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Sample GSM4905064 Query DataSets for GSM4905064
Status Public on Feb 04, 2021
Title CON_2
Sample type SRA
 
Source name Ovarian granulosa cells
Organism Homo sapiens
Characteristics cell line: KGN
cell type: Ovarian granulosa cells
genotype/variation: control
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 SAMN16779385
SRA SRX9491556

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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