Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
AR

Cell type

Cell type Class
Prostate
Cell type
R1-AD567
NA
NA

Attributes by original data submitter

Sample

source_name
prostate cancer cell line
cell type
R1-D567
agent
Ethanol (vehicle control)
chip antibody
AR -N20 (Santa Cruz, SC-816 lot B1012)
biological replicate number
rep3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was performed for three independent biological replicate experiments exactly as described (PMID: 21602788) with the exception fo the following modifications: R1-AD1 and R1-D567 cells (PMID 24101480) were seeded at 5x10^6 cells/plate on 10 cm plates in RMPI 1640 + 10% CSS, allowed to settle for 72h, then re-fed for 4h with RMPI 1640 + 5% CSS containing vehicle (ETH) or 1nM DHT prior to fixation. 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. Libraries were prepared according to Illumina's instructions accompanying the TruSeq Sample Preparation Kit (Illumina cat#IP-202-1012).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
23397429
Reads aligned (%)
30.5
Duplicates removed (%)
68.5
Number of peaks
943 (qval < 1E-05)

hg38

Number of total reads
23397429
Reads aligned (%)
32.6
Duplicates removed (%)
66.7
Number of peaks
957 (qval < 1E-05)

Base call quality data from DBCLS SRA