|
| Status |
Public on Feb 01, 2019 |
| Title |
Uninfected rice plants, bio rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
25 days old rice seedlings
|
| Organism |
Oryza sativa |
| Characteristics |
genotype: Rice line carrying bacterial blight and blast resistance gene Xa21, xa13 and Pi54 respectively
age: 25 days old rice seedlings
infection: uninfected
|
| Treatment protocol |
For bacterial blight infection, the rice leaves were clip inoculated with Xanthomonas oryzae pv. oryzae isolate (DX-020), by dipping the scissors in saturated culture of Xoo and cutting the leaf tips so that the cells are deposited at the site of incision. For blast infection, the fungal spore suspension of Magnaporthe oryzae isolate (SP-28) was sprayed in conditions of hight humidity to facilitate heavy infection.
|
| Growth protocol |
Rice plants were grown in platic trays under green house conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
2 cm rice tissue was collected from the leaves below the point of Xoo inocluation and where the fungal spores were sprayed, 10-15 such leaf pieces for each biological replicate were collected and processed for RNA isolation using TRIZOL (Invitrogen). The tissue was collected and RNA was extracted at two time points 24 and 72 hrs post infection, RNA was then pooled from these two time points.
|
| Label |
Biotin
|
| Label protocol |
250ng of total RNA from pooled sample was 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 uninfected rice plants, 24 and 72 hrs post infection.
|
| Data processing |
The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to GeneSpring 13.1 - GX - PA (Agilent Technology) for further analysis. The PLIER 16 algorithm was used for data normalization
|
| |
|
| Submission date |
Feb 02, 2018 |
| Last update date |
Feb 01, 2019 |
| 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) |
| GSE110088 |
Transcriptional profiling of rice gene expression changes upon co-infection with pathogens Magnapothe oryzae and Xanthomonas oryzae pv. oryzae that causes rice blast and bacterial blight respectively. |
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