|
| Status |
Public on Mar 01, 2011 |
| Title |
stomach vs. pool |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
stomach
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: stomach
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA isolated using Qiagen RNeasy spin columns with DNAse treatment; polyA+ RNA isolated from total RNA via magnetic bead-based mRNA extraction (Ambion, Poly(A) Purist)
|
| Label |
Cy3
|
| Label protocol |
custom automated version of the aminoallyl MessageAmp II kit from Ambion.
|
| |
|
| Channel 2 |
| Source name |
Pool
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Pool of 20 adult tissues
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA isolated using Qiagen RNeasy spin columns with DNAse treatment; polyA+ RNA isolated from total RNA via magnetic bead-based mRNA extraction (Ambion, Poly(A) Purist)
|
| Label |
Cy5
|
| Label protocol |
custom automated version of the aminoallyl MessageAmp II kit from Ambion.
|
| |
|
| |
| Hybridization protocol |
Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.
|
| Scan protocol |
Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.
|
| Description |
42 diverse human tissues were hybridized. Samples were purchased as pools from multiple donors, typically over 10 (Clontech, Mountainview, CA). Pooled RNA from 20 diverse disease-free adult tissue pools comprised the reference pool.
|
| Data processing |
Data were processed using the Rosetta Resolver® system.
|
| |
|
| Submission date |
Feb 20, 2009 |
| Last update date |
Mar 01, 2011 |
| Contact name |
Xinwei She |
| E-mail(s) |
[email protected]
|
| Phone |
206-802-6422
|
| Fax |
206-802-6411
|
| Organization name |
Rosetta Inpharmatics, Merck
|
| Department |
Molecular Informatics
|
| Street address |
401 Terry Ave. N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL8217 |
| Series (1) |
| GSE14938 |
Definition, conservation and epigenetics of housekeeping and tissue-enriched genes |
|
