Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

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

Attributes by original data submitter

Sample

ENA first public
2013-10-18
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA2224586
INSDC center alias
Cambridge University
INSDC center name
Cambridge University
INSDC first public
2013-10-18T17:01:30Z
INSDC last update
2018-03-08T16:47:47Z
INSDC status
public
Submitter Id
E-MTAB-1579:HepG2
broker name
ArrayExpress
cell type
HepG2
common name
human
developmental stage
adult
organism part
liver
sample name
E-MTAB-1579:HepG2
sex
male

Sequenced DNA Library

library_name
do2618_H3K4me3_HepG2_05-1339_hsa
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Samples were prepared by direct perfusion of the tissue with buffered salt solution, followed by % formaldehyde. After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde. After homogenization, the cells were rinsed with PBS. The animal tissues were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA was not further fragmented. After end-repair and addition of an A base to the 3prime ends, the adapters were ligated to the ends of the DNA Fragments using 2 ul of fortyfold diluted Adapter oligo mix in a total reaction volume of 25 ul. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 ul of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturers protocols, with paired end sequencing for 75 cycles.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
9456536
Reads aligned (%)
86.3
Duplicates removed (%)
34.4
Number of peaks
5104 (qval < 1E-05)

hg19

Number of total reads
9456536
Reads aligned (%)
85.8
Duplicates removed (%)
34.7
Number of peaks
5070 (qval < 1E-05)

Base call quality data from DBCLS SRA