WashU Epigenome Browser » Browser Metadata

GSM520875_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520876 (pirrota_482_B2_Input(14cyc).293.CEL)

GSM621339_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM390064_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575368_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575369_pirrota_354_E6_Input.182.CEL

GSM432583_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686709_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM575393_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575394_pirrota_345_E7_Input.173.CEL

GSM520929_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520930 (pirrota_482_B2_Input(14cyc).293.CEL)

GSM847771_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM570038_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM575380_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575381_pirrota_729_OR_Head_Prep3_Input_20cyc.493.CEL

GSM461206_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627336_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM847659_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM669543_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM451804_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using TopHat (http://tophat.cbcb.umd.edu/).  The bed file was generated by thresholding the bedgraph file (tag count>=1; minimum run length=50; maximum gap=50).

GSM333849_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM621333_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM461210_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM853480_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461179_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927232_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM408988_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM520939_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520940 (pirrota_292_A9_Input.136.CEL)

GSM624674_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624675_pirrota_1088_A21_Input.846.CEL

GSM942055_1	Detail=Normalization_and_smoothing_of_log2_ratios:DM:1 protocol. Two-color Agilent tiling arrays were processed by Bioconductor primarily with the Ringo package (Toedling et al., 2007, PMID: 17594472).  Briefly, each array was loess normalized and then probe log2 ratios were smoothed by running medians across windows of 10kb along the genome, requiring at least 3 probes within a window.

GSM853474_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM575508_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575509_pirrota_506_A12_Input_20cyc.328.CEL

GSM624887_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM439451_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM851706_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM942054_1	Detail=Normalization_and_smoothing_of_log2_ratios:DM:1 protocol. Two-color Agilent tiling arrays were processed by Bioconductor primarily with the Ringo package (Toedling et al., 2007, PMID: 17594472).  Briefly, each array was loess normalized and then probe log2 ratios were smoothed by running medians across windows of 10kb along the genome, requiring at least 3 probes within a window.

GSM400656_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686729_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM686551_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM432580_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM694128_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq_analysis:DM:1 protocol. *  BEDGRAPH Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

GSM520861_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520862 (pirrota_208_S12_Input.58.CEL)

GSM575384_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575385_pirrota_726_Larvae_Prep4_Input_14cyc.490.CEL

GSM881218_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq analysis BEDGRAPH Generation:DM:1 protocol. BEDGRAPH Track Generation:    * Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.    * Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.    * Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.    * To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.

GSM461210_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624880_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM694124_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ORC_ChIPseq_analysis:DM:1 protocol. *  BEDGRAPH Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

GSM627396_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627411_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM401412_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM461176_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575386_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575387_pirrota_725_Larvae_Prep3_Input_14cyc.489.CEL

GSM520800_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520801 (pirrota_212_A8_Input.62.CEL)

GSM521086_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521087 (pirrota_602_B5_Input(20cycles).391.CEL)

GSM627407_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521102_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521103 (pirrota_540_A12_Input18.362.CEL)

GSM521033_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521034 (pirrota_682_KC2_Input(14cycles).451.CEL)

GSM461187_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686762_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM408986_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686759_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM628252_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627417_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627387_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521015_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521016 (pirrota_621_B5_Input-18cycles.406.CEL)

GSM401420_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM451806_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using TopHat (http://tophat.cbcb.umd.edu/).  The bed file was generated by thresholding the bedgraph file (tag count>=1; minimum run length=50; maximum gap=50).

GSM520955_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520956 (pirrota_620_B3_Input-18cycles.405.CEL)

GSM927233_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM521031_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521032 (pirrota_681_KC1_Input(14cycles).450.CEL)

GSM451808_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using TopHat (http://tophat.cbcb.umd.edu/).  The bed file was generated by thresholding the bedgraph file (tag count>=1; minimum run length=50; maximum gap=50).

GSM853488_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM521017_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521018 (pirrota_620_B3_Input-18cycles.405.CEL)

GSM569800_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM927171_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM387596_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM521041_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521042 (pirrota_684_A15_Input.453.CEL)

GSM847674_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM401401_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM451807_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using TopHat (http://tophat.cbcb.umd.edu/).  The bed file was generated by thresholding the bedgraph file (tag count>=1; minimum run length=50; maximum gap=50).

GSM686743_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627411_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM333833_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM686707_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM432592_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM624868_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM847752_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM624888_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM520828_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520829 (pirrota_481_B1_Input(14cyc).292.CEL)

GSM461193_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627380_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM439464_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM439462_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM461208_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575437_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575438_pirrota_602_B5_Input_20cycles.391.CEL

GSM333838_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM575446_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575447_pirrota_684_A15_Input.453.CEL

GSM686606_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520790_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520791 (pirrota_478_C18-2_Input(14cyc).289.CEL)

GSM627360_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624620_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624621_pirrota_454_E4_Input.276.CEL

GSM461191_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927176_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM461209_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575391_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575392_pirrota_824_E_late_1_inputDNA_20cyc.595.CEL

GSM621328_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM624882_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM853468_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461209_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927202_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM927208_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM575510_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575511_pirrota_243_S12_Input_20_cycles.86.CEL

GSM451805_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using TopHat (http://tophat.cbcb.umd.edu/).  The bed file was generated by thresholding the bedgraph file (tag count>=1; minimum run length=50; maximum gap=50).

