The Eukaryotic Hybridization control mix contains non-eukaryotic transcripts, which serve as controls for hybridization quality and array performance. A synthetic control oligonucleotide (B2) provides alignment signals used by the scanner software to position the grid over the array image. Addition of the Eukaryotic Hybridization control mix to the hybridization cocktail is not compulsory, but the B2 control oligo-nucleotide must be added to every cRNA sample to be hybridized. In this protocol we use 15 |g of cRNA for the hybridization of standard GeneChip® arrays. Use only RNAse-free plasticware (Eppendorf tubes, pipette tips) and DEPC-treated water. All the buffers used in this protocol must be sterile-filtered (0.22 |m filter).

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