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
Mdr2-WT_liver
strain
FVB.129P2
genotype/variation
Mdr2-WT
treated with
none
tissue
Liver tissue
antibody
IgG (Santa Cruz, sc-2027)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Tissues were chopped and fixed in 1% formaldehyde for 15min. Lysates were immunoprecipitated with 5ug of antibody. Antibodies were pre-bound overnight to 50ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (after an overnight preclearing step) and the mix was incubated overnight at 4°C. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by overnight incubation at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters and PCR with index primers. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
26387628
Reads aligned (%)
87.5
Duplicates removed (%)
8.9
Number of peaks
712 (qval < 1E-05)

mm9

Number of total reads
26387628
Reads aligned (%)
87.3
Duplicates removed (%)
9.0
Number of peaks
781 (qval < 1E-05)

Base call quality data from DBCLS SRA