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Sample GSM5720867 Query DataSets for GSM5720867
Status Public on Feb 08, 2022
Title 1511-3-2_S15_L004
Sample type SRA
Source name Metadcarc1511.3 rep2
Organism Canis lupus familiaris
Characteristics cell line: TihoDProMetadcarc1511.3
breed: Dobermann
description: male neutered
age: 6 years
cell line short name: Metadcarc1511.3
histopathological classification: metastasis of prostate adenocarcinoma
patient id: 4
original tumor tissue, from which the cell line was established: Ln4.3
Treatment protocol Each cell line was seeded in T25 flasks in triplicate beyond passage 60. At 70-80% confluency, cells were detached with TrypLE™Express (Life Technologies GmbH, Darmstadt, Germany), pelleted, fresh frozen in liquid nitrogen and stored at ‑80°C until further use.
Growth protocol Culturing conditions were Medium 199 (Life Technologies GmbH, Darmstadt, Germany) containing 10% fetal calf serum (FBS Superior, Biochrom GmbH, Berlin, Germany), 200 IU/ml penicillin and 200 mg/ml streptomycin (Biochrom GmbH) at 37°C in humidified air.
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 passage 86
Data processing Bases were called with Illumina Casava bcl2fastq (version
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
BioSample SAMN23787576
SRA SRX13340511

Supplementary file Size Download File type/resource
GSM5720867_1511-3-2_S15_L004_rsem_quant.txt.gz 494.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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