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 cells LNCaP
tissue
prostate
cell line
LNCaP
chip-antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei were purified after formaldehyde crosslinking, collected and resuspended in SDS Lysis buffer before sonication. Chromatin was sonicated to generate a majority of fragments between 200 and 600 bp. 10µg of each antibody was used per ChIP. Libraries for ChIP-Seq were prepared following Illumina protocols. The resulting libraries were sequenced on the Illumina HiSeq 2000 platform configured for 50bp single-end reads.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
45165589
Reads aligned (%)
97.2
Duplicates removed (%)
10.2
Number of peaks
1280 (qval < 1E-05)

hg19

Number of total reads
45165589
Reads aligned (%)
96.2
Duplicates removed (%)
11.9
Number of peaks
1168 (qval < 1E-05)

Base call quality data from DBCLS SRA