Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
REST

Cell type

Cell type Class
Liver
Cell type
Hepatocytes
MeSH Description
The main structural component of the LIVER. They are specialized EPITHELIAL CELLS that are organized into interconnected plates called lobules.

Attributes by original data submitter

Sample

Alias
E-MTAB-437:human NRSF ChIP 1
Broker name
ArrayExpress
CellType
hepatocytes
Description
Protocols: The animal livers 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 and input DNA were not further fragmented. After end-repair and addition of an A base to the 3 prime ends, the adapters were ligated to the ends of the DNA Fragments using 2 ml of fourtyfold diluted Adapter oligo mix in a total reaction volume of 25 ml. 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 ml of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2 percent agarose gel and a gel slice containing the 200-300 bp fragments was excised. Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution followed by percent formaldehyde. After 10 minutes the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde. After homogenization the hepatocytes were rinsed with PBS.
INSDC center alias
CRUK-CRI
INSDC center name
CRUK-CRI
INSDC first public
2011-11-01T17:00:34Z
INSDC last update
2018-03-08T15:32:33Z
INSDC status
public
SRA accession
ERS066527
Sample Name
ERS066527
Sex
male
Tissue
liver
Title
human NRSF ChIP 1

Sequenced DNA Library

library_name
human ChIP 3
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The animal livers 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 and input DNA were not further fragmented. After end-repair and addition of an A base to the 3 prime ends, the adapters were ligated to the ends of the DNA Fragments using 2 ml of  fourtyfold diluted Adapter oligo mix in a total reaction volume of 25 ml. 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 ml of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2 percent agarose gel and a gel slice containing the 200-300 bp fragments was excised. Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution followed by percent formaldehyde. After 10 minutes the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde. After homogenization the hepatocytes were rinsed with PBS.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
30500610
Reads aligned (%)
63.2
Duplicates removed (%)
27.6
Number of peaks
1861 (qval < 1E-05)

hg38

Number of total reads
30500610
Reads aligned (%)
65.3
Duplicates removed (%)
25.9
Number of peaks
1619 (qval < 1E-05)

Base call quality data from DBCLS SRA