Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Digestive tract
Cell type
Intestines
MeSH Description
The section of the alimentary canal from the STOMACH to the ANAL CANAL. It includes the LARGE INTESTINE and SMALL INTESTINE.

Attributes by original data submitter

Sample

source_name
Whole Intestine
antibody
none, DNA input control
strain
C57BL/6
age
E14.5
genotype
wild type

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed following a previously described protocol (Vokes et. Al, 2007). Intestines wer snap-frozen in liquid and ground in a mortar and pestle to dissociate the tissue to single cells. DNA and protein were then crosslinked and sonicated to an average 500 bp fragment size. cJUN bound regions were immunoprecipitated overnight using anti cJUN Polyclonal Rabbit antibody (Santa Cruz sc-44) bound to Protein G Dyanabeads). Input control consisted of sonicated DNA. ChIP libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
50800575
Reads aligned (%)
94.0
Duplicates removed (%)
23.8
Number of peaks
538 (qval < 1E-05)

mm9

Number of total reads
50800575
Reads aligned (%)
93.8
Duplicates removed (%)
23.8
Number of peaks
576 (qval < 1E-05)

Base call quality data from DBCLS SRA