Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Liver
Cell type
Hep G2
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular

Attributes by original data submitter

Sample

source_name
HepG2
cell line
HepG2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Exponentially growing cells from ENCODE Tier 1 and Tier 2 cell lines were crosslinked in 1% formaldehyde and harvested in batches of 20 million cells per replicate.  Prepared nuclei were resuspended in RIPA buffer and chromatin shearing was performed on a Bioruptor Twin instrument (Diagenode). Antibody (5 µg/rxn) was coupled to M-280 Dynabeads (ThermoFisher Scientific; 11201) overnight prior to addition of sheared chromatin. A small aliquot of the sheared chromatin was reserved as an input control. Following incubation and wash steps, captured chromatin and input control were reverse crosslinked overnight at 65°C and recovered using the QIAquick PCR Purification System (Qiagen; 28104). ChIP-seq libraries (illumina) were prepared and run on an Illumina HiSeq 2500 instrument.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
44394778
Reads aligned (%)
97.6
Duplicates removed (%)
6.0
Number of peaks
984 (qval < 1E-05)

hg19

Number of total reads
44394778
Reads aligned (%)
97.1
Duplicates removed (%)
6.7
Number of peaks
1043 (qval < 1E-05)

Base call quality data from DBCLS SRA