|
| Status |
Public on Feb 13, 2008 |
| Title |
ctrl_vs_herb_EMITTER_3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
STQ0004
|
| Organism |
Solanum lycopersicum |
| Characteristics |
Solanum lycopersicum, Leaves, Biotic stress
|
| Treatment protocol |
Herbivory
|
| Growth protocol |
Grown 2 weeks in greenhouse, 1 aditional week in the field
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)
|
| Label |
Cy3
|
| Label protocol |
Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)
|
| |
|
| Channel 2 |
| Source name |
STQ0001
|
| Organism |
Solanum lycopersicum |
| Characteristics |
Solanum lycopersicum, Leaves, Biotic stress
|
| Treatment protocol |
EMITTER control
|
| Growth protocol |
Grown 2 weeks in greenhouse, 1 aditional week in the field
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)
|
| Label |
Cy5
|
| Label protocol |
Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)
|
| |
|
| |
| Hybridization protocol |
Hybridization with indirectly labeled mRNA (SGED_SOP_6.1.1, SGED_SOP_6.2.1-4)
|
| Scan protocol |
Axon 4000B scanner. Both the 635nm (red, Cy5) and 532nm (green, Cy3) channels are scanned simultaneously at 100% laser power, the PMT set between 600 and 950. Slides are scanned at a resolution of 10micron
|
| Description |
In plants, an increase in resource allocation to growth (primary metabolism) associated with the presence of neighbors is likely to reduce defense-related production (secondary metabolism), making plants more vulnerable to herbivory. Even though there is increasing evidence supporting this “trade-off hypothesis”, the underlying mechanisms are still unclear. Far red (FR) radiation reflected from plant tissues serves as an early warning signal of future competition, triggering a suite of plastic morphological adjustments that improve plant’s ability to compete for light in crowded populations. Recent evidence from our lab showed that, when competition signals are present, plant defenses are severely reduced. Besides direct effects of herbivory and competition signals on target plants, second order effects occurs on neighboring plants through plant volatiles (PVs) communication. PVs play a key role in plant-plant and plant-insect interactions, changing its content and composition in response to environmental conditions. To increase our understanding of the molecular mechanisms underlying those interacting signaling webs, we performed a field study with tomato plants (cv Moneymaker), in which plants of EMITTER plots (six plants plot-1) were subjected to herbivory (nine larvae of Spodoptera eridania plant-1) and competition signals (increased FR radiation) in a factorial design. Light treatment started 28 days after sowing (DAS), and herbivory treatment and volatiles conduction started 34 DAS. Volatiles were conducted from EMITTER to RECEIVER plots (five plants plot-1) using a 5 inch, 1.4 m long tube fitted with a computer-type fan. 40 and 45 DAS, larval performance was measured on EMITTER plots as well as naturally-occurring insect colonization on RECEIVER plots. Finally (46 DAS), samples for bulk phenolic content were taken on every plot, and plant material from 4th and 5th leaves was collected for microarray analysis. There were three real biological replicates.
|
| Data processing |
The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.
|
| |
|
| Submission date |
Feb 12, 2008 |
| Last update date |
Feb 12, 2008 |
| Contact name |
Jia Liu |
| E-mail(s) |
[email protected]
|
| URL |
http://www.tigr.org/tdb/potato
|
| Organization name |
Plant Genomics
|
| Street address |
9712 Medical Center Drive
|
| City |
Rockville |
| State/province |
MD |
| ZIP/Postal code |
20850 |
| Country |
USA |
| |
|
| Platform ID |
GPL3838 |
| Series (1) |
| GSE10486 |
Transcriptional rearrangements in tomato in response to herbivory and signals of competition |
|
| Data table header descriptions |
| ID_REF |
Spot identifier for each feature |
| VALUE |
Normalized log2 ratio of normalized intensities defined by CH2/CH1. This value is set to null if it is flagged with "M" or "X" |
| CH1_NORMALIZED |
Normalized background subtracted CH1 intensity (RED channel) |
| CH1_RAW |
Background (CH1_BACKGROUND) subtracted raw intensity (F635 Mean - B635 Media) |
| CH1_BACKGROUND |
CH1 background median intensity (B635 Media) |
| CH2_NORMALIZED |
Normalized background subtracted CH2 intensity (GREEN channel) |
| CH2_RAW |
Background (CH2_BACKGROUND) subtracted raw intensity (F532 Mean - B532 Media) |
| CH2_BACKGROUND |
CH2 background median intensity (B532 Media) |
| FLAG |
B: no flag, good spot; X: undetectable spot; M: flagged for diameter < 70 microns, the percentage of saturated pixels > 30% or not validated PCR product |
