|
| Status |
Public on Aug 07, 2015 |
| Title |
empty vector [1B] |
| Sample type |
RNA |
| |
|
| Source name |
brown adipocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
|
| Growth protocol |
Immortalized brown preadipocytes were transduced with lentivirus expressing NT-PGC-1α or empty vector. Preadipocytes were grown to become confluent in growth mediem (DMEM+FBS) and differentiation was induced for 2 days in the growth medium containing 20 nM insulin, 1 nM triiodothyronine, 0.5 mM isobutylmethlyxanthine, 2 µg/ml dexamethasone and 250 µM indomethacin. Thereafter, cells were maintained in the growth medium containing 20 nM insulin and 1 nM triiodothyronine for additional 5 days (Zhang Y et al, 2009, JBC 284(47):32813).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Tri-Reagent (Molecular Research Center) with modifications to remove DNA using Qiagen RNAeasy columns.
|
| Label |
digoxigenin-11-UTP
|
| Label protocol |
One microgram of RNA was amplified and labeled using the NanoAmp IVT-Amplification Kit (Applied Biosystems).
|
| |
|
| Hybridization protocol |
Ten micrograms of digoxigenin-11-UTP-labeled (Roche Diagnostics) cRNA was fragmented using the Applied Biosystems Chemiluminescent Detection Kit protocol. Pooled samples were hybridized onto ABI Mouse Genome Survey arrays.
|
| Scan protocol |
The microarray slides were scanned and gridded, and the images were digitized and analyzed using an Applied Biosystems 1700 Chemiluminescent Microarray Analyzer.
|
| Description |
immortalized cells
|
| Data processing |
Data files were analyzed using the package ABarray v1.36.0 (Applied Biosystems, Foster City, CA), the statistical program R v.2.2.1 (http://www.r-project.org) and the quantile-quantile method for normalization across arrays (http://www.bioconductor.org). Parameters for feature control were set at signal/noise ratio ≥3 and quality flags <5,000 in order to generate fold changes for features.
The Sample table contains quantile normalized signal, SN-signal to noise ratio and flag-flagged defect in the array oligonucleotide spot. The RawData Matrix contains non-normalized data exported from the package ABarray v1.36.0. 1A and 1B represent technical replicates of control samples (empty vector) and 4A and 4B of NT-PGC-1α-expressing samples.
|
| |
|
| Submission date |
Aug 06, 2015 |
| Last update date |
Aug 07, 2015 |
| Contact name |
Ji Suk Chang |
| Organization name |
Pennington Biomedical Research Center
|
| Department |
Gene Regulation and Metabolism
|
| Street address |
6400 Perkins Rd.
|
| City |
Baton Rouge |
| State/province |
LA |
| ZIP/Postal code |
70808 |
| Country |
USA |
| |
|
| Platform ID |
GPL2995 |
| Series (1) |
| GSE71774 |
Remodeling of Brown and White Adipose Tissue by NT-PGC-1α-Mediated Gene Regulation |
|
