|
| Status |
Public on Mar 26, 2020 |
| Title |
prostate cancer case with archival biopsy tissue 716-4a |
| Sample type |
SRA |
| |
|
| Source name |
prostate tissue
|
| Organism |
Homo sapiens |
| Characteristics |
disease stage: M0-NP
metastasis: No metastasis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Diagnostic hematoxylin and eosin (H&E) PNBX slides were reviewed by a genitourinary pathologist, and high-grade tumor areas (Gleason grade 4, 5, or neuroendocrine/small cell) were encircled. Transfer of annotated areas to the paraffin-embedded tissue blocks was performed and 1-2mm sterile circular biopsy punches enabled manual procurement of formalin-fixed tissue from the block. A minimum of 2 (1mm) cancer cores were used from each high-grade tumor area for RNA and/or DNA preparation. Total RNA was extracted from tissue cores using the Ambion Recover All Total Nucleic Acid Isolation Kit for FFPE (ThermoFisher). Samples were eluted with H20 and quantitated with nanodrop and bioanalyzer.
Approximately 40-100ng of RNA was used to generate the libraries using the TruSeq RNA Access Library Prep Kit (Illumina) according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
the quality of sequence reads from the RNAseq data were assessed and low quality reads were filtered using the FastQC tool (Babraham Bioinformatics, Cambridge, UK) and ShortRead (v. 1.30.0) package from R bioconductor (version 3.3).
Quantification of gene level expression from preprocessed RNA-seq results were performed with the UCSC hg19 build of the Homo Sapiens genome, through the use of the Subread aligner and the featureCounts software
To reduce systemic bias between samples, the Trimmed Mean Method (TMM) was applied to gene level expression counts
Genome_build: hg19
|
| |
|
| Submission date |
Mar 24, 2020 |
| Last update date |
Mar 26, 2020 |
| Contact name |
Sungyong You |
| E-mail(s) |
Sungyong.You@cshs.org
|
| Organization name |
Cedars-Sinai Medical Center
|
| Department |
Surgery
|
| Lab |
Freeman Lab.
|
| Street address |
Beverly Blvd 8400
|
| City |
LA |
| State/province |
CA |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE147493 |
Transcriptome analysis in a unique cohort of untreated primary tumors collected from diagnostic prostate needle biopsies (PNBX) of localized (M0) and metastatic (M1) cases |
|
| Relations |
| BioSample |
SAMN14442257 |
| SRA |
SRX7988226 |
