|
| Status |
Public on Mar 29, 2012 |
| Title |
DR0199-deletion strains vs. wildtype strains (Cy5/Cy3) rep 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from DR0199-deletion strains labeled with Cyanine-5 (red).
|
| Organism |
Deinococcus radiodurans |
| Characteristics |
genotype/variation: DR0199-deletion
phenotype: growth delay
|
| Growth protocol |
Cells were grown in an normal condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
16 µg of total RNA were primed with 9 µg of Hexadeoxyribonucleotide mixture at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe
|
| |
|
| Channel 2 |
| Source name |
Total RNA from wildtype strains labeled with Cyanine-3 (green).
|
| Organism |
Deinococcus radiodurans |
| Characteristics |
genotype/variation: Wildtype
phenotype: normal growth rate
|
| Growth protocol |
Cells were grown in an normal condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
16 µg of total RNA were primed with 9 µg of Hexadeoxyribonucleotide mixture at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe
|
| |
|
| |
| Hybridization protocol |
Samples were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed sequential. Dye-swap is carried out.
|
| Scan protocol |
Scanned on an Genepix 4000B scanner.
Images were quantified using Genepix (version 5.0).
|
| Description |
Biological replicate 3 of 3.
|
| Data processing |
Prior to channel normalization, microarray outputs were fitered to remove spots of poor signal quality by excluding those data points with a signal mean intensity less than two standard deviations above background in both channels. LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Limma software was used. Furthemore, the replicate spots on each array were merged to one value using lmFit function within Limma (this step is not done in this submission).
|
| |
|
| Submission date |
Nov 16, 2011 |
| Last update date |
Mar 29, 2012 |
| Contact name |
Yuejin Hua |
| E-mail(s) |
[email protected]
|
| Organization name |
Zhejiang University
|
| Department |
Institute of Nuclear-Agricultural Sciences
|
| Street address |
268 KaiXuan Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310029 |
| Country |
China |
| |
|
| Platform ID |
GPL9466 |
| Series (1) |
| GSE33758 |
Deinococcus radiodurans R1: wildtype strains vs. DR0199-deletion strains |
|