GSM847673_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461187_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927212_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM520935_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520936 (pirrota_479_Kc-1_Input(14cyc).290.CEL)

GSM927224_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM390062_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575382_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575383_pirrota_730_OR_Head_Prep4_Input_20cyc.494.CEL

GSM499657_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM686477_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM521061_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521062 (pirrota_760_A17_Input.530.CEL)

GSM390059_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927197_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM575475_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575476_pirrota_879_E_early_1_Input.650.CEL

GSM624646_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624647_pirrota_1205_B5_Input.936.CEL

GSM461203_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461184_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686555_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM927210_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM847706_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM636835_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627382_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627392_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM694120_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ORC_ChIPseq_analysis:DM:1 protocol. *  BEDGRAPH Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

GSM520949_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520950 (10.pirrota_142_A3_Input_HD.CEL)

GSM575401_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575402_pirrota_620_B3_Input-18cycles.405.CEL

GSM521003_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521004 (pirrota_620_B3_Input-18cycles.405.CEL)

GSM520775_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520776 (pirrota_208_S12_Input.58.CEL)

GSM521039_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521040 (pirrota_683_A11_Input.452.CEL)

GSM686600_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520854_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: no input (NA)

GSM621329_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM627407_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM614652_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM927181_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM520873_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520874 (pirrota_482_B2_Input(14cyc).293.CEL)

GSM521063_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521064 (pirrota_761_A18_Input.531.CEL)

GSM686475_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM570045_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM569791_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM499638_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM401416_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM627363_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627374_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575433_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575434_pirrota_298_S11_Input.143.CEL

GSM627398_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM499643_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM499635_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM387597_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM624884_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM521037_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521038 (pirrota_836_CL8-1_Input_DNA(14cyc).607.CEL)

GSM521100_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521101 (pirrota_196_S9_Input.46.CEL)

GSM847658_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461193_3	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927216_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM686739_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM624861_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM624628_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624629_pirrota_915_A17_Input-18cycles.670.CEL

GSM627413_3	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM401421_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM575479_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575480_pirrota_424_B1_Input.250.CEL

GSM881221_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq analysis BEDGRAPH Generation:DM:1 protocol. BEDGRAPH Track Generation:    * Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.    * Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.    * Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.    * To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.

GSM627356_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686717_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM333846_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM686755_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM847675_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627337_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686612_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM401413_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM522360_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1    Processed data are obtained using following parameters: read length is 36   ORC_ChIPseq_analysis:DM:1 protocol. Processing and peaking calling for ORC solexa data.

GSM853469_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM520796_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520797 (pirrota_292_A9_Input.136.CEL)

GSM624876_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM843544_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627406_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624892_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is R5.27.

GSM575411_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575412_pirrota_916_B4_Input-18cycles.671.CEL

GSM624897_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is R5.27.

GSM927223_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM575431_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575432_pirrota_284_Input.137.CEL

GSM520881_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520882 (pirrota_480_Kc-2_Input(14cyc).291.CEL)

GSM628255_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627388_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM669545_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM575417_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575418_pirrota_620_B3_Input-18cycles.405.CEL

GSM686547_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM927177_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM333866_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM927222_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627395_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM851729_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461190_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM401410_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM621341_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM627349_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM400672_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM627391_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627364_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM432594_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM520921_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520922 (pirrota_425_B2_Input.251.CEL)

GSM461192_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520852_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520853 (pirrota_190_A3_Input.38.CEL)

GSM627353_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624664_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624665_pirrota_621_B5_Input-18cycles.406.CEL

GSM333850_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM521071_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521072 (pirrota_647_Kc2_Input(20cycles).424.CEL)

GSM853472_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM927194_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM432593_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM624865_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM520818_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520819 (pirrota_264_S13_Input.116.CEL)

GSM575448_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575449_pirrota_835_E_late1_Input_DNA_14cyc.606.CEL

GSM333837_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM400666_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM390066_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM333847_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM686751_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM848956_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM686685_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627335_3	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM432584_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM333868_2	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM686479_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM686776_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM461183_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM594222_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie version 0.12.5. Signal files were generated with the R package version 2.7.1 SPP 1.0. Peaks were called with MACS version 1.3.7.

GSM694129_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq_analysis:DM:1 protocol. *  BEDGRAPH Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

GSM461181_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686782_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM847578_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM636830_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM575419_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575420_pirrota_873_S15_Input-18cycles.644.CEL

GSM401409_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM439443_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM432586_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM624862_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM624885_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is R5.27.

