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]

Dec

22

Happy Holidays from LC Sciences

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Dec

21

LC Sciences’ Customers Publish in Science Magazine

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One of the highlights in the Dec 11th issue of Science Magazine was a paper published by LC Sciences’ customers Andrew H. Williams and Eric N. Olsen from the Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas. 

Williams AH, Valdez G, Moresi V, Qi X, McAnally J, Elliott JL, Bassel-Duby R, Sanes JR, Olson EN.  (2009) MicroRNA-206 delays ALS progression and promotes regeneration of neuromuscular synapses in mice.  Science 326(5959), 1549-54 [abstract]

This groundbreaking work identified miR-206 as a modifier of Amyotrophic lateral sclerosis (ALS)  pathogenesis  and provides a new perspective on the mechanisms underlying this neurodegenerative disease.  More broadly, the findings provide insight into the molecular basis of neuromuscular junction plasticity and also into determinants of rates of disease progression in motor neuron disease.

Additionally, a perspective on these important findings was published in the same Dec 11th issue of Science, by Robert H. Brown of the UMASS Medical School.

Brown, RH. (2009) A Reinnervating  MicroRNA. Science 326(5959), 1494-95. [abstract]

Dec

17

microRNAs Inform Cancer Research

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Alterations in the Expression of miRNA Genes Contribute to Pathogenesis on Broad Basis

Elizabeth Lipp

MicroRNA (miRNA) has a significant role in controlling developmental and cancer processes like cell proliferation, differentiation, cell cycle, apoptosis, and metastasis. This ubiquitousness and their recently revealed role as key regulators of gene expression during development has boosted their use as agents in the fight against cancer. It’s a hot topic “and it’s getting hotter,” said Frank Slack, associate professor of molecular, cellular, and developmental biology at Yale University … (read more)

Dec

15

Supplier Comparison – microRNA Microarray Content

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mirbase_supplier_comparisonLC Sciences’ microRNA microarrays cover all species for which sequence data are available in the miRBase Sequence Database and the Plant MicroRNA Database.  Other suppliers are not covering miRs from the Plant MicroRNA database and their arrays covering the miRBase are somewhat out of date.  Since miRBase is being continually updated, a flexible microarray platform is necessary to keep current with the latest miRBase version (14.0 released in September of 2009).

Supplier miRBase             Version           Coverage Total        miRBase     Entries miRBase           Release Date
LC Sciences 14.0 10883 Sept 2009
Agilent 12.0 8619 Sept 2008
Affymetrix 11.0 6396 April 2008
Exiqon 11.0 6396 April 2008
Invitrogen 9.0 4361 Oct 2006

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Dec

10

Featured Customer Publication – Expression Profile of MicroRNAs in Young Stroke Patients

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Plos-One---2009---ExpressioResearchers at the University of Malaya, Kuala Lumpur and the National University of Singapore demonstrate that peripheral blood miRNAs and their profiles can be developed as biomarkers in diagnosis and prognosis of cerebral ischaemic stroke. MicroRNA microarrays were utilized to detect dysregulated miRNAs even after several months from the onset of stroke in what is usually regarded as neurologically stable patients.

Tan KS, Armugam A, Sepramaniam S, Lim KY, Setyowati KD, Wang CW, Jeyaseelan K.  (2009) Expression profile of MicroRNAs in young stroke patients. PLoS One 4(11), e7689.  [article]

Dec

2

UNLOCKING THE SECRETS OF microRNA

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Science-Nov-2009-Life-ScienBy Anne Harding
Microarrays are a vital tool in research on microRNAs, the tiny noncoding stretches of genetic material that regulate messenger RNA. They can’t be beat for reading the microRNA “fingerprints” unique to disease states. But keeping up with this super hot field is a challenge for commercial microarray makers, and competition is fierce. (read more)