Analysis of the effect of constitutive expression of AtGLK1 and AtGLK2 on the transcriptome of tomato fruits

Hybridization: GLK2

Hybridization protocol
Hybridization solution
Solution concentration
Blocking agent
Wash procedureThe chips were washed and stained with a phycoerythrin-strepavidin conjugate using the GeneChip Fluidics Station (Affymetrix) with the FS450-0001 protocol
Labeled Target Quantity300 ng of total RNA from each sample were labeled using the Ambion WT expression array kit (Ambion Inc.)
Hybridization Time17hr
Hybridization Volume
Hybridization Temperature45C
Hybridization InstrumentAffymetrix Hybridization Oven 640

Scan information
Scan hardwareAffymetrix GeneChip Scanner 3000 7G
scan softwareAffymetrix GeneChip Command Console software

Image analysis information
SoftwareAffymetrix GeneChip Command Console software
Analysis algorithm

Normalization information
Normalization softwarePartek Genomic Suite software v6.6
Normalization algorithmData 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.
Normalization strategyTotal array