Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Rorc

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
time
ZT22
experiment_type
ChIP-seq
target
RORgamma
genome build
mm9
genotype
C57BL/6J RORg KO

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP experiments were performed as described (Feng et al. 2011) with minor changes. Mouse liver, brain (ventral tegmental area), and epididymal white adipose tissue (eWAT) were harvested, minced and cross-linked in 1% formaldehyde for 20min, followed by quenching with 1/20 volume of 2.5M glycine solution for 5 min, and two washes with 1×PBS. Nuclear extracts were prepared by Dounce homogenization in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC). Chromatin fragmentation was performed by sonication in lysis buffer (50mM Tris-HCL ph 8.0, 0.1%SDS, 10mM EDTA), using the Bioruptor (Diagenode). Proteins were immune-precipitated in ChIP buffer, and crosslinking was reversed overnight at 65°C in SDS buffer (50mM Tris-HCL, 10mM EDTA, 1% SDS, pH 8), and DNA isolated using phenol/chloroform/isoamyl alcohol. DNA was amplified according to ChIP Sequencing Sample Preparation Guide provided by Illumina, using adaptor oligo and primers from Illumina, enzymes from New England Biolabs and PCR Purification Kit and MinElute Kit from Qiagen.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
27683291
Reads aligned (%)
70.5
Duplicates removed (%)
28.3
Number of peaks
1687 (qval < 1E-05)

mm9

Number of total reads
27683291
Reads aligned (%)
70.2
Duplicates removed (%)
28.4
Number of peaks
1645 (qval < 1E-05)

Base call quality data from DBCLS SRA