|
Status |
Public on Jun 01, 2016 |
Title |
BS2339 cancer Trop2+ CD49f Hi |
Sample type |
SRA |
|
|
Source name |
prostate
|
Organism |
Homo sapiens |
Characteristics |
patient: BS2339 tissue type: cancer cell type: basal cell population: Trop2+ CD49f Hi
|
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 3
|
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 |
SAMN05191790 |
SRA |
SRX1810493 |