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

2016-11-16

ENA last update

2016-08-11

ENA-CHECKLIST

ERC000011

External Id

SAMEA4378436

INSDC center alias

Cancer Research UK Cambridge Institute University of Cambridge

INSDC center name

Cancer Research UK Cambridge Institute University of Cambridge

INSDC first public

2016-11-16T17:02:46Z

INSDC last update

2016-08-11T16:38:46Z

INSDC status

public

Submitter Id

E-MTAB-4913_2:do4332

broker name

ArrayExpress

common name

house mouse

genotype

[129S8xB6]F1xTc1

individual

74467

organism part

liver

phenotype

Male Germline

sample name

E-MTAB-4913_2:do4332

sex

male

strain

Tc1

Sequenced DNA Library

library_name

do4332_s

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

The Tc1 mouse line was obtained from Dr. E. Fisher and Dr. V. Tybulewizc and housed in the Biological Resources Unit (BRU) in the Cancer Research UK – Cambridge Institute under the Home Office Licence (PPL 70/7535). For maintenance of the transgenic line, the human chromosome 21 (HsChr21) was transmitted through the female germline by breeding female Tc1 mice to male (129S8 x C57BL/6J) F1 mice (conventional breeding setup). For male germline transmission, female (129S8 x C57BL/6J) F1 mice were crossed with male Tc1 mice. Samples were harvested after direct perfusion of the liver with buffered salt solution and cross-linked in 1% formaldehyde for 20 minutes, followed by quenching with 1/20 volume of 2.5M glycine to neutralise formaldehyde. Cross-linked tissues were homogenised in dounce tissue grinder and lysed according to published protocols (10.1016/j.ymeth.2009.03.001). Sonication was performed on a Misonix sonicator 3000 with a 418 tip to fragment chromatin to an average length of 300bp. 50 ul of cell lysate after sanitation were removed as input control DNA and processed alongside ChIP samples. The following antibodies were used for immuno-precipitation: H3K4me3 (Millipore 05-1339 CMA304, Lot numbers 236661 and 2504863), H3K27ac (abcam ab4729, Lot numbers GR150367 and GR200563), CEBPA (Santa Cruz sc-9314, Lot L1113), HNF4A (ARP31946, Lot numbers QC22894 and QC1455(R1)100317), RNA polymerase II (abcam, ab5408, Lot number GR106949). Immuno-precipitated DNA or 50ng of input DNA was used for library preparation following the standard Illumina TruSeq ChIP Sample preparation protocol.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

17001941

Reads aligned (%)

96.7

Duplicates removed (%)

18.0

Number of peaks

339 (qval < 1E-05)

mm9

Number of total reads

17001941

Reads aligned (%)

96.4

Duplicates removed (%)

18.1

Number of peaks

369 (qval < 1E-05)