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Sample GSM607560 Query DataSets for GSM607560
Status Public on Dec 15, 2011
Title Fg_8h_BR1_cy5
Sample type RNA
 
Channel 1
Source name Liquid Fg culture treated with SA for 8h biorep 1
Organism Fusarium graminearum
Characteristics strain: DAOM 180378
treatment: treated with SA for 8h
Treatment protocol After initial 40h growth, 300 ul of 1 M Salicylic Acid in methanol was added to the test samples and 300 ul of methanol was added to the reference samples and the cultures grown for an additional 8h and 24h prior to sampling.
Growth protocol 100ml PDB (potato dextrose broth) media was inoculated with ground Fusarium graminearum mycelia (strain DAOM 180378; about 1/4 of the ground mycelia scrapped from a confluent PDA plate), grown for 40hrs at 28ºC and 170 rpm, then supplemented with salicylic acid (test samples) or not (reference samples) and grown for an additional 8h or 24h.
Extracted molecule total RNA
Extraction protocol Mycelia were harvested by vacuum filtration and ground in liquid nitrogen. Total RNA was extracted using the guanidine isothiocyanate-cesium chloride method (Ohan and Heikkila, 1995).
Label cy5
Label protocol 500ng of total RNA was labelled using reagents and procedure described in the Two-color Quick Amp Labeling protocol version 5.7 (Agilent Technologies) except only half the amounts of reagents were used in Step 2 of the labelling reaction.
 
Channel 2
Source name Liquid Fg culture untreated for 8h biorep 1
Organism Fusarium graminearum
Characteristics strain: DAOM 180378
treatment: untreated, incubated for 8h
Treatment protocol After initial 40h growth, 300 ul of 1 M Salicylic Acid in methanol was added to the test samples and 300 ul of methanol was added to the reference samples and the cultures grown for an additional 8h and 24h prior to sampling.
Growth protocol 100ml PDB (potato dextrose broth) media was inoculated with ground Fusarium graminearum mycelia (strain DAOM 180378; about 1/4 of the ground mycelia scrapped from a confluent PDA plate), grown for 40hrs at 28ºC and 170 rpm, then supplemented with salicylic acid (test samples) or not (reference samples) and grown for an additional 8h or 24h.
Extracted molecule total RNA
Extraction protocol Mycelia were harvested by vacuum filtration and ground in liquid nitrogen. Total RNA was extracted using the guanidine isothiocyanate-cesium chloride method (Ohan and Heikkila, 1995).
Label cy3
Label protocol 500ng of total RNA was labelled using reagents and procedure described in the Two-color Quick Amp Labeling protocol version 5.7 (Agilent Technologies) except only half the amounts of reagents were used in Step 2 of the labelling reaction.
 
 
Hybridization protocol Hybridizations were incubated overnight at 65ºC in a Robbins 400 oven outfitted with a Hybridization Oven Rotator (Agilent G2530-60029). Slides were washed as described in the Supplemental Procedures: Wash with Stabilization and Drying Solution.
Scan protocol Slides were scanned on the Genepix4200a (Molecular Devices) at 5µ resolution. Images were quantified using Genepix Pro 6.0 (Molecular Devices)
Description 8h SA treatment. Technical rep 1. Biorep 1 of 3
Data processing Array results files (.gpr) were imported in Acuity 4.0 and Lowess M log ratio normalized. A dataset was formed with all arrays. Features that had Lowess A intensities lower that 7.5 in at least 50% of the arrays were removed. Spike-in controls were removed. Cy3 test array data were swapped to cy5. Candidate genes that were significantly differentially expressed were identifed using the following cut-off parameters: t-test p-value<0.05 and fold changes >2 in expression rations (SA vs control), and signal value>1000.
 
Submission date Oct 12, 2010
Last update date Dec 15, 2011
Contact name Linda J Harris
E-mail(s) Linda.Harris@agr.gc.ca
Phone 613-759-1314
Organization name Agriculture & Agri-Food Canada (AAFC)
Department Eastern Cereal & Oilseed Research Centre
Lab Building #21
Street address 960 Carling Ave.
City Ottawa
State/province Ontario
ZIP/Postal code K1A 0C6
Country Canada
 
Platform ID GPL11046
Series (1)
GSE24636 Effect of salicylic acid on Fusarium graminearum, the major causal agent of fusarium head blight in wheat

Data table header descriptions
ID_REF
VALUE normalized log2 ratio test to reference

Data table
ID_REF VALUE
1 0.239
2 0.31
3 0.227
4 -0.941
5 -1.797
6 -3.568
7 0.776
8 -0.234
9 0.316
10 -0.352
11 0.106
12 -0.872
13 0.192
14 0.123
15 -0.101
16 -0.172
17 -0.08
18 -0.025
19 0.352
20 -1.575

Total number of rows: 41448

Table truncated, full table size 481 Kbytes.




Supplementary file Size Download File type/resource
GSM607560_252071710056_1.gpr.gz 4.3 Mb (ftp)(http) GPR
Processed data included within Sample table

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