Data sheet, GeneChip® miRNA 2.0 Array

Data SheetGeneChip ® miRNA 2.0 ArrayYour gene expression experiment has given you the “what”—now discover the “why.”Benefits of the GeneChip ® miRNA 2.0 Array:• Comprehensive content – Provides complete coverageof miRBase V15, including snoRNA and scaRNA probes• Unique content – Designed to independentlyinterrogate pre-miRNA and mature miRNA in thesame experiment• High sensitivity – Detects 85 percent of miRNAtranscripts at 1.0 amol• High reproducibility – 0.95 reproducibility(inter- and intra-lot)• Easiest workflow – 45-minute assay withoutpre-amplification or purification steps• Low sample input – Requires as little as 100 ngtotal RNA• Affordable – Meets the budget needs of every lifescience researcherIntroductionSince their discovery in 1993, small non-coding RNAs(microRNA, scaRNA, and snoRNA) have emerged as a majorcomponent in the regulatory circuitry that underlies thedevelopment and physiology of complex organisms.As a result, it is becoming increasingly important to complementmessenger RNA (mRNA) gene expression studies with miRNAanalysis to understand the biological context of differentiallyexpressed genes. These key functional gene products are estimatedto regulate approximately 30 percent of all protein-coding genes.These small-non-coding RNA molecules cover the broadestspectrum of developmental and physiological mechanisms inthe cell, including:• Protein translation inhibition•Ribosomal RNA processing• Alternative splicing• mRNA degradation1

Unique array contentThe GeneChip ® miRNA 2.0 Array provides the most sensitive,accurate, and complete measurement of small non-codingRNA transcripts involved in gene regulation.It is the only array with:• 100 percent miRBase v15coverage, all 135 organisms(15,644 probe sets)Data analysisData analysis with the GeneChip miRNA 2.0 Array is simple.You can use one of our GeneChip-compatible programs youalready use for analyzing expression data today, or downloadthe free Affymetrix miRNA QCTool from www.affymetrix.com.• 2,334 snoRNAs and scaRNAs• 2,202 probe sets unique topre-miRNA hairpin sequencesThe easiest and most affordable solution availableCoupled with the simple and affordable FlashTag BiotinHSR RNA Labeling Kit from Genisphere, the GeneChipmiRNA 2.0 Array offers easy target preparation and themost affordable solution available.The 45-minute assay does not involve complex enzymology(amplification) or purification steps that can reduce theyield or bias your results by introducing false positives orfalse negatives.SpecificationsReproducibility>0.95 Within lot>0.95 Between lotsTranscripts detected at 1.0 amol 85%Dynamic rangeTotal RNA inputFeature size>3 logs100 ng11 μmProbe length 25-mer; less, if the miRNA is less than 25Array contentUnique probe sets Number SourceMature miRNA probes from miRBase V15 15,644Human, mouse, and rat hairpin pre-miRNA 2,202Content is derived from the Sanger miRBase miRNA(http://microrna.sanger.ac.uk).Content is derived from the Sanger miRBase miRNA(http://microrna.sanger.ac.uk).Retrospective miRNA, scaRNA, and snoRNAprobe sets from the previous-generation array107Retrospective probe sets include miRNA, snoRNA, and scaRNA RNAfrom the previous version of the array.snoRNA and scaRNA probes 2,334Probe sets targeting human snoRNAs and scaRNAs are derived from thesnoRNABase (www.snorna.biotoul.fr/coordinates.php) and the EnsemblArchive (www.ensembl.org/biomart/martview).2

