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Topic: Microarray

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	Microarrays Factsheet
		Microarrays are a significant advance both because they may contain a very large number of genes and because of their small size.
		Microarrays are therefore useful when one wants to survey a large number of genes quickly or when the sample to be studied is small.
		Microarrays may be used to assay gene expression within a single sample or to compare gene expression in two different cell types or tissue samples, such as in healthy and diseased tissue.
	www.ncbi.nlm.nih.gov /About/primer/microarrays.html (3611 words)

	genome.gov \| DNA Microarray Fact Sheet
		Microarray technology will help researchers to learn more about many different diseases, including heart disease, mental illness and infectious diseases, to name only a few.
		With the help of microarray technology, however, they will be able to further classify these types of cancers based on the patterns of gene activity in the tumor cells.
		DNA microarrays are created by robotic machines that arrange minuscule amounts of hundreds or thousands of gene sequences on a single microscope slide.
	www.genome.gov /10000533 (518 words)

	Microarray Technology
		Microarray is one such technology which enables the researchers to investigate and address issues which were once thought to be non traceable.
		Microarray technology has empowered the scientific community to understand the fundamental aspects underlining the growth and development of life as well as to explore the genetic causes of anomalies occurring in the functioning of the human body.
		Now, with the evolution of microarray technology, it will be possible for the researchers to further classify the types of cancer on the basis of the patterns of gene activity in the tumor cells.
	www.premierbiosoft.com /tech_notes/microarray.html (972 words)

	Tissue microarray recommended references
		Sections of the microarray provide targets for parallel in situ detection of DNA, RNA and protein targets in each specimen on the array, and consecutive sections allow the rapid analysis of hundreds of molecular markers in the same set of specimens.
		A major obstacle to broad acceptance of microarrays is that they reduce the amount of tissue analyzed from a whole tissue section to a disk, 0.6 mm in diameter, that may not be representative of the protein expression patterns of the entire tumor.
		We compared the staining of 2 to 10 microarray disks and the whole tissue sections from which they were derived and determined that analysis of two disks is comparable to analysis of a whole tissue section in more than 95% of cases.
	www.beecherinstruments.com /references.html (1310 words)

	Microarrays
		Microarrays that consist of ordered sets of DNA fixed to solid surfaces provide pharmaceutical firms with a means to identify drug targets.
		Microarray analysis permits scientists to detect thousands of genes in a small sample simultaneously and to analyze the expression of those genes.
		A basic difference between microarray data analysis and much traditional biomedical research is the dimensionality of the data.
	www.geocities.com /bioinformaticsweb/microarrays.html (1283 words)

	CiteULike: Tag microarray (Site not responding. Last check: 2007-10-11)
		Microarrays reveal distinct gene signatures in the thymus of seropositive and seronegative myasthenia gravis patients and the role of CC chemokine ligand 21 in thymic hyperplasia.
		Segmentation and intensity estimation of microarray images using a gamma-t mixture model.
		MotifScorer: using a compendium of microarrays to identify regulatory motifs.
	www.citeulike.org /tag/microarray (1367 words)

	DNA Microarrays (Genome Chips) (by Leming Shi, PhD)
		Base-pairing (i.e., A-T and G-C for DNA; A-U and G-C for RNA) or hybridization is the underlining principle of DNA microarray.
		Microarrays require specialized robotics and imaging equipment that generally are not commercially available as a complete system.
		DNA microarray, or DNA chips are fabricated by high-speed robotics, generally on glass but sometimes on nylon substrates, for which probes* with known identity are used to determine complementary binding, thus allowing massively parallel gene expression and gene discovery studies.
	www.gene-chips.com (2281 words)

	Anatomy of a Comparative Gene Expression Study
		DNA microarrays are perfectly suited for comparing gene expression in different populations of cells.
		The reporters currently used in comparative hybridization to microarrays are fluorescent dyes (fluors), represented by the red and green circles attached to the cDNA's in the diagram [2].
		One advantage of current microarray technology over its predecessors is that the background is extremely low; consequently, the signal-to-noise ratio of the scanned data can be quite high.
	www.cs.wustl.edu /~jbuhler/research/array (2945 words)

	Affymetrix - GeneChip® Technology
		GeneChip microarrays consist of small DNA fragments (referred to here as probes), chemically synthesized at specific locations on a coated quartz surface.
		By extracting and labeling nucleic acids from experimental samples, and then hybridizing those prepared samples to the array, the amount of label can be monitored at each feature, enabling a wide range of applications on a whole-genome scale — including gene- and exon-level expression analysis, novel transcript discovery, genotyping, and resequencing.
		Microarray analysis can also be combined with chromatin immunoprecipitation to perform genome-wide identification of transcription factors and their respective binding sites.
	www.affymetrix.com /technology/index.affx (145 words)

