Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
-
treatment 2
-
antibody
none (input)

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
46340669
Reads aligned (%)
99.1
Duplicates removed (%)
7.8
Number of peaks
1219 (qval < 1E-05)

hg19

Number of total reads
46340669
Reads aligned (%)
98.2
Duplicates removed (%)
9.2
Number of peaks
1178 (qval < 1E-05)

Base call quality data from DBCLS SRA