GSM621331_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM333859_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM390065_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM621326_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM686516_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520885_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520886 (12.pirrota_144_A7_Input_HD.CEL)

GSM439450_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM624652_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624653_pirrota_1088_A21_Input.846.CEL

GSM843545_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM521059_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521060 (pirrota_761_A18_Input.531.CEL)

GSM520802_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520803 (pirrota_292_A9_Input.136.CEL)

GSM575454_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575455_pirrota_935_Eearly2_Input_20cyc.690.CEL

GSM461191_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM694125_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ORC_ChIPseq_analysis:DM:1 protocol. *  BEDGRAPH Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

GSM927180_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM461185_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520985_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520986 (pirrota_499_S14_Input18.320.CEL)

GSM575498_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575499_pirrota_600_Kc1_Input_20cycles.389.CEL

GSM621338_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM520830_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520831 (pirrota_480_Kc-2_Input(14cyc).291.CEL)

GSM521090_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521091 (pirrota_641_S12_input_gk2.417.CEL)

GSM627355_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM847657_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM333855_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM624890_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM570051_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM521088_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521089 (pirrota_803_A14.input.566.CEL)

GSM408992_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM627379_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627346_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM499640_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM627389_3	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686508_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM621342_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM521035_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521036 (pirrota_837_CL8-2_Input_DNA(14cyc).608.CEL)

GSM575483_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575484_pirrota_825_CL8-1_InputDNA_20cyc.596.CEL

GSM669472_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461207_3	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461186_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM942053_1	Detail=Normalization_and_smoothing_of_log2_ratios:DM:1 protocol. Two-color Agilent tiling arrays were processed by Bioconductor primarily with the Ringo package (Toedling et al., 2007, PMID: 17594472).  Briefly, each array was loess normalized and then probe log2 ratios were smoothed by running medians across windows of 10kb along the genome, requiring at least 3 probes within a window.

GSM686745_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM575469_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575470_pirrota_723_OR_Head_Prep3_Input_14cyc.487.CEL

GSM851849_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM686737_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM847773_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM439463_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686749_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520913_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520914 (pirrota_424_B1_Input.250.CEL)

GSM333842_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM520832_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520833 (pirrota_479_Kc-1_Input(14cyc).290.CEL)

GSM686510_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627359_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM499661_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM575514_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575515_pirrota_873_S15_Input-18cycles.644.CEL

GSM624869_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM627408_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686492_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627335_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM499649_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM621327_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM390063_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520919_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520920 (pirrota_424_B1_Input.250.CEL)

GSM461183_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM853485_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM624632_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624633_pirrota_1058_L3_3_Input(20cyc).798.CEL

GSM439459_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM387600_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM686741_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM686691_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM847775_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM927195_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627365_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575366_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575367_pirrota_345_E7_Input.173.CEL

GSM461200_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM439445_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM927184_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM432591_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM408982_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM520947_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520948 (pirrota_212_A8_Input.62.CEL)

GSM927175_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM847702_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM499636_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM521082_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521083 (pirrota_620_B3_Input-18cycles.405.CEL)

GSM628259_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM847699_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM686719_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM694132_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ORC_ChIPseq_analysis:DM:1 protocol. *  BEDGRAPH Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

GSM627371_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520981_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520982 (pirrota_499_S14_Input18.320.CEL)

GSM439442_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686561_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM621332_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM432579_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM627343_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461205_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521043_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521044 (pirrota_602_B5_Input(20cycles).391.CEL)

GSM520915_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520916 (pirrota_196_S9_Input.46.CEL)

GSM521001_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521002 (pirrota_761_A18_Input.531.CEL)

GSM627359_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624886_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is R5.27.

GSM669537_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM521096_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521097 (pirrota_837_CL8-2_Input_DNA(14cyc).608.CEL)

GSM575370_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575371_pirrota_353_E4_Input.181.CEL

GSM439449_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM401415_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM847952_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627366_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686711_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM686483_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM575450_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575451_pirrota_263_E3_Input.108.CEL

GSM686679_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627393_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM387594_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM853473_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM686764_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520905_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520906 (40.pirrota_182_S8_Input_HD.CEL)

GSM847954_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM621337_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM627383_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624650_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624651_pirrota_1362_Kc-5_Input.1114.CEL

GSM624872_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM627352_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461182_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM451813_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using TopHat (http://tophat.cbcb.umd.edu/).  The bed file was generated by thresholding the bedgraph file (tag count>=1; minimum run length=50; maximum gap=50).

GSM927227_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM520917_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520918 (pirrota_242_S12_Input(14_cycles).85.CEL)

GSM847619_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM521084_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521085 (pirrota_646_B3_Input2(20cycles).423.CEL)

GSM333870_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM432581_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM333836_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM569798_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM686565_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627414_3	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461182_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520869_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520870 (pirrota_499_S14_Input18.320.CEL)

GSM432587_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686689_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627415_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627334_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM847676_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM624672_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624673_pirrota_1089_A20_Input.847.CEL

GSM439446_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM520836_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520837 (pirrota_292_A9_Input.136.CEL)

GSM627385_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627356_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627389_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520903_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520904 (pirrota_208_S12_Input.58.CEL)

GSM594213_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie version 0.12.5. Signal files were generated with the R package version 2.7.1 SPP 1.0. Peaks were called with MACS version 1.3.7.

GSM451809_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using TopHat (http://tophat.cbcb.umd.edu/).  The bed file was generated by thresholding the bedgraph file (tag count>=1; minimum run length=50; maximum gap=50).

GSM686733_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520871_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520872 (pirrota_481_B1_Input(14cyc).292.CEL)

GSM401424_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM927183_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM927192_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627343_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927229_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627402_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM333867_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM461189_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627412_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM451811_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using TopHat (http://tophat.cbcb.umd.edu/).  The bed file was generated by thresholding the bedgraph file (tag count>=1; minimum run length=50; maximum gap=50).

