Next-generation sequencing analysis

Different variations of ChIP experiments are now rapidly evolving. This is mainly due to the rapid progress in the field of microarrays and next-generation sequencing that can be used for the analysis of the immunopreciptated DNA. We discuss here the most important variations of the standard ChIP protocol with a focus on ChIP-on-chip and ChIP-sequencing technologies. 

Xiao, M., et al, Transcriptome analysis based on next-generation sequencing of nonmodel plants producing specialized metabolites of biotechnological interest. Journal of Biotechnology, 2013. 166(3) p. 122-134. 

Nam, Y. D., Lee, S. Y., Lim, S. I. (2012). Microbial community analysis of Korean soybean pastes by next-generation sequencing. International Journal of Food Microbiology, 155, 36-42. 

In summary, we presented a detailed overview of microarray studies. We introduced the mechanism, the associated statistical analysis, and the potential substitution for microarray-next generation sequencing. Several examples of microarray studies to identify biomarkers are also presented. We hope this chapter can serve as a guide for beginners in the field of biomarker identification and drug discovery. 

Fig. 5 Taxonomic profiles frran the superkingdom bacteria of different biogas mitaobial communities based on analysis of metagenome sequcmce reads created by next-generation sequencing techniques. Phylogenetic class is indicated. The authms ctnnpared eithCT 16S-rDNA sequences or environmental gene tags (EGTs) with different referoice data sets, e.g., Ribosomal Database Project Classifier or ARB Database (modified aftta- Wirth et al. 2012 Krbber et al. 2009 Krause et al. 2008)...

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