Fig. 2

Mapping open chromatin by ATAC-Seq in iMG and human primary microglia. A. Displays distribution of DNA accessible sites (DAS) across each genomic feature in human iMG and primary microglia (pMG). B. Illustrates the relative distance of DAS from transcriptional start sites human iMG and primary microglia (pMG). C. ATAC-Seq abundance tracks identify accessible chromatin regions (DAS) around the BIN1 gene in iMG (blue tracks) and pMG (pink tracks). D. Principal component analysis (PCA) of ATAC-Seq signal at a microglia specific gene set (see Table S1). Data sets include iMG, pMG and monocytes and HMC3 cells from another study in our laboratory. E-F. De novo (E) and known (F) motif discovery analysis (HOMER) on common DAS in iMG and pMG are presented. G. AD-linked APOE variants concentrate on genomic regulatory regions (DAS) in iMG and pMG. ADVP track shows the AD-associated single nucleotide variants around APOE from ADVP database. DAS detected in the vicinity of APOE gene in iMG are shown as blue dashes. H. Gene ontology (GO) enrichment analysis for 250 genes associated with most significant common peaks between iMG and pMG is depicted. ATAC-Seq was performed on iMG derived from C1-iPSC line. Abbreviations: UTR untranslated region; TSS transcription start site; kb kilobase; HMC3 human microglia cell line 3