Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants
Hybridization: 10 h post inoculation
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Hybridization protocol
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| Hybridization solution | N/A |
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| Solution concentration | 5 X SSPE, 62.8% formamide, 0.8% SDS, 4 X Denhardt's solution |
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| Blocking agent | N/A |
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| Wash procedure | At room temperature for 10 minutes twice with 2 X SSC and 0.1% SDS, twice with 0.2 X SSC and 0.1% SDS, and twice with 0.2 X SSC. A final wash with 0.2 X SSC at 50C for 10 minutes |
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| Labeled Target Quantity | N/A |
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| Hybridization Time | Over night (12 h) |
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| Hybridization Volume | 45 ul |
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| Hybridization Temperature | 42C |
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| Hybridization Instrument | Corning microarray hybridization chamber in 42C incubator |
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Scan information
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| Scan hardware | Affymetrix 428 Array Scanner |
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| Scan software | Jaguar ver 2.0 |
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Image analysis information
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| Software | ImaGene ver 5.5 |
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| Analysis algorithm | 1) Images
Cy5 = Red Cy3 = Green
2) Spot Finding
Find negative spots = yes
Enforce grid constraints = yes
Local flexibility = 5.0
Global flexibility = 50%
3) Segmentation
Background buffer = 3.0
Background width = 5.0
Autosegmentation = yes
4) Quality Flags
Empty spots = yes
Negative spots = yes
Poor spots = yes
5) Poor Spot Parameters
Contamination of background/signal = no
Ignored pixels percentage = no
Open perimeter ratio = no
Shape regularity = no
Area to perimeter ratio = no
Offset value = no |
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Normalization information
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| Normalization software | GeneSight ver 3.5 |
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| Normalization algorithm | Using the mean of signals |
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| Normalization strategy | Total array |
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