|
| Status |
Public on Feb 01, 2019 |
| Title |
Orseola oryzae and Xanthomonas oryzae pv. oryzae infected rice plants, biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
25 days old rice seedlings
|
| Organism |
Oryza sativa |
| Characteristics |
genotype: Rice line carrying bacterial blight and gall midge resistance gene Xa21, xa13, xa5 and Gm1, Gm4 Gm8, gm3 respectively.
age: 25 days old rice seedlings
infection: co-infection with insect Orseola oryza and pathogen Xanthomonas oryzae pv. oryzae
|
| Treatment protocol |
Gall midge biotype 1 (GMB1) is maintained on rice var. TN1 under greenhouse conditions. Test plants along with suitable controls were raised in trays and 21 day old plants were exposed to freshly emerged flies (30 females and 10 males) obtained from nucleus culture under mesh cage for 48h for oviposition. Infested plants in the trays were later transferred to high humidity chamber and left for two days for the eggs to hatch. On 5 th day after release of adults, plants were examined for the presence of maggots at apical meristem which was considered as ‘ 0 day’ of larval infestation. At '0 day' larval infestation the rice leaves were challenged with Xoo. 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.
|
| Growth protocol |
Rice plants were grown in platic trays under green house conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
2 cms rice tissue was collected from the leaves below the point of Xoo inocluation, 10-15 such leaf pieces were collected from each biological replicate and processed for RNA isolation using TRIZOL (Invitrogen). Similarly 2 cms rice tissue from the apical meristem where the larvae reside were collected and processed for RNA isolation using TRIZOL (Invitrogen). The tissue was collected from two time points 24 and 72 hrs post infection. The RNA from the two tissue samples and from the two time points were pooled for the experiment.
|
| Label |
Biotin
|
| Label protocol |
250ng of total RNA from the 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)
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| |
|
| 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 infected 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 was used for data normalization
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| |
|
| 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) |
| GSE110068 |
Transcriptional profiling of rice gene expression changes upon co-infection with insect Orseola oryza and pathogen Xanthomonas oryzae pv. oryzae that causes gall midge and bacterial blight respectively. |
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