title: GSM9135159: MCF10A PM shCHD1 A 72h dox, biol rep 1; Homo sapiens; ATAC-seq
library_construction_protocol: 50,000 live cells were sorted and then centrifuged at 500xg for 5 minutes at 4˚C. Cell pellets were then resuspended in 50 µL of cold resuspension buffer (RSB; 10 mMTris-HCl at pH 7.4, 10mM NaCl, 3 mM MgCl2) supplemented with 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin, to dissociate cell membrane. Samples were incubated on ice for 3 minutes and then washed with 1 mL of ATAC RSB with 0.1% NP-40 by inverting the tube. The nuclei were subsequently pelleted by centrifugation at 500xg for 10 minutes at 4˚C and then resuspended in 50 µL of transposition mixture (25 µL of 2x TD buffer, 2.5 µL of transposase [100nM final], 16.5 µL of 1x PBS, 0.5 µL of 1% digitonin, 05 µL of 10% Tween-20, 5 µL of nuclease-free water) for tagmentation. Tagmentation was performed at 37˚C for 30 minutes at 1000 RPM on a thermomixer. DNA clean-up was performed following the tagmentation using the Zymo DNA Clean and Concentrator 5 kit (Zymo #D4014) and DNA was eluted in 21 µL of elution buffer Library amplification was performed as per the Omni-ATAC protocol52. After five initial amplification cycles, an additional qPCR surveillance step was included to determine the optimal number of extra PCR amplification cycles,  enough to generate sufficient material for library sequencing, without over-amplifying and introducing duplicate artifacts. Amplified libraries were then purified with AMPure XP beads (Beckman Coulter #A63880) using a double-sided bead purification approach, to remove smaller primer dimers as well as large >1000bp fragments. Finally, libraries were quantified using the Qubit dsDNA high-sensitivity kit (Invitrogen #Q32854) and pooled at equimolar concentrations to be sequenced paired-end on a single lane of an Illumina NovaSeqX 10B flow cell.