|
| Status |
Public on Feb 20, 2014 |
| Title |
DGAT1_Study4_Vehicle_2 |
| Sample type |
RNA |
| |
|
| Source name |
Skin
|
| Organism |
Mus musculus |
| Characteristics |
treatment: vehicle
tissue: dorsal skin
genotype: C57BL/6
age: 8 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.
|
| Label |
biotin
|
| Label protocol |
The reverse 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-cDNA.
|
| |
|
| 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 45C 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 |
Gene expression data from dorsal skin taken after 14 days of treatment with DGAT1 inhibitor.
|
| Data processing |
Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/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://0-bioinformatics-oxfordjournals-org.brum.beds.ac.uk/cgi/content/full/22/9/1111).
|
| |
|
| Submission date |
Jul 30, 2013 |
| Last update date |
Feb 21, 2014 |
| Contact name |
eric muise |
| E-mail(s) |
eric_muise@merck.com
|
| Organization name |
Merck
|
| Department |
Genetics and Pharmacogenomics
|
| Street address |
33 Ave Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL9734 |
| Series (1) |
| GSE49375 |
DGAT1 Inhibitor-Induced Gene Expression in Mouse Skin |
|
