|
| Status |
Public on Mar 22, 2013 |
| Title |
Aged Gastroc Muscle Replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
Diseased
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Muscle
strain: Sprague Dawley
age: 24 mo
|
| Growth protocol |
Five 24-month old male Sprague-Dawley rats served as the aged group to compare with five 6-month old male Sprague-Dawley rats as young controls. All animals were housed in a 12:12 hour light cycle with ad lib food and water for at least a month (Age at necropsy was 28 months and 7 months for old and young, respectively). Animals were euthanized with CO2 and exanguination and the whole hind limb lateral gastrocnemius muscle from the left leg was dissected and snap frozen in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from muscle using Qiagen RNeasy Midi kit as described by the manufacturer. Samples were treated with DNaseI on-column (Qiagen) for 30 minutes. RNA concentration was measured using a NanoDrop ND-1000 and RNA integrity was determined with a 2100 Bioanalyzer.
|
| Label |
Biotin
|
| Label protocol |
The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cRNA.
|
| |
|
| Hybridization protocol |
GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45?C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.
|
| Scan protocol |
Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.
|
| Description |
Aged Muscle Replicate 3
|
| Data processing |
Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260). Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value. The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).
|
| |
|
| Submission date |
May 21, 2012 |
| Last update date |
Mar 22, 2013 |
| Contact name |
I-Ming Wang |
| E-mail(s) |
i_ming_wang@merck.com
|
| Phone |
215-652-1287
|
| Organization name |
Merck Research Lab
|
| Department |
Genetics and Pharmacogenomics
|
| Lab |
Discovery Pharmacogenomics
|
| Street address |
770 Sumneytown Pike
|
| City |
West Point |
| State/province |
PA |
| ZIP/Postal code |
19486 |
| Country |
USA |
| |
|
| Platform ID |
GPL15572 |
| Series (2) |
| GSE31559 |
Various mice and rat tissues subjected to various treatments |
| GSE38077 |
Profiling muscle from aged rat model for sarcopenia |
|
