|
| Status |
Public on May 02, 2011 |
| Title |
carcinoma_C03 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Prostate cancer tissue
tumor stage: Gleason score 7
sequencing protocol: paired-end, 36-mer sequencing
|
| Treatment protocol |
Tissue was extracted from patients before treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol and mRNA enriched using oligo(dT) capture and ds cDNA was prepared. The ds cDNA was fragmented via nebulization. The fragmented DNA was end polished and ligated with Illumina methylated PE adaptors. Average insert size is 150 bp (median = 152 bp), standard deviation is 38 bp.
Illumina mRNA-seq protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
ds cDNA from polyA selected mRNA
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the hg18 (March, 2006) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained
|
| |
|
| Submission date |
Jun 09, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
LIGUO WANG |
| E-mail(s) |
wang.liguo@mayo.edu
|
| Organization name |
Mayo Clinic
|
| Department |
Division of Computational Biology
|
| Street address |
200 1st St SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE22260 |
Comparative transcriptomic analysis of prostate cancer and matched normal tissue using RNA-seq |
|
| Relations |
| SRA |
SRX022061 |
| BioSample |
SAMN00015147 |
