|
| Status |
Public on Nov 23, 2005 |
| Title |
Characterization of an Arabidopsis mutant deficient in the non-phosphorylating of GAPN gene-2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
WT arabidopsis plant
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
The experimental RNA sample was directly labeled with Cy3-dUTP fluorescent dye
|
| Extracted molecule |
total RNA |
| Label |
Cy3-dUTP
|
| |
|
| Channel 2 |
| Source name |
GAPN mutant arabidopsis plant
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
The experimental RNA sample was directly labeled with Cy5-dUTP fluorescent dye
|
| Extracted molecule |
total RNA |
| Label |
Cy5-dUTP
|
| |
|
| |
| Hybridization protocol |
Labeled samples were mixed and then hybridized to a microarray for 15 h at 60C. The slides were washed at room temperature in three wash steps: 2x SSC, 0.5% SDS; 0.5x SSC; and 0.05x SSC for 5 min each with gentle shaking.
|
| Scan protocol |
The slides were scanned with a GenePix 4000B Scanner
|
| Description |
Normalization between the Cy3 and Cy5 fluorescent dye emission channels was achieved by adjusting the levels of both image intensities. The experiments were repeated three times with samples from different experiments, as biological replicates. In dye swapping experiments, the RNA samples from different experiments were labeled reciprocally, both as a biological and technical repetition for comparing the reproducibility of the experiments.The hybridization intensities of each microarray element were measured using ScanAlyze 4.24 (available at http://genome-www4.stanford.edu/MicroArray/SMD /restech.html). The two channels were normalized in log space using the z-score normalization on a 95% trimmed data set. We removed unreliable spots according to the following criteria: spots flagged as having false intensity caused by dust or background on the array were removed; and spots for which intensity was less than three fold above background were also eliminated. Data from multiple experiments were normalized (Bolstad et al., 2003) and signals from spots from different experiments were analyzed using Significance Analysis of Microarrays using the one class response (SAM, Tusher et al., 2001, http://www-stat.stanford.edu/~tibs/SAM/.), with a false discovery rate <10%.
|
| Data processing |
Significance Analysis of Microarrays
|
| |
|
| Submission date |
Oct 31, 2005 |
| Last update date |
Nov 23, 2005 |
| Contact name |
Paula Casati |
| E-mail(s) |
casati@cefobi-conicet.gov.ar
|
| Phone |
54-341-4371955
|
| Organization name |
Universidad Nacional de Rosario
|
| Department |
Biological Sciences
|
| Lab |
Casati
|
| Street address |
Suipacha 531
|
| City |
Rosario |
| State/province |
Santa Fe |
| ZIP/Postal code |
2000 |
| Country |
Argentina |
| |
|
| Platform ID |
GPL1941 |
| Series (1) |
| GSE3539 |
Characterization of an Arabidopsis mutant deficient in the non-phosphorylating of GAPN gene. |
|
