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
strain
C57BL/6J/129 SV mixed background
Sex
male
age
10-20 weeks
genotype
Wild-type
chip antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated (for BAF180 ChIP-Seq) or MNase-digested (for REV-ERBα ChIP-Seq) nuclei and Protein-DNA complexes were isolated with antibody. Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina NextSeq 500 (75 nt reads, single-end for BAF180 ChIP-Seq). The resulting DNA libraries were quantified and sequenced on Illumina HiSeq 2500 Sequencing system (50nt reads, single end for REV-ERBα ChIP-Seq).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
13096585
Reads aligned (%)
85.1
Duplicates removed (%)
13.0
Number of peaks
209 (qval < 1E-05)

mm9

Number of total reads
13096585
Reads aligned (%)
84.9
Duplicates removed (%)
13.0
Number of peaks
223 (qval < 1E-05)

Base call quality data from DBCLS SRA