Time course of DC3000 vs delta hrp on tomato Prf-3
Hybridization: DC3000/delta hrp 24h |
| Hybridization protocol |
| Hybridization solution | SDS Genisphere Hybridization Solution |
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| Solution concentration | 0.25m NaPO4, 4.5%SDS, 1mm EDTA, 1x SSC, 2x Denhardt's Solution |
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| Blocking agent | ssDNA and Oligo dT |
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| Wash procedure | 2x15 minutes
1) 2x SSC + 0.2% SDS at 55 C.
2) 2x SSC at RT.
3) 0.2x SSC at RT (+ 0.5mM DTT) |
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| Labeled Target Quantity | 6 ul labeled cDNA |
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| Hybridization Time | (1) 14 hours (2) 2 hours |
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| Hybridization Volume | 65 ul |
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| Hybridization Temperature | 60 C / 55 C for secondary hyb |
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| Hybridization Instrument | Corning hybridization chambers in water bath |
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| Scan information |
| Scan hardware | Scan Array 5000 |
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| scan software | Scan Array ver 3.1 |
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| Image analysis information |
| Software | ImaGene ver 5.1 |
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| Analysis algorithm | 1) Images
Cy5 = Red Cy3 = Green
Default settings for image analysis algorithms were used, according to manufacturer's protocol |
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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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