Monitoring the Trascriptome

Monitoring the Trascriptome

Stilianos Arhondakis (Biomedical Research Foundation of the Academy of Athens, Greece), Georgia Tsiliki (Biomedical Research Foundation of the Academy of Athens, Greece) and Sophia Kossida (Biomedical Research Foundation of the Academy of Athens, Greece)
DOI: 10.4018/978-1-60960-483-7.ch006
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Abstract

The technologies monitoring the transcriptome are under a continuous status of development and implementation, producing high amounts of expression data which require reliable and well structured databases. This chapter provides a general overview and a reliable guide of these technologies, as developed from the early ‘90s until today, and of the most important available expression databases. The first part aims at introducing to the reader the fundamental functional aspects of these technologies, which are under a continuous development in order to obtain a more accurate description of the transcriptome. The second part offers the necessary information to those who are interested in further exploiting expression data in their research.
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Introduction: From The Genome To The Transcriptome

After the complete sequencing of the human genome, and that of other organisms (Venter et al., 2001; Lander et al., 2001, 2002) there was an unavoidable increase of genomic information which allowed the development of different technologies, in order to achieve a complete use of this large information, and a faithful identification of the transcriptome, i.e. the combined variability of all transcripts produced by the genome. Since the official announcement from the International Human Genome Sequence Consortium (IHGSC) in 2001 that there are only 32,000 genes in the human genome, new sequences are still being added into the chromosome maps and their relative locations are being adjusted (Kidd et al., 2008; The ENCODE project Consortium, 2007; Jobling et al., 2004). Furthermore, the overall gene fragmentation has rapidly decreased the number of genes originally identified. For example, the number of genes located by Ensembl genome annotation system (http://www.illumina.com). The second category, named hybridization-based techniques, is mainly referred to the microarray technology. Microarray technology can be classified based on different attributes such as, commercial or custom made arrays, probes’ length arrays, spotted or in situ synthesized, glass or membrane based, one- or two-colour arrays. Here, arrays will be classified in two major categories, the 3’-based arrays and the recently developed exon arrays. The former arrays will be examined in this chapter, given their probes’ length, particularly, we can distinguish three principal types: spotted cDNA arrays (Schena et al., 1995), long-oligonucleotide arrays (50-80 mer: Blanchart et al., 1999, Hughes et al., 2001), and short-oligonucleotides (25-30 mer: Lockhart et al., 1996).

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