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
iPSC_96h
cell type
Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP
time
96h

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Nuclei were isolated from 50,000 cells and incubated with Tn5 transposase (Illumina) for 30 min at 37°C. DNA was purified and PCR-amplified using customized Nextera PCR primers. A size range of 200-1000 base pairs was selected for sequencing on the Illumina Hiseq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
22890629
Reads aligned (%)
93.7
Duplicates removed (%)
82.2
Number of peaks
5628 (qval < 1E-05)

mm9

Number of total reads
22890629
Reads aligned (%)
93.6
Duplicates removed (%)
82.3
Number of peaks
5618 (qval < 1E-05)

Base call quality data from DBCLS SRA