|
| Status |
Public on Feb 04, 2021 |
| Title |
TOX3_2 |
| Sample type |
SRA |
| |
|
| Source name |
Ovarian granulosa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KGN
cell type: Ovarian granulosa cells
genotype/variation: TOX3 overexpression
|
| Treatment protocol |
Control (lentiviral-control, LV-CON) and TOX3 (lentiviral-TOX3, LV-TOX3) overexpression lentiviruses (Genechem Company, Shanghai, CHN) carrying the puromycin resistance gene were synthesized. Lentiviruses were added at a ratio of 1:200 into the cell culture medium when cell fusion reached 60–70%. Positive cells were screened using 2 mg/mL of puromycin for two passages.
|
| Growth protocol |
Cells were cultured in Dulbecco’s Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F12) (Hyclone Corporation, South Logan, UT, USA) supplemented with 10% fetal bovine serum (Hyclone Corporation) and 100 U/mL penicillin (Hyclone Corporation) and 100 mg/mL streptomycin (Hyclone Corporation) at 37 °C in a humidified atmosphere containing 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by removing the culture medium and lysing the remaining cells using TRIzol™ Reagent (Takara Bio, Beijing, CHN) according to the manufacturer’s instructions. RNA concentration and integrity number were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The sequencing data were filtered with SOAPnuke by removing reads containing sequencing adapters
Reads whose low-quality base ratio, i.e., a base quality less than or equal to 5, was above 20%
Reads whose unknown base ('N' base) ratio was more than 5%, after which clean reads were obtained and stored in the FASTQ format.
Genome_build: RefSeq hg38
Supplementary_files_format_and_content: The expression levels were calculated using RNA-Seq by Expectation Maximization
|
| |
|
| Submission date |
Nov 12, 2020 |
| Last update date |
Feb 04, 2021 |
| Contact name |
Yuanyuan Man |
| E-mail(s) |
manyuanyuan_0018@163.com
|
| Phone |
+8617865139105
|
| Organization name |
Shandong University
|
| Department |
Center for Reproductive Medicine
|
| Street address |
No.157, Jingliuweiwu Road
|
| City |
Jinan |
| State/province |
Shandong |
| ZIP/Postal code |
250100 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE161341 |
The Breast Cancer Susceptibility Gene TOX3 Promotes Estrogen Synthesis: An RNA-sequencing and Network Study |
|
| Relations |
| BioSample |
SAMN16779383 |
| SRA |
SRX9491558 |
