Mapping 250K/500K SNP assay

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268 GeneChip ® Mapping 500K Assay Manual
Fragmentation of PCR product before hybridization onto
GeneChip ® probe arrays has been shown to be critical in obtaining
optimal assay performance. Due to the sensitive nature of the
Fragmentation Reagent (DNase I), these general rules need to be
followed to ensure the success of the step:
Store the Fragmentation Reagent stock at –20°C until ready for
use.
Make sure the purified PCR products are in RB buffer with proper
volume (45 µL).
Pre-heat the thermal cycler to 37°C before setting up the
fragmentation reaction.
Prepare the Fragmentation Reagent dilution immediately prior to
use.
Prepare diluted Fragmentation Reagent in excess to avoid errors
in taking a small volume of Fragmentation Reagent.
Perform all the dilution, addition and mixing steps ON ICE.
Perform all the steps AS QUICKLY AS POSSIBLE.
Discard remaining Diluted Fragmentation Reagent after use.
Tips on handling the Fragmentation Reagent:
Store Fragmentation Reagent stock at –20°C until ready for use.
Transfer Fragmentation Reagent in a –20°C cooler and keep in the
cooler until used. Return to the cooler immediately after use.
Work efficiently while preparing mixes for the fragementation
reaction.
Briefly spin down Fragmentation Reagent tube. Do not vortex.
Avoid excess enzyme on the outside of the pipette tip while
preparing mixes.