|
| Status |
Public on Aug 17, 2021 |
| Title |
C11P2_T2_0.5mM |
| Sample type |
SRA |
| |
|
| Source name |
COVCAR cells designated as C11 in 2ndpassage
|
| Organism |
Gallus gallus |
| Characteristics |
cell line: COVCAR
cell type: Ovarian cancer cells derived fom ascites of chickens with ovarian cancer
tumor type: Ovarian endometrioid adenocarcinoma
treatment: 0.5mM metfromin
|
| Treatment protocol |
Approximately 200,000 COVCAR cells from each of 4 primary ovarian cancer lines designated as C5, C7, C9, and C11 were treated with 0, 0.5, 1, or 2 mM metformin dissolved in serum-free medium [SCM, X-VIVO 20 culture medium supplemented with 5 µg/ml bovine insulin, 20 ng/ml recombinant human epidermal growth factor and antibiotic-antimycotic solution] in 24-well ultra-low attachment plate for 24 h at 37ºC under 5% CO2 atmosphere.
|
| Growth protocol |
COVCAR cells were cultured on gelatinized 75cm cell culture flasks at 37ºC under 5% CO2 atmosphere. When the COVCAR cells reached 100% confluence, the cells were dissociated from the flask using 0.05% trypsin (Invitrogen) and used for metformin treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells and spheres following the metformin treatment were harvested by centrifugation followed by resuspension in Trizol and stored at -80C until RNA extraction. Total RNA was extracted using the RNeasy Micro kit (Qiagen) using the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Truseq Stranded mRNA Librarykit was used and data was sequnced using Illumina HiSeq2500. Base calling was done using bcl2fastq v2.20.0 software and quality reports were generated using fastqc.
Raw data was mapped to chicken reference genome using hisat2 (v.2.1.0)
Mapping was visualized and inspected in IGV.
Gene-level read counts were obtained using featureCounts
Differential expression analysis was done using DESeq2
Genome_build: Gallus_gallus.GRCg6a
Supplementary_files_format_and_content: Gene-level raw read counts
Supplementary_files_format_and_content: Normalized counts and differential expression results
|
| |
|
| Submission date |
Aug 13, 2021 |
| Last update date |
Aug 17, 2021 |
| Contact name |
Aswathy Sebastian |
| E-mail(s) |
azs13@psu.edu
|
| Phone |
5204613475
|
| Organization name |
PennState
|
| Street address |
University Park
|
| City |
State College |
| ZIP/Postal code |
16801 |
| Country |
USA |
| |
|
| Platform ID |
GPL19005 |
| Series (1) |
| GSE182084 |
Metformin affects transcriptomic pathways involved in cell survival, metabolism and angiogenesis in ovarian cancer cells |
|
| Relations |
| BioSample |
SAMN20773841 |
| SRA |
SRX11745824 |
