|
| Status |
Public on Jun 01, 2016 |
| Title |
BS2771 cancer Trop2+ CD49f Lo |
| Sample type |
SRA |
| |
|
| Source name |
prostate
|
| Organism |
Homo sapiens |
| Characteristics |
patient: BS2771
tissue type: cancer
cell type: luminal
cell population: Trop2+ CD49f Lo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from human prostate basal (Trop2+ CD49f Hi) and luminal (Trop2+ CD49f Lo) populations using the RNeasy Mini kit (QIAGEN). Samples with a RNA integrity number (RIN) > 8 were used for construction of RNA-seq libraries.
RNA-seq libraries were constructed using the Ovation RNA-seq V2 (Nugen) and PrepX ILM DNA (IntegenX) kits.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 11
|
| Data processing |
Illumina CASAVA 1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads were mapped to UCSC hg19 using MapSplice 2.1.8 software.
Gene expression was quantified using RSEM 1.2.25 and quantile normalized.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes normalized RSEM quantification for each Sample
|
| |
|
| Submission date |
May 31, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bryan Smith |
| Organization name |
UCLA
|
| Department |
Microbiology, Immunology, and Molecular Genetics
|
| Lab |
Laboratory of Owen Witte
|
| Street address |
MRL 5-720, 675 Charles E. Young Drive South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE82071 |
A Basal Stem Cell Signature Identifies Aggressive Prostate Cancer Phenotypes |
|
| Relations |
| BioSample |
SAMN05191798 |
| SRA |
SRX1810501 |
