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/6
tissue
Liver
age
3-4 month old
genotype
wild type
chip antibody
Rabbit IgG (Jackson Immuno Res)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Livers were removed and flash frozen in liquid nitrogen. They were later homogenized in 1% PFA and the nuclei were isolated via sucrose density centrifugation. They were resuspended in SDS buffer and sonicated. The sonicated chromatin (major DNA fragment size ~150-400 bp) was aliquoted and used for ChIP. For Pol II ChIP, rabbit IgG was used as the control. For Nelf-A ChIP, goat IgG was used as the control. ChIP-seq SE50 libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
31196529
Reads aligned (%)
92.7
Duplicates removed (%)
20.2
Number of peaks
596 (qval < 1E-05)

mm9

Number of total reads
31196529
Reads aligned (%)
92.5
Duplicates removed (%)
20.2
Number of peaks
612 (qval < 1E-05)

Base call quality data from DBCLS SRA