Mapping 250K/500K SNP assay

Before You Begin
MASTER MIX PREPARATION
38 GeneChip ® Mapping 500K Assay Manual
Carefully follow each master mix recipe. Use pipettes that have been
calibrated to ± 5%. When molecular biology-grade water is specified,
be sure to use the AccuGENE® water listed in Appendix A, Reagents,
Equipment, and Consumables Required for 96-Well Plate Protocol. Using
in-house ddH2O or other water can negatively affect your results. The
enzymatic reaction in Stage 7: Fragmentation is particularly sensitive to
pH and metal ion contamination.
If you run out of master mix during any of these procedures, a volume
error has been made or the pipettes are not accurate. We recommend
that you stop and repeat the experiment.
REAGENT HANDLING AND STORAGE
Follow these guidelines for reagent handling and storage.
• When working on the bench top, keep all reagents (except enzymes)
on ice in a cooling chamber that has been chilled to 4 °C.
• Always leave enzymes at –20 °C until immediately prior to adding
them to master mixes. When removed from the freezer, immediately
place in a cooler that has been chilled to –20 °C and placed on ice.
• Store the reagents used for the restriction digestion, ligation and
PCR steps in the Pre-PCR Clean Area.
• Do not re-enter the Pre-PCR Clean Area after entering the PCR-
Staging Room or the Main Lab. Aliquot each of the reagents in the
Pre-PCR Clean Area before starting the rest of the experiment.
• Dedicate one cooler for the Pre-PCR Clean Area and one for the
Main Lab (post-PCR).
• When performing the steps for Stages 2 through 8:
- Leave all of the tubes on ice or in a cooling chamber on ice.
- Keep all plates in a cooling chamber on ice.
• Consult the appropriate MSDS for reagent storage and handling
requirements.