Sample information curated by ChIP-Atlas

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.

Attributes by original data submitter

Sample

source_name
Liver
tissue
Liver
strain
C57BL/6
Sex
male
age
28
age unit
days
treatment
TCDD
dose
30
dose unit
ug/kg
duration
2
duration unit
hours
replicate
1
chip antibody
None
antibody vendor
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed as previously described (Dere et al., 2001. BMC Genomics 12, 365; Lo and Matthews, 2012. Toxicol Sci 130(2), 349-61). Briefly, mouse livers (~100 mg) were homogenized in 1% formaldehyde and incubated at room temperature for 10 minutes. Homogenates were centrifuged at 10,000 RPM for 3 minutes at 4°C and pellets washed with cold PBS followed by resuspension in TSEI with Protease Inhibitor Cocktail. Samples were sonicated 12 times for 10 seconds and supernatants transferred to new tubes and incubated with rabbit IgG and anti-AhR or just rabbit IgG overnight at 4°C. Protein A/G-Sepharose was added and samples incubated for 1.5h. Pellets were washed for 10 minutes in buffer 1, buffer 2, LiCl buffer, and TE. Protein-DNA complexes were then eluted using TE and cross-links reversed by overnight incubation at 65°C followed by DNA purification. Libraries were prepared using the MicroPlex kit (Diagenode) according to manufacturer's instructions

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
17500481
Reads aligned (%)
92.0
Duplicates removed (%)
21.8
Number of peaks
471 (qval < 1E-05)

mm9

Number of total reads
17500481
Reads aligned (%)
91.8
Duplicates removed (%)
21.9
Number of peaks
485 (qval < 1E-05)

Base call quality data from DBCLS SRA