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
cell type
mouse embryonic stem cell
cell line
J1 ES cells containing BirA
chip antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The cells were cross-linked with 1% formaldehyde, followed by sonication to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500bp to 1Kb were immunoprecipitated using different antibodies/beads. ChIP-sequencing libraries were generated using NEB ChIP-seq library prep kit (E6200L) according to the manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
10213469
Reads aligned (%)
91.7
Duplicates removed (%)
72.9
Number of peaks
124 (qval < 1E-05)

mm9

Number of total reads
10213469
Reads aligned (%)
91.6
Duplicates removed (%)
73.2
Number of peaks
107 (qval < 1E-05)

Base call quality data from DBCLS SRA