|
| Status |
Public on Dec 24, 2009 |
| Title |
Cellulase treated leaves, biological replicate3 |
| Sample type |
RNA |
| |
|
| Source name |
20 days old Taichung Native-1 rice seedlings
|
| Organism |
Oryza sativa |
| Characteristics |
Genotype: bacterial blight susceptible rice cultivar
Age: 20 days old rice seedlings
|
| Treatment protocol |
30-40μl of either cellulase (5μg/ml) purified from the culture supernatant of wild type Xoo or 10mM potassium phosphate buffer (pH 6.0) were infiltrated to the adaxial surfaces of rice leaves with a 1ml hypodermal syringe without the needle (as described in Jha et al. 2007; MPMI vol 20, pp 31-40)
|
| Growth protocol |
TN-1 rice seeds were germinated in petri plates containing moistened filter paper. Three days old seedlings were transferred to plastic pots containing soil and were grown for 15 days in a green house. Two days before the actual treatment, the pots containing the rice seedlings were transferred to a growth chamber (28oC; 80% relative humidity with 12/12h light/dark cycle)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
20-30 leaf pieces covering the infiltrated zone from each of the treatments were harvested 12h after infiltration and subjected to total RNA isolation using Trizol (Invitrogen)
|
| Label |
Biotin
|
| Label protocol |
8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
|
| |
|
| Hybridization protocol |
The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rice Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
|
| Scan protocol |
The gene chips were scanned on an Affymetrix Scanner 3000
|
| Description |
Expression profile of cellulase treated rice leaves, 12 h after infiltration
|
| Data processing |
The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization
|
| |
|
| Submission date |
Jun 21, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Ramesh V. Sonti |
| E-mail(s) |
sonti@ccmb.res.in
|
| Organization name |
Centre for cellular and molecular biology (CCMB)
|
| Department |
Plant Microbe Interactions
|
| Street address |
Uppal Road
|
| City |
Hyderabad |
| State/province |
Andhra Pradesh |
| ZIP/Postal code |
500007 |
| Country |
India |
| |
|
| Platform ID |
GPL2025 |
| Series (1) |
| GSE8216 |
Transcriptional profiling of Cellulase induced hypersensitive reaction like response in rice |
|
