|
| Status |
Public on Feb 15, 2013 |
| Title |
Cultured adipocytes, Day 4, bio rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
Cultured adipocytes, Day 4
|
| Organism |
Mus musculus |
| Characteristics |
sample type: Cultured white pre-adipocytes+differentiation medium
cell type: differentiated cultured white pre-adipocytes
strain: C57BL/6
|
| Growth protocol |
White pre-adipocytes are isolated from subcutaneous fat pat from young mice (2 weeks old). After collagenase digestion and fractionation, pre-adipocytes,enriched in bottom stromal vascular fraction (VSC)s, are resuspended and cultured to confluence in DMEM supplemented with 10% New-born Bovine Serum. The cells arethen exposed to differentiation medium: 10%FBS DMEM, Insulin 850nM (Sigma), Dexamethasone 0.5uM (Sigma), IBMX 250uM (Sigma), Rosiglitazone 1uM (Cayman Chemical). After 2 days, cells are incubated in culture medium containing insulin 160nM for another 2 days, and then are switched to 10% FBS DMEM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the samples was extracted via the MiRNeasy kit (Qiagen) according to manufacturer's instructions and normalized to 50 ng/ul. The GeneChip® 3’ IVT Express Protocol was used for amplification in a semi automated process. The total RNA underwent reverse transcription to synthesize first-strand cDNA. This cDNA was then converted into a double-stranded DNA template for transcription.
|
| Label |
biotin
|
| Label protocol |
In vitro transcription synthesized aRNA and incorporated a biotin-conjugated nucleotide. The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate.
|
| |
|
| Hybridization protocol |
Fragmentation of the biotin-labeled aRNA prepared the samples for hybridization on a custom designed GeneChip® Mouse 430 2.0 (PN 900496). The washing and staining were performed on the GeneChip® Fluidics Station
|
| Scan protocol |
The GeneChip® Scanner 3000 was used for scanning the arrays.
|
| Description |
Gene expresssion data from differentiated mouse pre-adipocytes
|
| Data processing |
R/Bioconductor, MAS5.0 background corrected, quantile normalized, pmonly & avgdiff probset summarization
|
| |
|
| Submission date |
Jun 10, 2011 |
| Last update date |
Feb 15, 2013 |
| Contact name |
Cole Trapnell |
| E-mail(s) |
[email protected]
|
| Organization name |
Harvard University
|
| Department |
Stem Cell and Regenerative Biology
|
| Lab |
John Rinn
|
| Street address |
7 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL8321 |
| Series (2) |
| GSE29897 |
Long non-coding RNAs regulate adipogenesis (Affymetrix) |
| GSE29899 |
Long non-coding RNAs regulate adipogenesis |
|