GSM520782_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520783 (pirrota_540_A12_Input18.362.CEL)

GSM847770_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM333843_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM636832_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461195_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575376_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575377_pirrota_731_Larvae_Prep_3_Input_20cyc.495.CEL

GSM927187_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM621340_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM520933_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520934 (pirrota_478_C18-2_Input(14cyc).289.CEL)

GSM627368_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521075_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: no input (NA)

GSM333851_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM575395_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575396_pirrota_344_E5_Input.172.CEL

GSM521094_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521095 (pirrota_303_S14_Input.148.CEL)

GSM627414_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627388_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM439440_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM575378_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575379_pirrota_732_Larvae_Prep_4_Input_20cyc.496.CEL

GSM853484_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM853490_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM575488_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575489_pirrota_584_A14_Input_20cycles.373.CEL

GSM627335_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624636_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624637_pirrota_1040_Kc4_Input(20cyc).814.CEL

GSM851744_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627339_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520816_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520817 (pirrota_499_S14_Input18.320.CEL)

GSM520977_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520978 (pirrota_292_A9_Input.136.CEL)

GSM927221_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM624670_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624671_pirrota_499_S14_Input18.320.CEL

GSM439461_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM461208_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624638_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624639_pirrota_1041_Kc5_Input(20cyc).815.CEL

GSM333861_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM927206_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627362_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM439457_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM847660_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM520777_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520778 (pirrota_303_S14_Input.148.CEL)

GSM575397_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575398_pirrota_999_Elate4_Input_20cyc.738.CEL

GSM575464_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575465_pirrota_721_E10_Input_14cyc.487.CEL

GSM575364_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575365_pirrota_344_E5_Input.172.CEL

GSM333858_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM390061_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520867_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520868 (pirrota_298_S11_Input.143.CEL)

GSM853489_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627367_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM401407_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM627405_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461199_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686573_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM521073_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521074 (pirrota_600_Kc1_Input(20cycles).389.CEL)

GSM847698_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM520838_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520839 (pirrota_424_B1_Input.250.CEL)

GSM520850_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520851 (pirrota_242_S12_Input(14_cycles).85.CEL)

GSM461204_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521057_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521058 (pirrota_760_A17_Input.530.CEL)

GSM624878_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM461196_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM628262_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM520812_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520813 (pirrota_619_A14_Input-18cycles.404.CEL)

GSM669547_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM522359_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1    Processed data are obtained using following parameters: read length is 36   ORC_ChIPseq_analysis:DM:1 protocol. Processing and peaking calling for ORC solexa data.

GSM570054_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM627375_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521013_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521014 (pirrota_761_A18_Input.531.CEL)

GSM927203_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627351_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM847753_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM927199_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM401418_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM627357_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627384_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521055_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521056 (pirrota_761_A18_Input.531.CEL)

GSM594225_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie version 0.12.5. Signal files were generated with the R package version 2.7.1 SPP 1.0. Peaks were called with MACS version 1.3.7.

GSM927193_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM575399_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575400_pirrota_916_B4_Input-18cycles.671.CEL

GSM627415_3	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM432589_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM847772_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627410_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521011_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521012 (pirrota_760_A17_Input.530.CEL)

GSM520931_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520932 (pirrota_477_C18-1_Input(14cyc).288.CEL)

GSM520844_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520845 (pirrota_242_S12_Input(14_cycles).85.CEL)

GSM520957_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520958 (pirrota_621_B5_Input-18cycles.406.CEL)

GSM333840_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM520969_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520970 (pirrota_478_C18-2_Input(14cyc).289.CEL)

GSM627360_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927230_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM686593_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520810_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520811 (pirrota_620_B3_Input-18cycles.405.CEL)

GSM627400_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627387_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM439465_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM627333_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461207_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM621336_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM521009_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521010 (pirrota_499_S14_Input18.320.CEL)

GSM520814_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520815 (pirrota_499_S14_Input18.320.CEL)

GSM520788_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520789 (pirrota_477_C18-1_Input(14cyc).288.CEL)

GSM569795_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM400668_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM575423_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575424_pirrota_880_E_late_2_Input.651.CEL

GSM432585_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM847696_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461206_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927182_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627358_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM451812_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using TopHat (http://tophat.cbcb.umd.edu/).  The bed file was generated by thresholding the bedgraph file (tag count>=1; minimum run length=50; maximum gap=50).

GSM627376_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM628251_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627366_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM408990_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686536_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM522354_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1    Processed data are obtained using following parameters: read length is 36   ORC_ChIPseq_analysis:DM:1 protocol. Processing and peaking calling for ORC solexa data.

