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Sample GSM4432042 Query DataSets for GSM4432042
Status Public on Mar 26, 2020
Title prostate cancer case with archival biopsy tissue 501-5a
Sample type SRA
Source name prostate tissue
Organism Homo sapiens
Characteristics disease stage: M0 poly
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
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
BioSample SAMN14442292
SRA SRX7988256

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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