Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Rara

Cell type

Cell type Class
Pluripotent stem cell
Cell type
F9
Tissue
Testis
Disease
Embryonal Carcinoma; Testicular Teratoma

Attributes by original data submitter

Sample

source_name
F9 cells, RA, 48h, RAR ChIP
cell line
F9
cell type
embryonal carcinoma cell line
treatment
all-trans retinoic acid
time after ra stimulation
48h
chip antibody
anti-panRAR (Santa Cruz, Sc-773)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Cells were cross-linked by a two-step procedure, with 2mM disuccinimidyl glutarate for 30 minutes at room temperature and then with 1% formaldehyde for 10 min at 37°C. The ChIP lysis buffer composition was 50mM Tris-HCl pH 8, 10mM EDTA, 1% SDS and 1X Protease Inhibitor Cocktail w/o EDTA. After lysis, chromatin extract were sonicated to reduce the length of DNA fragments to 200-400 bp using a Diagenode Bioruptor. ChIP-seq library: ChIP-seq libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Sequencing was performed on Illumina Genome Analyzer IIx (IGBMC) single-end 36bp.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
31760038
Reads aligned (%)
48.6
Duplicates removed (%)
31.4
Number of peaks
19010 (qval < 1E-05)

mm9

Number of total reads
31760038
Reads aligned (%)
48.5
Duplicates removed (%)
31.6
Number of peaks
19147 (qval < 1E-05)

Base call quality data from DBCLS SRA