Genome-wide Mapping of DNase I Hypersensitive Sites

DNaseI hypersensitivity mapping was performed using protocols developed by Duke^{7 (link)} or UW^{8 (link)} on a total of 125 cell-types (Supplementary Table 1). Datasets were sequenced to an average depth of 30 million uniquely mapping sequence tags (27-35 bp for UW and 20 bp for Duke) per replicate. For uniformity of analysis, some cell type data sets that exceeded 40M tag depth were randomly sub sampled to a depth of 30 million tags. Sequence reads were mapped using the Bowtie aligner, allowing a maximum of two mismatches. Only reads mapping uniquely to the genome were used in our analyses. Mappings were to male or female versions of hg19/GRCh37, depending on cell type, with random regions omitted. Data were analyzed jointly using a single algorithm^{7 (link)} (Supplementary Methods) to localize DNaseI hypersensitive sites. H3K4me3 ChIP-seq was performed using antibody 9751 (Cell Signaling) on 1% formaldehyde crosslinked samples sheared by Diagenode bioruptor. Gene expression measurements for each cell type were performed on Affymetrix Human Exon microarrays. 5C experiments were performed as described^{31 (link), 32} . Transcription factor recognition motif occurrences within DHSs were defined with FIMO^{38 (link)} at significance P < 10^-5 using motif models from the TRANSFAC database.