|
| Status |
Public on Sep 01, 2007 |
| Title |
c3tag.3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Gland mammary normal
|
| Organism |
Mus musculus |
| Characteristics |
Strain: FVB
Model: wild-type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA obtained by a two-step extraction method using TRIZOL® Reagent (Invitrogen) and RNeasy Mini protocol for RNA cleanup by QIAGEN (Valencia, CA).
|
| Label |
Cy3
|
| Label protocol |
The tumor RNA was labeled by using Cyanine 5-dUTP (Cy5), and reference normal samples were labeled with Cyanine 3-dUTP (Cy3) as described in Hegde P. et al. Biotechniques 2000;29(3):548-50, 52-4.
|
| |
|
| Channel 2 |
| Source name |
Gland mammary tumor
|
| Organism |
Mus musculus |
| Characteristics |
Strain: FVB
Model: C3(1)/SV40 T/t-antigen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA obtained by a two-step extraction method using TRIZOL® Reagent (Invitrogen) and RNeasy Mini protocol for RNA cleanup by QIAGEN (Valencia, CA).
|
| Label |
Cy5
|
| Label protocol |
The tumor RNA was labeled by using Cyanine 5-dUTP (Cy5), and reference normal samples were labeled with Cyanine 3-dUTP (Cy3) as described in Hegde P. et al. Biotechniques 2000;29(3):548-50, 52-4.
|
| |
|
| |
| Hybridization protocol |
Twenty micrograms of total RNA from each sample was was labeled and hybridized as described in Hegde P. et al. Biotechniques 2000;29(3):548-50, 52-4.
|
| Scan protocol |
The array slides were scanned with an Axon 4000 scanner (Axon Instruments, Foster City, CA)
Images were quantified using GenePix software.
|
| Description |
mAdbID.26634
|
| Data processing |
For each spot the channel signal was calculated as mean foreground minus median background. Bad and/or low intensity spots were excluded. Log2 ratios on each array were normalized with LOWESS. Insightful S-Plus 6.0 (Insightful Corp., Seattle, WA) was used for the data processing.
|
| |
|
| Submission date |
Aug 02, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Jeffrey E Green |
| E-mail(s) |
[email protected]
|
| Phone |
3014355193
|
| Fax |
3014968709
|
| Organization name |
NCI
|
| Street address |
Rm 4054, 37 Convent Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL5339 |
| Series (2) |
| GSE8663 |
Integrated SV40 T/t-antigen Cancer Signature in Aggressive Breast, Prostate and Lung Carcinomas with Poor Prognosis 2 |
| GSE8666 |
Integrated SV40 T/t-antigen Cancer Signature in Aggressive Breast, Prostate and Lung Carcinomas with Poor Prognosis |
|
