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 on day 5 of TT-only protocol
cell type
Human iPS cells
tissue
Dermal fibroblasts
days after differentiation
5
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, 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, cells were cross-linked with 1% formaldehyde, and after lysis of cells, chromatin was fragmented by sonication. Protein-DNA complexes were purified with antibody. For ATAC-seq, DNA fragments were PCR-amplified using previously-designed barcoded primers, as described previously (Buenrostro et al., 2013).For ChIP-seq, libraries were constructed with ThruPLEX DNA-seq Kit (Takara Bio), according to manufacturer's instruction.

Sequencing Platform

instrument_model
Illumina HiSeq X Ten

hg19

Number of total reads
70536429
Reads aligned (%)
114.4
Duplicates removed (%)
32.4
Number of peaks
9308 (qval < 1E-05)

hg38

Number of total reads
70536429
Reads aligned (%)
116.2
Duplicates removed (%)
31.9
Number of peaks
10616 (qval < 1E-05)

Base call quality data from DBCLS SRA