Transcription profiling of tomato shoots and roots from plants systemically infected by TSWV reveals organ-specific transcriptional responses
Hybridization: Leave_TSWV/Leave_mock |
| Hybridization protocol |
| Hybridization solution | |
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| Solution concentration | |
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| Blocking agent | |
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| Wash procedure | |
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| Labeled Target Quantity | 1.5 ug of Cy3- and Cy5-labelled cRNA |
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| Hybridization Time | |
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| Hybridization Volume | |
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| Hybridization Temperature | |
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| Hybridization Instrument | Agilent oven (G2545A) |
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| Scan information |
| Scan hardware | Agilent DNA microarray scanner |
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| scan software | N/A |
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| Image analysis information |
| 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 |
| 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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