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SRX5060074: GSM3488028: PT-9: Canine prostate tissue; Canis lupus familiaris; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 20.1M spots, 3G bases, 1.1Gb downloads

Submitted by: NCBI (GEO)
Study: Comparative transcriptomic characterisation of canine prostate fine-needle-aspiration and tissue samples - from sampling to sequencing
show Abstracthide Abstract
Ultrasound-guided fine-needle aspiration (US-FNA) biopsy is a widely used minimally invasive sampling procedure for cytological diagnosis. This study investigates the feasibility of using US-FNA samples for both cytological diagnosis and whole transcriptome RNA-sequencing analysis (RNA-Seq), with the ultimate aim of improving canine prostate cancer management. The feasibility of the US-FNA procedure was evaluated intra vitam on 43 dogs. Additionally, aspirates from 31 euthanised dogs were collected for standardising the procedure. Each aspirate was separated into two subsamples: for cytology and RNA extraction. Additional prostate tissue samples served as control for RNA quantity and quality evaluation, and differential expression analysis. The US-FNA sampling procedure was feasible in 95% of dogs. RNA isolation of US-FNA samples was successfully performed using phenol-chloroform extraction. The extracted RNA of 56% of a subset of US-FNA samples met the quality requirements for RNA-seq. Expression analysis revealed that only 153 genes were exclusively differentially expressed between non-malignant US-FNAs and tissues. Moreover, only 36 differentially expressed genes were associated with the US-FNA sampling technique and unrelated to the diagnosis. Furthermore, the gene expression profiles clearly distinguished between non-malignant and malignant samples. This proves US-FNA to be useful for molecular profiling. Overall design: Fine-needle aspirates of the canine prostate: non-malignant (n=5) and malignant (n=2); canine prostate tissues: non-malignant (n=9) and malignant (n=9). Aspirates and tissue samples of the canine prostate were used for RNA-sequencing. Non-malignant prostate tissue samples were used as control. Differentially expressed genes were used for evaluation of similarities and differences in aspirates and canine prostate tissues.
Sample: PT-9: Canine prostate tissue
SAMN10476598 • SRS4076044 • All experiments • All runs
Library:
Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Canine prostate tissue samples were collected post mortem from macroscopically representative areas after prostatectomy. The samples were immediately snap frozen in liquid nitrogen and stored at -80°C. Prostate tissue samples were disrupted using Buffer RLT Plus and 5mm stainless steel beads by tissueLyser II (Qiagen). Total RNA from prostate tissue samples was isolated using AllPrep® DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer's instructions. Ultrasound-guided fine-needle aspirates were collected intra vitam, snap frozen in liquid nitrogen and stored at -80°C. Total RNA from aspirates were isolated using Qiazol Lysis Reagent with Qiagen miRNeasy Micro Kit (Qiagen) according to the manufacturer's protocol. RNA libraries were prepared for sequencing using standard Illumina protocols.
Experiment attributes:
GEO Accession: GSM3488028
Links:
Runs: 1 run, 20.1M spots, 3G bases, 1.1Gb
Run# of Spots# of BasesSizePublished
SRR824189820,090,2163G1.1Gb2019-10-09

ID:
6829481

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