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| Status |
Public on Feb 05, 2013 |
| Title |
AR CPA rep2 |
| Sample type |
SRA |
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| Source name |
LNCaP-1F5 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Prostate epithelial cells derived from metastatic prostate carcinoma, genetically engineered to express rat glucocorticoid receptor (Cleutjens et al., 1997).
passages: 15-35
cell line: LNCaP-1F5 cells
treatment: 1000 nM CPA
chip antibody: AR (Kang et al. 2004; Sahu et al. 2011)
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| Treatment protocol |
Cells were treated with vehicle, 100 nM DHT, 1000 nM CPA, 1000 nM RU486, 1000 nM Bica or 100 nM DEX for 2 hours followed by Chromatin Immunoprecipitation. For combination experiments 100 nM DHT and 100 nM Dex were given concomittantly. CHIP antibodies: AR (Sahu et al. 2011), rat GR (Widen et al., Sahu et al. 2011), Human GR (BuGR2, Millipore and Mab-010-050, Diagenode), RNA Pol II (sc-899x, Santa Cruz), rabbit IgG (sc-2027, Santa Cruz) and mouse IgG (sc-2025, Santa Cruz).
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| Growth protocol |
LNCaP-1F5 and VCaP cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 10 mM HEPES supplemented with antibiotics (penicillin and streptomycin).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and DNA-protein complexes were isolated with respective antibodies. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Chromatin IP against AR in cells treated with 1000 nM CPA
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| Data processing |
Alignment: Sequence reads were obtained and mapped to the human (Feb, 2009) genomes using the Illumina Genome Analyzer Pipeline (ELAND) or BOWTIE. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) and overlapping peaks present in both biological replicates at a 2% FDR cutoff are used for further downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: aligned files are in BED and wig format
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| Submission date |
Aug 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Olli A. Jänne |
| E-mail(s) |
[email protected]
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| Phone |
+358919125040
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| Organization name |
University of Helsinki
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| Department |
Inst. of Biomedicine/Physiology
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| Lab |
Androgen Receptor Laboratory
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| Street address |
Haartmaninkatu-8
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| City |
Helsinki |
| ZIP/Postal code |
FI-00014 |
| Country |
Finland |
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| Platform ID |
GPL9052 |
| Series (2) |
| GSE39879 |
FoxA1 specifies unique androgen and glucocorticoid receptor binding events in prostate cancer cells (HTS) |
| GSE39880 |
FoxA1 specifies unique androgen and glucocorticoid receptor binding events in prostate cancer cells |
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| Relations |
| SRA |
SRX173192 |
| BioSample |
SAMN01096931 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM980648_AR_CPA_rep2_peaks_FDR2.bed.gz |
99.2 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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