Transcriptomics applications

K. F. (2005) An olignucleotide microarray for transcriptome analysis of Schistoma mansoni and its application/use to investigate gender-associated gene expression. Molecular and Biochemical Parasitology 141, 1-13. 

As a general trend, de novo transcriptome assembly studies reveal greater transcriptome complexity than expected and provide a blueprint for further studies. De novo transcriptome assembly of black pepper is a representative example of the application of SOLiD RNA-Seq technology in nonmodel species (29). In that study, 71 million short reads, representing a sequencing coverage per base (depth) of 62X, were used to assemble a total of 22,363 transcripts in root samples. Transcript and functional annotation was performed based on the sequence homology with other species. 

As it has been discussed in this chapter, transcriptomic profiling of food crops is a hot application for RNA-Seq technologies. Nevertheless, the applicability of RNA-Seq in Food Science and Nutrition is still in its infancy and it is not fully exploited yet. In the near future, it can be anticipated that many relevant topics in Food Science will benefit from RNA-Seq techniques. For instance in Nutrigenomics studies, it can be expected that RNA-Seq studies will improve our limited understanding of the roles of nutritional compounds... 

Foodomics involves the use of multiple tools to deal with its different applications. Thus, the use of omics tools (as e.g., transcriptomics, proteomics, or metabolomics) is a must in this new discipline. Although a detailed description on these tools is out of the scope of this chapter, some fundamental concepts on different omics techniques are provided below. 

Metabonomics has received considerable attention in the toxicological community, but based on published literature, metabonomic applications do not appear to be as widely used as transcriptomics (toxicogenomics). However, this is not a reflection on the utility of the approach, but more likely a consequence of the need to have a complex infrastructure, particularly with respect to data analysis and interpretation in order to carry out the technology. 

Coen M, Ruepp SU, Lindon JC, Nicholson JK, Pognan F, Lenz EM, Wilson ID. Integrated application of transcriptomics and metabonomics yields new... 

To use metabolic footprinting as a technique for high-throughput applications, benchmark spectra databases with identified peaks are required so that peak patterns obtained from MS or NMR analysis can be rapidly translated into relevant biological information. Common experimental procedures should, ideally, also be established for metabolite analysis [80] such as those existing in proteomics or transcriptomics. Nevertheless, the scientific community has only recently attempted to achieve these tasks. Several databases for identification of metabolomics signals by MS are now available, for instance, BIGG [81], BioCyc [82], MSlib [83], NIST [84], Metlin [85], and HMDB [86] databases. For a more comprehensive list of resources we refer to the review of Werner and coworkers [68]. 

Transcriptome Improvement of galactose uptake Brewing, baking application [343]... 

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