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Sample GSM5720878 Query DataSets for GSM5720878
Status Public on Feb 08, 2022
Title 27P1_S1_L003
Sample type SRA
 
Source name P6.1
Organism Canis lupus familiaris
Characteristics tissue: Prostate cancer
breed: Bolonka Zwetna
description: male neutered
age: 9 years
histopathological classification: transitional cell carcinoma
patient id: 6
Treatment protocol Each tissue sample was subsequently divided into three parts: The first part (“original tissue”) was fresh frozen in liquid nitrogen and stored at -80°C until RNA isolation. The second part was histopathologically classified into PAC or TCC by a certified and experienced pathologist.
Growth protocol Tissue samples of suspected prostate or bladder carcinomas were collected from ten patient dogs at the Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany between 2003 and 2015 with the consent of the patients’ owners.
Extracted molecule total RNA
Extraction protocol RNA from cell pellets was isolated using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany), in accordance with the manufacturer’s protocols. For tissue samples, the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen GmbH) was utilized.
Samples with RNA integrity numbers ≥ 5.2 measured with RNA 6000 Nano LabChip on an Agilent Bioanalyzer 2100 (Agilent Technologies Inc., Santa Clara, CA, USA) were further processed for library preparation using the NEBNext Ultra RNA preparation kit (New England Biolabs Inc., Ipswich, MA, USA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description total RNA, including miRNA
27P1_S1
Data processing Bases were called with Illumina Casava bcl2fastq (version 2.15.0.4).
Sequencing reads were trimmed and filtered using trimmomatic (v0.36) with parameters "-phred33, HEADCROP:11 LEADING:20 TRAILING:20 AVGQUAL:20 MINLEN:25". Reads were mapped to the dog reference genome (Ensembl CanFam 3.1) and corresponding gene model annotation (v94) using STAR (v2.5.3) with parameters: "--sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts". RSEM (v.1.3.0) was used to quantify gene expression with parameters "--bam --no-bam-output". Finally, for each library, read counts derived from multiple lanes were added together.
Genome_build: Ensembl CanFam 3.1
Supplementary_files_format_and_content: Tab-delimited text including raw gene counts for every gene Ensembl gene identifier
 
Submission date Dec 07, 2021
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
 
Platform ID GPL21400
Series (1)
GSE190374 RNA-seq of nine canine prostate cancer cell lines reveals diverse therapeutic target signatures
Relations
BioSample SAMN23787565
SRA SRX13340522

Supplementary file Size Download File type/resource
GSM5720878_27P1_S1_L003_rsem_quant.txt.gz 508.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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