Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
mESC derived neural cells
NA
NA

Attributes by original data submitter

Sample

source_name
RA-treated Mutant ESC
agent
1 uM all-trans retinoic acid (RA)
strain background
C57BL/6 (mixed)
chip antibody
NA
genotype/variation
GLP mutant (GLP 3A) homozygous

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
79698645
Reads aligned (%)
98.3
Duplicates removed (%)
15.2
Number of peaks
752 (qval < 1E-05)

mm9

Number of total reads
79698645
Reads aligned (%)
98.0
Duplicates removed (%)
15.1
Number of peaks
855 (qval < 1E-05)

Base call quality data from DBCLS SRA