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Sample GSM1327099 Query DataSets for GSM1327099
Status Public on Dec 14, 2018
Title 24h_RNA_SEQ
Sample type SRA
 
Source name VCaP cells, DHT 24h
Organism Homo sapiens
Characteristics cell line: VCaP
cell type: prostate cancer cell line
treatment: DHT for 24hrs
Treatment protocol Hormone-deprived VCaP cells were treated with ETOH/10nM DHT for the indicated time points.
Growth protocol VCaP cells were seeded in DMEM supplemented with 10% fetal bovine serum (FBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution for 3 days. Prior to ETOH/DHT stimulation, VCaP cells were washed and the medium was replaced with phenol red-free DMEM supplemented with 10% charcoal stripped fetal bovine serum (CDFBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution to starve the cells for 24 hours.
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent (Sigma) and purified according to the manufacturer's protocol in the PureLink RNA Mini Kit (Invitrogen).
Sequencing adaptors were ligated to the PET constructs, which were then amplified by PCR and sequenced by the Illumina platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description RNA-seq at 24 hours after DHT treatment.
Data processing Alignment: For ChIA-PET, GRO-seq, we use program called BATMIS - Basic Alignment Tool for Mismatches http://code.google.com/p/batmis/. For G-PET, sequence tags were uniquely mapped to the human reference sequence (NCBI Build 37) allowing 2 mismatches. For RNA-PET, we use the RNA alignment program TopHat. For G-PET, sequence tags were mapped to the human reference sequence (NCBI Build 37) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite (Applied Biosystems).
Interaction cluster calling: ChIA-PET data was processed with ChIA-PET Tool software: Li, G., Fullwood, M.J., Xu, H., Mulawadi, F.H., Velkov, S., Vega, V., Ariyaratne, P.N., Mohamed, Y.B., Ooi, H.S., Tennakoon, C., Wei, C.L., Ruan, Y. and Sung, W.K. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol, 11 (2). R22
Peak calling: ChIA-PET data was processed with ChIA-PET Tool software: Li, G., Fullwood, M.J., Xu, H., Mulawadi, F.H., Velkov, S., Vega, V., Ariyaratne, P.N., Mohamed, Y.B., Ooi, H.S., Tennakoon, C., Wei, C.L., Ruan, Y. and Sung, W.K. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol, 11 (2). R22
Coverage data: use bedtool "genomeCoverageBed" with the alignment data
SV calling: Detect all Structural Variations (deletions, inversions, insertions, tandem and translocations) for each library using SVGenModule program.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bed.gz: peak
Supplementary_files_format_and_content: bedpe.gz: chromatin interaction
Supplementary_files_format_and_content: bedgraph.gz: RNA-seq coverage
Supplementary_files_format_and_content: pet2+.txt: chromatin interaction
Supplementary_files_format_and_content: xls: structure variation
 
Submission date Feb 12, 2014
Last update date May 15, 2019
Contact name Edwin Cheung
E-mail(s) rnapolii@outlook.com
Organization name Genome Institute of Singapore
Department Cancer Biology and Pharmacology
Street address Genome Institute of Singapore 60 Biopolis Street, Genome, #02-01
City Singapore
State/province Singapore
ZIP/Postal code 138672
Country Singapore
 
Platform ID GPL11154
Series (1)
GSE54946 An AR-ERG co-mediated chromatin interactome defines the transcriptional network in prostate cancer cells
Relations
BioSample SAMN02640988
SRA SRX470045

Supplementary file Size Download File type/resource
GSM1327099_tophat_RHV008.ucsc.bedGraph.gz 26.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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