Antigen

Antigen Class

TFs and others

Antigen

RELA

Cell type

Cell type Class

Prostate

Cell type

LNCAP

Primary Tissue

Prostate

Tissue Diagnosis

Carcinoma

Sample

source_name

prostate cancer

cell line

LNCaP

treatment 1

TNF-alpha (1000 U/ml, 2h)

treatment 2

FOXA1 silencing (siRNA transfection)

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

hg38

Number of total reads

32606099

Reads aligned (%)

92.7

Duplicates removed (%)

17.5

Number of peaks

5930 (qval < 1E-05)

hg19

Number of total reads

32606099

Reads aligned (%)

91.8

Duplicates removed (%)

19.5

Number of peaks

6008 (qval < 1E-05)