Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

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

Attributes by original data submitter

Sample

source_name
hES-Derived Definitive Endoderm cells
passage
Between 40-50
line
H1
pulldown method
Input - N/A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked for 10 minutes with 1% formaldehyde, which was quenched with 125mM glycine. The cells were washed 3X with ice cold PBS+protease inhibitors+PMSF, and scraped into tubes. Chromatin was sheared in a Diagenode Bioruptor Pico to 150-600bp fragments. Input chromatin was saved for "input sample" and the remainder of the chromatin was pulled down using streptavidin beads. Bound chromatin and input DNA samples had the crosslinks reversed, the DNA was purified by phenol/chloroform extraction and ethanol precipitation, and the purified DNA samples were submitted to Beijing Genomics Institute for Library Generating and Sequencing. Library generated by Beijing Genomics Institute

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
47882009
Reads aligned (%)
98.8
Duplicates removed (%)
13.4
Number of peaks
1550 (qval < 1E-05)

hg19

Number of total reads
47882009
Reads aligned (%)
97.9
Duplicates removed (%)
15.0
Number of peaks
1438 (qval < 1E-05)

Base call quality data from DBCLS SRA