|
| Status |
Public on Jun 30, 2015 |
| Title |
Lipase/Esterase A treated leaves, biological replicate1 (120min_RMA) |
| Sample type |
RNA |
| |
|
| Source name |
two weeks old
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: bacterial blight susceptible rice cultivar (Taichung Native-1; TN-1)
age: two weeks old rice seedlings
tissue: leaves
agent: Lipase/Esterase A
time: 120 min
|
| Treatment protocol |
30-40μl of either Lipase/Esterase A (500μg/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 10 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 30 min. and 120 min. 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 |
Raw data file: 120 min Lipase-1.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 120 minafter infiltration
|
| Data processing |
The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to GeneSpring 12.6 - GX - PA (Agilent Technology) for further analysis. The PLIER 16 and RMA algorithms were used for data normalization
|
| |
|
| Submission date |
Jan 09, 2014 |
| Last update date |
Jun 30, 2015 |
| Contact name |
Ramesh V. Sonti |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE53940 |
Whole genome expression profiling of rice leaves treated with Xanthomonas oryzae pv. oryzae secreted cell wall degrading lipase/esteraseA (LipA) at early time points, 30 min. and 120 min. |
|
| Relations |
| Reanalysis of |
GSM1303775 |
