Data Sheet, GeneChip PrimeView Human Gene Expression Array

Data SheetGeneChip ® PrimeView Human Gene Expression ArrayIndustry leading technology for cost-effective expression profilingDesign and coverageThe PrimeView Array utilizes content with an emphasis onestablished, well-annotated genes. The array is for use with theGeneChip ® Scanner 3000 7G (GCS 3000 7G) and is supported byour premium reagents and software. The PrimeView Array, whichis a perfect-match-only (PM) array, yields data that is not directlycomparable with previous arrays, including the GeneChip ® HumanGenome U133 (HG-U133) Array or the GeneChip ® Human Gene1.0 ST Array.Table 1 lists the key data sources used to design the probes andassociated analysis files that contain the gene annotation for eachset of probes. Affymetrix frequently updates array annotationfiles to remain up to date with the current understanding of eachgenome. Please visit the Affymetrix website for the most recentarray annotation available.Table 1: Annotation and key data sources for PrimeView Human GeneExpression Array.The GeneChip ® PrimeView Human Gene ExpressionArray provides comprehensive coverage of the humangenome in a cartridge array format designed for usewith the GeneChip ® Scanner 3000 7G series.IntroductionThe PrimeView Human Gene Expression Array offers theindustry’s highest quality expression technology in a cartridgeformat, enabling comprehensive whole-genome geneexpression analysis. The array demonstrates extremely highperformance, with strong signal and fold change correlationbetween sample replicates; it is a powerful and cost-effectivetool for studying drug and disease regulatory mechanisms.Key benefits of the PrimeView Array:• Offers excellent gene expression specificity andreproducibility• Produces reliable results with multiple independentmeasurements per transcript—11 probes per set for wellannotatedsequences, 9 probes per set for the remainder• Provides complete coverage of the annotated genome• Highest transcript coverage in the industry withthe most recent annotation—covers all wellannotatedgenes and transcripts from RefSeqData sources (June 2011)UniGene (design time) 219RefSeq 41NCBI genome version 37UCSC 19Ensembl 57GenBank ® 177PrimeViewEntrez 6/2010PerformanceFigure 1 and Table 3 show that the PrimeView Array demonstratesthe same high level of performance as other 3’ gene expressionanalysis arrays. Affymetrix observed a median coefficient ofvariation (CV) of less than 10 percent. The Pearson correlationcoefficient for sample replicates was greater than 0.990.Hybridization targets were prepared from Microarray QualityControl (MAQC) A and B total RNA and HeLa (Table 2) using theGeneChip ® 3’ IVT Express Kit. Labeled target from each samplewas pooled and hybridized to the arrays. CEL files were quantilenormalized with Expression Console Software using the RMAalgorithm for probe set summarization.1

SpecificationsInput RNA requiredSensitivity 1Detectable fold changeDynamic range 1Probe length50–500 ng≥1:100,000≥2.0 fold≥3log25-mer1Sensitivity and dynamic range were determined using a Latin square experimental design with 61 in vitro transcribed (IVT), full-length transcripts added to HeLa totalRNA. For this experiment, 12 spike pools with different relative abundances were tested. Spike concentration differences were defined as significant if the t-statisticresults were greater than a threshold set based on three replicates and the alpha significance level of 0.95.Ordering informationPart number Product Description901837 GeneChip ® PrimeView Human Gene Expression Array Contains 10 arrays901838 GeneChip ® PrimeView Human Gene Expression Array Contains 30 arrays901839901840GeneChip ® PrimeView Human Gene Expression Arrayand 3’ IVT Express Kit BundleGeneChip ® PrimeView Human Gene Expression Arrayand 3' IVT Express Kit BundleSufficient for 10 reactionsSufficient for 30 reactionsRelated productsPart number Product Description901228 GeneChip ® 3' IVT Express Kit Sufficient for 10 reactions (manual preparation)901229 GeneChip ® 3' IVT Express Kit Sufficient for 30 reactions (manual preparation)900720 GeneChip ® Hybridization, Wash, and Stain Kit Sufficient for 30 reactions3