|
| Status |
Public on Mar 30, 2009 |
| Title |
559T.tumor.Cy3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Tumor epithelial tissue from murine mammary glands
|
| Organism |
Mus musculus |
| Characteristics |
Sample identifier: 559T; Diagnosis: solid nodular, erbb2-type carcinoma; Sex: Female; Strain: FVB/N
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Phenol-chloroform extraction
|
| Label |
Cy3
|
| Label protocol |
4ng of extracted RNA was subjected to two rounds of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy3-labeled cRNA was prepared from 4-5ug total RNA using Ambion's MessageAmp kit.
|
| |
|
| Channel 2 |
| Source name |
Stratagene universal mouse reference
|
| Organism |
Mus musculus |
| Characteristics |
None
|
| Biomaterial provider |
Stratagene
|
| Extracted molecule |
total RNA |
| Extraction protocol |
No extraction
|
| Label |
Cy5
|
| Label protocol |
4ng of extracted RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy5-labeled cRNA was prepared from 4-5 ug total RNA using Ambion's MessageAmp kit.
|
| |
|
| |
| Hybridization protocol |
Following fragmentation, 750ng of cRNA was hybridized to Agilent's Whole Mouse Genome expression array (G4122A) according to the protocols provided by the manufacturer.
|
| Scan protocol |
Array was scanned using Agilent's dual-laser microarray scanner (Model G2505B), and Cy5/Cy3-signals were quantified using Agilent's Feature Extraction software (Palo Alto, CA).
|
| Description |
RNA isolated from laser capture microdissected mammary tissue.
|
| Data processing |
Raw Cy5 and Cy3 intensities were background corrected using the RMA background correction algorithm. Data was transformed to log2 ratios and within array normalization was performed using spatial and intensity-dependent loess.
|
| |
|
| Submission date |
Feb 04, 2008 |
| Last update date |
Mar 30, 2009 |
| Contact name |
Robert Lesurf |
| Organization name |
Washington University in St. Louis
|
| Department |
McDonnell Genome Institute
|
| Lab |
Griffith Lab
|
| Street address |
4444 Forest Park Ave
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63112 |
| Country |
USA |
| |
|
| Platform ID |
GPL2872 |
| Series (1) |
| GSE10450 |
Met induces mammary tumors with diverse histologies and is associated with poor outcome and human basal breast cancer |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
-[INV_VALUE] |
| gMeanSignal |
The mean foreground signal in the Cy3 channel |
| gMedianSignal |
The median foreground signal in the Cy3 channel |
| gBGMeanSignal |
The mean background signal in the Cy3 channel |
| gBGMedianSignal |
The median background signal in the Cy3 channel |
| rMeanSignal |
The mean foreground signal in the Cy5 channel |
| rMedianSignal |
The median foreground signal in the Cy5 channel |
| rBGMeanSignal |
The mean background signal in the Cy5 channel |
| rBGMedianSignal |
The median background signal in the Cy5 channel |
| INV_VALUE |
log2 ratio of normalized Cy5 to Cy3 signal |
