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Sample GSM253248 Query DataSets for GSM253248
Status Public on Mar 01, 2008
Title ZM_12h_SG200_3inf_I
Sample type RNA
Source name leaf tissue
Organism Zea mays
Characteristics 3. leaf of maize seedlings 12 hours 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.
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 ZM_12h_SG200 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 Jan 25, 2008
Contact name Jörg Thomas Kämper
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)
GSE10023 Maize gene expression during infection with Ustilago maydis

Data table header descriptions
VALUE MAS 5.1 signal intensity

Data table
AFFX-BioB-5_at 81.4 P 0.000169
AFFX-BioB-M_at 152.9 P 0.000052
AFFX-BioB-3_at 104.5 P 0.000052
AFFX-BioC-5_at 274.7 P 0.000052
AFFX-BioC-3_at 369.9 P 0.000044
AFFX-BioDn-5_at 837.2 P 0.000044
AFFX-BioDn-3_at 1857.2 P 0.000052
AFFX-CreX-5_at 4494.7 P 0.000052
AFFX-CreX-3_at 5700.2 P 0.000044
AFFX-DapX-5_at 2.8 A 0.455413
AFFX-DapX-M_at 9.4 A 0.185131
AFFX-DapX-3_at 2.7 A 0.699394
AFFX-LysX-5_at 0.8 A 0.712274
AFFX-LysX-M_at 7.2 A 0.440646
AFFX-LysX-3_at 6.5 M 0.062929
AFFX-PheX-5_at 0.4 A 0.868639
AFFX-PheX-M_at 1.3 A 0.794268
AFFX-PheX-3_at 3.8 A 0.686277
AFFX-ThrX-5_at 1.3 A 0.916426
AFFX-ThrX-M_at 5.1 A 0.340661

Total number of rows: 17734

Table truncated, full table size 573 Kbytes.

Supplementary file Size Download File type/resource
GSM253248.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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