Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RXRA

Cell type

Cell type Class
Others
Cell type
JMSU1
Primary Tissue
Bladder
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
bladder cancer cells
cell type
JMSU-1
chip antibody
RXRA (Perseus Proteomics, K8508, lot A2)
genotype
RXRA S427F

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Crosslinking and ChIP were performed as described for adherent cells in the ENCODE experiment summary for ENCSR000BJW (https://www.encodeproject.org/experiments/ENCSR000BJW/) . Chromatin was sonicated using the Diagenode Pico Bioruptor. DNA-protein complexes were precipitated with antibodies against RXRA (PP-K8508-00 R&D Systems) and H3K27Ac (ab4729 Abcam).

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg19

Number of total reads
42840051
Reads aligned (%)
49.3
Duplicates removed (%)
47.6
Number of peaks
3522 (qval < 1E-05)

hg38

Number of total reads
42840051
Reads aligned (%)
51.0
Duplicates removed (%)
46.1
Number of peaks
3513 (qval < 1E-05)

Base call quality data from DBCLS SRA