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Sample GSM209844 Query DataSets for GSM209844
Status Public on Apr 08, 2009
Title Mycelia/rice vs lesion biological rep 1.1
Sample type RNA
 
Channel 1
Source name 20% mycelial RNA mixed with 80% mock-inoculated rice RNA
Organisms Oryza sativa; Pyricularia oryzae
Characteristics Fungal and plant RNAs mixed in a similar proportion as in the infected samples
Biomaterial provider B. Valent Lab. Kansas State University
Treatment protocol Sheaths inoculated with gelatin solution. An approximately 1 cm square piece of agar containing fungus was excised from the surface of an oatmeal agar plate and blended in 25 ml of 3,3,3 liquid medium (3g/L of glucose, 3g/L of casamino acids, and 3g/L of yeast extract). The blended mycelium was mixed with 225 ml of fresh medium in 500 ml flasks.
Growth protocol Inoculated sheath tissues were incubated in high humidity at room temperature for 36 hours. The fungal culture was incubated at 24°C under continuous rotation at 120 RPM. Mycelium was collected by filtration after 24 h of incubation, and the blending treatment was repeated for 3 rounds of growth
Extracted molecule total RNA
Extraction protocol Trizol method as specified by the manufacturers.
Label cy5
Label protocol Total RNA was labeled using a linear amplification kit (Agilent Technologies). Five hundred nanograms were one-round amplified. Normal cRNA yields were 10-15 ug. The cRNA was labeled according to manufacturers specifications. Fluorescent cRNA was purified, quantified using the NanoDrop Spectrophotometer, and 1 µg of probe was hybridized to M. oryzae microarray slides.
 
Channel 2
Source name 36 hpi infected rice sheath
Organisms Oryza sativa; Pyricularia oryzae
Characteristics Biotrophic invasive hyphae in rice sheath epidermal cells
Biomaterial provider B. Valent Lab. Kansas State University
Treatment protocol Rice leaf sheath pieces were placed in wire supports in order to avoid contact with the wet paper, and to hold the pieces horizontally flat for even inoculum distribution over the mid-vein. Spore suspension (1 X 105 spores/mL in gelatin solution) was injected in one end of the leaf sheath using a 1 mL pipet.
Growth protocol Inoculated tissues were kept in high humidity at room temperature for 36 hours.
Extracted molecule total RNA
Extraction protocol Trizol method as specified by the manufacturers.
Label cy3
Label protocol Total RNA was labeled using a linear amplification kit (Agilent Technologies). Five hundred nanograms were one-round amplified. Normal cRNA yields were 10-15 ug. The cRNA was labeled according to manufacturers specifications. Fluorescent cRNA was purified, quantified using the NanoDrop Spectrophotometer, and 1 µg of probe was hybridized to M. oryzae microarray slides.
 
 
Hybridization protocol The labeled samples (1ug each cy3 and cy5 labeled cRNA) were defragmented by the addition of 25X Agilent Defragmentation buffer and incubated for 30 min, 60°C. The sample was adjusted to a final volume of 450 µl with formamide-containing hybridization buffer (Hughes et al., 2001) and then added to the microarray slides. Slides were incubated for 18 hours with continuous rotation at 40°C. After hybridization, slides were washed in 6X SSPE, 0.005% sarcosyl for 1 min, in 0.06X SSPE for 30 sec, in water for 30 sec and then air dried.
Scan protocol Slides were scanned on an Agilent G2565BA DNA microarray scanner, and the TIFF images extracted using the Agilent Feature Extraction software (version 8.5). The resultant .xml and .jpeg files were imported into Rosetta Resolver
Description This experiment was designed to compare gene expression
by biotrophic invasive hyphae in planta to gene expression
by mycelium in nutrient medium.
Data processing Data from individual biological replicates and also the combined data were analyzed. The data was then plotted as an intensity scatter plot (background subtracted/dye normalized cy3channel vs background subtracted/dye normalized cy5 channel). “Signature sequences” (features which were 1.5 fold differentially regulated, P-values <0.01) were identified by Resolver, and exported to Excel.
 
Submission date Jul 11, 2007
Last update date Aug 14, 2011
Contact name Barbara Valent
E-mail(s) bvalent@ksu.edu
Phone 785-532-2336
Fax 785-532-5692
Organization name Kansas State University
Department Department of Plant Pathology
Street address 4024 Throckmorton Plant Sciences
City Manhattan
State/province KS
ZIP/Postal code 66506-5502
Country USA
 
Platform ID GPL892
Series (2)
GSE8518 Rice Gene Expression During Biotrophic Invasion by Magnaporthe oryzae (Agilent Array G4138A)
GSE8670 Analysis of the Interaction Transcriptome During Biotrophic Invasion of Rice by the Blast Fungus, Magnaporthe oryzae

Data table header descriptions
ID_REF
VALUE log ratio of test/control
green_raw Raw signal in green channel
red_raw Raw signal in red channel
green_normalized Normalized signal in green channel
red_normalized Normalized signal in red channel
INV_VALUE Log Ratio

Data table
ID_REF VALUE green_raw red_raw green_normalized red_normalized INV_VALUE
1 1.12 4.38E+03 3.33E+02 4380.85 333.36 -1.12E+00
2 0.822 4.18E+03 6.30E+02 4183.24 630.053 -8.22E-01
3 0.804 1.77E+03 2.78E+02 1770.57 276.261 -8.04E-01
4 0.12 9.83E+01 7.46E+01 98.2614 -2.68548 -1.20E-01
5 0.689 3.99E+02 8.16E+01 399.156 81.6292 -6.89E-01
6 0.341 3.63E+02 1.65E+02 362.599 165.196 -3.41E-01
7 1.6 3.22E+03 8.06E+01 3223.62 80.5868 -1.60E+00
8 0.227 5.35E+02 3.17E+02 534.943 317.177 -2.27E-01
9 0.188 2.52E+03 1.63E+03 2515.23 1631.5 -1.88E-01
10 0.62 2.96E+02 7.10E+01 295.731 71.0008 -6.20E-01
11 0.692 9.41E+03 1.91E+03 9406.35 1909.89 -6.92E-01
12 0.507 8.18E+02 2.54E+02 817.756 254.368 -5.07E-01
13 0.0434 1.89E+02 1.71E+02 189.481 171.452 -4.34E-02
14 1.61 3.44E+03 8.54E+01 3438.95 85.3905 -1.61E+00
15 -0.2 7.50E+02 1.19E+03 750.448 1188.62 2.00E-01
16 0.00E+00 7.20E+00 7.80E+01 -21.8413 -2.30575 0.00E+00
17 0.0936 2.60E+02 2.10E+02 260.383 209.893 -9.36E-02
18 0.0519 9.68E+02 8.59E+02 968.47 859.356 -5.19E-02
19 0.215 1.79E+04 1.09E+04 17905.6 10921.9 -2.15E-01
20 0.244 1.62E+03 9.26E+02 1624.01 925.503 -2.44E-01

Total number of rows: 22575

Table truncated, full table size 1224 Kbytes.




Supplementary file Size Download File type/resource
GSM209844.txt.gz 5.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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