|
| Status |
Public on Jan 24, 2022 |
| Title |
C30-ALDU1MINUSUL |
| Sample type |
SRA |
| |
|
| Source name |
COVCAR cells designated as C30 SORTED FOR ALDH- CELLS Replicate 3
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: Ovarian cancer cells derived fom ascites of chickens with ovarian cancer
tumor type: Ovarian adenocarcinoma
treatment: ALDH- cells
|
| Treatment protocol |
Approximately 5 million COVCAR cells from each of 3 primary ovarian cancer lines designated as C27, C29, and C30 were sorted using FACS for the presence of ALDH activity. Cells sorted for ALDH+ or ALDH- were seperated and total RNA was extracted.
|
| 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 sorting ALDH+ and ALDH- cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy 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 |
125 base pair paired-end reads were sequenced. Quality reports were generated with FastQC.
Adapter sequence and low quality bases were trimmed using trimmomatic. Reads with length <35 bp after trimming were discarded.
Trimmed data was mapped to the Gallus_gallus.GRCg6a assembly using hisat2 program. Coverage files were generated and alignments were visualized in IGV.
Transcript level abundances were genereated by the pseudoalignment of the dataset to the chicken transcriptome using Kallisto.Transcript level read counts and TPMs were generated.
Transcript level raw read counts were normalized and differentially expressed transcripts were identified using DESeq2 package in R.
Genome_build: Gallus_gallus.GRCg6a
Supplementary_files_format_and_content: Transcript-level raw counts and TPMs
Supplementary_files_format_and_content: Deseq2 normalized counts and differential expression results
|
| |
|
| Submission date |
Jan 21, 2022 |
| Last update date |
Jan 24, 2022 |
| 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) |
| GSE194175 |
Transcriptomic profile of ovarian cancer stem cells dervived from ascites of chickens. |
|
| Relations |
| BioSample |
SAMN25159814 |
| SRA |
SRX13858836 |