Organisms on the arrayOrganismNo. ofRNAsAcyrthosiphon pisum 10Aedes aegypti 126Amphimedon queenslandica 16Anopheles gambiae 65Apis mellifera 58Aquilegia caerulea 45Arabidopsis thaliana 224Arachis hypogaea 32Ateles geoffroyi 54BK polyomavirus 2Bombyx mori 562Bos taurus 679Bovine herpesvirus 12Brachypodium distachyon 19Branchiostoma floridae 73Brassica napus 48Brassica oleracea 7Brassica rapa 23Brugia malayi 31Caenorhabditis briggsae 131Caenorhabditis elegans 233Caenorhabditis remanei 137Canis familiaris 291Capitella teleta 134Carica papaya 1Cerebratulus lacteus 2Chlamydomonas reinhardtii 85Ciona intestinalis 514Ciona savignyi 25Citrus clementine 5Citrus reticulata 4Citrus sinensis 11Citrus trifoliata 6Cricetulus griseus 1Culex quinquefasciatus 93Danio rerio 248Daphnia pulex 44Dictyostelium discoideum 2Drosophila ananassae 75Drosophila erecta 78Drosophila grimshawi 72Drosophila melanogaster 186Drosophila mojavensis 71Drosophila persimilis 69Drosophila pseudoobscura 274Drosophila sechellia 76OrganismNo. ofRNAsDrosophila simulans 178Drosophila virilis 74Drosophila willistoni 72Drosophila yakuba 75Epstein-Barr virus 44Equus caballus 361Fugu rubripes 109Gallus gallus 544Glycine max 86Glycine soja 13Gorilla gorilla 81Gossypium arboretum 1Gossypium herbacium 1Gossypium hirsutum 36Gossypium raimondii 4Haliotis rufescens 5Herpes B virus 3Herpes simplex virus 49Herpesvirus of Turkeys 28Homo sapiens (miRNA) 1,105Homo sapiens (pre-miRNA) 1,105Homo sapiens (scaRNA) 32Homo sapiens (snoRNA) 2,302Human cytomegalovirus 17Human immunodeficiency virus 4Hydra magnipapillata 20Infectious laryngotracheitis 10Ixodes scapularis 34JC polyomavirus 2Kaposi sarcoma-associated virus 25Lagothrix lagotricha 45Lemur catta 15Locusta migratoria 14Lottia gigantean 64Lotus japonicas 4Macaca mulatta 505Macaca nemestrina 71Malus domestica 2Mareks disease virus 62Medicago truncatula 383Merkel cells 2Monodelphis domestica 146Mouse cytomegalovirus 29Mouse gammaherpesvirus 10Mus musculus 722Mus musculus (pre-miRNA) 690OrganismNo. ofRNAsNasonia vitripennis 53Nematostella vectensis 78Oikopleura dioica 63Ornithorhynchus anatinus 532Oryza sativa 496Oryzias latipes 4Ovis aries 4Pan paniscus 84Pan troglodytes 531Phaseolus vulgaris 10Physcomitrella patens 281Pinus taeda 38Pongo pygmaeus 608Populus euphratica 8Populus trichocarpa 237Pristionchus pacificus 99Pygathrix bieti 9Rattus norvegicus 389Rattus norvegicus (pre-miRNA) 389Rhesus lymphocryptovirus 48Rhesus monkey 11Ricinus communis 63Saccharum officinarum 16Saccoglossus kowalevskii 45Saguinus labiatus 40Schistosoma japonicum 78Schistosoma mansoni 5Schmidtea mediterranea 257Selaginella moellendorffii 64Simian virus 2Solanum lycopersicum 30Sorghum bicolor 148Strongylocentrotus purpuratus 46Sus scrofa 189Symphalangus syndactylus 10Taeniopygia guttata 212Tetraodon nigroviridis 109Tribolium castaneum 56Triticum aestivum 32Vigna unguiculata 2Vitis vinifera 138Xenopus laevis 22Xenopus tropicalis 169Zea mays 3193

Instrument and software requirementsCritical specificationsHybridization volumeInstrumentationSoftwareLibrary filesFluidics scriptDescription100 μLGeneChip ® Hybridization Oven 645, GeneChip® Fluidics Station 450, and GeneChip® Scanner 3000 7GGeneChip ® Command Console® Software (AGCC), miRNA QCToolmiRNA2_0FS450_0003Ordering informationPart number Product DescriptionArrays901753 GeneChip ® miRNA 2.0 Array 2 arrays901754 GeneChip ® miRNA 2.0 Array 6 arrays901755 GeneChip ® miRNA 2.0 Array 30 arraysReagents900301 Control Oligo B2, 3nM Sufficient for 30 reactions900720 GeneChip ® Hybridization, Wash, and Stain Kit Sufficient for 30 reactionsHSR10FTAHSR30FTAFlashTag Biotin HSR RNA Labeling Kit(available from Genisphere)FlashTag Biotin HSR RNA Labeling Kit(available from Genisphere)Sufficient for 10 reactionsSufficient for 30 reactionsThe GeneChip ® miRNA 2.0 Array is covered by Affymetrix’ limited warranty as set forth under the “Limited Warranty” section below. Affymetrix will provide no support for thearray. Affymetrix will not support any assay protocol used by the customer with the array. The array is not functionally tested by Affymetrix, and Affymetrix provides no warrantyregarding the functional performance of the array in any specific customer application.Limited warranty. Affymetrix warrants to you (but not to any third party) that GeneChip ® Arrays shall be free from physical defects. Affymetrix’ sole and exclusive liability and yoursole and exclusive remedy under the foregoing warranty, is to provide you with a replacement array provided if the following conditions are met: (i) you used the affected array priorto its expiration date and notify Affymetrix promptly after you become aware of the defect; (ii) you cooperate with Affymetrix in Affymetrix’ investigation as to the cause of the allegedphysical defect and provide any information required by Affymetrix; and (iii) Affymetrix shall make the final determination in good faith, as to whether: (a) any physical defectin fact exists; and (b) if so, whether such physical defect was caused by Affymetrix’ manufacturing process, and not user error, improper storage or handling, or any other cause forwhich Affymetrix is not responsible.Affymetrix, Inc. Tel: +1-888-362-2447 •Affymetrix UK Ltd. Tel: +44-(0)-1628-552550 •Affymetrix Japan K.K. Tel: +81-(0)3-6430-4020Panomics Products Tel: +1-877-PANOMICS www.panomics.com •USB Products Tel: +1-800-321-9322 www.usb.affymetrix.comwww.affymetrix.com Please visit our website for international distributor contact information.For Research Use Only. Not for use in diagnostic procedures.P/N EXP00180 Rev 1©2011-12 Affymetrix, Inc. All rights reserved. Affymetrix ® , Axiom , Command Console ® , DMET , GeneAtlas , GeneChip ® , GeneChip-compatible , GeneTitan ® , Genotyping Console , myDesign ,NetAffx ® , OncoScan , Powered by Affymetrix , Procarta ® , and QuantiGene ® are trademarks or registered trademarks of Affymetrix, Inc. Luminex ® and xMAP ® are registered trademarks of Luminex Corp.All other trademarks are the property of their respective owners.4