Mapping 250K/500K SNP assay

appendix D | Reagents, Instruments, and Supplies Required for Low Throughput Protocol 287
Reagents and Instruments Required
Table D.1
Reagents Supplied by Affymetrix - 30 Reaction Kit
The following reagents and equipment are required to process the
GeneChip Mapping 500K Array Set.
Affymetrix GeneChip ® Mapping 250K Nsp Assay Kit P/N 900766
This kit includes sufficient reagent for 30 arrays.
Component Volume Concentration Description Box #
Adaptor, Nsp I 25 µL 50 µM Two annealed oligonucleotides,
specific for ligation to Nsp restriction
site.
PCR Primer, 002 450 µL 100 µM PCR primer, to amplify ligated genomic
DNA
Reference Genomic DNA,
103
GeneChip ®
Fragmentation Reagent
30 µL 50 ng/µL Human genomic DNA (single source) 2
25 µL See label on tube DNase I enzyme, formulated to
fragment purified PCR amplicons
10X Fragmentation Buffer 250 µL 10X Buffer for fragmentation reaction 3
GeneChip ® DNA Labeling
Reagent (30 mM)
Terminal
Deoxynucleotidyl
Transferase
5X Terminal
Deoxynucleotidyl
Transferase Buffer
Oligo Control Reagent,
0100 (OCR, 0100)
60 µL 30 mM Biotin-labeled reagent for end-labeling
fragmented PCR amplicons
105 µL 30 U/µL Enzyme used to end-label fragmented
PCR amplicons with the GeneChip ®
DNA Labeling Reagent (30 mM)
420 µL 5X Buffer for labeling reactio 3
60 µL See protocol
Chapter 4 (high
throughput) or
Appendix C (low
throughput)
Mixture of five biotin-labeled
oligonucleotides, which hybridize to
control regions (gridding controls and
array controls) on the GeneChip ®
Mapping 250K Arrays.
1
1
3
3
3
3