Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTNNB1

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
hepatocellular carcinoma cells
tissue
liver
cell type
HCC-derived liver cancer cells
cell line
HepG2
treatment
Control
chip antibody
β-catenin (CST)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
35965298
Reads aligned (%)
82.9
Duplicates removed (%)
3.6
Number of peaks
981 (qval < 1E-05)

hg38

Number of total reads
35965298
Reads aligned (%)
84.5
Duplicates removed (%)
2.4
Number of peaks
822 (qval < 1E-05)

Base call quality data from DBCLS SRA