Mapping 250K/500K SNP assay

STEP 7: Fragmentation
REAGENTS AND EQUIPMENT
appendix C | Low Throughput Protocol 267
The amount of DNA in each well will differ. For optimal
performance, it is critical that the contents of each well be
normalized to 2 µg of DNA/µL before proceeding to the next step.
If necessary, bring the volume of each well to 45 µL by adding
RB Buffer; do not add water.
• Fragmentation Reagent (DNase I): Affymetrix, P/N 900131
• 10X Fragmentation Buffer: Affymetrix, P/N 900422 for 30 Rxns
and P/N 900695 for 100 Rxns
• Molecular Biology Grade Water: Bio Whittaker Molecular
Applications/Cambrex, P/N 51200
• 4% TBE Gel: BMA Reliant precast (4% NuSieve 3:1 Plus Agarose):
Cambrex, P/N 54929
• All Purpose Hi-Lo DNA Marker: Bionexus, Inc.; 50 - 10000bp;
P/N BN2050
• Gel Loading Solution: Sigma, P/N G2526
• 96-well plate: Bio-Rad, P/N MLP-9601
• 96-well PLT. Clear Adhesive Films: Applied Biosystems,
P/N 4306311
• Thermal cycler
- DNA Engine Tetrad ®1 : MJ Research, or
- GeneAmp ® PCR System 9700 with gold-plated block
1 In 2004 MJ GeneWorks, Inc. and its subsidiary MJ Research, Inc. were purchased by Bio-Rad Laboratories, Inc.
This model is no longer available. Bio-Rad has indicated that the DNA Engine Tetrad 2 gives similar performance
with the same progams. Affymetrix has not tested the newer version.