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 derived chondrocytes
NA
NA

Attributes by original data submitter

Sample

source_name
Human iPS-derived cells during chondrocyte differentiation by the 2C method at day 3
cell type
Human iPS cells
tissue
Foreskin
days after differentiation
3
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
52434382
Reads aligned (%)
143.6
Duplicates removed (%)
13.5
Number of peaks
4303 (qval < 1E-05)

hg38

Number of total reads
52434382
Reads aligned (%)
145.7
Duplicates removed (%)
13.3
Number of peaks
5275 (qval < 1E-05)

Base call quality data from DBCLS SRA