Transcription profiling of roots and leaves of tomato plants colonized by the arbuscular mycorrhizal fungus Glomus mosseae

Hybridization: Root_MYC/Root_Non_MYC

Hybridization protocol
Hybridization solution
Solution concentration
Blocking agent
Wash procedure
Labeled Target Quantity1.5 ug of Cy3- and Cy5-labelled cRNA
Hybridization Time
Hybridization Volume
Hybridization Temperature
Hybridization InstrumentAgilent oven (G2545A)

Scan information
Scan hardwareAgilent DNA microarray scanner
scan softwareN/A

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