title: GSM9022888: MCF-7 cells treated with DMSO for 30 min, Rep3; Homo sapiens; ATAC-seq
library_name: GSM9022888
library_construction_protocol: ATAC-seq libraries were generated as previously described with a few modifications. Cells were collected by trypsinization counted at experimental endpoint, and 50,000 live cells were used for each experimental condition. Nuclei were purified by resuspending cell pellets in hypotonic lysis buffer and incubating on ice for 3 minutes. Nuclei were then washed once with hypotonic lysis buffer without NP-40 or digitonin. Nuclei were then resuspended in transposition mix containing 100 mM Tn5 transposase and incubated at 37°C for 30 minutes shaking at 1000 rpm. Resulting tagmented DNA fragments were purified by column purification using the Qiagen PCR purification kit (cat. 28104). Final amplification of libraries was performed using the NEBNext High-Fidelity Master Mix, and Nextera i5 and i7 primers for a total of 7 cycles. Final samples were purified of excess adapters by using 1.3X volume of AMPure beads.  The libraries were subjected to quality control analyses, such as optimizing the number of PCR cycles required to amplify each set of libraries, quantifying the final library yield by Qubit fluorometer (Invitrogen, Q32851), and checking the size distribution of the final library by DNA ScreenTape system (Agilent Technologies, G2964AA, 5067–5584, and 5067–5603). The libraries were barcoded with indices as described for the Nextera i5/i7 indexed barcodes, multiplexed, and sequenced using Illumina NextSeq 2000 by 100 bp paired-end sequencing.