GSM7898252: ATAC-seq_Group3_SMARCA4KO_rep1; Homo sapiens; ATAC-seq
ATAC-seq was performed as described previously (Buenrostro et al., 2013; Corces et al., 2017) with some modifications. To quantitatively analyze ATAC-seq data between experimental conditions, we used a fixed number of Drosophila S2 cells as a spike-in control for each sample. The read counts for the spike-in were used to internally calibrate ATAC-seq data, as described previously (Bonhoure et al., 2014; Hu et al., 2015; Orlando et al., 2014). In brief, 1x104 (for group1) or 2.5x103 S2 cells (for group2) were first mixed with 1x105 eHAP cells in a tube, washed with cold PBS, and centrifuged at 935 x g for 5 min. Cells were permeabilized with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Then cells were transposed using Tn5 complex with MEAB34 adaptors in TAPS-DMF buffer at 37 ˚C for 30 min. Genomic DNA was purified with Monarch PCR & DNA Cleanup Kit (NEB). After amplification of transposed DNA using Q5 High-Fidelity 2X Master Mix (NEB), DNA was size-selected using SPRI beads to produce libraries with fragments between 150 and 600 bp. To reduce a contamination of mitochondrial DNA, the libraries for group2 were treated with an anti-mitochondrial DNA CRISPR/Cas9 library to specifically digest mitochondrial DNA as described previously (Montefiori et al., 2017). The libraries were sequenced on HiSeq3000 or HiSeq2500 for 100 bp or 50 bp paired-end reads, respectively. Two biological replicates were analyzed for each experimental condition.