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Sample GSM253278 Query DataSets for GSM253278
Status Public on Mar 01, 2008
Title ZM_8d_SG200_3inf_II
Sample type RNA
 
Source name leaf tissue
Organism Zea mays
Characteristics 3. leaf of maize seedlings 8 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.
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_8d_SG200 II
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
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)
GSE10023 Maize gene expression during infection with Ustilago maydis

Data table header descriptions
ID_REF
VALUE MAS 5.1 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 123.5 P 0.00006
AFFX-BioB-M_at 136.2 P 0.000044
AFFX-BioB-3_at 114.8 P 0.000052
AFFX-BioC-5_at 355.4 P 0.000052
AFFX-BioC-3_at 468.5 P 0.000044
AFFX-BioDn-5_at 850.7 P 0.000044
AFFX-BioDn-3_at 1860.8 P 0.000044
AFFX-CreX-5_at 4811.6 P 0.000052
AFFX-CreX-3_at 5794.2 P 0.000044
AFFX-DapX-5_at 7.2 A 0.067661
AFFX-DapX-M_at 4.4 A 0.327023
AFFX-DapX-3_at 0.6 A 0.945787
AFFX-LysX-5_at 1.3 A 0.544587
AFFX-LysX-M_at 4 A 0.659339
AFFX-LysX-3_at 1.5 A 0.455413
AFFX-PheX-5_at 0.2 A 0.916426
AFFX-PheX-M_at 0.6 A 0.843268
AFFX-PheX-3_at 0.8 A 0.814869
AFFX-ThrX-5_at 1.3 A 0.783496
AFFX-ThrX-M_at 4.1 A 0.354441

Total number of rows: 17734

Table truncated, full table size 574 Kbytes.




Supplementary file Size Download File type/resource
GSM253278.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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