Transcriptional profiles of drought-responsive genes in modulating transcription, signal transduction and biochemical pathways in tomato

Hybridization: IL9-1 drought stress/control

Hybridization protocol
Hybridization solutionN/A
Solution concentrationN/A
Blocking agentN/A
Wash procedurethe arrays were washed with 0.2% SDS, 2×SSC at 42oC for 5 min, followed by washing with 0.2% SSC for 5 min at room temperature.
Labeled Target QuantityN/A
Hybridization Timeovernight
Hybridization VolumeN/A
Hybridization Temperature42oC
Hybridization InstrumentN/A

Scan information
Scan hardwareLuxScan 10KA confocal laser 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