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
RA-treated WT ESC
agent
1 uM all-trans retinoic acid (RA)
strain background
C57BL/6 (mixed)
chip antibody
NA
genotype/variation
wild type

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin Immunoprecipitation were performed according to Diagenode IDeal ChIP-seq Kit with minor modifications. Briefly, 2 million cells were harvested in PBS and crosslinked in 1% formaldehyde for 2 minutes. After sonication, chromatin from 1 million cells was subjected to ChIP using IDeal ChIP-seq Kit. For RNA-Seq, RNA samples were extracted using Trizol reagent, and genomic DNA contaminations were eliminated with TurboTM DNase (Life technologies). ChIP-seq libraries were constructed with KAPA Library Preparation Kits and single-end sequenced with Hiseq 2000. For RNA-Seq, total RNA were extracted and the subsequent library preparation steps were carried out according to standard Illumina procedures at the NIBS sequencing center and subjected to single-end sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
87417918
Reads aligned (%)
98.2
Duplicates removed (%)
11.9
Number of peaks
681 (qval < 1E-05)

mm9

Number of total reads
87417918
Reads aligned (%)
98.0
Duplicates removed (%)
11.8
Number of peaks
804 (qval < 1E-05)

Base call quality data from DBCLS SRA