|
| Status |
Public on Mar 22, 2013 |
| Title |
Dox-treated lung Replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Diseased
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
strain: BALB/c
transgene: IL-1b
treatment: doxycyline
|
| Growth protocol |
Lungs were harvested from water- or Dox-treated mice after 7 days at ~12-week of age. IL-1b is induced in Dox-treated mice which showed increased inflammation and emphysema in lung.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.
|
| 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 |
Dox-treated lung replicate 2
|
| 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 |
GPL6794 |
| Series (2) |
| GSE31559 |
Various mice and rat tissues subjected to various treatments |
| GSE38075 |
Profiling whole lung from lung-specific IL-1b-Tg mice |
|
