Mapping 250K/500K SNP assay

Fragmentation and
Labeling
appendix D | Reagents, Instruments, and Supplies Required for Low Throughput Protocol 297
Table D.6
Reagents, Equipment and Supplies Not Supplied by Affymetrix
Assay Step Reagents Equipment
GeneChip ® 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 -
10000 bp; P/N BN2050
Gel Loading Solution: Sigma, P/N G2526
96-well plate: Bio-Rad, P/N MLP-9601
96-well Clear Adhesive Films: Applied Biosystems,
P/N 4306311
GeneChip ® DNA Labeling Reagent (30 mM):
Affymetrix, P/N 900778 for 30 Rxns and P/N
900699 for 100 Rxns, available in the Nsp and
Sty GeneChip ® Mapping 250K Assay Kits:
Nsp 30 Rxn Kit P/N 900766
Nsp 100 Rxn Kit P/N 900753
Sty 30 Rxn Kit P/N 900765
Sty 100 Rxn Kit P/N 900754
Terminal Deoxynucleotidyl Transferase
(30 U/µL): Affymetrix, P/N 900508 for 30 Rxns
and P/N 900703 for 100 Rxns, available in the
Nsp and Sty GeneChip ® Mapping 250K Assay
Kits:
Nsp 30 Rxn Kit P/N 900766
Nsp 100 Rxn Kit P/N 900753
Sty 30 Rxn Kit P/N 900765
Sty 100 Rxn Kit P/N 900754
5X Terminal Deoxynucleotidyl Transferase
Buffer: Affymetrix, P/N 900425 for 30 Rxns
and P/N 900696 for 100 Rxns, available in the
Nsp and Sty GeneChip ® Mapping 250K Assay
Kits:
Nsp 30 Rxn Kit P/N 900766
Nsp 100 Rxn Kit P/N 900753
Sty 30 Rxn Kit P/N 900765
Sty 100 Rxn Kit P/N 900754
PCR Thermal Cycler*
(Ramp speeds on these
models are critical - assay
protocols have been
optimized for these two
thermal cycler models
only):
MJ Research DNA
Engine Tetrad ®**
(PTC-225) 96 well
block, or
ABI GeneAmp ® PCR
System 9700 - goldplated
96 well block