tomato Never-ripe mutant fruit development
Hybridization: 57DAP/7DAP
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Hybridization protocol
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| Hybridization solution | Corning Universal Hybridization Solution (catalog # 40090) |
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| Solution concentration | Proprietary |
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| Blocking agent | Proprietary |
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| Wash procedure | 3 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 |
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| Labeled Target Quantity | 25 pmol of Cy3, 25 pmol of Cy5 |
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| Hybridization Time | 12-16 hours |
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| Hybridization Volume | 63 ul |
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| Hybridization Temperature | 43 C |
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| Hybridization Instrument | Corning Hybridization Chamber (catalog # 2551) |
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Scan information
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| Scan hardware | Scan Array 5000 |
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| Scan software | Scan Array ver 3.1 |
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Image analysis information
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| Software | ImaGene ver 5.5.4 |
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| Analysis algorithm | 1) 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) |
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Normalization information
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| Normalization software | marray package under R |
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| Normalization algorithm | Print-tip specific Lowess Normalization |
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| Normalization strategy | Total Array |
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