ATAC-Seq analysis of the effect of hypoxia and acetate supplementation on chromatin accessibility in CHP134 cells

ATAC-Seq was utilized to investigate chromatin accessibility under normoxia, hypoxia, and hypoxia with acetate supplementation in CHP134 cells. For each replicate, 50,000 cells were lysed in lysis buffer containing 0.01% IGEPAL CA-630 to obtain nuclei, which were directly used in the Tn5 transposition reaction (reagents from Illumina, FC-121-1030). Immediately following transposition, DNA fragments were purified (MinElute Kit, Qiagen) and PCR amplified for a total of 10-11 cycles using previously-designed primer sequences that include Illumina compatible adapters and barcodes. The resulting ATAC-seq libraries were purified (MinElute Kit, Qiagen), pooled and final library-pool concentrations were assessed (Bioanalyzer) prior to next-generation sequencing. The quality of ATAC-seq libraries was confirmed by a shallow sequencing run using a MiSeq v3 (Stanford Functional Genomics Facility, 2x75bp reads) before deep sequencing was performed on a NextSeq 500 (2x75bp reads).