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Microarray Spots Web sites that explain the basic and advanced techniques. Laura Ruth
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nterpreting the red, yellow, and green spots of a DNA gene expression microarray can be tricky. Fortunately, international standards for microarray experiments and information storage databases are being developed, which will help scientists worldwide share individual laboratory microarray data. But what is a microarray? The Web offers a wealth of information describing microarrays and how they are used, along with examples, protocols, analysis software, databases, and standards that help in reading microarray signal spots. The best place to start is the European Bioinformatics Institute’s online slideshow (http://industry.ebi.ac.uk/ ~alan/MicroArray/IntroMicroArrayTalk/ sld001.htm), which describes how a microarray is prepared and used to detect complementary DNA (cDNA), the different DNA microarray technologies, and the various microarray gene expression experiments. Next, read about the differences between a biochip, DNA chip, DNA microarray, gene array, and macroarrays. Leming Shi, head of informatics at the start-up ChipScreen Biosciences, explains array terminology, synthesis, and design (http://www.gene-chips.com). To find out more about chip fabrication methods and slide array technologies, investigate the more than 35 companies listed on Bernd Weisshaar’s DNA microarray links on the Max Planck Institute for Plant Breeding Research Web site (http://www.mpiz-koeln.mpg.de/ ~weisshaa/Adis/DNA-array-links.html). D E C E M B E R 1 , 2 0 0 1 / A N A LY T I C A L C H E M I S T R Y
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What makes microarray technology so exciting? “Being able to place thousands of cDNA probes on a microarray,” according to Charles Sugnet’s online microarray FAQ (http://www.cse.ucsc. edu/~sugnet/microarray/microarray_ FAQ.html). Sugnet gives quick and easy-to-read details about the differences between types of microarrays and experimental variables, such as sensitivity, reverse transcription, and ratios versus cohybridizations.
tips and probe labels; and preparing specific microarray DNA, RNA, and hybridization protocols. After running a microarray experiment, what do the sea of red, yellow, and green signal spots mean? The virtual library of plant arrays at the Institut National de la Recherche Agronomique (France) lists 19 public and commercial microarray gene expression software analysis programs (http://www.ensam.inra.fr/ biochimie/plant_arrays/Plant-Arrays_
Microarray users can communicate with each other through a variety of e-mail and Web-based microarray newsgroups. Want to build a DNA microarray chip and run a hybridization experiment? Tune in to the Davidson College Department of Biology site to watch an animated presentation on how DNA microarray experiments are performed and interpreted (http://www.bio.davidson.edu/ courses/genomics/chip/chip.html). The use of robots and pins for microarray chip synthesis and spot quality, as well as other stages of microarray data collection and analysis, are clearly discussed in BioRobotics’ genomic microarrays review (http://www.biorobotics.com/ Pages/micover.html). The microarrays.org protocols section, mainly derived from the Cold Spring Harbor’s laboratory course manual, leads you through building a chip, preparing RNA, cDNA probe production and labeling, array hybridization, and data analysis (http://www.microarrays.org/ protocols.html). Researchers at Albert Einstein College of Medicine have posted one specific protocol that includes steps for RNA preparation, probe preparation, slide preparation, and hybridization (http://sequence.aecom.yu.edu/ bioinf/microarray/protocol4.html). Pat Brown at Stanford University supplies a complete guide to microarraying for the molecular biologist (http://cmgm. stanford.edu/pbrown/mguide/index. html). The guide includes information on assembling microarrays; using print 690 A
Software.html). Cluster analysis, scatter plots, and histograms are a few of the mathematical software analysis methods available. Wentian Li at Rockefeller University describes many microarray analysis methods, such as partial least squares and parametric versus nonparametric analysis, in a comprehensive collection of papers (http://linkage.rockefeller. edu/wli/microarray). Learn about a few more normalization statistical methods on the Arabidopsis functional genomics consortium Web site (http://afgc. stanford.edu/afgc_html/site2Stat.htm). Scientists are developing databases to store and analyze the growing mountain of microarray gene expression data. The department of biology at Ecole Normale Superieure (ENS, France) lists public and private general microarray databases (http://www.biologie.ens.fr/en/ genetiqu/puces/bddeng.html). Microarrays allow investigation of DNA in many organisms. The ENS’s microarray selected links section lists specific microarray experiments and databases for ⬎15 organisms (http://www.biologie.ens.fr/en/ genetiqu/puces/microarraysframe.html). Look up information about the National Cancer Institute’s screening of 60 human cancer cell lines for anticancer activity patterns with ⬎70,000 compounds (http://discover.nci.nih.gov). The University of Arizona has been investigating spermatogenesis genes
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(http://www.mcb.arizona.edu/wardlab/ microarray.html). Microarray users can communicate with each other through a variety of e-mail and Web-based microarray newsgroups. Lab-on-a-chip.com offers a free e-mail newsletter subscription. The online newsletter includes information about jobs, industry, government, patents, meetings, and other online resources all related to microarrays. The e-mail listserv
[email protected] is a heavily trafficked microarray news community that discusses meetings, protocols, data analysis, and other topics of interest. The European Bioninformatics Institute’s (EBI’s) microarray-request@ ebi.ac.uk and the newer e-mail group bionet.molbio.genearrays are other microarray information highways. Group listings of microarray listservs and newsgroups, as well as information about microarray articles, laboratories, software, companies, and databases, can be found on Web pages, such as the DNA microarrays site (http://www.deathstarinc. com/science/biology/chips.html) and the expression profiler EBI microarray information page (http://ep.ebi.ac.uk/ links.html). Scientists are creating international standards for microarray experiments so that data generated using different technologies and techniques can be compared and collectively interpreted. Consult the Association of Biomolecular Resource Facilities microarray research group survey for information about microarray facilities, spotting arrays, and Affymetrix photolithography arrays (http://brcweb. biotech.cornell.edu/marg2000/). Experimental design, array design, samples, hybridization conditions, measurements, and normalization are all important for microarray experiments. Lastly, the microarray gene expression database group outlines what information to include for depositing results in a database or publication, so that the scientific community can steer through the traffic of red, yellow, and green array signals (http:// www.mged.org/Annotations-wg/ MGEDmiameApr2001.1.0.doc). Laura Ruth is a freelance writer based in Los Angeles, CA.
