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| Status |
Public on Aug 07, 2014 |
| Title |
NC_rep2 |
| Sample type |
SRA |
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| Source name |
adipocytes
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| Organism |
Mus musculus |
| Characteristics |
transfection: control
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| Treatment protocol |
For transfection, primary preadiocytes were kept in culture medium until 80-90% confluence. Then Locked Nucleic Acid (LNAs) miRNA inhibitors (100nM) were transfected by Lipofectaimine RNAi Max (Invitrogen) according to the manufacturer’s instruction. 8 hours after transfection, cells were recovered in full culture media and induced to differentiation. Four days after differentiation RNAs were harvested for analysis.
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| Growth protocol |
Briefly, tissue depots were digested in 0.2% collagenase at 37ºC for 25-30min. Digested tissues were filtered through a 100um membrane and SVF cells were collected by centrifugation at 1500rpm for 5min. After centrifugation, the mature adipocytes floating on top were collected for genotying analysis. The freshly isolated SVF cells were seeded and cultured in DMEM containing 10% new born calf serum and 0.5% penicillin/streptomycin at 37ºC with 5% CO2. On confluence, the cells were induced to differentiate for 2 days with DMEM containing 10% FBS, 850nM of insulin, 0.5uM of dexamethasone (Sigma), 250uM of 3-isobutyl-methylxanthine (IBMX) (Sigma) and 1VM of rosiglitazone (Sigma) in DMEM. The induction medium was replaced with DMEM containing 10% FBS and 160nM insulin for 2 days. Then cell were incubated in DMEM with 10% FBS.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen miRNeasy Mini Kit
NEBNext® Ultra™ Directional RNA Library Prep Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Reads were aligned to mm10, using Tophat (version tophat-2.0.9) . Differential expression was performed using Cuffdiff (version 2.1.1).
Genome_build: mm10
Supplementary_files_format_and_content: RPKM and fold-change
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| Submission date |
Aug 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Lei Sun |
| E-mail(s) |
[email protected]
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| Organization name |
Duke-NUS
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| Street address |
8 College Road
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| City |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE60165 |
MicroRNAs are required for the feature maintenance and differentiation of brown adipocytes |
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| Relations |
| BioSample |
SAMN02953563 |
| SRA |
SRX670806 |
| 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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