Antigen

Antigen Class

No description

Antigen

NA

Cell type

Cell type Class

Liver

Cell type

Liver

MeSH Description

A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Sample

ENA-FIRST-PUBLIC

2012-05-30T17:00:31Z

ENA-LAST-UPDATE

2018-03-08T15:46:21Z

External Id

SAMEA1325114

INSDC center name

Max-Delbrueck-Center, MDC, Berlin

INSDC first public

2012-05-30T17:00:31Z

INSDC last update

2018-03-08T15:46:21Z

INSDC status

public

StrainOrLine

HXB02

Submitter Id

E-MTAB-1102:liver-H3K4me3-HXB02-male-bio1-tech1.bam

age

6 week

broker name

ArrayExpress

common name

Norway rat

developmental stage

adult

organism part

liver

sample name

E-MTAB-1102:liver-H3K4me3-HXB02-male-bio1-tech1.bam

scientific_name

Rattus norvegicus

Sequenced DNA Library

library_name

DNA_Extract_liver-H3K4me3-HXB02-male-bio1-tech1

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Rats were kept in the animal facility of the Institute of Physiology, Czech Academy of Science (Prague, Czech Republic) in a climate-controlled environment with 12h light/dark cycles. Rats were housed in polystyrene cages containing wood shavings and fed standard rodent chow and water ad libitum. Six weeks old male rats were sacrificed by cervical dislocation and tissue (left ventricle of the heart and liver) was collected between 8 and 10 am, snap frozen in liquid nitrogen and stored at -80 C. All animal procedures were in accordance with the Animal Protection Law of the Czech Republic. ChIP samples were prepared as previously described (Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-37, 2007) with following changes: Frozen LV and liver tissue was crunched using pestle and mortar. 125mg tissue was homogenized in a Potter- Elvehjem tissue grinder, nuclei were isolated and digested with MNase (Sigma- Aldrich) to generate native chromatin templates consisting mainly of mononucleosomes. Chromatin was precipitated with anti-H3K4me3 (NEB, 9751 S), anti-H3K27me3 (Millipore, 07-449), anti-H3K4me1 (Abcam, ab8895), or anti- H4K20me1 (Abcam, ab9051) and antibody-bound DNA fragments were purified by MinElute PCR Purification Kit (QIAGEN). Specificity of immunoprecipitation was confirmed with known genes by qPCR. 50ng of DNA was used for construction of ChIP-seq libraries according to the manufacturer's protocol (Illumina/Solexa).

Sequencing Platform

instrument_model

Illumina Genome Analyzer II

rn6

Number of total reads

115066223

Reads aligned (%)

98.2

Duplicates removed (%)

68.5

Number of peaks

61918 (qval < 1E-05)