Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS cells
NA
NA

Attributes by original data submitter

Sample

source_name
mouse iPSCs
strain
129SV/Jae/C57BL6J
cell type
iPSC

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
50,000 sorted cells were resuspended in nuclear isolation buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL). Nuclei were then treated with Tn5 transposase (Illumina). DNA was isolate using the MinElute Kit (Qiagen) and PCR-amplified using barcoded Nextera primers (Illumina). The DNA libraries were validated using a bioanalyzer (Agilent).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
39202864
Reads aligned (%)
91.4
Duplicates removed (%)
42.8
Number of peaks
4631 (qval < 1E-05)

mm9

Number of total reads
39202864
Reads aligned (%)
91.3
Duplicates removed (%)
42.9
Number of peaks
4350 (qval < 1E-05)

Base call quality data from DBCLS SRA