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 cells (ESC)
esc strain
R1 ESC
mouse strain
129SV
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
cells were fixed with 1% Formaldehyde for 10 minutes, then quenched with 0.125M Glycine. After nuclei extraction as described in Rada et al, Nature 2011. Sonication was carried out using Diagenode bioruptor in 15ml Falcon tubes. Each ChIP was validated using q-PCR against selected loci. libraries were prepared for Illumina sequencing using descibed protocols. All libraries were sequenced as single reads, 36bp length on the Illumina Genome Analyzer Iix.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
27620089
Reads aligned (%)
97.1
Duplicates removed (%)
15.9
Number of peaks
463 (qval < 1E-05)

mm9

Number of total reads
27620089
Reads aligned (%)
96.9
Duplicates removed (%)
16.0
Number of peaks
523 (qval < 1E-05)

Base call quality data from DBCLS SRA