tomato Never-ripe mutant fruit development

Hybridization: 42DAP/41DAP

Hybridization protocol
Hybridization solutionCorning Universal Hybridization Solution (catalog # 40090)
Solution concentrationProprietary
Blocking agentProprietary
Wash procedure3 x 10 minutes each:
1) 1x SSC + 0.2% SDS at 43 C.
2) 0.1x SSC + 0.2% SDS at 22 C.
3) 0.1x SSC at 22 C
Labeled Target Quantity25 pmol of Cy3, 25 pmol of Cy5
Hybridization Time12-16 hours
Hybridization Volume63 ul
Hybridization Temperature43 C
Hybridization InstrumentCorning Hybridization Chamber (catalog # 2551)

Scan information
Scan hardwareScan Array 5000
scan softwareScan Array ver 3.1

Image analysis information
SoftwareImaGene ver 5.5.4
Analysis algorithm1) Images
Cy5 = Red Cy3 = Green

2) Grid Flexibility
Enforce grid constraints = yes
Local flexibility = 6.0 pixels
Flexibility = 75%

3) Quality Control
Empty spots = no
Poor spots = yes
Find negative spots = no

4) Measurements
Background buffer = 2.25
Background width = 5.0
Auto seqmentation = no
Signal low cutoff = 20%
Signal high cutoff = 100%
Background low cutoff = 0%
Background high cutoff = 88%

5) Poor Spot Parameters
Contamination of Background/Signal = no
Ignored pixels % = yes (setting = 69)
Open perimeter = no
Shape regularity = no
Area to perimeter = yes (setting = 0.6)
Off-set value = yes (setting = 17.5)

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