|
Status |
Public on Jun 03, 2009 |
Title |
grape buds 1500hr vs 2000hr chilling rep 2 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
axillary buds collected at 1500 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 1500 hr of chilling.
|
Biomaterial provider |
Kathy Mathiason, South Dakota State University, Brookings, SD
|
Treatment protocol |
Axillary buds were collected from intact plants after 1500 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 2000 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 2000 hr of chilling.
|
Biomaterial provider |
Kathy Mathiason, South Dakota State University, Brookings, SD
|
Treatment protocol |
Axillary buds were collected from intact plants after 2000 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
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|
|
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 |
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