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Learn more about the assay:
The Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0
The Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0 [P/N 901152, 901015] was developed and validated for use in conjunction with the Genome-Wide Human SNP Array 5.0 [P/N 901167, 901071] and SNP Array 6.0 [P/N 901153, 901150]. Briefly, total genomic DNA (500 ng) is digested with Nsp I and Sty I restriction enzymes and ligated to adaptors that recognize the cohesive 4 bp overhangs. All fragments resulting from restriction enzyme digestion, regardless of size, are substrates for adaptor ligation. A generic primer that recognizes the adaptor sequence is used to amplify adaptor-ligated DNA fragments. PCR conditions have been optimized to preferentially amplify fragments in the 200 to 1,100 bp size range. PCR amplification products for each restriction enzyme digest are combined and purified using polystyrene beads. The amplified DNA is then fragmented, labeled and hybridized to the array.
The Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0 contains validated and qualified reagents for the most critical steps in the assay. This includes the PCR primer and adaptors, reagents to fragment and label the PCR products and several control reagents. Kits are available for either 50 or 100 reactions (see Ordering Information).
Whole-genome-amplified material prepared by the Qiagen REPLI-g® kits may also be used as the starting material for the Genome-Wide Human SNP Assay Kit 5.0/6.0.
Figure 1: Overview of the Genome-Wide Human SNP Assay Kit 5.0/6.0
| Affymetrix® Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0 Components |
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Adaptor, Nsp I or Adaptor, Sty l |
Two annealed oligonucleotides specific for
ligation to the Nsp l or Sty l restriction site |
| PCR Primer 002 |
PCR primer to amplify ligated genomic DNA |
| Reference Genomic DNA, 103 |
Human genomic DNA control, with consensus genotypes |
| GeneChip® Fragmentation Reagent |
DNasel enzyme, formulated to fragment purified PCR amplicons |
| 10X Fragmentation Buffer |
Buffer for fragmentation reaction |
| GeneChip® DNA Labeling Reagent (30 mM) |
Proprietary biotin-labeled reagent for end- labeling fragmented PCR amplicons |
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| Terminal Deoxynucleotidyl Transferase |
Enzyme used to end-label-fragmented PCR
amplicons with the GeneChip® DNA Labeling Reagent |
| 5X Terminal Deoxynucleotidyl Transferase |
Buffer Buffer for labeling reaction |
| Oligo Control Reagent, 0100 |
Mixture of five biotin-labeled oligonucleotides, which hybridize to control regions (gridding and array controls) on the SNP Array 5.0 and SNP Array 6.0 |
Find out more about Clontech's Titanium™ DNA Amplification Kit, functionally validated for PCR amplification in the Whole-genome Sampling Assay.
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