Next-generation-sequencing

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. 

Finally, if no reference genome is available, one can try to assemble the raw read sequences to regions of enrichment. A combination of Sanger sequencing and next-generation sequencing may be helpful here. 

Applications of Next-Generation Sequencing Technologies to the Study of the Human Microbiome... 

Krupp M, Marquardt JU, Sahin U et al (2012) RNA-Seq atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing. Bioinformatics 28 1184-1185... 

Hackenberg M, Barturen G, Oliver JL (2011) NGSmethDB a database for next-generation sequencing single-cytosine-resolution DNA methylation data. Nucleic Acids Res 39 D75-D79... 

Quail MA, Smith M, Coupland P et al (2012) A tale of three next generation sequencing platforms comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13 341... 

In recent years, new reports suggest that novel next-generation sequencing (NGS) technology has the potential to quickly supersede microarrays in a wide range of applications (80,87). This seems reasonable because in principle NGS can overcome the limitations (1-3) cited above (88). Although it may seem a reasonable evolution, especially when NGS becomes more robust and affordable, the fact is that in 2013 microarrays are still in use and, indeed, microarrays are still the option of choice for many studies where the flexibility of NGS may not be necessary. Whether they will disappear or will stay as one more technique is something that is yet to be seen. 

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