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
strain
back-crossed to the BALB/c
chip antibody
None (Input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Liver tissue isolated from sacrificed mice was immediately frozen in liquid nitrogen. To process for ChIP, the tissue was thawed, minced and crosslinked in 1 % formaldehyde/PBS. Cells were disrupted and nuclei purified by dounce homogenization in a hypotonic buffer (20 mM HEPES/NaOH pH 7.5, 0.25 M sucrose, 3 mM MgCl2, 0.2% NP-40, 3 mM 2-mercaptoethanol, Complete protease inhibitor cocktail). To prepare ChIP extracts, nuclei were suspended SDS lysis buffer (50 mM HEPES/NaOH pH 7.5, 1% SDS, 10 mM EDTA, Complete protease inhibitor), incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency. ChIP-Seq libraries were produced and sequenced according to Illumina protocols. ChIP-exo libraries were produced for Illumina sequencing. Libraries were multiplexed for sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
17290019
Reads aligned (%)
97.3
Duplicates removed (%)
10.4
Number of peaks
523 (qval < 1E-05)

mm9

Number of total reads
17290019
Reads aligned (%)
97.1
Duplicates removed (%)
10.5
Number of peaks
531 (qval < 1E-05)

Base call quality data from DBCLS SRA