Antigen

Antigen Class

TFs and others

Antigen

AHR

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

liver

tissue

liver

cell type

hepatocytes

treatment

vehicle control (0.1% DMSO) for 24h

chip antibody

AhR (ENZO Lifesciences, BML-SA210, Lot# 01031447)

Sequenced DNA Library

library_name

GSM6213902

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Cells were fixed with 1% formaldehyde at room temperature for 15 min and quenched with 0.125 M glycine and shipped to Active Motif (Carlsbad, CA, U.S.A) for ChIP-seq analysis. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated using a Misonix Sonicator 3000. For each ChIP reaction, 30 μg of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reactions were set up using precleared chromatin and a rabbit polyclonal antibody against AhR (ENZO Lifesciences, BML-SA210, Lot# 01031447) and incubated overnight at 4 °C. Protein A agarose beads were added and incubation at 4 °C was continued for another 3 h. Immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. Immune complexes were eluted from the beads with SDS buffer and subjected to RNase treatment and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 °C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by phenol/chloroform extraction and ethanol precipitation. Purified DNA was quantified on a NanoDrop spectrophotometer. .equipped with a microtip in order to shear the DNA to an average length of 300–500 bp. Lysates were cleared by centrifugation and stored at −80 °C. ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3′-ends. Illumina genomic adapters were ligated and the sample was size-fractionated (200–250 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on HiSeq 2000.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

hg38

Number of total reads

37498205

Reads aligned (%)

87.3

Duplicates removed (%)

20.5

Number of peaks

1135 (qval < 1E-05)

hg19

Number of total reads

37498205

Reads aligned (%)

86.7

Duplicates removed (%)

21.5

Number of peaks

1019 (qval < 1E-05)