Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
embryonic stem cell
genotype
wild type
cell line
E14
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP-seq has been carried out as previously described6,7. Briefly, 2 million cells were crosslinked with 1% formadehyde for 10 min at RT. The reaction was quenched by adding 125 mM of Glycine and incubating for 5 min at RT. Cells were lysed in RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with protease inhibitor (Roche). And chromatin was sonicated into short fragments (300-700 bp). The fragmented chromatin was incubated with antibodies to pull down the specific DNA bound TFs or histones. After intensive wash, DNA was purified and prepared as sequencing library using illumina Truseq LT kit. TruSeq

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
6054242
Reads aligned (%)
96.3
Duplicates removed (%)
10.3
Number of peaks
350 (qval < 1E-05)

mm9

Number of total reads
6054242
Reads aligned (%)
96.1
Duplicates removed (%)
10.6
Number of peaks
320 (qval < 1E-05)

Base call quality data from DBCLS SRA