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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 06, 2023 |
| Title |
NR-1 |
| Sample type |
SRA |
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| Source name |
cell line
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| Organism |
Tupaia chinensis |
| Characteristics |
tissue: cell line
cell line: home made
cell type: spermatogonial stem cells
genotype: wild type
treatment: 100 uM nicotinamide ribose
passage number: None
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| Treatment protocol |
100 uM nicotinamide ribose was added to medium.
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| Growth protocol |
Tree shrew spermatogonial stem cells were routinely maintained on inactivated tree shrew sertoli cells in the culture medium:StemPro-34 SFM supplemented with StemPro supplement, 10% FBS, 1 mM penicillin, 2 mM L-Glutamine, 0.1 mM β-mercaptoethanol, 1 mM sodium pyruvate, 1 mM NEAA (nonessential amino acid), 60 μM putrescine, 40 ng/mL human GDNF (recombinant human glial cell line-derived neurotrophic factor), 10 ng/mL human EGF (epidermal growth factor), 1 000 U mouse LIF (leukemia inhibitory factor), 2 ng/mL human bFGF (basic fibroblast growth factor). To harvest tree shrew SSCs, cells were cultured on gelatin-coated dishes about 3-5 hours to avoid contamination of somatic cells.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using standard Trizol procedure.
RNA libraries were constructed by Novogene Corporation (Beijing, China). RNA-seq libraries were constructed using Illumina NEBNext® UltraTM RNA Library Prep Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
NR-1
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| Data processing |
Basecalls performed using CASAVA version 2.19
Reads were mapped to Treeshrew genome using tophat2 (version 2.0.8) with default parameters.
For RNA-seq, fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using cufflinks version 2.1.1; Differentialy expressed genes were determined using cuffdiff (version 2.1.1).
Assembly: TS_3.0 from Treeshrew database (http://www.treeshrewdb.org/)
Supplementary files format and content: tab-delimited text files include FPKM values for each RNA-seq Sample
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| Submission date |
Apr 02, 2023 |
| Last update date |
Apr 07, 2023 |
| Contact name |
Ping Zheng |
| E-mail(s) |
zhengp@mail.kiz.ac.cn
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| Organization name |
Kunming Institute of Zoology, Chinease Academy of Sciences
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| Street address |
Qingsong Road 21
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| City |
Kunming |
| ZIP/Postal code |
650000 |
| Country |
China |
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| Platform ID |
GPL33302 |
| Series (1) |
| GSE228744 |
Characterization of long-term ex vivo expansion of tree shrew spermatogonial stem cells |
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| Relations |
| BioSample |
SAMN34041312 |
| SRA |
SRX19845002 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7135809_NR-1.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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