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
Enzalutamide, replicate 1
cell line
LNCaP
cancer
Prostate adenocarcinoma
sample type
Androgen-sensitive
chip antibody
anti-AR (N20) from Santa Cruz Biotechnology (Santa Cruz, CA)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For LNCaP AR ChIP-exo, after treatment with 10 nm DHT or vehicle for 4 h, LNCaP cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-AR antibody. For AR ChIP-exo, T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
199838233
Reads aligned (%)
101.9
Duplicates removed (%)
40.9
Number of peaks
12628 (qval < 1E-05)

hg38

Number of total reads
199838233
Reads aligned (%)
104.7
Duplicates removed (%)
39.9
Number of peaks
15039 (qval < 1E-05)

Base call quality data from DBCLS SRA