|
| Status |
Public on Sep 01, 2007 |
| Title |
Stage12_vs_PF2_1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
NTA0007
|
| Organism |
Nicotiana langsdorffii x Nicotiana sanderae |
| Characteristics |
Nicotiana langsdorffii x sanderae, Nectary, Development
|
| Treatment protocol |
None
|
| Growth protocol |
Green house grown, 16h light, 8h darkness
|
| 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 |
NTA0010
|
| Organism |
Nicotiana langsdorffii x Nicotiana sanderae |
| Characteristics |
Nicotiana langsdorffii x sanderae, Nectary, Development
|
| Treatment protocol |
None
|
| Growth protocol |
Green house grown, 16h light, 8h darkness
|
| 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 |
Floral Nectaries – Many plants secrete a rich floral nectar to entice visitation by insect and avian pollinators. In turn, these pollinators transfer pollen between flowers increasing plant fecundity. The nectary is the floral organ that secretes nectar into the base of the flower. The size and abundance of the ornamental tobacco nectaries (Nicotiana sp.) will permit us to isolate up to several grams of nectaries at each stage to obtain the necessary amounts of RNA for probe preparation. Our primary goals to understand the biochemistry the nectary, so that we can manipulate nectary function to increase pollinator visitation. We have previously conducted an EST study and have identified 13596 cDNAs from three different stages of nectary development (Stage 6, immature, presecretory nectaries; Stage 12, mature nectaries at floral anthesis; and nectaries, 44 hours after fertilization. In our efforts to evaluate the transcriptional program for the Nicotiana nectary we are proposing to evaluate nectary mRNAs by hybridization with the potato microarrays. We have preliminary evidence that wholesale transcriptional reprogramming (60% of the transcriptome) occurs during nectary maturation and again following fertilization. Our goal is to understand these processes at a biochemical level so that we can begin manipulating nectary function to improve nectar quality and quantity thereby increasing the attractiveness of flowers to insect pollinators. Such improvements have the potential to result in increases in insect visitation, seedset, and ultimately yield for insect pollinated crops. We are also making significant efforts to understand the restructuring of the nectary during its lifecycle. Many changes occur during nectary development and the observed transcriptional reprogramming makes sense the when these many changes are accounted for.
|
| 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 |
Jun 22, 2007 |
| Last update date |
Aug 14, 2011 |
| 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) |
| GSE8245 |
Nicotiana nectary development |
|
| 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 |
