Mapping 250K/500K SNP assay

272 GeneChip ® Mapping 500K Assay Manual
8. Vortex the fragmentation plate at medium speed for 2 seconds, and
spin briefly at 2,000 rpm at 4°C.
9. Place the fragmentation plate in pre-heated thermal cycler (37°C)
as quickly as possible.
Make sure the reaction tubes/plates are securely sealed prior to
running this program in order to minimize solution loss due to
evaporation at the DNase I inactivation step (95°C).
Seal the tubes/plates to make sure all reaction tubes fit snugly into
the wells of the heating block. Do not use a low-quality substitute
of the 96-well plate or PCR tubes that do not fit with the thermal
cycler.
10. Run the 500K Fragment program:
500K Fragment Program
Temperature Time
37ºC 35 minutes
95ºC 15 minutes
4ºC Hold
11. Spin the plate briefly after fragmentation reaction.
12. Dilute 4 µL of fragmented PCR product with 4 µL gel loading dye
and run on 4% TBE gel at 120V for 30 minutes to 1 hour. (See
Figure C.3.)
13. Proceed immediately to Labeling step, if your gel matches the
example below.