Mapping 250K/500K SNP assay

RUNNING GELS
72 GeneChip ® Mapping 500K Assay Manual
Before Running Gels
To ensure consistent results, take 3 µL aliquot from each PCR before
adding EDTA.
Wear the appropriate personal protective equipment when
handling ethidium bromide.
Run the Gels
When the 500K PCR program is finished:
1. Remove each plate from the thermal cycler.
2. Spin down plates at 2000 rpm for 30 sec.
3. Place plates in cooling chambers on ice or keep at 4 °C.
4. Label three fresh 96-well reaction plates P1Gel, P2Gel and P3Gel.
5. Aliquot 3 µL of 2X Gel Loading Dye to each well of the three
plates.
6. Using a 12-channel P20 pipette, transfer 3 µL of each PCR product
from plates P1, P2 and P3 to the corresponding plate, row and
wells of plates P1Gel, P2Gel and P3Gel.
Example: 3 µL of each PCR product from each well of row A on
plate P1 is transferred to the corresponding wells of row A on plate
P1Gel.
7. Seal plates P1Gel, P2Gel and P3Gel.
8. Vortex the center of plates P1Gel, P2Gel and P3Gel, then spin
down at 2000 rpm for 30 sec.
9. Load all 6 µL from each well of plates P1Gel, P2Gel and P3Gel onto
2% TBE gels.
10. Run the gels at 120V for 40 minutes to 1 hour.
11. Verify that the PCR product distribution is between ~250 bp to
1100 bp (see Figure 4.3).
90 µg of PCR product is needed for fragmentation.