|
| Status |
Public on Oct 08, 2019 |
| Title |
US-4: Canine prostate fine-needle aspirate |
| Sample type |
SRA |
| |
|
| Source name |
Canine prostate fine-needle aspirate
|
| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: canine prostate carcinoma
diagnosed by: Diagnosed by cytology as canine prostate carcinoma
sample type: FNA
diagnosis: malignant
reproductive status: male neutered
breed: Miniature Pinscher
age: 9 years
|
| Extracted molecule |
total RNA |
| Extraction 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Bases were called with Illumina Casava bcl2fastq (version 2.15.0.4).
Adaptors and low-quality bases were trimmed using Trimmomatic (v0.32) with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Trimmed reads were then mapped to the CanFam3.1 assembly of the dog genome using TopHat2 with default parameters and supplying the Ensembl GTF annotation (Ensembl release 85) through the -G option.
Read counts for each protein-coding gene were calculated for each sample using the htseq-count tool of the Python package HTSeq with default parameters.
Genome_build: CanFam 3.1
Supplementary_files_format_and_content: Tab-delimited text files that include counts for each Ensembl gene.
|
| |
|
| Submission date |
Nov 26, 2018 |
| Last update date |
Oct 08, 2019 |
| Contact name |
Leila Taher |
| Organization name |
Graz University of Technology
|
| Street address |
Stremayrgasse 16/I
|
| City |
Graz |
| ZIP/Postal code |
8010 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21400 |
| Series (1) |
| GSE122916 |
Comparative transcriptomic characterisation of canine prostate fine-needle-aspiration and tissue samples - from sampling to sequencing |
|
| Relations |
| BioSample |
SAMN10476585 |
| SRA |
SRX5060087 |