GSM669474_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461198_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521019_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521020 (pirrota_277_S12_Input.122.CEL)

GSM624874_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM627349_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575468_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575465_pirrota_721_E10_Input_14cyc.487.CEL

GSM439454_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM927231_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM686721_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM624863_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM621335_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM451801_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM810644_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461202_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM401408_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM636838_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM520822_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520823 (pirrota_264_S13_Input.116.CEL)

GSM686494_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520857_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520858 (pirrota_437_B3_INPUT.253.CEL)

GSM627381_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686553_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM461205_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927225_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627413_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520911_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520912 (pirrota_425_B2_Input.251.CEL)

GSM520979_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520980 (pirrota_540_A12_Input18.362.CEL)

GSM686538_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM851839_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM881223_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq analysis BEDGRAPH Generation:DM:1 protocol. BEDGRAPH Track Generation:    * Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.    * Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.    * Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.    * To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.

GSM570049_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM575409_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575410_pirrota_879_E_early_1_Input.650.CEL

GSM851817_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM621334_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM439438_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM499647_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM624624_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624625_pirrota_377_LarvaeTrial_Input.193CEL

GSM624680_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624681_pirrota_212_A8_Input.62.CEL

GSM521053_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521054 (pirrota_683_A11_Input.452.CEL)

GSM927207_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM520983_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520984 (pirrota_619_A14_Input-18cycles.404.CEL)

GSM627350_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM451810_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using TopHat (http://tophat.cbcb.umd.edu/).  The bed file was generated by thresholding the bedgraph file (tag count>=1; minimum run length=50; maximum gap=50).

GSM694134_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ORC_ChIPseq_analysis:DM:1 protocol. *  BEDGRAPH Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

GSM401422_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM627337_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520961_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520962 (pirrota_365_B2_Input.208.CEL)

GSM333871_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM942057_1	Detail=Normalization_and_smoothing_of_log2_ratios:DM:1 protocol. Two-color Agilent tiling arrays were processed by Bioconductor primarily with the Ringo package (Toedling et al., 2007, PMID: 17594472).  Briefly, each array was loess normalized and then probe log2 ratios were smoothed by running medians across windows of 10kb along the genome, requiring at least 3 probes within a window.

GSM520999_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521000 (pirrota_760_A17_Input.530.CEL)

GSM847707_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM686524_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627362_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627373_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520877_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520878 (pirrota_481_B1_Input(14cyc).292.CEL)

GSM520891_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520892 (pirrota_540_A12_Input18.362.CEL)

GSM624654_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624655_pirrota_1089_A20_Input.847.CEL

GSM927215_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM614655_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM333839_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM624870_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM387598_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM624895_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is R5.27.

GSM520923_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520924 (pirrota_242_S12_Input(14_cycles).85.CEL)

GSM447608_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM520997_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520998 (pirrota_441_A12_INPUT.267.CEL)

GSM621330_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM439456_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM853479_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM624660_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624661_pirrota_1059_L3_6_Input.799.CEL

GSM628268_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM927213_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM624875_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM401419_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686557_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM686532_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM499637_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM387593_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM432590_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM520804_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520805 (pirrota_619_A14_Input-18cycles.404.CEL)

GSM575405_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575406_pirrota_916_B4_Input-18cycles.671.CEL

GSM439441_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM520794_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520795 (pirrota_480_Kc-2_Input(14cyc).291.CEL)

GSM520786_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520787 (pirrota_481_B1_Input(14cyc).292.CEL)

GSM624867_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM499641_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM686484_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520899_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520900 (pirrota_365_B2_Input.208.CEL)

GSM624622_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624623_pirrota_262_E2_Input.107.CEL

GSM461190_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461202_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686481_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520824_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520825 (40.pirrota_182_S8_Input_HD.CEL)

GSM627348_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521023_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521024 (pirrota_836_CL8-1_Input_DNA(14cyc).607.CEL)

GSM575477_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575478_pirrota_646_B3_Input2_20cycles.423.CEL

GSM627361_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520842_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520843 (pirrota_190_A3_Input.38.CEL)

GSM847701_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM400658_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM847704_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM575500_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575501_pirrota_646_B3_Input2_20cycles.423.CEL

GSM686735_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM847703_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM927209_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM575372_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575373_pirrota_380_OR_HeadTrial_Input.197.CEL

GSM432588_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM520973_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520974 (pirrota_480_Kc-2_Input(14cyc).291.CEL)

GSM333834_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM669539_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM520943_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520944 (pirrota_292_A9_Input.136.CEL)

GSM521080_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521081 (pirrota_621_B5_Input-18cycles.406.CEL)

GSM627342_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575456_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575457_pirrota_454_E4_Input.276.CEL

GSM521007_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521008 (pirrota_540_A12_Input18.362.CEL)

GSM451803_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using TopHat (http://tophat.cbcb.umd.edu/).  The bed file was generated by thresholding the wiggle file (tag count>=1; minimum run length=50; maximum gap=50).

GSM927214_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM927173_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM333832_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM522357_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1    Processed data are obtained using following parameters: read length is 36   ORC_ChIPseq_analysis:DM:1 protocol. Processing and peaking calling for ORC solexa data.

