|
| Status |
Public on Dec 31, 2010 |
| Title |
ZM_4dpi_dfox1_1 |
| Sample type |
RNA |
| |
|
| Source name |
Maize leaf tissue 4 days post infection with Ustilago maydis strain SG200∆fox1
|
| Organism |
Zea mays |
| Characteristics |
tissue: leaf
|
| Biomaterial provider |
Alexander Zahiri and Jörg Kämper
|
| Treatment protocol |
U. maydis strain SG200∆fox1 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; 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. Samples were taken 4 days post infection at 1 h before end 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/phycoerythrin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
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| |
|
| 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 Ustilago maydis infection. Infection was performed 7 days post sowing. Dissected leaf tissue from 30 plants was pooled. Samples were harvested in the evening.
Identification of differentially regulated maize genes in maize leaves infected with the SG200∆fox1 strain 4 days post infection. The experiments GSM253265 (ZM_4d_SG200_3inf_I), GSM253266 (ZM_4d_SG200_3inf_II), GSM253267 (ZM_4d_SG200_3inf_III) of series GSE10023 ( Maize gene expression during infection with Ustilago maydis) were used as wild-type controls.
|
| 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.
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| |
|
| Submission date |
Dec 18, 2009 |
| Last update date |
Dec 31, 2010 |
| 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 (1) |
| GSE19559 |
Maize gene expression during infection with Ustilago maydis strain SG200∆fox1 |
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