Comprehensive maps of transcription factor (TF) binding sites in mouse (ATAC-Seq)

Mammalian genome encodes approximately 1,700 transcription factors (TFs), 1,300 out of which have sequence specific binding motifs. Transcription in mammalian cells is regulated by the recruitment of TFs to specific cis-regulatory elements. In spite of consistent efforts on the function of individual TF, the question still remains how TFs bind to DNA and form enhancer. Here, we try to solve this problem by investigating the relationship between TF binding pattern and chromatin accessibility (ATAC-Seq). We first systematically acquired ATAC-Seq dataset as well as matched RNA-Seq dataset from different mouse primary tissues. A comprehensive TF binding map was built for each tissue/cell type by genomic approaches. Overall design: We have analyzed 239 ATAC-Seq samples from mouse primary cells and tissues, which include 151 samples from ENCODE and GEO (listed in metadata_ALLsamples.xlsx - YELLOW), and 88 newly generated samples. Third-party reanalysis was performed on 151 samples from ENCODE and GEO. The 151 processed data files are linked below as supplementary files.