title: GSM3671078: ATACseq_HUDEP2_CRISPR_115edit_bulk; Homo sapiens; ATAC-seq
library_construction_protocol: ATAC-seq was performed with Illumina Nextera DNA Preparation kit   (Illumina, FC-121-1030) as previously described (Buenrostro et al.,   2015). 50,000 cells of expansion phase HUDEP-2 or derived cell lines   were collected, and permeabilized with 50 mL ice cold lysis buffer (10   mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-360) for 10   minutes. The transposition reaction was carried out at 37 degrees for 60   minutes in 50 mL volume containing 25 mL 2x TD buffer and 2.5 mL   transpose enzyme (contained in Illumina Nextera DNA Preparation kit).   DNA was purified with QIAGEN MinElute PCR purification kit. Library amplification was  done with NEBNext Ultra II Q5 Master Mix   (contained in NEBNext Ultra II DNA Library Prep Kit). PCR amplification   was carried out as follow: 72 degrees 5 min, 98 degrees 30 s, 98 degrees   10 s, 63 degrees 30 s, 72 degrees 1 min, repeat steps 3-5 for another 7   cycles, hold at 4 degrees. The resulting libraries were purified using   QIAGEN MinElute PCR purification kit, and quantified with Qubit   fluorometer and bioanalyzer, and then sequenced in NextSeq 500 platform.   Sequencing parameter was paired end 2x41 bp reads, 8 bp index.
attributes.tag: GEO Accession
attributes.value: GSM3671078