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

strain

C57BL/6 x Sv129

tissue

Liver

age

postnatal 2-3 months

chip antibody

none

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Liver tissue was fixed with formaldehyde, lysed, sonicated, and GATA4-DNA complexes were isolated with antibody. DNA was purified using phenol/chloroform extraction and ethanol precipitation. Libraries were prepared with Illumina ChIP-Seq DNA Sample Prep kit Cat # IP-102-1001. The input (liver) and ChIP DNA fragments were repaired to generate blunt ends, with a single adenine added to each end. Illumina genomic adaptors were ligated to both ends of the fragments, ligation products were amplified by 18 cycles of PCR, and the PCR products between 250 and 450 bp were gel purified according to standard Illumina protocols. The quantity and quality of each library was evaluated by qPCR and Bioanalyzer (Agilent Technologies, Santa Clara, CA). Cluster generation and sequencing chemistry were performed using Illumina-supplied kits as appropriate. The ChIP DNA library was sequenced in single-read mode on the Illumina HiSeq 2000 platform.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

113713520

Reads aligned (%)

94.9

Duplicates removed (%)

11.8

Number of peaks

702 (qval < 1E-05)

mm9

Number of total reads

113713520

Reads aligned (%)

94.7

Duplicates removed (%)

11.8

Number of peaks

815 (qval < 1E-05)