Mapping 250K/500K SNP assay

106 GeneChip ® Mapping 500K Assay Manual
CHECK THE FRAGMENTATION REACTION
To ensure that fragmentation was successful:
1. When the 500K Fragment program is finished:
A. Remove the plate from the thermal cycler.
B. Spin down the plate at 2000 rpm for 30 sec, and place in a
cooling chamber on ice.
2. Dilute 4 µL of each fragmented PCR product with 4 µL gel loading
dye.
3. Run on 4% TBE gel with the BioNexus All Purpose Hi-Lo ladder
at 120V for 30 minutes to 1 hour.
4. Inspect the gel and compare it against the example shown in
Figure 4.7 below.
Figure 4.7
Typical example of fragmented PCR products run on 4% TBE agarose gel at 120V
for 30 minutes to 1 hour. Average fragment size is < 180 bp.