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SRX7988306: GSM4432092: prostate cancer case with archival biopsy tissue 22; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina HiSeq 3000) run: 86.3M spots, 4.3G bases, 1.5Gb downloads

Submitted by: NCBI (GEO)
Study: Transcriptome analysis in a unique cohort of untreated primary tumors collected from diagnostic prostate needle biopsies (PNBX) of localized (M0) and metastatic (M1) cases
show Abstracthide Abstract
PNBX were collected from 99 patients treated in the VA Greater Los Angeles (GLA-VA) Healthcare System between 2000-2016 Overall design: 99 prostate cancer cases with archival biopsy tissue available were selected for RNA sequencing (RNAseq) from a total cohort 1927 cases identified within the GLA-VA cancer registry or procedure logs. The selected cases were divided into sub-cohorts based upon tumor burden at diagnosis or recurrence/progression documented in imaging reports, including 99mTc-methylene disphosphonate (99mTc-MDP) planar bone scintigraphy, 18F-NaF positron emission tomography (18F-NaF PET), ultrasounds, magnetic resonance imaging (MRI), computed tomography (CT) scans, and plain radiographs. Cases were designated clinical stage M1 if metastatic lesions were identified on imaging scans performed within 1 year of the diagnostic PNBX. Osteoblastic, osteolytic, and/or sclerotic bone lesions observed on bone scan were confirmed or by the presence of overlapping lesions on plain radiographs, CT or MRI imaging. Oligometastatic “oligo” disease was defined by <5 extrapelvic lymph node and/or bone metastases and no visceral metastases. Polymetastatic “poly” disease was defined as >5 metastases or any visceral involvement. M1 cases were designated M1-oligo or M0-poly based on the aforementioned tumor burden assessment. Cases that were considered M0 at diagnosis, but demonstrated eventual metastatic progression (M0-M) were designated M0-oligo or M0-poly based on tumor burden on imaging scans at the time of follow-up. Cases were designated as clinical stage M0 non-metastatic (M0-NM) if no metastatic lesions were identified at the time of last follow-up. If imaging scans were not performed, or equivocal results were obtained, the cases were categorized as MX and excluded from analysis. A significant subset of M0 cases from the original 1927 cohort did not have an indication for diagnostic imaging due to diagnosis of low- or intermediate-risk PC according to D'Amico classification
Sample: prostate cancer case with archival biopsy tissue 22
SAMN14442320 • SRS6371888 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina HiSeq 3000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction 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.
Experiment attributes:
GEO Accession: GSM4432092
Links:
Runs: 1 run, 86.3M spots, 4.3G bases, 1.5Gb
Run# of Spots# of BasesSizePublished
SRR1140960486,344,0094.3G1.5Gb2020-03-27

ID:
10424749

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