Mapping 250K/500K SNP assay

PCR STAGING AREA
260 GeneChip ® Mapping 500K Assay Manual
A PCR negative control can be included in the experiment to assess
the presence of contamination. Refer to Chapter 2 and Chapter 7 for
more information.
Prepare fresh PCR Master Mix just prior to use.
2. Transfer 10 µL of each diluted ligated DNA from the 96-well plate
into the corresponding three individual wells of the PCR plates
using an 8- or 12-channel pipette. Be sure to change tips between
samples.
3. Add 90 µL PCR Master mix to obtain a total volume of 100 µL.
Final volume for each PCR is listed in the table below.
It is convenient to dispense the PCR Master Mix with a repetitive
dispenser (such as Gilson Distriman, available from Rainin) or
pipet the PCR Master Mix from a solution basin (Labcor Products,
Inc., Cat. No. 730-014; available from PGC Scientifics) with an 8channel
or 12-channel pipette.
Table C.8
Reagent Volume/PCR
PCR Master Mix 90 µL
Diluted ligated DNA (from Ligation step) 10 µL
Total 100 µL
Three PCR reactions are needed to produce sufficient product for
hybridization to one array (each reaction = 100 µL).
4. Seal the plate with plate cover, vortex at medium speed for
2 seconds, and spin at 2,000 rpm for 1 minute.