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Sample GSM3488039 Query DataSets for GSM3488039
Status Public on Oct 08, 2019
Title US-7: Canine prostate fine-needle aspirate
Sample type SRA
Source name Canine prostate fine-needle aspirate
Organism Canis lupus familiaris
Characteristics tissue: normal to hyperplastic canine prostate tissue
diagnosed by: Diagnosed by cytology as normal to hyperplastic canine prostate tissue
sample type: FNA
diagnosis: non-malignant
reproductive status: male intact
breed: Mixed breed
age: 5 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
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
BioSample SAMN10476587
SRA SRX5060085

Supplementary file Size Download File type/resource
GSM3488039_US3_S1_dir.accepted_hits.bam.proper.bam.nsorted.bam.Canis_familiaris.CanFam3.1.85.chr.gtf.htseq_counts.txt.gz 113.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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