Time course of DC3000 vs delta hrp on tomato Prf-3

Hybridization: DC3000/delta hrp 12h

Hybridization protocol
Hybridization solutionNEN Hybridization buffer
Solution concentrationunknown-NEN micromax labeling system buffer
Blocking agentincluded in buffer-unknown
Wash procedure3 10 minute washes at RT:
1)10 0.5X SSC, 0.01% SDS.
2) 0.06% SSC, 0.01% SDS.
3) 0.06X SSC
Labeled Target Quantity50ug
Hybridization Time12-16h
Hybridization Volume65ul
Hybridization Temperature65C
Hybridization InstrumentCorning microarray hybridization chamber

Scan information
Scan hardwareScan Array 5000
scan softwareScan Array ver 3.1

Image analysis information
SoftwareImaGene ver 5.5
Analysis algorithm1) Images
Cy5 = Red Cy3 = Green

2) Spot Finding
Find negative spots = no
Enforce grid constraints = yes
Local flexibility = 6.0
Global flexibility = 75%

3) Segmentation
Background buffer = 2.25
Background width = 5.0
Autosegmentation = no
Signal low cutoff = 20%
Signal high cutoff = 100%
Background low cutoff = 0%
Backgound high cutoff = 88%

4) Quality Flags
Empty spots = no
Negative spots = yes
Poor spots = yes

5) Poor Spot Parameters
Contamination of background/signal = no
Ignored pixels percentage = yes (setting = 69%)
Open perimeter ratio = no
Shape regularity = no
Area to perimeter ratio = yes (setting = 0.6)
Offset value = yes (setting = 17.5)

Normalization information
Normalization softwaremarray package under R
Normalization algorithmPrint-tip specific Lowess Normalization
Normalization strategyTotal Array