 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 14, 2018 |
| Title |
2h_GRO_seq |
| Sample type |
SRA |
| |
|
| Source name |
VCaP cells, DHT 2hr
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: VCaP
cell type: prostate cancer cell line
treatment: DHT for 2hrs
|
| Treatment protocol |
Hormone-deprived VCaP cells were treated with 100nM 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 |
Nuclei were isolated from VCaP cells with or without DHT treatment.
GRO-seq libraries were prepared from 10 million cells based on previously published protocols (Core et al., 2008). After harvesting the cells, RNA polymerases were allowed to run-on for 5 minutes at 30C (~100bp) in the presence of sarkosyl and BrUTP. The RNA was then base hydrolyzed, end-repaired and immunopurified with anti-BrdUTP-coated agarose beads thrice. The affinity-enriched RNAs are then reverse transcribed, amplified, and PAGE purified for deep sequencing on the Illumina Genome Analyzer and HiSeq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GRO-seq after DHT treatment. "XXX.plusgraph" is the bedgraph file for the groseq coverage of forward strand. "XXX.minusgraph" is the bedgraph file for the groseq coverage of reverse strand.
|
| 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 |
SAMN02640986 |
| SRA |
SRX470042 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1327096_RHV002_s_8_qseq.txt.fastq.sam.bed.minusgraph.bedGraph.gz |
66.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM1327096_RHV002_s_8_qseq.txt.fastq.sam.bed.plusgraph.bedGraph.gz |
74.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
