GSM6431141: Eahy926, IL1b, 1.1; Homo sapiens; ATAC-seq
One well of a 12-well plate (~200,000 cells) was directly lysed using a custom TN5 buffer (33mM Tris Acetate pH 7.8, 66mM Potassium Acetate, 10 mM Magnesium Acetate, 16% dimethylformamide & 0.1% NP40). 47.5 ul of lysed cells was added to 2.5 ul Tn5 tagmentation enzyme (Illumina) & incubated at 37C for 1hr, and the reaction stopped by addition of 20 ul buffer RLT (Qiagen). Products were purified by addition of 1.8 volumes Ampure XP beads (Beckman-Coulter) & magnetic separation of beads, followed by two 80% ethanol washes, brief drying of pellets & resuspension in 23 ul water. Barcoded ATAC-seq libraries were then generated as described in (Fulco, C. P., Nasser, J., Jones, T. R. & Munson, G. Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations. Nature (2019)), and sequenced to a depth of 10-20 million reads per library. Amplification with custon ATAC-seq oligos to give ATAC fragments flanked by read1, read2 sequences, and an 8 base index sequence specific to each library. Libraries were prepared on two different days, designated (under library name & title) as CELLLINE_CONDITION_0 & _1. Biological replicate numbers are indicated after a dot, e.g. _1.1, _1.2 & _1.3.