GSM686579_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM686747_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM847700_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM521027_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521028 (pirrota_837_CL8-2_Input_DNA(14cyc).608.CEL)

GSM333869_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM461194_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927179_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627389_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520820_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520821 (40.pirrota_182_S8_Input_HD.CEL)

GSM520927_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520928 (pirrota_481_B1_Input(14cyc).292.CEL)

GSM401404_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM927186_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM624644_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624645_pirrota_1204_B3_Input.935.CEL

GSM575425_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575426_pirrota_263_E3_Input.108.CEL

GSM401414_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM575494_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575495_pirrota_825_CL8-1_InputDNA_20cyc.596.CEL

GSM686602_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM521005_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521006 (pirrota_621_B5_Input-18cycles.406.CEL)

GSM520887_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520888 (pirrota_208_S12_Input.58.CEL)

GSM400670_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686540_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM461185_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM853477_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM521025_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521026 (pirrota_837_CL8-2_Input_DNA(14cyc).608.CEL)

GSM401402_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM520840_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520841 (pirrota_425_B2_Input.251.CEL)

GSM400664_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM432578_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM461178_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627354_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627386_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM669477_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM686512_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM439439_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM627359_3	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624877_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM521067_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521068 (pirrota_620_B3_Input-18cycles.405.CEL)

GSM881222_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq analysis BEDGRAPH Generation:DM:1 protocol. BEDGRAPH Track Generation:    * Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.    * Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.    * Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.    * To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.

GSM624662_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624663_pirrota_1058_L3_3_Input(20cyc).798.CEL

GSM520951_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520952 (pirrota_212_A8_Input.62.CEL)

GSM927201_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM851707_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM624658_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624659_pirrota_825_CL8-1_InputDNA(20cyc).596.CEL

GSM851705_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM686577_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520806_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520807 (pirrota_499_S14_Input18.320.CEL)

GSM847576_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM624676_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624677_pirrota_364_B1_Input.207.CEL

GSM627397_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927168_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM333863_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM520883_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520884 (10.pirrota_142_A3_Input_HD.CEL)

GSM853470_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM686715_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520863_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520864 (pirrota_435_B4_INPUT.255.CEL)

GSM451799_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM927174_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM520879_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520880 (pirrota_479_Kc-1_Input(14cyc).290.CEL)

GSM520846_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520847 (pirrota_425_B2_Input.251.CEL)

GSM520897_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520898 (pirrota_208_S12_Input.58.CEL)

GSM851743_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM927217_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM851840_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM686693_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM686773_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM461184_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520937_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520938 (pirrota_480_Kc-2_Input(14cyc).291.CEL)

GSM624626_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624627_pirrota_284_Input.137.CEL

GSM575435_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575436_pirrota_303_S14_Input.148.CEL

GSM575512_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575513_pirrota_584_A14_Input_20cycles.373.CEL

GSM575452_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575453_pirrota_880_E_late_2_Input.651.CEL

GSM669541_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM927189_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM686610_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM621128_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM521104_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521105 (pirrota_365_B2_Input.208.CEL)

GSM333868_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM390060_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM453867_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using TopHat (http://tophat.cbcb.umd.edu/).  The bed file was generated by thresholding the bedgraph file (tag count>=1; minimum run length=50; maximum gap=50).

GSM853481_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM847705_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM575473_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575474_pirrota_935_Eearly2_Input_20cyc.690.CEL

GSM461197_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624860_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM627347_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927204_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM621130_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM853482_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM499644_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM408984_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686683_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM461190_3	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575374_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575375_pirrota_285_Input.138.CEL

GSM408994_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686530_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520909_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520910 (pirrota_242_S12_Input(14_cycles).85.CEL)

GSM686506_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM851818_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM927165_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM522353_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1    Processed data are obtained using following parameters: read length is 36   ORC_ChIPseq_analysis:DM:1 protocol. Processing and peaking calling for ORC solexa data.

GSM439455_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM927200_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627401_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520993_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520994 (pirrota_437_B3_INPUT.253.CEL)

GSM851841_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM694121_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ORC_ChIPseq_analysis:DM:1 protocol. *  BEDGRAPH Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

GSM520893_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520894 (40.pirrota_182_S8_Input_HD.CEL)

GSM461201_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM333856_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM853476_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627413_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627372_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461204_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575415_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575416_pirrota_621_B5_Input-18cycles.406.CEL

GSM686731_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM333860_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM461207_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520959_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520960 (pirrota_436_B5_INPUT.254.CEL)

GSM461188_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461189_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM853478_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627376_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM628224_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM520941_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520942 (pirrota_212_A8_Input.62.CEL)

GSM853491_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM927226_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM461199_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461188_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM851730_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM575441_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575438_pirrota_602_B5_Input_20cycles.391.CEL

GSM624640_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624641_pirrota_825_CL8-1_InputDNA(20cyc).596.CEL

GSM624879_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM333844_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM522363_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1    Processed data are obtained using following parameters: read length is 36   ORC_ChIPseq_analysis:DM:1 protocol. Processing and peaking calling for ORC solexa data.

GSM575504_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575505_pirrota_684_A15_Input.453.CEL

GSM847656_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461180_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461177_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575460_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575461_pirrota_879_E_early_1_Input.650.CEL

GSM575444_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575445_pirrota_584_A14_Input_20cycles.373.CEL

GSM627378_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM594245_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie version 0.12.5. Signal files were generated with the R package version 2.7.1 SPP 1.0. Peaks were called with MACS version 1.3.7.

