|
| Status |
Public on Apr 03, 2007 |
| Title |
Salt Susceptible2 shoot 48hpt |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Treatment
|
| Organism |
Cicer arietinum |
| Characteristics |
Genotype: ICC 08161 (ATC 40707)
Age: 18 days
Tissue type: leaf/shoot
|
| Biomaterial provider |
Dr. Bob Redden, ATFCC, Horsham, Victoria, Australia
|
| Treatment protocol |
At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s with 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). Leaf/shoot tissues were collected from five treatment plants at 48 h post-treatment (hpt).
|
| Growth protocol |
The treatment plants were cultivated in a hydroponic system using 50 L plastic crates. Forty holes (8 x 5 grid) of 5 cm diameter were drilled in the crates’ lid and rock wool plugs were placed in them. The germinated seeds were transplanted in alternate plugs within the crate. The seedlings were watered normally from above for four days. The following day, the crates were filled with 0.5 X modified Hoagland’s nutrient medium (pH 6.5; Taiz and Zeiger 2002). The medium was aerated using two aquarium pumps. The nutrient medium was subsequently replaced with 1.0 X Hoagland’s solution (pH 6.5) after a further seven days.
|
| 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: ICC 08161 (ATC 40707)
Age: 18 days
Tissue type: leaf/shoot
|
| Biomaterial provider |
Dr. Bob Redden, ATFCC, Horsham, Victoria, Australia
|
| Treatment protocol |
At day 18, the nutrient medium for the control plants was replaced with just 1.0 X modified Hoagland’s medium (pH 6.5). Leaf/shoot tissues were collected from five control plants at 48 h post medium change.
|
| Growth protocol |
The control plants were cultivated in a hydroponic system using 50 L plastic crates. Forty holes (8 x 5 grid) of 5 cm diameter were drilled in the crates’ lid and rock wool plugs were placed in them. The germinated seeds were transplanted in alternate plugs within the crate. The seedlings were watered normally from above for four days. The following day, the crates were filled with 0.5 X modified Hoagland’s nutrient medium (pH 6.5; Taiz and Zeiger 2002). The medium was aerated using two aquarium pumps. The nutrient medium was subsequently replaced with 1.0 X Hoagland’s solution (pH 6.5) after a further seven days.
|
| 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 |
Mar 31, 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) |
| GSE7418 |
Gene expression profiling of chickpea responses to high-salinity 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 |
| Salt Susceptible2 Shoot 48h pairMedian (locBGC) ratio |
Log (base 2) transformed median expression ratio of treatment/control |
| Salt Susceptible2 Shoot 48h (control)Mean (locBGC) |
Log (base 2) control channel mean with local background correction |
| Salt Susceptible2 Shoot 48h (control)Median (locBGC) |
Log (base 2) control channel median with local background correction |
| Salt Susceptible2 Shoot 48hMean (locBGC) |
Log (base 2) treatment channel mean with local background correction |
| Salt Susceptible2 Shoot 48hMedian (locBGC) |
Log (base 2) treatment channel median with local background correction |
| Salt Susceptible2 Shoot 48h pairMean (locBGC) ratio cv |
Log (base 2) transformed mean expression ratio of treatment/control coefficient of variation (cv) |
| Salt Susceptible2 Shoot 48h pairMedian (locBGC) ratio cv |
Log (base 2) transformed median expression ratio of treatment/control coefficient of variation (cv) |
| Salt Susceptible2 Shoot 48h (control)Mean (locBGC) cv |
Log (base 2) control channel mean with local background correction coefficient of variation (cv) |
| Salt Susceptible2 Shoot 48h (control)Median (locBGC) cv |
Log (base 2) control channel median with local background correction coefficient of variation (cv) |
| Salt Susceptible2 Shoot 48hMean (locBGC) cv |
Log (base 2) treatment channel mean with local background correction coefficient of variation (cv) |
| Salt Susceptible2 Shoot 48hMedian (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 |
