Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
AR

Cell type

Cell type Class
Prostate
Cell type
R1-AD1
NA
NA

Attributes by original data submitter

Sample

source_name
R1-AD1 prostate cancer cell line treated with VPC14449 and DHT
cell type
prostate cancer cell line
cell line
R1-AD1
chip antibody
AR-Antibody [Santa Cruz sc-816 (N-20)]

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
R1-AD1 and R1-D567 cells were seeded at 5 x 106 cells/10 cm plate in RPMI 1640, settled for 48 hrs, then treated with vehicle (0.1% DMSO) or VPC14449 (50 µM) in RPMI 1640 for 24 hrs. Cells were re-fed with RPMI 1640 + 10% CSS supplemented with 50 µM VPC-14449 (or DMSO control) and 1 nM DHT (or ethanol control) for an additional 4 hrs prior to cross-linking. Nuclear pellets were sonicated on ice for 8 cycles at 40% amplitude using a 450 Sonifer (Branson). Each cycle consisted of 10 sec pulse/10 sec rests for 1 min, with 2 min rests between cycles. Lysates were immunoprecipitated with Protein A/G Plus agarose beads (Santa Cruz Biotechnology) pre-blocked with tRNA (Sigma). DNA was purified using a PCR purification kit (Qiagen). For ChIP-seq, 2-10ng of DNA (ChIP-enriched or input) was used for library creation with a TruSeq ChIP Sample Preparation Kit (Illumina cat #IP-202-1012) and sequenced at the Univeristy of Minnesota Genomics Center using an Illumina HiSeq2000 at 1X50bp. 2 ng of DNA (ChIP-enriched and input) was used for library creation with a Truplex ChIP sample Preprarion Kit (Rubicon Genomics).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
74894930
Reads aligned (%)
75.7
Duplicates removed (%)
21.4
Number of peaks
1740 (qval < 1E-05)

hg38

Number of total reads
74894930
Reads aligned (%)
78.0
Duplicates removed (%)
19.5
Number of peaks
1895 (qval < 1E-05)

Base call quality data from DBCLS SRA