Mar

19

Seq-Array is Here!

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seqarrayl_brochure_coverSeq-ArraySM offers a customized solution to high-throughput genome-wide miRNA discovery and profiling, especially in species with limited or no miRNA sequence information available. This unique combination of the latest deep sequencing technology, advanced bioinformatics, and our innovative µParaflo® custom microarray platform leverages all these technologies to form a comprehensive service package tailored to your specific research needs.

Seq-ArraySM provides an efficient pathway from an initial broad miRNA search to focused biological insights.

Mar

17

microRNA Focused Meeting

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microrna

3/22/10 – 3/24/10  Boston, MA

TOPICS INCLUDE:

microRNA in Cancer
microRNA in Biomarker and Diagnostic Development
microRNA in Therapeutic Development
microRNA in Human Development and Disease
microRNA Pathways and Mechanisms

Don’t miss the Technology Showcase Wed 3/24/10

12:35-12:50 Seq-Array – miRNA Discovery and Profiling Using a Customizable Workflow

Christoph Eicken, Ph.D., Head of Technical Services – Microarrays, LC Sciences
Current miRNA profiling methods rely on the limited sequence information available, hence the focus on a few model species. Seq-Array is a customized solution high-throughput genome-wide miRNA profiling to overcome these limitations. It combines and leverages three technologies: the latest deep sequencing technology, advanced bioinformatics, and μParaflo™ custom microarrays. This talk will present the workflow and a case study with 777 newly discovered miRNAs.

Jan

20

Seminar – MicroRNA Discovery & Profiling

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Presented by – Dr. Christoph Eicken & Dr. Qi Zhu, LC Sciences
12:00 pm Conference Room 2

as part of – Texas Medical Center BioResearch Product Faire

Houston, TX (Marriott Medical Center) – January 16, 2010

Jan

8

Deep Sequencing is Enabling microRNA Study in Any Species

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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.

Jan

8

Plant & Animal Genomes Conference

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p&ag_2010_header

Plant & Animal Genomes XVIII Conference
Jan 9 – 13, 2010 – San Diego, CA     Visit LC Sciences at Booth #509

The Premier and Largest Ag-Genomics Meeting in the World

5 Reasons to Select LC Sciences for your microRNA Profiling Studies in Agriculturally Important Species

  • 100% miRBase Coverage – Version 14.0 – 10883 microRNAs – 115 species
  • 100% Plant Database Coverage – Version 1.0 of the Plant microRNA Database – 8433 microRNAs covering 121 plant species
  • Experience – More than 6000 samples processed since 2005 – Over 130 customer publications
  • Custom Microarrays – Expression profiling of any species
  • Deep Sequencing – Discovery or novel small RNAs in any species

Dec

23

MicroRNA Discovery & Analysis by High-Throughput Sequencing

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For profiling microRNA expression, microarrays have been the standard technology. However, the recent introduction of deep sequencing technology, enabling the simultaneous sequencing of up to millions of DNA or RNA molecules, has provided another option for profiling microRNAs. Deep sequencing utilizes massively parallel sequencing, generating millions of small RNA sequence reads from a given sample. Profiling of microRNAs by deep sequencing measures absolute abundance and allows for the discovery of novel microRNAs that have eluded previous cloning and standard sequencing efforts.[1]

There are many web-based tools available for handling microRNA deep sequencing data:

mirTools – a web server for microRNA profiling and discovery based on high-throughput sequencing data.

miRDeep – Discovering known and novel miRNAs from deep sequencing data

deepBase – a database for deeply annotating and mining deep sequencing data

miRExpress – Analyzing high-throughput sequencing data for profiling microRNA expression

miRanalyzer – A microRNA detection and analysis tool for next-generation sequencing experiments

CID-miRNA – Computational Identification of microRNA

miRCat – miRNA Categorizer

  1. Creighton CJ, Reid JG, Gunaratne PH. (2009) Expression profiling of microRNAs by deep sequencing. Brief Bioinform 10(5), 490-97. [abstract]