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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 14, 2018 |
| Title |
6h_RNA_SEQ |
| Sample type |
SRA |
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| Source name |
VCaP cells, DHT 6hr
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| Organism |
Homo sapiens |
| Characteristics |
cell line: VCaP
cell type: prostate cancer cell line
treatment: DHT for 6hrs
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| Treatment protocol |
Hormone-deprived VCaP cells were treated with ETOH/10nM DHT for the indicated time points.
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
RNA-seq at 6 hours after DHT treatment.
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| 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
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| Submission date |
Feb 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Edwin Cheung |
| E-mail(s) |
rnapolii@outlook.com
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| Organization name |
Genome Institute of Singapore
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| Department |
Cancer Biology and Pharmacology
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| Street address |
Genome Institute of Singapore 60 Biopolis Street, Genome, #02-01
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| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE54946 |
An AR-ERG co-mediated chromatin interactome defines the transcriptional network in prostate cancer cells |
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| Relations |
| BioSample |
SAMN02640985 |
| SRA |
SRX470044 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1327098_tophat_RHV007.ucsc.bedGraph.gz |
25.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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