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
cell line
J1
antibody
-
genotype/variation
WT

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin Immunoprecipitation (ChIP) was performed as described previously (Kim et al., 2009; Das et al., 2014). For bioChIP reactions, streptavidin beads (Dynabeads MyOne Streptavidin T1- Invitrogen) were used for the precipitation of chromatin, and 2% SDS was applied for first washing step. All other steps were same as conventional ChIP protocol. 2-10 ng of purified ChIP DNA was used to prepare sequencing libraries, using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB) and NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
34945774
Reads aligned (%)
98.2
Duplicates removed (%)
14.6
Number of peaks
528 (qval < 1E-05)

mm9

Number of total reads
34945774
Reads aligned (%)
98.0
Duplicates removed (%)
14.6
Number of peaks
589 (qval < 1E-05)

Base call quality data from DBCLS SRA