|
| Status |
Public on Jun 03, 2009 |
| Title |
grape buds 0hr vs 500hr chilling rep 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
axillary buds collected at 0 hr of accumulated chilling
|
| Organism |
Vitis riparia |
| Characteristics |
Axillary buds harvested from shoot basal nodes 3 to 12. Buds were harvested from plants that had accumulated 0 hr of chilling.
|
| Biomaterial provider |
Kathy Mathiason, South Dakota State University, Brookings, SD
|
| Treatment protocol |
Axillary buds were collected from intact plants after 0 hours of chilling. Buds were excised, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.
|
| Growth protocol |
Potted, spur-pruned, 5- to 6-year old V. riparia Michx vines were grown in climated controlled greenhouses under a natural long photoperiod at 25/20C day/night temperatures for 45 to 60 days. Endodormancy was induced by natural daylength shortening. Once periderm had developed up through 15 nodes and leaves had senesced from the bottom 4 nodes, canes were trimmed to 15 nodes, defoliated, and the pots were moved to cold storage (4C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from ground axillary buds using the Pine tree extraction method (Chang et al. 1993).
|
| Label |
Cy3
|
| Label protocol |
Indirect labelling of 1 ug total RNA using Ambion Amino Allyl MessageAmp II aRNA amplification kit, and Amersham Pharmacia's monoreactive dyes.
|
| |
|
| Channel 2 |
| Source name |
axillary buds collected at 500 hr of accumulated chilling
|
| Organism |
Vitis riparia |
| Characteristics |
Axillary buds harvested from shoot basal nodes 3 to 12. Buds were harvested from plants that had accumulated 500 hr of chilling.
|
| Biomaterial provider |
Kathy Mathiason, South Dakota State University, Brookings, SD
|
| Treatment protocol |
Axillary buds were collected from intact plants after 500 hours of chilling. Buds were excised, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.
|
| Growth protocol |
Potted, spur-pruned, 5- to 6-year old V. riparia Michx vines were grown in climated controlled greenhouses under a natural long photoperiod at 25/20C day/night temperatures for 45 to 60 days. Endodormancy was induced by natural daylength shortening. Once periderm had developed up through 15 nodes and leaves had senesced from the bottom 4 nodes, canes were trimmed to 15 nodes, defoliated, and the pots were moved to cold storage (4C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from ground axillary buds using the Pine tree extraction method (Chang et al. 1993).
|
| Label |
Cy5
|
| Label protocol |
Indirect labelling of 1 ug total RNA using Ambion Amino Allyl MessageAmp II aRNA amplification kit, and Amersham Pharmacia's monoreactive dyes.
|
| |
|
| |
| Hybridization protocol |
University of Arizona 2006 International Microarray Workshop http://www.ag.arizona.edu/microarray/
|
| Scan protocol |
Arrays were scanned with a GenePix 4000B Microarray Scanner. Spots were identified and signal intensities calculated using GenePix Pro 6.0 software provided with the scanner.
|
| Description |
This experiment compares the differences in gene expression of grape buds during the chilling requirement fulfillment period.
|
| Data processing |
Signal intensities were normalized and analyzed using the R software package LIMMA. Within-array normalization was performed by print-tip loess normalization. Differential expression analysis, based on the single channel intensities, used a mixed model representation. ANOVA (p<0.05) identified significant expression
|
| |
|
| Submission date |
Dec 14, 2007 |
| Last update date |
Jun 03, 2009 |
| Contact name |
Kathy Mathiason |
| E-mail(s) |
kathy.mathiason@sdstate.edu
|
| Phone |
605-688-4765
|
| Fax |
605-688-4713
|
| Organization name |
South Dakota State University
|
| Department |
Horticulture, Forestry, Landscape, Parks
|
| Lab |
Fruit Crops Research
|
| Street address |
NPB 201 Box 2140A
|
| City |
Brookings |
| State/province |
SD |
| ZIP/Postal code |
57007 |
| Country |
USA |
| |
|
| Platform ID |
GPL6275 |
| Series (1) |
| GSE9903 |
Chilling requirement fulfillment in Vitis riparia overwintering buds |
|
