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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 26, 2024 |
| Title |
Liver, Young-veh, rep1 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: C57BL/6
treatment: Veh.
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| Treatment protocol |
(Cell lines) To induce quiescence, IMR-90 ER:Ras cells were cultured with the above medium containing 0.1% FBS for 2 days. To induce oncogene-induced senescence, IMR-90 ER:Ras cells were treated with 100 nM 4-Hydroxytamoxifen (4-OHT) for 6 days or 8 days. Transfection of siRNA was performed using RNAiMAX (Invitrogen). (Mouse) Young (8–9 weeks old) and aged (89–90 weeks old) male C57BL/6J mice (JAXON LABORATORY JAPAN) were intraperitoneally injected with 10,11-Dehydrocurvularin (DCV; 10 mg/kg/ 200 l), JQ1 (50 mg/kg/ 200 l), or vehicle control (200 l corn oil) two or three times a week for 1 month, and the liver and kidney tissue was then collected.
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| Growth protocol |
(Cell lines) IMR-90 ER:Ras cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 200 mM L-glutamine, 1 mM sodium pyruvate, 10% (v/v) heat-inactivated fetal bovine serum (FBS), and penicillin/streptomycin. (Mouse) Animal experiments were approved by the Animal Care and Use Committee of Kumamoto University (A2019-098), and conducted in accordance with its guidelines.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
(Cell lines) Total RNA was extracted using RNeasy Mini Kit (QIAGEN). (Mouse) Total RNA was extracted using Trizol reagent.
Messenger RNA was purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were synthesized using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Basecalls and conversion to FASTQ files were performed using BaseSpace Onsite (Illumina)
Adaptor trimming and QC were done using Trim galore (v0.5.0).
Mapping of the trimmed reads on the reference genome was done using rsem-calculate-expression (RSEM v1.3.1).
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.1).
Differentially expressed gene (DEG) analysis was done using RNAseqChef (Etoh K et al., 2023)
Assembly: hg19 or mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes TPM values for each sample.
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| Submission date |
Nov 13, 2023 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Mitsuyoshi Nakao |
| E-mail(s) |
mnakao@gpo.kumamoto-u.ac.jp
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| Phone |
+81963736800
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| Organization name |
Kumamoto University
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| Department |
Institute of Molecular Embryology and Genetics
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| Lab |
Medical Cell Biology
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| Street address |
2-2-1 Honjo, Chuo-ku
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| City |
Kumamoto |
| ZIP/Postal code |
860-0811 |
| Country |
Japan |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE247607 |
Transcriptome analysis to investigate the role of ACLY pathway in senescent cells. |
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| Relations |
| BioSample |
SAMN38237873 |
| SRA |
SRX22513132 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7897902_Liver-Young-veh_1.genes.results.gz |
446.0 Kb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
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