|
| Status |
Public on Jun 02, 2010 |
| Title |
GrKP4 T16 biological rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
Triticum aestivum flag leaf symptomatic
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: leaf
genotype/variation: GrKP4
treatment: T16
age: Zadoks stages 85-87 of wheat growth
|
| Treatment protocol |
A concentrated aqueous suspension of T. caries teliospores was made of each pathogenic race. A few drops of the suspension were added to the seeds in a 50 ml test tube and then vortexed to evenly distribute spores on the seeds and to adhere spores to seeds. The spores were applied at a high rate to the point seeds were visibly darkened with spores to generate a high infection pressure. Flag leaves from 20 plants were collected from each plot from plants showing smut symptoms on the ears, in the case of treated plots, while flag leaves from asymptomatic ears from untreated plots. One plot was considered a biological replicate and RNA extraction was performed from a mix of all the leaves collected.
|
| Growth protocol |
The field experiment was designed in randomized complete blocks with four replicates. Each plot was seeded by hand and consisted of two 10 foot rows with 3.5 grams of seed per row. A total of 8 treatments were tested. These included two wheat genotypes (null segregant Greina and KP4-Greina) each inoculated with the 3 bunt races (T1/T5/T16) and each with no inoculation (Untreated). In addition to a high inoculum load, plots were seeded early in the spring when soil temperatures were cool which are most favorable to induce high levels of infection. Individual plants were scored for bunt symptoms 16 weeks after sowing, during dough stages of the new formed seeds
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
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| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Wheat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
Gene expression data from flag leaf of GrKP4 inoculated with T16
|
| Data processing |
The data were analyzed with Microarray AGCC software. Probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002) and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. Log ratio data for the comparisons are included in supplementary files on the series record.
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| |
|
| Submission date |
Jun 01, 2010 |
| Last update date |
Jun 01, 2010 |
| Contact name |
Alessandro Fammartino |
| E-mail(s) |
alessandro.fammartino@gmail.com
|
| Organization name |
ETHZ
|
| Department |
IPAS
|
| Lab |
Plant Biotechnology
|
| Street address |
Universitaettstrasse 2
|
| City |
Zurich |
| ZIP/Postal code |
8092 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL3802 |
| Series (1) |
| GSE22080 |
Pleiotropic expression of endogenous genes upon fungus infection of wheat plants containing anti-fungal transgenes |
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