 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 08, 2022 |
| Title |
0840-2_S7_L004 |
| Sample type |
SRA |
| |
|
| Source name |
TCC0840 rep1
|
| 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 350; cell line's former name: DT08/40
0840-2_S7
|
| 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 |
SAMN23787636 |
| SRA |
SRX13340407 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5720787_0840-2_S7_L004_rsem_quant.txt.gz |
491.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
