|
| Status |
Public on Dec 27, 2007 |
| Title |
BY4742 Non-Quiescent DDR2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
BY4742 Non-Quiescent DDR2
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
BY4742 Non-Quiescent DDR2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected as quiescent or non-quiescent cell fractions. All RNA isolation was accomplished with a modified Gentra protocol followed by Qiagen RNeasy Mini Kit reagents. As a control, exponential and stationary phase RNA were mixed 1:1.
|
| Label |
Cy5
|
| Label protocol |
RNA (20 µg) was annealed with 2 µg oligo dT, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.25 mM dCTP, 0.5 mM dATP, 0.5 mM dTTP. RNA was degraded using RNase H and RNase A.
|
| |
|
| Channel 2 |
| Source name |
Yeast stationary phase and Exponental mix 1:1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
As a control Yeast stationary phase and Exponental mix 1:1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected as quiescent or non-quiescent cell fractions. All RNA isolation was accomplished with a modified Gentra protocol followed by Qiagen RNeasy Mini Kit reagents. As a control, exponential and stationary phase RNA were mixed 1:1.
|
| Label |
Cy3
|
| Label protocol |
RNA (20 µg) was annealed with 2 µg oligo dT, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.25 mM dCTP, 0.5 mM dATP, 0.5 mM dTTP. RNA was degraded using RNase H and RNase A.
|
| |
|
| |
| Hybridization protocol |
The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and re-suspended in 30 µl of the hybridization solution.
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 6.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios were normalized to exogonus controls.
|
| Description |
Yeast
|
| Data processing |
After background correction based on negative controls and removal of flaged valuse, data was normalized to Arabidopsis thaliana controls.
|
| |
|
| Submission date |
Jul 20, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Sushmita Roy |
| E-mail(s) |
sroy@cs.unm.edu
|
| Phone |
5052779340
|
| Organization name |
Biology, University of New Mexico
|
| Street address |
|
| City |
Albuquerque |
| State/province |
NM |
| ZIP/Postal code |
87106 |
| Country |
USA |
| |
|
| Platform ID |
GPL5627 |
| Series (2) |
| GSE8560 |
Mutant1 |
| GSE8624 |
Quiescent and non-quiescent deletion-mutant strains |
|
