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Sample GSM323170 Query DataSets for GSM323170
Status Public on Sep 25, 2008
Title Zm_SG200Dpep1_24hpi_I
Sample type RNA
 
Source name infected leaf tissue
Organism Zea mays
Characteristics 3. leaf of maize seedlings 24 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 SG200Dpep1 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 pep1_24hpi_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 Sep 23, 2008
Last update date Sep 24, 2008
Contact name Gunther Doehlemann
E-mail(s) g.doehlemann@uni-koeln.de
Phone +49-6421-178 530
Organization name Max Planck Institue for Terrestiral Microbiology
Department Organismic Interactions
Street address Karl von Frisch Str.
City Marburg
State/province Hessen
ZIP/Postal code 35041
Country Germany
 
Platform ID GPL4032
Series (1)
GSE12892 Maize gene expression during infection with Ustilago maydis strain SG200Dpep1

Data table header descriptions
ID_REF
VALUE MAS5.1 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 145.607 P 8.14279e-05
AFFX-BioB-M_at 196.372 P 5.16732e-05
AFFX-BioB-3_at 143.002 P 4.42873e-05
AFFX-BioC-5_at 373.852 P 5.16732e-05
AFFX-BioC-3_at 543.425 P 4.42873e-05
AFFX-BioDn-5_at 796.571 P 4.42873e-05
AFFX-BioDn-3_at 1746 P 5.16732e-05
AFFX-CreX-5_at 4649.48 P 5.16732e-05
AFFX-CreX-3_at 5768.57 P 4.42873e-05
AFFX-DapX-5_at 0.721574 A 0.617401
AFFX-DapX-M_at 2.33853 A 0.354441
AFFX-DapX-3_at 0.220845 A 0.986196
AFFX-LysX-5_at 0.119444 A 0.645547
AFFX-LysX-M_at 6.94228 A 0.327079
AFFX-LysX-3_at 4.45121 M 0.0584438
AFFX-PheX-5_at 2.07422 A 0.327079
AFFX-PheX-M_at 3.37254 A 0.354441
AFFX-PheX-3_at 5.89448 A 0.58862
AFFX-ThrX-5_at 0.873204 A 0.916408
AFFX-ThrX-M_at 0.772737 A 0.686277

Total number of rows: 17734

Table truncated, full table size 655 Kbytes.




Supplementary file Size Download File type/resource
GSM323170.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM323170.CHP.gz 97.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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