	Beecher Instruments Tissue Microarray Technology
		Beecher's tissue microarray instruments allow generation of multiple specimen slides that contain hundreds of individual tissues.
		The term tissue array could perhaps be most suitable for arrays containing relatively large specimens (also called tissue macroarrays) whereas the term "tissue microarray" is descriptive of the arrays made with small, 0.6 mm punches.
		For example, reagents and conditions that worked well with regular sections may not be optimal for tissue microarrays simply because tissue arrays contain many different tissues types on the same slide.
	www.beecherinstruments.com (374 words)

	EBI Databases: Microarray Databases
		Microarrays are one of the most important breakthroughs in experimental life sciences that allow snapshots to be made of gene expression levels at a genomic scale.
		The microarray data can be accessed through ArrayExpress which is a public repository for microarray based gene expression data.
		Microarray technology makes use of the sequence resources created by the genome projects efforts to answer the question, what genes are expressed in a particular cell type of an organism, at a particular time, under particular conditions.
	www.ebi.ac.uk /Databases/microarray.html (154 words)

	Microarray Scanner
		Microarray Cleanroom Gloves should be used at all times when handling and scanning microarrays.
		The portion of the microarray selected for scanning is indicated as X and Y coordinates on the left side of the “Scanner Settings” section.
		A microarray was manufactured on a SuperProtein hydrophobic membrane coated substrate using SMP4 pins and a SpotBot®.
	arrayit.com /Products/MicroarrayI/Scanner/scanner.html (2705 words)

	Microarry Faq
		A generic microarray consists of multiple features (spots) of DNA which will be used to determine the levels of mRNA expression in a collection of cells.
		When the microarray is scanned, number of photons in the experimental dye's spectrum is compared to the number of photons in the reference dye's spectrum.
		It can be difficult using microarrays to show that there is a relationship between the absolute intensity of a hybridized probe and the absolute number of target molecules bound.
	www.cse.ucsc.edu /~sugnet/microarray/microarray_FAQ.html (2032 words)

	MICRO ARRAY CORE INFORMATION
		Microarrays are miniature arrays of gene fragments attached to glass slides.
		In the basic sciences, microarray technology will permit researchers to elucidate the genetic pathways that are followed in the development, aging, and pathology of specific cells or tissues of the body.
		In many instances, the use of microarray technology will be a prerequisite for funding for proposed studies in functional genomics.
	cgb.utmem.edu /cores/chiparray.htm (564 words)

	SRC Microarray Facility - Home Page (Site not responding. Last check: 2007-10-11)
		Samples determined by the Microarray Facity to be unsuitable for further analysis may be processed at the discretion of the submitting investigator.
		In “two colour” microarray experiments two samples are labelled with distinct fluorescent dyes, commonly Cy3 and Cy5, and combined prior to hybridization.
		The microarray is scanned to detect the fluorescent signals generated by each of the fluorescent dyes.
	microarray.imb.uq.edu.au /Illumina/faq.html (1978 words)

	protein microarray chips
		Due to the limitations of 3D-gel separation technology, increasing attention is focusing on the development of the second approach, the development of protein microarrays as an alternative and complementary approach (10-12).
		According to the model, antibody microarrays not only would permit simultaneous screening of an analyte panel, but would also be more sensitive and rapid than conventional screening methods.
		Protein microarray biochips extract and retain targets from liquid media and are distinct from microfluidic biochips, which separate and process proteins in a transport medium in situ using microfluidic devices (24,25).
	www.molecularstation.com /protein-microarrays (816 words)

	DecisionSite for Microarray Analysis - Spotfire, Inc.
		Microarray analysis continues to evolve based on new technology platforms, analysis techniques and methods for refining lists of prospective gene targets.
		DecisionSite for Microarray Analysis combines DecisionSite's visual analytics with high-power statistics that are at the leading edge of how scientists want to be able to analyze gene expression and biomarker data.
		DecisionSite for Microarray Analysis is powered by S-PLUSÂ® to provide multiple methods of probe level analysis, normalization, quality assessment and advanced statistics for secondary analysis of both Affymetrix and 2-Channel microarray experiments.
	www.spotfire.com /products/decisionsite_microarray_analysis.cfm (252 words)

	NIEHS Microarray Home Page
		Recent developments in genome sciences have led to the development of DNA microarray technology, a tool of unprecedented power for the study of gene sequence, structure, and expression.
		Using microarrays, the expression of thousands of genes can be monitored simultaneously in two biological samples of interest, and the expression patterns compared.
		The National Institute of Environmental Health Sciences has established a Microarray Group which provides access to this technology for the intramural and extramural community.
	dir.niehs.nih.gov /microarray (120 words)

