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Sample GSM618466 Query DataSets for GSM618466
Status Public on Aug 02, 2011
Title CA-HPV-10_pe_rep1
Sample type SRA
Source name prostate gland
Organism Homo sapiens
Characteristics read type (single/paired-end): paired_end
sample pool name: CA-HPV-10
sample type: Cell Line
cell line: CA-HPV-10
disease state: cancer
patient id: NA
ets fusion status: ETS-
tissue harvest site: None
read length (bp): 40
insert size (bp): 267
insert size standard deviation (bp): 36
Treatment protocol None
Extracted molecule polyA RNA
Extraction protocol Messenger RNA (1 microgram) was fragmented at 70 °C for 2 min in a fragmentation buffer (Ambion) and converted to single- stranded cDNA using SuperScript II reverse transcriptase (Invitrogen), followed by second-strand cDNA synthesis using Escherichia coli DNA polymerase I (Invitrogen). The double- stranded cDNA was further processed by Illumina mRNA- sequencing Prep kit. Briefly, double-stranded cDNA was end repaired by using T4 DNA polymerase and T4 polynucleotide kinase, monoadenylated using a Klenow DNA polymerase I (3' to 5' exonucleotide activity), and ligated with adaptor oligo mix (Illumina) using T4 DNA ligase. The adaptor-ligated cDNA library was then fractioned on a 4% agarose gel, and a smear corresponding to 300 nt was excised, purified, and PCR amplified (15 cycles) by Pfu polymerase (Stratagene). The PCR product was again size selected on a 4% agarose gel by cutting out the library smear at 300 base pairs. The library was then purified with the Qiaquick Minelute PCR Purification Kit (Qiagen) and quantified with the Agilent DNA 1000 kit on the Agilent 2100 Bioanalyzer following the manufacturer’s instruc- tions. Library (10 nM) was used to prepare flowcells with 100,000–130,000 clusters per lane for analysis on the Illumina Genome Analyzer II.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Data processing Reads were aligned to the human genome (hg18, downloaded from UCSC) using TopHat v0.1.3. Only uniquely aligned reads were considered "-g 1". In cases where insert size was not available, we assumed an insert of 200bp. We used a insert size standard deviation of 20bp for all lanes. In addition to standard human chromosomes, adapter sequences and human ribosomal sequences were included in the initial reference in order to filter out the corresponding reads in subsequent processing steps.
Submission date Nov 08, 2010
Last update date May 15, 2019
Contact name Matthew Iyer
Phone 7346154503
Organization name University of Michigan
Department Michigan Center for Translational Pathology
Lab Chinnaiyan Lab
Street address 5316 CCGC 0940 1400 E. Medical Center Drive
City Ann Arbor
State/province MI
ZIP/Postal code 48109-0940
Country USA
Platform ID GPL9115
Series (2)
GSE25183 Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression (RNA-Seq data)
GSE31728 Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
SRA SRX031910
BioSample SAMN00138496

Supplementary file Size Download File type/resource
GSM618466_mctp_429T4AAXX_5.bam 757.0 Mb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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