GSM439452_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM624648_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624649_pirrota_1361_Kc-4_Input.1113.CEL

GSM927198_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM520826_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520827 (pirrota_482_B2_Input(14cyc).293.CEL)

GSM927185_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM686757_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520895_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520896 (pirrota_303_S14_Input.148.CEL)

GSM401417_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM521045_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521046 (pirrota_646_B3_Input2(20cycles).423.CEL)

GSM847955_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM575486_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575487_pirrota_826_CL8-2_Input_DNA_20cyc.597.CEL

GSM624666_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624667_pirrota_620_B3_Input-18cycles.405.CEL

GSM333835_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM927169_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM520967_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520968 (pirrota_477_C18-1_Input(14cyc).288.CEL)

GSM520963_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520964 (pirrota_264_S13_Input.116.CEL)

GSM686713_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627370_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521051_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521052 (pirrota_684_A15_Input.453.CEL)

GSM627400_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM401405_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM927211_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627383_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575490_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575491_pirrota_243_S12_Input_20_cycles.86.CEL

GSM461197_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM499633_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM521078_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521079 (pirrota_482_B2_Input(14cyc).293.CEL)

GSM439447_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686784_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM927191_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM499631_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM333852_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM520792_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520793 (pirrota_479_Kc-1_Input(14cyc).290.CEL)

GSM333845_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered.  The supplementary file 'GSM333845_gene_expr.txt' contains per-gene processed expression data.

GSM333854_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM628226_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM624656_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624657_pirrota_826_CL8-2_Input_DNA(20cyc).597.CEL

GSM853471_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627338_3	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575403_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575404_pirrota_437_B3_INPUT.253.CEL

GSM521106_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521107 (pirrota_436_B5_INPUT.254.CEL)

GSM624864_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM686522_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520975_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520976 (pirrota_212_A8_Input.62.CEL)

GSM520834_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520835 (pirrota_212_A8_Input.62.CEL)

GSM520889_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520890 (pirrota_619_A14_Input-18cycles.404.CEL)

GSM847697_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM624873_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM927188_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM942058_1	Detail=Normalization_and_smoothing_of_log2_ratios:DM:1 protocol. Two-color Agilent tiling arrays were processed by Bioconductor primarily with the Ringo package (Toedling et al., 2007, PMID: 17594472).  Briefly, each array was loess normalized and then probe log2 ratios were smoothed by running medians across windows of 10kb along the genome, requiring at least 3 probes within a window.

GSM400662_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686591_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM570040_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM927167_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM575496_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575497_pirrota_647_Kc2_Input_20cycles.424.CEL

GSM627418_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM847776_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM621343_1	Detail=.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks. .bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.

GSM847575_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM624678_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624679_pirrota_365_B2_Input.208.CEL

GSM627394_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927170_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM624881_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM627401_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627345_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520925_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520926 (pirrota_196_S9_Input.46.CEL)

GSM521029_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521030 (pirrota_836_CL8-1_Input_DNA(14cyc).607.CEL)

GSM627418_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520808_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520809 (pirrota_621_B5_Input-18cycles.406.CEL)

GSM521092_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521093 (pirrota_298_S11_Input.143.CEL)

GSM624682_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624683_pirrota_142_A3_Input_HD.10.CEL

GSM521076_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521077 (pirrota_481_B1_Input(14cyc).292.CEL)

GSM686753_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627338_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686559_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627414_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM847774_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM520971_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520972 (pirrota_479_Kc-1_Input(14cyc).290.CEL)

GSM570043_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM942056_1	Detail=Normalization_and_smoothing_of_log2_ratios:DM:1 protocol. Two-color Agilent tiling arrays were processed by Bioconductor primarily with the Ringo package (Toedling et al., 2007, PMID: 17594472).  Briefly, each array was loess normalized and then probe log2 ratios were smoothed by running medians across windows of 10kb along the genome, requiring at least 3 probes within a window.

GSM520848_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520849 (pirrota_424_B1_Input.250.CEL)

GSM520859_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520860 (40.pirrota_182_S8_Input_HD.CEL)

GSM461200_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM571140_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM520995_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520996 (pirrota_499_S14_Input18.320.CEL)

GSM594216_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie version 0.12.5. Signal files were generated with the R package version 2.7.1 SPP 1.0. Peaks were called with MACS version 1.3.7.

GSM686534_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM461209_3	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927172_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM521047_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521048 (pirrota_684_A15_Input.453.CEL)

GSM499639_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM461186_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM522356_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1    Processed data are obtained using following parameters: read length is 36   ORC_ChIPseq_analysis:DM:1 protocol. Processing and peaking calling for ORC solexa data.

GSM927196_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM927166_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627363_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM401411_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM627377_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627338_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM520953_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520954 (pirrota_292_A9_Input.136.CEL)

GSM627348_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM621134_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM853486_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461195_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM432582_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686687_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520907_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520908 (pirrota_190_A3_Input.38.CEL)

GSM627399_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM499653_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM624630_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624631_pirrota_873_S15_Input-18cycles.644.CEL

GSM627412_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624883_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM521021_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521022 (pirrota_540_A12_Input18.362.CEL)

GSM881217_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq analysis BEDGRAPH Generation:DM:1 protocol. BEDGRAPH Track Generation:    * Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.    * Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.    * Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.    * To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.

