Mapping 250K/500K SNP assay

PREPARE THE PCR MASTER MIX
68 GeneChip ® Mapping 500K Assay Manual
Prepare enough PCR Master Mix to run three PCR reactions per
sample.
Location
Pre-PCR Clean Room
Prepare the PCR Master Mix
To prepare the PCR Master Mix:
The PCR reaction is sensitive to the concentration of primer used. It
is critical that the correct amount of primer be added to the PCR
Master Mix to achieve the correct distribution of fragments (200 to
1100 bp) in the products.
Check the PCR reactions on a gel to ensure that the distribution is
correct (see Figure 4.3). 90 µg of PCR product is needed for
fragmentation.
1. Keeping the 50 mL Falcon tube in the cooling chamber, add the
reagents in Table 4.16 in the order shown.
2. Remove the TITANIUM Taq DNA Polymerase from the freezer
and immediately place in a cooler.
3. Pulse spin the Taq DNA polymerase for 3 sec.
4. Immediately add the Taq DNA polymerase to the master mix;
then return the tube to the cooler on ice.
5. Vortex the master mix at high speed 3 times, 1 sec each time.
6. Pour the mix into the solution basin, keeping the basin on ice.