|
| Status |
Public on Jul 16, 2008 |
| Title |
Xac infiltrated leaves at 6h_biol replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Xac infiltrated leaves at 6h
|
| Organism |
Citrus sinensis |
| Characteristics |
adult leaves
|
| Treatment protocol |
Plant leaves were infiltrated with suspensions of Xac (strain 306, da Silva et al., 2002) or Xaa pathotype C (strain ICMP 8435). Bacterial cells grown in LB medium without NaCl (LBON) for 48h at 28oC and 200 rpm were recovered by centrifugation and ressuspended in sterile water (OD600nm= 0.6). Leaf sectors were infiltrated with approximately 0.3 mL of the bacterial suspensions or water as control.
|
| Growth protocol |
Six-month-old plants of sweet orange (C. sinensis) “Pêra” cultivar were obtained from certified nurseries and kept in growth room at 25-28oC under 14h/day fluorescent light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from sweet orange leaves at different time intervals after water and bacterial infiltration treatments using Trizol (Invitrogen), followed by mRNA purification with FastTrack 2.0 (Invitrogen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.4 µg of mRNA (Expression Analysis Technical Manual, Affymetrix 2005-2006).
|
| |
|
| Hybridization protocol |
After fragmentation, 15 µg of cRNA were hybridized for 16hs at 45ºC on a GeneChip hybridization oven 640. Subsequently, genechips were washed and stained in the Affymetrix fluidics station 450.
|
| Scan protocol |
Scanned using the Affymetrix genechip scanner 7G.
|
| Description |
To identify defense response genes, sweet orange leaves were infiltrated with water (mock control) and bacterial pathogens Xanthomonas axonopodis pv. citri and Xanthomonas axonopodis pv. aurantifolii.
|
| Data processing |
All data were acquired and processed using the GeneChip Operating Software (GCOS - Affymetrix). The CEL files of each hybridization chip were obtained with the GCOS and subsequently imported to the ArrayAssist software (Stratagene) for further normalization and statistical analyses. The matrix tables containing the statistical data for each experiment were performed through the significance analysis (“Multiple treatments vs Control”) of the ArrayAssist. These microarray-hybridization comparisons identified the genes with 3.0 or 2.0 fold change up- or down- regulation with a p-value ≤ 0.05.
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| |
|
| Submission date |
Mar 12, 2008 |
| Last update date |
Jul 16, 2008 |
| Contact name |
Celso Eduardo Benedetti |
| E-mail(s) |
[email protected]
|
| Phone |
+55-19 35121111
|
| URL |
http://www.lnls.br
|
| Organization name |
Brazilian Synchrotron Light Laboratory
|
| Department |
Center for Molecular and Structural Biology
|
| Street address |
R. Giuseppe Maximo Scolfaro, 10000
|
| City |
Campinas |
| State/province |
São Paulo |
| ZIP/Postal code |
13083-970 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL5731 |
| Series (1) |
| GSE10798 |
Transcriptional analysis of the sweet orange interaction with the citrus canker pathogens |
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