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| Status |
Public on Aug 02, 2011 |
| Title |
DU145_sr_rep3 |
| Sample type |
SRA |
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| Source name |
prostate gland
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| Organism |
Homo sapiens |
| Characteristics |
read type (single/paired-end): single_read
sample pool name: DU145
sample type: Cell Line
cell line: DU145
disease state: cancer
patient id: NA
ets fusion status: ETS-
tissue harvest site: None
read length (bp): 45
insert size (bp): 108
insert size standard deviation (bp): NA
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| Treatment protocol |
None
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| 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.
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| Submission date |
Nov 08, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew Iyer |
| E-mail(s) |
mkiyer@med.umich.edu
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| Phone |
7346154503
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| Organization name |
University of Michigan
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| Department |
Michigan Center for Translational Pathology
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| Lab |
Chinnaiyan Lab
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| Street address |
5316 CCGC 0940 1400 E. Medical Center Drive
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109-0940 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| 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 |
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| Relations |
| SRA |
SRX031914 |
| BioSample |
SAMN00138500 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM618470_mctp_30DJDAAXX_3.bam |
271.6 Mb |
(ftp)(http) |
BAM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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