|
| Status |
Public on Mar 01, 2008 |
| Title |
ZM_4d_Mock_3inf_I |
| Sample type |
RNA |
| |
|
| Source name |
leaf tissue
|
| Organism |
Zea mays |
| Characteristics |
tissue: leaf
|
| Treatment protocol |
U. maydis strain SG200 (Nature 444:97-101) was grown in liquid culture overnight to an OD600 of 1.0, harvested by centrifugation, and resuspended in water to an OD600 of 3.0; compatible strains were mixed in equal amounts immediately before infection; 0.2 ml of cell suspension mixes were injected into the leaf whorl of 6–7-day-old corn plants (as described in Mol Microbiology 42:1047-1063). Plants were infected 7 days after sowing 1 h before end of the light period with the exception of the 12 hpi samples were plants were infected during the beginning of the light period.
|
| Growth protocol |
Maize plants of the cultivar Early Golden Bantam were grown in a phytochamber in a 15 h / 9 h light-dark cycle; light period started with a continuous increase from 0% to 100% light for 1h, and ended 13h later with a continuous decrease from 100% to 0% light for 1 h. Temperature was 28°C and 20°C, relative humidity 40% and 60% during light and dark periods, respectively, with a 1 h ramping for both values. Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) to avoid shading of the plants.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA isolation, material from 30 plants was pooled and subsequently ground in liquid nitrogen by mortar and pestle. RNA was extracted from the powder with Trizol (Invitrogen) and purified using the Qiagen RNeasy kit, according to the manufacturer’s instructions, respectively.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (Expression Analysis Technical Manual, 2001, Affymetrix)
|
| Scan protocol |
Microarrays were scanned on an Affymetrix GSC3000.
|
| Description |
3. leaf of maize seedlings 4 days post mock infection. Infection was performed 7 days post sowing. Dissected leaf tissue from 30 plants was pooled. Samples were harvested in the evening.
ZM_4d_Mock I
|
| Data processing |
Data were analyzed with Microarray Suite version 5.1 (MAS 5.1) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.
|
| |
|
| Submission date |
Dec 26, 2007 |
| Last update date |
Jun 28, 2013 |
| Contact name |
Jörg Thomas Kämper |
| E-mail(s) |
joerg.kaemper@kit.edu
|
| Phone |
+49 721 608 5670
|
| Organization name |
Karlsruhe Institute of Technology
|
| Department |
Department for Applied Biosciences
|
| Street address |
Hertzstrasse 16, Geb. 06.40
|
| City |
Karlsruhe |
| ZIP/Postal code |
76187 |
| Country |
Germany |
| |
|
| Platform ID |
GPL4032 |
| Series (3) |
| GSE10023 |
Maize gene expression during infection with Ustilago maydis |
| GSE19559 |
Maize gene expression during infection with Ustilago maydis strain SG200∆fox1 |
| GSE48406 |
Maize gene expression during infection with the Ustilago maydis mutant for cluster 19A and subdeletions for individual genes of cluster 19A |
|
