Edited by David Bowtell and Joseph Sambrook Cold Spring Harbor Laboratory Press (2003) 712 pages. ISBN 0-870969-625-7£100/US$135
I have to admit that I felt quite daunted when this book arrived on my desk. Over 700 pages long and weighing more than 2 kilos, it is quite a document. Is there really that much to know about microarrays? It seems there is. Just as the Molecular Cloning Manual(Sambrook et al., 2001) became a 'must have' reference in many labs, DNA Microarrays from Cold Spring Harbor Laboratory Press is set to provide the same type of in-depth information to researchers working in this relatively new field.
Bowtell and Sambrook have assembled a comprehensive collection of protocols, covering many aspects of microarray application. The protocols have been supplied by a number of contributors, many of whom are well-known authorities in the field of microarray technology. The protocols are well written and easy to follow, with extensive introductory sections to each chapter. Information panels distributed throughout the book contain very helpful and detailed background information and explain some of the jargon used in the field.
The editors have chosen to concentrate on the production of cDNA microarrays on glass surfaces and the hybridisation of cDNA and oligonucleotide arrays, both of which are covered in great detail. However,they also include a short chapter on membrane-based spotted arrays, as these seem to be more accessible for many academic labs. A large section of the book covers different methods for isolating RNA from cells and tissues, including preparing polysomal RNA for the enrichment of transcribed genes or amplifying RNA from single cells and small amounts of tissue. The description of target labelling and hybridisation methods is equally detailed, including a step-by-step guide to the tricky task of applying labelled target to glass slides. I found the troubleshooting guide at the end of the chapter particularly useful. It consists of a collection of images illustrating common problems (many of which I had come across myself) with cDNA arrays and oligonucleotide chips and lists potential causes and solutions.
In addition to the more widely used expression analysis of RNA, the manual also contains chapters on genomic analysis using microarrays, including detection of copy number and SNP genotyping and the use of microarrays in conjunction with chromatin immunoprecipitations, albeit only in yeast.
The most interesting chapter for me was the introduction to microarray bioinformatics. The authors cover every step from experimental design, image analysis, normalisation and quality control to cluster analysis and data management. In addition to excellent descriptions of different strategies and potential problems that can arise at different stages of data analysis,Bowtell and Sambrook also include examples of good and bad data, as well as references to available commercial and academic software packages.
One can argue that more and more academic labs are using microarrays from commercial sources rather than embarking on the expensive and time-consuming task of manufacturing their own. And commercial systems would usually come with recommended protocols and technical support. However, even when using an off-the-shelf system, it is very important to understand the potential of the technology and the possible pitfalls. Careful experimental design and statistical scrutiny are essential for generating usable data and can save unnecessary expense. A number of protocols in this manual also cover specialist applications that have been developed in academic labs to investigate particular biological questions. It is invaluable as a guide to how a protocol can be adjusted or optimised and to what problems can occur. Now that microarrays have evolved into a widely used technology, the appearance of this reference is timely. Bowtell and Sambrook have managed to assemble an excellent manual that should be on the shelf of anybody intending to get seriously involved in this powerful and exciting field.
