|
| Status |
Public on May 17, 2013 |
| Title |
RW-SS_3 |
| Sample type |
RNA |
| |
|
| Source name |
Regular weight mice exposed to sidestream smoke (SS), biological rep3
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: heart
body weight: regular weight
treatment: Sidestream smoke (SS)
|
| Treatment protocol |
Groups (N=6-8 biological replicates) of RW and DIO C57BL/6 mice (15-weeks old at start of exposures) were exposed to either filtered air (sham controls, SC), mainstream (MS) or sidestream (SS) cigarette smoke by nose-only inhalation exposure for 5 hr/day for a total of eight exposures over two weeks as follows: 5 consecutive days of exposure, followed by 2 days with no exposure, then three days of exposure, with necropsies occurring the day following the last exposure.
|
| Growth protocol |
Control, i.e., nonobese or regular weight (RW) and diet-induced obese (DIO) male C57BL/6 mice at 13 weeks of age were purchased from the Jackson Laboratories (Bar Harbor, ME). For this study, RW mice are defined as those mice fed a regular diet consisting of pelleted PMI® 5002 Certified Rodent Diet (PMI 5002 Rodent Diet®, Richmond, IN; ~5kcal% fat) throughout the study. DIO mice were fed a high calorie/high fat diet consisting of pelleted D12492 Rodent Diet (Research Diets Inc., New Brunswick, NJ; 60kal% fat) throughout the study starting at six weeks of age for a total of nine weeks prior to the start of the 4-day LPS exposure study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).
|
| |
|
| Hybridization protocol |
Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
|
| Scan protocol |
The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
|
| Description |
Gene expression data from regular weight mice exposed to sidestream smoke (SS)
503
|
| Data processing |
Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.
|
| |
|
| Submission date |
May 16, 2013 |
| Last update date |
Aug 16, 2013 |
| Contact name |
Susan C. Tilton |
| E-mail(s) |
[email protected]
|
| Organization name |
Oregon State University
|
| Department |
AG Envr & Molec Toxicology
|
| Street address |
1007 ALS Bldg
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
| |
|
| Platform ID |
GPL8321 |
| Series (1) |
| GSE47022 |
Impaired Transcriptional Response of the Murine Heart To Cigarette Smoke in the Setting of High Fat Diet and Obesity |
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