Expression data from roots and first two leaves of tomato seedlings growing on regular MS medium or MS medium supplemented with multi-wall carbon nanotubes (0, 50, 100, 200 ug/ml) or activated carbon (50 mg/ml)
Hybridization: Roots-100 ug/ml of CNTs
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Hybridization protocol
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| Hybridization solution | 1X hybridization buffer |
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| Solution concentration | 100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20 |
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| Blocking agent | Herring sperm DNA (final concentration 100ng) |
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| Wash procedure | Automated fluidics station consisting of wash buffers A and B. Wash buffer A is a non-stringent buffer containing 6X SSPE, 0.01% Tween 20. Wash buffer B is a stringent buffer containing 100 mM MES, 0.1 M NaCl, 0.01% Tween 20 |
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| Labeled Target Quantity | 5 ug |
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| Hybridization Time | 16 hours |
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| Hybridization Volume | 80 ul |
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| Hybridization Temperature | 45C |
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| Hybridization Instrument | Hybridization oven 640 (Affymetrix) |
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Scan information
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| Scan hardware | Affymetrix GeneChip Scanner 3000 7G |
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| Scan software | Affymetrix GeneChip Command Console software |
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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 | RMA |
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| Normalization algorithm | N/A |
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| Normalization strategy | Total array |
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