Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC derived endodermal cells
NA
NA

Attributes by original data submitter

Sample

source_name
dEN
cell line background
HUES64
cell type
Definitive Endoderm (ES derived)
genotype/variation
wildtype

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Tagmentation was performed on whole nuclei at 37C for 45 minutes as previously described in (Buenrostro et al., 2013). DNA was isolated on PCR min-elute columns (Qiagen) and a small amount of the DNA was amplified for 9, 12 and 15 cycles to determine optimal cycling conditions. Nextera amplified

Sequencing Platform

instrument_model
Illumina MiSeq

hg38

Number of total reads
95388288
Reads aligned (%)
99.2
Duplicates removed (%)
1.9
Number of peaks
25627 (qval < 1E-05)

hg19

Number of total reads
95388288
Reads aligned (%)
98.6
Duplicates removed (%)
1.6
Number of peaks
25406 (qval < 1E-05)

Base call quality data from DBCLS SRA