One of the limitations of microarray expression profiling is the requirement of prior sequence information, to be used for probe design. Until recently, this has been limited mostly to that found in public databases (i.e. miRBase), these data having been gathered mainly through a combination of bioinformatics and extensive cloning experiments. In contrast, deep sequencing is not dependent on any prior sequence information, instead providing information about all RNA species in the sample and allowing for discovery of novel microRNAs or other types of small RNAs. Thus providing an excellent tool for those studying species where limited sequence information is currently available. Additionally, new sequence information provided by deep sequencing can be used to design microarray probe content for future large scale expression studies.
Deep sequencing identifies novel and conserved microRNAs in peanut (Arachis hypogaea L.).
Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, Li AQ, Li MJ, Li CS, Zhang BH, Wang XJ.
BMC Plant Biol. 2010 Jan 5;10(1):3.
Genome-wide identification of Schistosoma japonicum microRNAs using a deep-sequencing approach.
Huang J, Hao P, Chen H, Hu W, Yan Q, Liu F, Han ZG.
PLoS One. 2009 Dec 8;4(12):e8206.
Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv.
Wei B, Cai T, Zhang R, Li A, Huo N, Li S, Gu YQ, Vogel J, Jia J, Qi Y, Mao L.
Funct Integr Genomics. 2009 Nov;9(4):499-511.
Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis.
Armisen J, Gilchrist MJ, Wilczynska A, Standart N, Miska EA.
Genome Res. 2009 Oct;19(10):1766-75.
Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response.
Zhang J, Xu Y, Huan Q, Chong K.
BMC Genomics. 2009 Sep 23;10:449.
Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules.
Lelandais-Brière C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C, Gouzy J, Crespi M.
Plant Cell. 2009 Sep;21(9):2780-96.
High throughput sequencing of microRNAs in chicken somites.
Rathjen T, Pais H, Sweetman D, Moulton V, Munsterberg A, Dalmay T.
FEBS Lett. 2009 May 6;583(9):1422-6.
Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening.
Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, Moulton V, Dalmay T.
Genome Res. 2008 Oct;18(10):1602-9.
Identification of novel and candidate miRNAs in rice by high throughput sequencing.
Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK.
BMC Plant Biol. 2008 Feb 29;8:25.