|
| Status |
Public on Jul 13, 2022 |
| Title |
SKOV3_OCSCs_ LY500307_2 |
| Sample type |
SRA |
| |
|
| Source name |
SKOV3 ovarian cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Treatment
|
| Treatment protocol |
Total RNA was isolated from SKOV3 OCSCs after treatmet with either vehicle or LY500307 for 24 hours.
|
| Growth protocol |
OCSCs from SKOV3 cells were FACS sorted using the ALDEFLUOR kit. OCSCs were cultured as spheroids in DMEM-F12 medium supplemented with B27 serum free supplement, EGF (20ng/ml), bFGF (20ng/ml), hydrocortisone, and insulin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
OCSCs from SKOV3 cells were FACS sorted using the ALDEFLUOR kit. SKOV3-ALDH+ OCSCs were treated with vehicle or LY500307 (5 µM) for 24 h and the total RNA was isolated using RNeasy Mini Kit (Qiagen, Valencia, CA).
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
SKOV3 ovarian cancer stem cells (OCSCs) treated with ERβ agonist LY500307
|
| Data processing |
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
|
| |
|
| Submission date |
Feb 23, 2022 |
| Last update date |
Jul 13, 2022 |
| Contact name |
YI ZOU |
| E-mail(s) |
zou@uthscsa.edu
|
| Organization name |
UTHSA-GCCRI
|
| Street address |
8403 Floyd Curl Drive
|
| City |
SAN ANTONIO |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE197320 |
Therapeutic Targeting of Ovarian Cancer Stem Cells Using Estrogen Receptor Beta Agonist |
|
| Relations |
| BioSample |
SAMN26200457 |
| SRA |
SRX14266689 |
