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Sample GSM5720791 Query DataSets for GSM5720791
Status Public on Feb 08, 2022
Title 0840-3_S8_L004
Sample type SRA
 
Source name TCC0840 rep2
Organism Canis lupus familiaris
Characteristics cell line: TihoDProCarc/TCC0840
breed: Pitbull Terrier
description: male neutered
age: 10 years
cell line short name: TCC0840
histopathological classification: transitional cell carcinoma
patient id: 5
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 352; cell line's former name: DT08/40
0840-3_S8
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 SAMN23787632
SRA SRX13340411

Supplementary file Size Download File type/resource
GSM5720791_0840-3_S8_L004_rsem_quant.txt.gz 496.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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