|
| Status |
Public on Apr 03, 2007 |
| Title |
Cold Susceptible1 flowers |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Treatment
|
| Organism |
Cicer arietinum |
| Characteristics |
Genotype: Amethyst (ATC 42331)
Age: 2 weeks after flowering
Tissue type: flowers/buds/early pods
|
| Biomaterial provider |
Dr. Heather Clarke, CLIMA, Australia
|
| Treatment protocol |
To simulate cold stress, the treatment plants were exposed to a 12h day/12h night temperature cycle of 15-25oC and 5oC (Dr. H. Clarke, 2005, pers comm.; Croser et al. 2003; Clarke and Siddique 2004). The flowers/buds/early pods were harvested after the seventh night at 5oC.
|
| Growth protocol |
Five treatment plants were cultivated (one plant per 15 cm pot) in sterile potting mix in a glasshouse at 15-25oC. All plants were watered to keep the soil moist but excess watering was avoided. The plants were fertilized twice with urea during establishment and once with Nitrosol® (Amgrow, Australia) 10 days before flowering.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666
|
| Label |
Cy3/Cy5
|
| Label protocol |
See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666
|
| |
|
| Channel 2 |
| Source name |
Control
|
| Organism |
Cicer arietinum |
| Characteristics |
Genotype: Amethyst (ATC 42331)
Age: 2 weeks after flowering
Tissue type: flowers/buds/early pods
|
| Biomaterial provider |
Dr. Heather Clarke, CLIMA, Australia
|
| Treatment protocol |
The control plants were maintained in Glasshouse conditions at 15-25oC while the treatment plants were exposed to cold stress. The flowers/buds/early pods were harvested at the same time as treatment plants (after seventh night of cold stress to treatment plants)
|
| Growth protocol |
Five control plants were cultivated (one plant per 15 cm pot) in sterile potting mix in a glasshouse at 15-25oC. All plants were watered to keep the soil moist but excess watering was avoided. The plants were fertilized twice with urea during establishment and once with Nitrosol® (Amgrow, Australia) 10 days before flowering.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666
|
| Label |
Cy3/Cy5
|
| Label protocol |
See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666
|
| |
|
| |
| Hybridization protocol |
See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666
|
| Scan protocol |
See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666
|
| Description |
The data submitted represents the mean data from three biological replications that inlcuded dye swaps between control and treatment samples
|
| Data processing |
Data transformations consisted of a local background correction (mean intensity of background was subtracted from mean signal intensity for each spot), omitting flagged spots, Lowess normalisation of the entire population, creating a Cy5/Cy3 mean signal ratio, taking a shifted log (base 2), and combination of duplicated spot data. To identify differentially expressed (DE) genes, expression ratio results were filtered to eliminate genes whose 95% confidence interval for mean fold change (FC) did not extend to 2-fold up or down, followed by Students t test with False Discovery Rate (FDR) multiple testing correction to retain only genes in which expression changes versus untreated control were significant at P < 0.05.
|
| |
|
| Submission date |
Apr 01, 2007 |
| Last update date |
Apr 02, 2007 |
| Contact name |
Nitin Mantri |
| E-mail(s) |
nitin_mantri@rediffmail.com
|
| Phone |
+61 3 9925 7140
|
| Fax |
+61 3 9925 7110
|
| Organization name |
RMIT University
|
| Department |
Biotechnology & Environmental Biology
|
| Street address |
Bldg 223, Level 1, Plenty Road
|
| City |
Bundoora |
| State/province |
Victoria |
| ZIP/Postal code |
3083 |
| Country |
Australia |
| |
|
| Platform ID |
GPL3649 |
| Series (2) |
| GSE7417 |
Gene expression profiling of chickpea responses to cold stress |
| GSE7504 |
Gene expression profiling of chickpea responses |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
Log (base 2) transformed mean expression ratio of treatment/control with flagged values removed |
| FLAG |
Quality control where 0 indicates a good spot and 1 is a bad spot |
| Cold Susceptible1 Flowers pairMedian (locBGC) ratio |
Log (base 2) transformed median expression ratio of treatment/control |
| Cold Susceptible1 Flowers (control)Mean (locBGC) |
Log (base 2) control channel mean with local background correction |
| Cold Susceptible1 Flowers (control)Median (locBGC) |
Log (base 2) control channel median with local background correction |
| Cold Susceptible1 Flowers Mean (locBGC) |
Log (base 2) treatment channel mean with local background correction |
| Cold Susceptible1 Flowers Median (locBGC) |
Log (base 2) treatment channel median with local background correction |
| Cold Susceptible1 Flowers pairMean (locBGC) ratio cv |
Log (base 2) transformed mean expression ratio of treatment/control coefficient of variation (cv) |
| Cold Susceptible1 Flowers pairMedian (locBGC) ratio cv |
Log (base 2) transformed median expression ratio of treatment/control coefficient of variation (cv) |
| Cold Susceptible1 Flowers (control)Mean (locBGC) cv |
Log (base 2) control channel mean with local background correction coefficient of variation (cv) |
| Cold Susceptible1 Flowers (control)Median (locBGC) cv |
Log (base 2) control channel median with local background correction coefficient of variation (cv) |
| Cold Susceptible1 Flowers Mean (locBGC) cv |
Log (base 2) treatment channel mean with local background correction coefficient of variation (cv) |
| Cold Susceptible1 Flowers Median (locBGC) cv |
Log (base 2) treatment channel median with local background correction coefficient of variation (cv) |
| UNF_VALUE |
Log (base 2) transformed mean expression ratio of treatment/control |
