Analysis of the effect of constitutive expression of AtGLK1 and AtGLK2 on the transcriptome of tomato fruits
Hybridization: GLK1 |
| Hybridization protocol |
| Hybridization solution | |
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| Solution concentration | |
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| Blocking agent | |
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| Wash procedure | The chips were washed and stained with a phycoerythrin-strepavidin conjugate using the GeneChip Fluidics Station (Affymetrix) with the FS450-0001 protocol |
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| Labeled Target Quantity | 300 ng of total RNA from each sample were labeled using the Ambion WT expression array kit (Ambion Inc.) |
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| Hybridization Time | 17hr |
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| Hybridization Volume | |
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| Hybridization Temperature | 45C |
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| Hybridization Instrument | Affymetrix Hybridization Oven 640 |
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| Scan information |
| 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 |
| Software | Affymetrix GeneChip Command Console software |
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| Analysis algorithm | |
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| Normalization information |
| Normalization software | Partek Genomic Suite software v6.6 |
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| Normalization algorithm | Data was pre-processed and analyzed using Partek Genomic Suite software v6.6 (Partek Inc.) with the probes matching only once with the iTAG annotation v2.3. The configuration consisted of a pre-background adjustment for GC content, Robust Multi-array Analysis for background correction, quantile normalization and probe set summarization using median polishing. All signals were log2 transformed. Library files were eutom3gene_v2_ucprobes.cdf and the annotation file version was eutom3-annotation-per-scaffold-modif.txt which represents 30,000 genes of tomato genome. |
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| Normalization strategy | Total array |
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