DC3000 effector mutants

Hybridization: DC3000 delta A/DC3000 delta AB

Hybridization protocol
Hybridization solutionCorning Universal Hybridization Solution (catalog #40090, Corning Inc.)
Solution concentrationCorning hybridiation buffer
Blocking agentUnknown
Wash procedureSee Protocol Pronto Plus! TM Promega/Corning
Labeled Target QuantityStarting material 7ug RNA
Hybridization Time14-16 hours
Hybridization Volume70ul
Hybridization Temperature42C
Hybridization InstrumentCorning microarray hybridization chamber in 42C water bath

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