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

2013-06-03

ENA last update

2018-03-08

External Id

SAMEA1906588

INSDC center alias

Cambridge University

INSDC center name

Cambridge University

INSDC first public

2013-06-03T13:10:15Z

INSDC last update

2018-03-08T16:23:06Z

INSDC status

public

Submitter Id

E-MTAB-1579:Mmu5

broker name

ArrayExpress

common name

house mouse

developmental stage

adult

organism part

liver

sample name

E-MTAB-1579:Mmu5

sex

male

strain

C57BL/6

Sequenced DNA Library

library_name

do1948_H3K4me3_liver_CMA304_mmuBL653663

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

mm10

Number of total reads

10347630

Reads aligned (%)

98.5

Duplicates removed (%)

6.1

Number of peaks

12312 (qval < 1E-05)

mm9

Number of total reads

10347630

Reads aligned (%)

98.4

Duplicates removed (%)

6.3

Number of peaks

12279 (qval < 1E-05)