Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Pluripotent stem cell
Cell type
Differentiated hESCs
NA
NA

Attributes by original data submitter

Sample

source_name
ES-derived progenitors
tissue
ES-derived progenitors
differentiation stages
Definitive Endoderm
genotype
wild type

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked by formaldehyde and lysated by SDS lysis buffer. Sonicated nuclei were incubated with antibody overnight and then pulled down by dynabeads. After washing, decrosslinking was performed to isolate DNA. Libraries were prepared using the NEBNext® ChIP-seq Library Prep Master Mix Set for Illumina ® (NEB, E6240L)

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
23025265
Reads aligned (%)
98.8
Duplicates removed (%)
5.9
Number of peaks
45083 (qval < 1E-05)

hg19

Number of total reads
23025265
Reads aligned (%)
98.3
Duplicates removed (%)
6.5
Number of peaks
45014 (qval < 1E-05)

Base call quality data from DBCLS SRA