Dna Microarrays And Related Genomics Techniques

Considered highly exotic tools as recently as the late 1990s, microarrays are now ubiquitous in biological research. Traditional statistical approaches to design and analysis were not developed to handle the high-dimensional, small sample problems posed by microarrays. In just a few short years the number of statistical papers providing approaches

DNA Microarrays: Methods Express covers the very latest in DNA microarray technology, with a clear focus on how these techniques can be used in the lab to gain the very best results. The authors are from some of the leading laboratories in the field and write with real authority on the latest methodology. Every chapter provides detailed step-by-step protocols with valuable hints and tips for success, as well as giving typical experimental results and selected literature citations. This book is a 'must have' manual for researchers in all fields of biology, medicine and agriculture.

Modern DNA microarray technologies have evolved over the past 25 years to the point where it is now possible to take many million measurements from a single experiment. These two volumes, Parts A & B in the Methods in Enzymology series provide methods that will shepard any molecular biologist through the process of planning, performing, and publishing microarray results. Part A starts with an overview of a number of microarray platforms, both commercial and academically produced and includes wet bench protocols for performing traditional expression analysis and derivative techniques such as detection of transcription factor occupancy and chromatin status. Wet-bench protocols and troubleshooting techniques continue into Part B. These techniques are well rooted in traditional molecular biology and while they require traditional care, a researcher that can reproducibly generate beautiful Northern or Southern blots should have no difficulty generating beautiful array hybridizations. Data management is a more recent problem for most biologists. The bulk of Part B provides a range of techniques for data handling. This includes critical issues, from normalization within and between arrays, to uploading your results to the public repositories for array data, and how to integrate data from multiple sources. There are chapters in Part B for both the debutant and the expert bioinformatician. Provides an overview of platforms Includes experimental design and wet bench protocols Presents statistical and data analysis methods, array databases, data visualization and meta-analysis

Using chips composed of thousands of spots, each with the capability of holding DNA molecules corresponding to a given gene, DNA microarray technology has enabled researchers to measure simultaneously gene expression across the genome. As with other large-scale genomics approaches, microarray technologies are broadly applicable across disciplines of life and biomedical sciences, but remain daunting to many researchers. This guide is designed to demystify the technology and inform more biologists about this critically important experimental technique. Cohesive overview of the technology and available platforms, followed by detailed discussion of experimental design and analysis of microarray experiments Up-to-date description of normalization methods and current methods for sample amplification and labeling Deep focus on oligonucleotide design, printing, labeling and hybridization, data acquisition, normalization, and meta-analysis Additional uses of microarray technology such as ChIP (chromatin immunoprecipitation) with hybridization to DNA arrays, microarray-based comparative genomic hybridization (CGH), and cell and tissue arrays

Massive data acquisition technologies, such as genome sequencing, high-throughput drug screening, and DNA arrays are in the process of revolutionizing biology and medicine. Using the mRNA of a given cell, at a given time, under a given set of conditions, DNA microarrays can provide a snapshot of the level of expression of all the genes in the cell. Such snapshots can be used to study fundamental biological phenomena such as development or evolution, to determine the function of new genes, to infer the role individual genes or groups of genes may play in diseases, and to monitor the effect of drugs and other compounds on gene expression. Originally published in 2002, this inter-disciplinary introduction to DNA arrays will be of value to anyone with an a interest in this powerful technology.

Microarray technology provides a highly sensitive and precise te- nique for obtaining information from biological samples, with the added advantage that it can handle a large number of samples simultaneously that may be analyzed rapidly. Researchers are applying microarray technology to understand gene expression, mutation analysis, and the sequencing of genes. Although this technology has been experimental, and thus has been through feasibility studies, it has just recently entered into widespread use for advanced research. The purpose of DNA Arrays: Methods and Protocols is to provide instruction in designing and constructing DNA arrays, as well as hybridizing them with biological samples for analysis. An additional purpose is to p- vide the reader with a broad description of DNA-based array technology and its potential applications. This volume also covers the history of DNA arrays—from their conception to their ready off-the-shelf availability—for readers who are new to array technology as well as those who are well versed in this field. Stepwise, detailed experimental procedures are described for constructing DNA arrays, including the choice of solid support, attachment methods, and the general conditions for hybridization. With microarray technology, ordered arrays of oligonucleotides or other DNA sequences are attached or printed to the solid support using au- mated methods for array synthesis. Probe sequences are selected in such a way that they have the appropriate sequence length, site of mutation, and T .

In the early years of microarray technology, efforts were directed mainly at profiling expressed genes, while recently the microarray platform has been adapted into diverse applications directed toward the investigation of the physical genome. In Microarray Analysis of the Physical Genome: Methods and Protocols, experts in the field cover DNA microarray applications for the detection and characterization of genomic DNA-associated copy number alteration, loss of heterozygosity (LOH), cytosine methylation, protein binding sites, regulatory elements, and replication timing, with an emphasis on higher eukaryote (animal) and cancer genomes. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include a brief introduction to their respective subjects, lists of the necessary materials and reagents, step-by-step protocols, and time-saving notes on troubleshooting and avoiding known pitfalls. Authoritative and easy-to-use, Microarray Analysis of the Physical Genome: Methods and Protocols is of great value to the molecular biologist or computational biologist interested in understanding the principles of these analyses or in planning future experiments using microarrays to characterize the physical genome.