GSM6190465: ATAC-Seq R35A_0h_rep1; Mus musculus; ATAC-seq
ATAC-seq was performed as previously published (Buenrostro et al., 2015). Briefly, cells were harvested at the mentioned timepoints, feeder-depleted and lysed at 50.000 cells per condition. Immediately, transposition was performed using Nextera Tn5 Transposase (15027865, Illumina) at 37ºC for 30 minutes. Chromatin was then purified using Qiagen MinElute PCR Purification Kit (28004, Qiagen). DNA was then amplified using NEBNext High Fidelity PCR Master Mix (M0541S, New England Biolabs Inc.) and barcoded primers (see table MMX). qPCR was performed to determine the optimal number of cycles for each condition to stop amplification prior to saturation. Quality was analyzed by gel electrophoresis and in a fragment Bioanalyzer (Agilent 2100 Bioanalyzer DNA 7500 assay).