Antigen

Antigen Class

Input control

Antigen

Input control

Cell type

Cell type Class

Liver

Cell type

Hepatocytes

MeSH Description

The main structural component of the LIVER. They are specialized EPITHELIAL CELLS that are organized into interconnected plates called lobules.

Sample

source_name

primary culture of hepatocytes

strain

C57Bl6J

cell type

hepatocytes

antibody

none (input)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Fixation: 10 min 1% formaldehyde. Nuclear extracts sonication: Bioruptor 14 time 30s on / 30s off and cleared by centrifugation. Decrosslinking 65°C overnight. DNA purification: minielute (Qiagen) . E2F1 ChIP, samples were precleared with protein A agarose / salmon sperm DNA and chromatin was immunoprecipitated with anti–E2F1 c-20 antibody (santa cruz sc-193). Immunoprecipitated chromatin was washed (low salt, high salt, LiCl and TE buffer), reverse-crosslinked (65°C overnight) and purified with mini elute columns (Qiagen). Qubit fluorometric quantification (Life Technology) was used to quantify DNA. Illumina TruSeq ChIP Sample Prep reagents, according to the provider's protocol

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

133390343

Reads aligned (%)

98.1

Duplicates removed (%)

51.0

Number of peaks

496 (qval < 1E-05)

mm9

Number of total reads

133390343

Reads aligned (%)

97.9

Duplicates removed (%)

51.0

Number of peaks

539 (qval < 1E-05)