GSM7871991: S169 6h; Homo sapiens; ATAC-seq
ATAC-seq was implemented as outlined previously (Corces et al 2017). After thawing on ice, 50,000 cells were washed, chemically lysed (1% Digitonin, 10% Tween-20 & 10% NP-40) and pelleted. 50ul of transposition reaction mix (Tn5 transposase, Tagment DNA buffer, Tween-20, & Digitonin) was added to the pellet and incubated at 37 ˚C for 30 minutes. DNA was then isolated using Qiagen MinElute Reaction Cleanup kit. Libraries were generated using the Ad1 noMX and Ad2.1–2.20 barcoded primers by Illumina before purification with AMPure beads to remove primer dimers. Amplified libraries were quantified Using Qubit HS DNA Assay (Thermo Fisher Scientific, Paisley, United Kingdom). Library sizes were assessed on an Agilent Technologies 2100 Bioanalyzer before sequencing on the Illumina Nextseq platform paired-end reads (35 bp (R1) and 40 bp (R2)). One cartridge was used per 2 patients i.e. 20 multiplexed samples per cartridge.