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/.本数据集为造血增强子的整合集合。我们从BLUEPRINT数据库下载了所有H3K27ac染色质免疫沉淀测序（ChIP-seq）与脱氧核糖核酸酶I（DNase I）测序数据，并从ROADMAP数据库获取了造血系统DNase I测序数据。所有DNase I测序数据均使用Kundaje实验室DNase分析流程版本0.3.0（https://github.com/kundajelab/atac_dnase_pipelines）完成预处理。ChIP-seq样本则通过Kundaje实验室的AQUAS转录因子与组蛋白ChIP-seq分析流程（https://github.com/kundajelab/chipseq_pipeline）进行处理。针对BLUEPRINT的全部实验数据，我们直接使用欧洲生物信息研究所（EBI）提供的比对后reads数据。所有ROADMAP样本均使用bowtie2比对至hg38参考基因组。使用MACS2并遵循该DNase分析流程的默认参数调用DNase I峰。我们将所有DNase I峰文件进行合并，并将每个合并后的峰的中心对齐至对应最强单峰的峰顶位置。在以峰顶为中心的2kb区域内统计H3K27ac测序reads的数目。更多细节可参阅GimmeMotifs相关手稿：https://github.com/simonvh/gimmemotifs-manuscript/。