	The Institute for Genomic Research -- Software Tools
		TIGR Microarray Data Analysis System (MIDAS) is a microarray data quality filtering and normalization tool that allows raw experimental data to be processed through various data normalizations, filters, and transformations via a user-designed analysis pipeline.
		Microarray experiments produce large amounts of data for even the simplest of experiments.
		MADAM (MicroArray DAta Manager) is a java-based application designed to load and retrieve microarray data to and from a database (also supplied with the software).
	www.tigr.org /software/microarray.shtml (283 words)

	Corning® Microarray Surfaces
		Corning offers a choice of three optimized surfaces for creating microarrays as well as two printing solutions and two hybridization solutions further optimized for these surfaces (Table 1).
		All Corning® Microarray Slides are manufactured under the most stringent conditions, cleaned and individually examined for mechanical defects and the presence of dust and glass particles.
		Surfaces are applied in an environmentally controlled, HEPA-filtered ISO Class 5 facility, resulting in coated slides with highly uniform surface properties and low autofluorescence.
	www.corning.com /lifesciences/products__services/surfaces/microarray (140 words)

	The Scientist : The DNA Microarray
		Schena saw in Brown's spotted microarrays a chance to take a far broader look at gene expression than was possible with traditional techniques; Brown saw in Schena's work the kind of biological problem that would prove his technology in action.
		Before long, the do-it-yourself microarray movement had taken hold in many academic labs, where researchers wanted custom slides without the high cost of commercial arrays, and were willing to tinker to get results.
		The Microarray Quality Control (MAQC) Project, for instance, is collecting gene-expression data (both microarray and quantitative RT-PCR) from two human reference RNA samples to establish benchmarks against which new platforms, procedures, or algorithms can be tested.
	www.the-scientist.com /2005/08/29/27/1 (2367 words)

	microarray
		The primary objective of TARP is to develop and disseminate Multi-Tumor Tissue Microarray slides and the related technology to the cancer research investigators.
		survey in 1999-2000 to construct a current portrait of the microarray field that reflects the ongoing dynamic changes in both microarray methodologies and instrumentation and reflects the expanding range of investigators utilizing the technology.
		Key objectives are to provide a guide to the rapidly developing resources and technology in genomics and its impact on biological research, to publish large datasets and extensive results that are not readily accommodated in traditional journals, and to help establish new standards and nomenclature for post-genomic biology.
	ihome.cuhk.edu.hk /~b400559/array.html (5894 words)

	Microarray Platforms
		We are pleased to announce our flagship microarray platform, a "turn-key" solution for both fluorescent and colorimetric protein microarray detection.
		Of course our microarray platforms can be taylored to low-, medium- and high-throughput microarray analysis of nucleic acids, proteins and other biomolecules.
		The Colorimetric Protein Microarray Platform can empower a user perform a variety of micro multiplexed protein microarray assays including microarray based multiplex ELISA assays.
	arrayit.com /Products/Microarray_Platforms (159 words)

	Public microarray database
		Public microarray database is a public repository of microarray data.
		Microarray databases: storage and retrieval of microarray data.
		A public repository for microarray based gene expression data maintained by European Bioinformatics Institute.
	ihome.cuhk.edu.hk /~b400559/arraysoft_public.html (730 words)

	Amazon.com: Microarray Analysis: Books: Mark Schena (Site not responding. Last check: 2007-10-11)
		If you need help with that (and you are a biologist) I would suggest "Data analysis tools for DNA Microarrays" by Sorin Draghici, which is a very good intro book to data analysis and is not too hard on the math side (actually it is as simple as possible but without oversimplifying it).
		The Microarray Analysis book by Dr. Mark Schena does an excellent job of taking the reader thru the multiple technologies and science disciplines required to understand and use the power of the microarray.
		Chapter 13, which talks about the use of microarrays in genetic screening, testing and diagnostics, is one of Schena's greatest accomplishments, in a historic and socio-economic sense.
	www.amazon.com /Microarray-Analysis-Mark-Schena/dp/0471414433 (1440 words)

	Microarray data extraction software: News from Agilent Technologies Europe
		Researchers can use Agilent's new Feature Extraction 7.1 software to extract microarray data in less than 10 minutes per microarray, claimed to be two to three times faster than with independent software packages.
		Previously, these facilities could scan third-party microarrays with the Agilent scanner, but they needed to extract such data with a separate feature extraction tool.
		The new software reduces the time required to extract microarray data by allowing researchers to process any mix of 1x3" slide microarrays scanned on the Agilent microarray scanner.
	www.laboratorytalk.com /news/agi/agi263.html (428 words)

	Microarray Expression Data Analysis References
		Microarray data can be analysed using several approaches (Claverie, 1999).
		The use of standard clustering methods is most appropriate when the microarrays arise from some common source cell type, for example from a common tissue type from animals in some controlled cross.
		Statistical methods are emerging to account for multiple sources of variation when trying to pool information from many microarrays and to identify genes exhibiting significant differential expression between cell types.
	www.stat.wisc.edu /~yandell/statgen/reference/array.html (2812 words)

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