Antigen

Antigen Class

Input control

Antigen

Input control

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

source_name

Liver

tissue

liver

chip antibody

IgG (Santa Cruz, sc-2027)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies. For Myc, TEAD, Histone Marks, RNAPol2 ChIP, 3T9 fibroblasts or dissected liver/tumors were fixed with 1% formaldehyde. For YAP ChIP, fixation was performed by a double step approach with 0.5 M DSG (Di-(N-succinimidyl)-glutarate) and 1% formaldehyde (FA). Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

280376928

Reads aligned (%)

94.6

Duplicates removed (%)

21.2

Number of peaks

1383 (qval < 1E-05)

mm9

Number of total reads

280376928

Reads aligned (%)

94.3

Duplicates removed (%)

21.1

Number of peaks

1652 (qval < 1E-05)