title: GSM5819002: induced MCF10A-YAP5SA replicate 2; Homo sapiens; ATAC-seq
library_construction_protocol: For ATAC-seq, cells were washed with ice cold PBS and lysed in ATAC lysis buffer (10mM Tris pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% Tween 20 and freshly added protease inhibitor cocktail (Sigma)) by incubating on ice for 10 minutes. Nuclei were collected by spinning at 500 g for 10 minutes at 4°C. The transposition reaction mix (25 μl 2X TD buffer, 2.5 μl TDE1 Nextera transposase (Illumina), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl of nuclease free water) was added to nuclei and incubated at 37°C for 30 mins. Next, the reaction was cleaned using the MinElute PCR purification kit (Qiagen). For ATAC-seq, a PCR with 10-13 cycles was performed using the NEBNext High Fidelity 2X PCR Master Mix (NEB) and Ad1_noMX and Ad2.1–2.4 barcoded primers described in (Buenrostro et al., 2013). Size selection of the libraries was performed with Agencourt AMPure XP beads (Beckman Coulter). Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Paired end 2 x 75 bp sequencing was performed on the NextSeq 500 platform (Illumina).