GSM4437155: ATAC D13 NM REP 1; Homo sapiens; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Pluripotent stem cell
Cell type
iPSC intermediates
NA
NA
Attributes by original data submitter
Sample
source_name
human fibroblasts
cell type
human naive intermediates
passages
Passage 0
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Reprogramming intermediates and hiPSCs were isolated by FACS (Supplementary Table 4) and ~65k cells were washed and lysed in ATAC-seq lysis buffer (10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 10 mM Tris pH 7.4). The transposition reaction was then carried out by using 22.5 μl of UltraPure Distilled Water (ThermoFisher, Cat#10977-015), 25 μl of Tagment DNA Buffer (Illumina, Cat#15027866) and 2.5 μl of Tagment DNA Enzyme 1 (Illumina, Cat#15027865) for each sample, and then incubated for 30 min at 37°C, followed by immediate purification using a MinElute Reaction Cleanup Kit (Qiagen, Cat#28204) according to the manufacturer's instructions. 11 μl of transposed DNA, 25μl of the NEBNext High-Fidelity 2x PCR Master Mix (Cat#M0541S) and 1.25μM of the adaptor sequences as published previously were used in a 50 μl PCR reaction. PCR parameters were: 72°C for 5 min, 98°C for 30 s and 9 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. The prepared libraries were purified using a MinElute PCR purification kit (Qiagen, Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880) according to the manufacturer's specifications, where library fragments ranging from 200 to 700 bp were selected and sequenced on an Illumina HiSeq 1500 in 2x51 cycle paired-end mode