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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 08, 2022 |
| Title |
US20_S6_L004 |
| Sample type |
SRA |
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| Source name |
B7
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| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: Bladder cancer
breed: Labrador Retriever
description: female
age: 10 years
histopathological classification: transitional cell carcinoma
patient id: 7
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| 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.
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| 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.
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
total RNA, including miRNA
US20_S6
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| 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
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| Submission date |
Dec 07, 2021 |
| Last update date |
Feb 08, 2022 |
| Contact name |
Leila Taher |
| Organization name |
Graz University of Technology
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| Street address |
Stremayrgasse 16/I
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| City |
Graz |
| ZIP/Postal code |
8010 |
| Country |
Austria |
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| Platform ID |
GPL21400 |
| Series (1) |
| GSE190374 |
RNA-seq of nine canine prostate cancer cell lines reveals diverse therapeutic target signatures |
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| Relations |
| BioSample |
SAMN23732631 |
| SRA |
SRX13340447 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5720907_US20_S6_L004_rsem_quant.txt.gz |
499.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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