alias: GSM3528374
title: GSM3528374: NKL IL2 treated control Rep2; Homo sapiens; ATAC-seq
library_construction_protocol: ATAC-seq in GM12878 and NKL cells was performed using Illumina Tn5 transposase (Nextera kit; cat# FC-121-1030, Illumina), and GM12878 with Fluoro-Tn5 was performed as described previously. Briefly, 50,000 cells were centrifuged at 500 g for 5 min at 4 °C and washed once in cold PBS. The cell pellet was gently resuspended in 50 μl pre-chilled lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630) and centrifuged immediately at 500 g for 10 min at 4 °C. The cell pellet was resuspended in 50 μl transposase mixture (25 μl 2× TD buffer (Nextera kit), 2.5 μl Illumina Tn5 transposase or final concentration of 100 nM Fluoro-Tn5, and nuclease-free water to a final volume of 40 μl) and incubated at 37 °C for 30 min. After purification with Qiagen Min-Elute PCR purification kit (cat# 28004, Qiagen), DNA was eluted in 10 μl Qiagen buffer EB. Sequencing libraries were prepared following the original ATAC-seq protocol with slight modification1. A PCR library amplification step was performed with a final forward and reverse primer concentration of 0.625 µM. An AMPure XP (Beckman Coulter) purification step (1.8X volume) was performed in place of a PCR purification step after the PCR library amplification. Sequencing libraries were assessed via the 2100 Bioanalyzer (Agilent) for nucleosome profiles, and the library concentration estimated by analysis of library fragments between 50 bp and 450 bp. The sequencing was performed on Illumina NextSeq or HiSeq at the Stanford Functional Genomics Facility.
identifiers.namespace: GEO
identifiers.id: GSM3528374