Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

Hybridization: 10 h post inoculation

Hybridization protocol
Hybridization solutionN/A
Solution concentration5 X SSPE, 62.8% formamide, 0.8% SDS, 4 X Denhardt's solution
Blocking agentN/A
Wash procedureAt 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
Labeled Target QuantityN/A
Hybridization TimeOver night (12 h)
Hybridization Volume45 ul
Hybridization Temperature42C
Hybridization InstrumentCorning microarray hybridization chamber in 42C incubator

Scan information
Scan hardwareAffymetrix 428 Array Scanner
scan softwareJaguar ver 2.0

Image analysis information
SoftwareImaGene ver 5.5
Analysis algorithm1) 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

Normalization information
Normalization softwareGeneSight ver 3.5
Normalization algorithmUsing the mean of signals
Normalization strategyTotal array