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Sample GSM143503 Query DataSets for GSM143503
Status Public on Feb 01, 2007
Title Thatcher_Lr34 (resistant), rust inoculated basal leaf, replication 2
Sample type RNA
Source name Fully expanded wheat flag leaves, basal half, rust inoculated
Organism Triticum aestivum
Characteristics Genotype: Thatcher_Lr34
Growth stage: mid-anthesis
Treatment protocol Plants were heavily inoculated with the Puccinia triticina race MFBL suspended in Soltrol 170 light oil (Chevron Phillips Chemical Company, The Woodlands, TX), and were then incubated in a mist chamber with 100% RH for 12 hr. The plants were returned to the growth chamber until sampling at 48 hr after removal from the mist chamber.
Growth protocol Plants were grown in 4-liter pots in growth chamber (Conviron PGW-36) under 15C night/20C day (+/- 1C) with a 16 hr photoperiod. Pots were fertilized at planting with 5 g/pot 14-14-14 Osmocote (The Scotts Company, Marysville, OH) and thereafter every two weeks with 0.5 g/pot 15-30-15 Miracle-Gro All Purpose Plant Food (Scott's Miracle-Gro Products, Inc., Marysville, OH) and 0.1 ml/pot Fertilome Chelated Liquid Iron and Other Micronutrients (Voluntary Purchasing Groups, Inc., Bonham, TX).
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip wheat Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description Wheat fully expanded flag leaf, rust inoculated basal half, biological replication 2.
Data processing The data were analyzed with Affymetrix GCOS software using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Submission date Nov 02, 2006
Last update date Nov 08, 2006
Contact name Jianfa Bai
Phone 785-532-4332
Organization name Kansas State University
Department Diagnostic Medicine and Pathobiology
Street address 1800 Denison Ave
City Manhattan
State/province KS
ZIP/Postal code 66506-5502
Country USA
Platform ID GPL3802
Series (1)
GSE6227 Expression data from rust or mock inoculated, fully expanded flag leaf halves

Data table header descriptions
ID_REF Affymetrix probe set ID
VALUE GCOS-calculated signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
AFFX-BioB-5_at 438.5 P 0.000754
AFFX-BioB-M_at 461.9 P 0.000754
AFFX-BioB-3_at 273.5 P 0.000297
AFFX-BioC-5_at 1394.8 P 0.000070
AFFX-BioC-3_at 1682.2 P 0.000044
AFFX-BioDn-5_at 3119.9 P 0.000052
AFFX-BioDn-3_at 7015.6 P 0.000060
AFFX-CreX-5_at 19331.8 P 0.000052
AFFX-CreX-3_at 26570.5 P 0.000044
AFFX-DapX-5_at 225.6 P 0.000446
AFFX-DapX-M_at 536.6 P 0.000972
AFFX-DapX-3_at 606.6 P 0.000662
AFFX-LysX-5_at 15.6 A 0.327079
AFFX-LysX-M_at 108.5 A 0.116113
AFFX-LysX-3_at 163.9 P 0.000195
AFFX-PheX-5_at 50.5 A 0.116113
AFFX-PheX-M_at 59.7 A 0.514890
AFFX-PheX-3_at 83.3 A 0.165861
AFFX-ThrX-5_at 30.1 A 0.588620
AFFX-ThrX-M_at 113.4 P 0.004017

Total number of rows: 61290

Table truncated, full table size 2136 Kbytes.

Supplementary file Size Download File type/resource
GSM143503.CEL.gz 4.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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