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| Status |
Public on Oct 06, 2020 |
| Title |
immature Sertoli cells, C2 |
| Sample type |
SRA |
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| Source name |
Testis
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| Organism |
Sus scrofa |
| Characteristics |
cell type: immature Sertoli cells
age: 80 to 90 days gestation
treatment: control group of immature Sertoli cells
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| Treatment protocol |
The cells were seeded at a density of approximately 1×10e5 cells/mL, and cultured for 6h, before treated with the L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (AA2P, Sigma, USA) at 250μM.
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| Growth protocol |
iSCs were cultured in Minimum Essential Medium (MEM) with Eagle's balanced salt solution (HyClone, USA), supplementing with 10% fetal bovine serum (Clark, Australia) and 1% penicillin-streptomycin (Gibco, USA), in a 5% CO2 incubator at 37°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol reagent (Sigma) was used to isolate the total RNA of samples collected from three controls (C1, C2 and C3) and three AA2P-treated (V1, V2 and V3) iSC cells.
The libraries were constructed and sequenced on an Illumina Hiseq X-Ten (Illumina, San Diego, CA, USA) in a single lane.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
illumina bcl2fastq2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sus scrofa11.1 whole genome using Hisat2 v2.0.5 with parameters --rna-strandness RF --dta -t -p 4.
Fragments per Kilobase per Million Mapped Fragments of(FPKM) were calculated using a protocol from Trapnell, C. et al, 2010.FPKM method can eliminate the influence of gene length and sequencing amount on the calculated gene expression.
Genome_build: Sus scrofa11.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Jun 24, 2020 |
| Last update date |
Oct 06, 2020 |
| Contact name |
Liang Hao |
| E-mail(s) |
lianghaoYangtze@outlook.com
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| Phone |
18800463461
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| Organization name |
Yangtze University
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| Street address |
JingMi road
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| City |
Jingzhou |
| State/province |
Hubei |
| ZIP/Postal code |
434025 |
| Country |
China |
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| Platform ID |
GPL22918 |
| Series (1) |
| GSE153157 |
Ascorbic acid promotes the reproductive function of porcine immature Sertoli cells through transcriptome reprogramming |
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| Relations |
| BioSample |
SAMN15357404 |
| SRA |
SRX8609222 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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