GSM333864_1	Detail=Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

GSM575439_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575440_pirrota_646_B3_Input2_20cycles.423.CEL

GSM439448_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM575442_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575443_pirrota_967_A18_Input_20cyc.728.CEL

GSM439458_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM575502_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575503_pirrota_602_B5_Input_20cycles.391.CEL

GSM853483_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM686518_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM927219_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM624642_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624643_pirrota_826_CL8-2_Input_DNA(20cyc).597.CEL

GSM627391_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927234_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM461192_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM439453_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM627390_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624859_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM927228_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM686571_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520779_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: no input (NA)

GSM499642_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM627416_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575516_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575517_pirrota_499_S14_Input18.320.CEL

GSM686486_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627404_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461198_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624871_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM575421_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575422_pirrota_540_A12_Input18.362.CEL

GSM624896_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is R5.27.

GSM847577_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM400674_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686528_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM439460_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM851848_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM400660_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM686473_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM624889_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM686541_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM575388_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575389_pirrota_363_E6_Input.206.CEL

GSM847767_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM686681_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM520901_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520902 (pirrota_437_B3_INPUT.253.CEL)

GSM461193_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM627390_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM628264_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM461203_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM569793_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM520798_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520799 (pirrota_212_A8_Input.62.CEL)

GSM686488_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627403_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521098_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521099 (pirrota_836_CL8-1_Input_DNA(14cyc).607.CEL)

GSM521065_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521066 (pirrota_760_A17_Input.530.CEL)

GSM624866_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

GSM627409_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM461201_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM686526_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM621132_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

GSM522362_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1    Processed data are obtained using following parameters: read length is 36   ORC_ChIPseq_analysis:DM:1 protocol. Processing and peaking calling for ORC solexa data.

GSM333841_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM520991_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520992 (pirrota_435_B4_INPUT.255.CEL)

GSM686604_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM401423_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM401406_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM575492_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575493_pirrota_826_CL8-2_Input_DNA_20cyc.597.CEL

GSM847769_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM927205_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM401403_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM927218_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM575471_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575472_pirrota_724_OR_Head_prep4_Input_14cyc.488.CEL

GSM847953_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM439444_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

GSM627340_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM521069_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521070 (pirrota_621_B5_Input-18cycles.406.CEL)

GSM461196_2	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575413_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575414_pirrota_621_B5_Input-18cycles.406.CEL

GSM847768_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM520965_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520966 (pirrota_298_S11_Input.143.CEL)

GSM333853_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM686490_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM627402_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575407_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575408_pirrota_935_Eearly2_Input_20cyc.690.CEL

GSM575481_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575482_pirrota_425_B2_Input.251.CEL

GSM624891_1	Detail=NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is R5.27.

GSM461194_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM669694_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM575458_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575459_pirrota_262_E2_Input.107.CEL

GSM387595_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM520945_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520946 (pirrota_212_A8_Input.62.CEL)

GSM520855_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520856 (pirrota_436_B5_INPUT.254.CEL)

GSM520784_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520785 (pirrota_482_B2_Input(14cyc).293.CEL)

GSM520865_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520866 (pirrota_437_B3_INPUT.253.CEL)

GSM627415_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM927220_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM521049_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM521050 (pirrota_683_A11_Input.452.CEL)

GSM575506_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575507_pirrota_683_A11_Input.452.CEL

GSM575429_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575430_pirrota_964_Larvae_Prep5_Input_14cyc.725.CEL

GSM927190_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM627344_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM881219_1	Detail=Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq analysis BEDGRAPH Generation:DM:1 protocol. BEDGRAPH Track Generation:    * Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.    * Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.    * Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.    * To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.

GSM853475_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627341_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575462_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575463_pirrota_722_E11_Input_14cyc.486.CEL

GSM333848_1	Detail=Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

GSM499651_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

GSM927178_1	Library strategy=RIP-Seq; Base calling and demultiplexing was performed using CASAVA 1.8.; Alignments were performed using TopHat version 1.4.0 with the following parameters=-p 8 -G ginormous.100806.gtf --no-novel-juncs -a 6 -m 2 --min-intron-length 28 -I 200000 -F 0 -g 1 --library-type fr-unstranded --transcriptome-index ginormous_transcriptome -x 60 -n 2. Ginormous refers to the annotation published in Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., et al. (2011). The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (PMID 21179090).; bedGraph files were generated from bam files using bedTools with the following parameters=genomeCoverageBed -bg -split; Genome_build=Dm3; Supplementary_files_format_and_content=Genome browser files are presented in bedGraph format.

GSM851842_1	Detail=Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

GSM627350_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM624634_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624635_pirrota_1059_L3_6_Input.799.CEL

GSM520780_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.   input sample: GSM520781 (pirrota_499_S14_Input18.320.CEL)

GSM624668_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM624669_pirrota_298_S11_Input.143.CEL

GSM627369_1	Detail=Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

GSM575390_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575389_pirrota_363_E6_Input.206.CEL

GSM686563_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

GSM575427_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575428_pirrota_377_LarvaeTrial_Input.193.CEL

GSM575485_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.  input: GSM575484_pirrota_825_CL8-1_InputDNA_20cyc.596.CEL

GSM686549_1	Detail=M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.