Dear Mangesh,

SOLiD (Sequencing by Oligonucleotide Ligation and Detection) is a next-generation DNA sequencing technology developed by Life Technologies. This next generation technology generates hundreds of millions to billions of small sequence reads at one time.

Naturally the technology will be used to sequence DNA, but because of the high parallel nature of all next generation technologies they also have applications in transcriptomics and epigenomics.

Microarrays have been the mainstay of the transcriptomics world for the last ten years and array based technology has branched out to other areas. But they are limited in that only information can be obtained for probes that are on the chip.  Any organism's entire transcriptome could be potentially sequenced in one run (for very small bacterial genomes) and not only would the identification of each transcript be available but expression profiling is possible as quantitative reads can also be achieved. Chromatin immunoprecipitation (ChIP) is a method for determining transcription factor binding sites and DNA-protein interactions. It has in the past been combined with array technology (ChIP-chip) with some success. Next gen sequencing can also be applied in this area. Methylation immunoprecipitation (MeDIP) can also be performed and also on arrays. The ability to learn more about methylation and TF binding sites on a genome wide scale is a valuable resource and could teach us much about disease and molecular biology in general.

References & links:

Valouev A, Ichikawa J, Tonthat T, et al. (July 2008). "A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning". Genome Research. 18 (7): 1051–63. doi:10.1101/gr.076463.108. PMC 2493394free to read. PMID 18477713.

Cloonan N, Forrest AR, Kolle G, et al. (July 2008). "Stem cell transcriptome profiling via massive-scale mRNA sequencing". Nature Methods. 5 (7): 613–9. doi:10.1038/nmeth.1223. PMID 18516046.

Tang F, Barbacioru C, Wang Y, et al. (May 2009). "mRNA-Seq whole-transcriptome analysis of a single cell". Nature Methods. 6 (5): 377–82. doi:10.1038/nmeth.1315. PMID 19349980.

 McKernan KJ, Peckham HE, Costa GL, et al. (September 2009). "Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding". Genome Research. 19 (9): 1527–41. doi:10.1101/gr.091868.109. PMC 2752135free to read. PMID 19546169.

Yu-Feng Huang; Sheng-Chung Chen; Yih-Shien Chiang & Tzu-Han Chen (2012). "Palindromic sequence impedes sequencing-by-ligation mechanism". BMC systems biology. 6 Suppl 2: S10. doi:10.1186/1752-0509-6-S2-S10. PMID 23281822.

https://en.wikipedia.org/wiki/ABI_Solid_Sequencing

https://en.wikipedia.org/wiki/2_base_encoding

http://www.nature.com/nrg/journal/v17/n6/fig_tab/nrg.2016.49_F2.html

http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=1308

Hoping this will be helpful,

Rafik