Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
AR

Cell type

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

Attributes by original data submitter

Sample

source_name
LNCaP_anti-AR
cell line
LNCaP
chip antibody
Santa Cruz sc-816 X

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
LNCaP cells were seeded at 3x10^6 cells/plate in 15cm plates in RMPI 1640 + 10% FBS and allowed to grow for 3 days prior to fixation with formaldehyde. Nuclear pellets were sonicated on ice for 10 cycles (30 sec on, 30 sec off) using a Diagenode Bioruptor. Lysates were immunoprecipitated with 4 ug GRHL2 antibody (Sigma HPA004820) or 5 ug AR antibody (Santa Cruz N20 ), which had been pre-coupled to Protein G Dynabeads (Life Technologies, 10004D). DNA was purified using a PCR purification kit (Qiagen) and eluted in 100 µl. Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Prep Kit

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
76892758
Reads aligned (%)
76.7
Duplicates removed (%)
11.5
Number of peaks
3054 (qval < 1E-05)

hg38

Number of total reads
76892758
Reads aligned (%)
79.4
Duplicates removed (%)
9.5
Number of peaks
4364 (qval < 1E-05)

Base call quality data from DBCLS SRA