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GSM870040	Read-alignment=Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters. If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped; Valid Pair computing=Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations. Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR. Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads

GSM870041	Read-alignment=Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters. If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped; Valid Pair computing=Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations. Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR. Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads

GSM870042	Read-alignment=Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters. If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped; Valid Pair computing=Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations. Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR. Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads

GSM870043	Read-alignment=Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters. If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped; Valid Pair computing=Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations. Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR. Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads

GSM870044	Read-alignment=Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters. If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped; Valid Pair computing=Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations. Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR. Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads

GSM870045	Read-alignment=Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters. If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped; Valid Pair computing=Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations. Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR. Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads

GSM870046	Read-alignment=Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters. If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped; Valid Pair computing=Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations. Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR. Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads