The Affymetrix GeneChip System
provides a systems biology perspective for both Gene Expression profiling and DNA analysis. This integrated system gives the flexibility to view the genome at a global level or focus on a specific subset of genes.
High-density array makes available multiple, independent measurements for each transcript and genotype call.
The Center bases its work on the following instruments:
Affymetrix Software in the Center:
- 3' IVT Expression Assay for eukaryotic
- 3' IVT Expression Assay for prokaryotic
- Whole Transcript Sense Target Assay
- Whole Exon Sense Target Assay
- miRNA Assay
SNP Genotyping and CNV analysis
- Genome-Wide SNP Array 6.0
3' Expression Assay- interrogate each gene with multiple independent probes. Probes selected from the 600 bases most proximal to the 3' end of each transcript. This technology presents the 3'-based gene-level expression profiling. Affymetrix offers different catalog arrays from Arabidopsis to Zebrafish and custom designed arrays. List of arrays
Whole Transcript Sense Target Assay –Multiple probes spread across the full length of the genes represented on the array by, providing a more complete and more accurate picture of gene expression than 3’ based expression array designs. Only Human, Mouse, Rat arrays are available. More...
Whole Exon Sense Target Assay - approximately four probes per exon and roughly 40 probes per gene for over 1 million exon clusters that enables two complementary levels of analysis—gene expression and alternative splicing. Only Human, Mouse, Rat arrays are available. More...
miRNA Assay - coverage of 71 organisms including all important species. Sanger miRNA database content and additional human snoRNAs and scaRNAs. More...
SNP-250K – single array from SNP 500K set which enable genotyping on average 250,000 SNPs (approximately 262,000 for Nsp arrays and 238,000 for Sty arrays). More...
SNP6 - features 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation (CNV). More...
For details and complete list of arrays:
Affymetrix Product manager
Eisenberg Bros. Ltd.
Amounts and concentrations
For Eukaryotic Expression assay: 50-500ng (concentration > 50ng/μl)
For Prokaryotic Expression assay: 10-13μg (concentration >500ng/μl)
For Whole Transcript Sense Target assay: 300ng (concentration > 100ng/μl)
For Exon Sense Target assay: 1μg (concentration >320ng/μl)
For miRNA assay: 0.2-3μg (concentration > 125ng/μl)
For SNP-250K assay: 250ng (concentration > 50ng/μl)
For SNP-6 assay: 500ng (concentration > 50ng/μl)
Quantification of RNA
Integrity of total RNA samples can be evaluated by running on 1% agarose gel or by Agilent 2100 Bioanalyzer. RIN (RNA Integrity Number)>7 is acceptable.
Spectrophotometric absorbance parameters of the sample should be:
The Center for Genomic Technologies