News and Events

12/9/2008

Affymetrix Technology Powers Cincinnati Children's Hospital's Innovative Test for Jaundice

12/8/2008

Affymetrix Completes Acquisition of Panomics

View All >

Plant and Animal Genome XVII Conference

1/10/2009-1/14/2009

View All >

Achieving ROI in Personalized Medicine: Barriers, Incentives, and Pathways to Commercialization

1/27/2009-1/28/2009

Scientific Publications

Search our database of 16170 publications.

Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0

Figure 1

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.

Affymetrix® Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0 Components
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

Terminal Deoxynucleotidyl Transferase	Enzyme used to end-label-fragmented PCR amplicons with the GeneChip® DNA Labeling Reagent
5X Terminal Deoxynucleotidyl Transferase	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. >

Data Sheets

Genome-Wide Human SNP Array 6.0 (pdf, 473 KB)

Technical Notes

SNP Concordance Across Affymetrix Genotyping Arrays (pdf, 168 KB)

Application Notes

A New Paradigm for Two-stage Association Studies (pdf, 144 KB)

Part #	Description	Details
901152	Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0	Sufficient for 50 reactions
901013	Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0	Sufficient for 30 reactions
901015	Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0	Sufficient for 100 reactions

Required Products

Part #	Description	Details
	Affymetrix® GeneChip® Command Console® Software	Available Via Download
	Genotyping Console™ Software	Available Via Download
00-0079	GeneChip® Fluidics Station 450
00-0331	GeneChip® Hybridization Oven 645
00-0211	GeneChip® Scanner 3000 7G