|
| Status |
Public on Apr 12, 2012 |
| Title |
Ppar-beta null DMSO rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Ppar-beta null DMSO
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primary keratinocyte
strain: C57/BL6
genotype: Ppar-beta NULL
hras: hRAS mock transduced
ligand: Control (DMSO)
|
| Treatment protocol |
Primary keratinocytes were treated with or without 1 uM GW0742 for 24 hours.
|
| Growth protocol |
Primary keratinocytes were cultured as previously described (Dlugosz et al., 1995) for 2 days before transduced with Hras virus.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIZOL reagent and subject to a further step of clean up using Rneasy kit.
|
| Label |
biotin
|
| Label protocol |
FragmentED the sense strand cDNA according to the manufacturer’s instructions using the Affymetrix GeneChip WT Terminal Labeling Kit (#900671) and confirmed proper fragmentation using an RNA Nano Chip on the Agilent Bioanalyzer. Labeled the resulting fragmented cDNA using the Affymetrix GeneChip WT Terminal Labeling Kit (#900671) according to the manufacturer’s protocol. Assessed labeling efficiency with the gel shift assay described by the manufacturer but utilizing an Agilent Bioanalyzer RNA Nano Chip instead of PAGE.
|
| |
|
| Hybridization protocol |
Hybridization cocktail prepared using the GeneChip Hybridization Wash and Stain Kit (#702232). Arrays hybridized according to the manufacturer’s instructions in the Affymetrix GeneChip Hybridization Oven 640.
|
| Scan protocol |
Arrays washed and stained using the Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’s protocol using the GeneChip Hybridization Wash and Stain Kit (#702232). Stained arrays were scanned with the GeneChip Scanner 3000 7G.
|
| Description |
Affymetrix Mouse Gene 1.0 ST Array
|
| Data processing |
Data was normalized using the Robust Multichip Average (RMA) approach as previously described (Do and Choi, 2006) with the CFM file provided by the manufacturer (mogene10stv1.r3cdf)
|
| |
|
| Submission date |
Sep 29, 2011 |
| Last update date |
Apr 12, 2012 |
| Contact name |
Combiz Khozoie |
| E-mail(s) |
[email protected]
|
| Organization name |
The Pennsylvania State University
|
| Street address |
312 Life Sciences Building
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16803 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE32498 |
Gene expression of wild-type and Ppar-beta null primary keratinocytes, with and without infection with an activated Hras retrovirus, with and without the Ppar-beta specific ligand GW0742 |
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