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

2019-11-20

ENA last update

2019-10-25

ENA-CHECKLIST

ERC000011

External Id

SAMEA6120183

INSDC center alias

EMBL-EBI

INSDC center name

EMBL-EBI

INSDC first public

2019-11-20T17:03:55Z

INSDC last update

2019-10-25T13:44:00Z

INSDC status

public

Submitter Id

E-MTAB-8471:do9912

broker name

ArrayExpress

common name

house mouse

developmental stage

adult

genotype

wild type genotype

individual

96733

organism part

liver

sample name

E-MTAB-8471:do9912

sex

male

strain

C57BL/6J

Sequenced DNA Library

library_name

do9912_s

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Liver samples were collected from two male C57BL/6J individuals Liver tissue was crosslinked, dounced and lysed as described in Schmidt et al. 2009 (PMID: 19275939). The chromatin was sonicated for 6 minutes (12 cycles of 30s on and 60s off) at a power-output 30 Watt using a Misonix sonicator 3000. Chromatin was immunoprecipitated using 10ul CTCF antibody (Merck-Millipore, cat# 07-729). Immunoprecipitated DNA and and 50ng of input DNA was used for library preparation using the ThruPLEX DNA-Seq library preparation protocol according to the manufacturer's instructions (Rubicon Genomics, UK). Library fragment size was determined using a 2100 Bioanalyzer (Agilent).

Sequencing Platform

instrument_model

Illumina HiSeq 4000

mm10

Number of total reads

46397032

Reads aligned (%)

98.4

Duplicates removed (%)

24.2

Number of peaks

39731 (qval < 1E-05)

mm9

Number of total reads

46397032

Reads aligned (%)

98.1

Duplicates removed (%)

24.2

Number of peaks

39828 (qval < 1E-05)