|
| Status |
Public on Feb 06, 2015 |
| Title |
Baseline.2 (II) |
| Sample type |
RNA |
| |
|
| Source name |
Aortic vascular smooth muscle cells_baseline
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 8 weeks-old
stimulus: none
cell type: primary aortic smooth muscle cells (SMCs)
|
| Treatment protocol |
Cells were either harvested at baseline or treated with 10 μg/mL Cholesterol:methyl-β-cyclodextrin complex (1:6 molar ratio) for 72 h and then harvested, or treated with cholesterol for 72 h and then treated with 100 μg/mL HDL for an additional 72 h and then harvested.
|
| Growth protocol |
Mouse aortic VSMCs were isolated from thoracic aortas of 8 week-old C57BL/6 mice (as described in Rong et al., Proc Nat Acad Sci USA, v100, pp13531–13536, 2003) and subconfluent cell preparations (≤ five passages) were grown in DMEM containing 10% FBS, 100 units/mL penicillin, and 100 μg/mL streptomycin, and incubated at 37 °C with 5% CO2 / 95% air.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (Invitrogen). RNA quality was analyzed with an Agilent Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
RNA samples were reverse transcribed to cDNA, transcribed to obtain labeled aRNA, purified, and fragmented using the GeneChip 3’ IVT Express kit.
|
| |
|
| Hybridization protocol |
Labeled aRNA was hybridized onto the GeneChip® Mouse Genome 430 2.0 using the GeneChip Hybridization Oven 640, and the GeneChip was stained in a GeneChip Fluidics Station 450 with streptavidin-phycoerythrin conjugate.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
Analysis (II)
|
| Data processing |
Probe-level intensities for all six samples (baseline, cholesterol-treated, and HDL-recovered) were background-adjusted and normalized using the Robust Multichip Average procedure.
Probe-level log2 intensities were combined into probesets using probe-to-probeset mappings from the University of Michigan CustomCDF project version 13, based on Ensembl Gene identifiers (release 58).
|
| |
|
| Submission date |
Jun 07, 2013 |
| Last update date |
Feb 06, 2015 |
| Contact name |
Stephen Ramsey |
| Organization name |
Oregon State University
|
| Department |
Biomedical Sciences
|
| Street address |
Dryden Hall 208A
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
| |
|
| Platform ID |
GPL14657 |
| Series (1) |
| GSE47744 |
Molecular mechanisms vascular smooth muscle cell (VSMC) acquisition of macrophage features in response to cholesterol loading |
|
