H3K27Ac Read Counts In Hematopoietic Enhancers

This dataset represents an integrated collection of hematopoietic enhancers. We downloaded all H3K27ac ChIP-seq and DNase I data from BLUEPRINT and hematopoietic DNase I data from ROADMAP. All DNase I data were processed using the Kundaje lab DNase pipeline version 0.3.0 https://github.com/kundajelab/atac_dnase_pipelines]. The ChIP-seq samples were processed using the Kundaje lab AQUAS TF and histone ChIP-seq pipeline https://github.com/kundajelab/chipseq_pipeline. For all experiments from BLUEPRINT we used the aligned reads provided by EBI. All ROADMAP samples were aligned using bowtie2 to the hg38 genome. DNase I peaks were called using MACS2 according to the default settings of the DNase pipeline. We merged all DNase I peak files and centered each merged peak on the summit of the strongest individual peak. H3K27ac reads were counted in a region of 2kb centered at the summit. For more details, see the GimmeMotifs manuscript: https://github.com/simonvh/gimmemotifs-manuscript/.