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Series GSE122916 Query DataSets for GSE122916
Status Public on Oct 08, 2019
Title Comparative transcriptomic characterisation of canine prostate fine-needle-aspiration and tissue samples - from sampling to sequencing
Organism Canis lupus familiaris
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Contributor(s) Taher L, Escobar HM, Nolte I, Thiemeyer H, Schille JT, Beck J, Schütz E, Brenig B, Hewicker-Trautwein M, Mischke R, Hungerbuehler SO, Harder L, Kielbowicz Z
Citation(s) 31519932, 34768937
Submission date Nov 26, 2018
Last update date Feb 08, 2022
Contact name Leila Taher
Organization name Graz University of Technology
Street address Stremayrgasse 16/I
City Graz
ZIP/Postal code 8010
Country Austria
Platforms (1)
GPL21400 Illumina NextSeq 500 (Canis lupus familiaris)
Samples (25)
GSM3488020 PT-1: Canine prostate tissue
GSM3488021 PT-2: Canine prostate tissue
GSM3488022 PT-3: Canine prostate tissue
BioProject PRJNA506907
SRA SRP170673

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE122916_RAW.tar 2.8 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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