Regulatory control of high levels of carotenoid accumulation in potato tubers
Hybridization: POR03/Atlantic
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Hybridization protocol
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| Hybridization solution | 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 | 3x15 minutes:
1) 2x SSC + 0.2% SDS at 60 C.
2) 2x SSC at 22 C.
3) 0.2x SSC at 22 C |
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| Labeled Target Quantity | 3 ul cDNA |
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| Hybridization Time | 12-16 hours |
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| Hybridization Volume | 60 ul |
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| Hybridization Temperature | 60C |
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| Hybridization Instrument | 50 ml tube in 60C chamber |
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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 | Affymetrix GeneChip Operating Software (GCOS) |
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| Analysis algorithm | MAS 5 software |
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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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