|
| Status |
Public on Sep 18, 2017 |
| Title |
ES2-control-1 |
| Sample type |
SRA |
| |
|
| Source name |
ES2 ovarian cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Control
|
| Treatment protocol |
Total RNA was isolated from ES2 cells that are trated with vehicle or liquiritigenin for 24 h were subjected to RNA-seq analysis
|
| Growth protocol |
ES2 were cultured in phenol red–free RPMI-1640 medium containing 5% dextran-charcoal treated FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ES2 cells were treated with either vehicle or liquiritigenin for 24 h, and total RNA was isolated using RNAesy mini kit (Qiagen) according to the manufacturer’s instructions. The purity of isolated RNA was determined using Agilent 2100 BioAnalyzer. Illumina TruSeq RNA Sample preparation was performed following manufacturer's protocol, and the samples were run on an Illumina HiSeq 2000 in duplicates.
Total RNA samples about 1-2 micrograms 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 100bp single-end (SE) sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
ES2 cells trated with vehicle
|
| Data processing |
Illumina bcl2fastq v2.17.1.14 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 |
Jan 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yidong Chen |
| E-mail(s) |
cheny8@uthscsa.edu
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE93807 |
Therapeutic utility of natural estrogen receptor beta agonists on ovarian cancer |
|
| Relations |
| BioSample |
SAMN06239800 |
| SRA |
SRX2501919 |
