The Affymetrix Gene Chip

Affymetrix uses a method that directly synthesizes an oligonucleotide sequence on a silicon slide/chip using a technique known as light-directed combinatorial chemical synthesis [11]. Affymetrix gene chips are more commonly used for eukaryotic research as they can achieve higher spot densities, allowing the incorporation of more probes to study the many more genes and splice variants that occur. Microbial researchers do not require as many genes or splice variants on an array so can use the more easily obtainable spotted arrays. The latest human oligonucleotide genechip by Affymetrix can incorporate up to 47000 probes [12], whereas the Mycobacterium tuberculosis whole-genome spotted array contains just 4410 probes [13]. However, it is worth noting that Affymetrix have just released a new Escherichia coli gene chip that contains 10 000 probes covering four common environmental and laboratory strains on the same array, thereby allowing micro-biologists to benefit from the higher density arrays.

In this chapter we will focus on spotted microarrays (PCR or long-oligo) as they are the most common platform for the analysis of microbial expression profiles. For more information on Affymetrix Gene Chip technology and their applications visit the company website [12] or see Ref. [11].

24 | 2 Transcriptome Analysis: Towards a Comprehensive Understanding of Global Transcription Activity 2.3.3

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