|
| Status |
Public on Oct 22, 2009 |
| Title |
wildtype strains vs. rpob 9-bp-deletion strains(Cy5/Cy3) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from wildtype strains labeled with Cyanine-5 (red).
|
| Organism |
Deinococcus radiodurans |
| Characteristics |
genotype: Wild-type
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 |
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 rpob 9-bp-deletion strains labeled with Cyanine-3 (green).
|
| Organism |
Deinococcus radiodurans |
| Characteristics |
genotype: rpob 9-bp-deletion
phenotype: low 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 2 of 2 with dye-swap.
|
| 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.
|
| |
|
| Submission date |
Oct 21, 2009 |
| Last update date |
Oct 21, 2009 |
| 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) |
| GSE18661 |
Deinococcus radiodurans R1: rpob 9-bp-deletion vs. wild-type |
|
