Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RARA

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS cells
NA
NA

Attributes by original data submitter

Sample

source_name
Human iPS cells before chondrocyte differentiation by the 2C method
cell type
Human iPS cells
tissue
Foreskin
days after differentiation
0
chip antibody
Mouse anti-human RARα antibody (Perseus Proteomics, PP-H1920-00)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ATAC-seq samples, 50,000 cells were lysed to obtain nuclei in cold lysis buffer, and incubated in the Tn5 transposase reaction mix, as described previously (Buenrostro et al., 2013). For ChIP-seq and input samples, cells were cross-linked with 1% formaldehyde, and after lysis of cells, chromatin was fragmented by sonication. Then, protein-DNA complexes were purified with anti-RARα antibody. For ATAC-seq samples, DNA fragments were PCR-amplified using previously-designed barcoded primers, as described previously (Buenrostro et al., 2013). For ChIP-seq and input samples, libraries were constructed with ThruPLEX DNA-seq Kit (Takara Bio), according to manufacturer's instruction.

Sequencing Platform

instrument_model
HiSeq X Ten

hg19

Number of total reads
56337356
Reads aligned (%)
140.8
Duplicates removed (%)
10.6
Number of peaks
553 (qval < 1E-05)

hg38

Number of total reads
56337356
Reads aligned (%)
142.9
Duplicates removed (%)
10.3
Number of peaks
1436 (qval < 1E-05)

Base call quality data from DBCLS SRA