Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RELA

Cell type

Cell type Class
Prostate
Cell type
LNCAP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
prostate cancer
cell line
LNCaP
treatment 1
DHT (100nM, 2h) + TNF-alpha (1000U/ml, 2h)
treatment 2
-
antibody
anti-p65 (Santa Cruz Biotechnology, sc-372)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei from approximately 10 million formaldehyde crosslinked (1%; 10min at room temperature for VCaP cells, and 8min. at room temperature for K562 cells) cells were isolated and chromatin was fragmented using sonicator (bioruptor). Lysates were cleared and protein-DNA complexes were isolated using target specific antibodies and protein-A/G magnetic beads. DNA fragments were purified and libraries were prepared accorcing to standard Illumina protocol. Samples were sequenced at BGI Tech Solutions (Shenzhen, China) or at the Gene Core in EMBL (Heidelberg, Germany).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
39207309
Reads aligned (%)
80.5
Duplicates removed (%)
18.0
Number of peaks
4465 (qval < 1E-05)

hg38

Number of total reads
39207309
Reads aligned (%)
82.6
Duplicates removed (%)
16.5
Number of peaks
4507 (qval < 1E-05)

Base call quality data from DBCLS SRA