miRNA array

Houston, TX (PRWEB)   –  A week after the latest miRBase update LC Sciences announced use of miRBase Version 17 probe content as new default for their miRNA microarrays. Arrays for all species included in the latest miRBase 17 release are available. Looking at the most common species: while the changes in probe content for rat are negligible, additions to the list of human miRNAs are substantial: 521 new unique human mature miRNA sequences were added (see our post miRBase Version 17 Update Released).

The full press release: http://www.prweb.com/releases/2011/5/prweb8404968.htm


Industry Press

by Chris on January 18, 2011

in News

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The study of microRNA (miRNA) is growing rapidly as researchers discover new miRNA sequences and uncover the importance of these small regulatory elements linked to a wide range of biological functions. The miRBase sequence database (1) is the primary public repository for newly discovered miRNAs and the number of miRBase entries has grown rapidly from a mere 218 in 2002 to almost 10,000 in the latest version, suggesting the existence of many more miRNAs yet to be discovered.
Contributing to the rapid rate of new discoveries is the development of several new advanced technologies such as high-throughput sequencing and custom microfluidic arrays. The increasing availability of these technologies makes the discovery of new sequences in lesser understood organisms now routinely possible. A straightforward process of discovery, confirmation, and validation is commonly employed:

Deep Sequencing – Discovery —> Microarray – Confirmation —> QPCR – Validation

In a recent study, many novel miRNAs were experimentally verified in the silkworm Bombyx mori, an industrially important insect, by researchers at the Chinese Academy of Sciences, Shanghai using this three step process (2).
Deep sequencing (Illumina GA sequencing-by-synthesis platform) revealed a total of 95,184 non-redundant tags that matched to the silkworm genome, and computational pipeline analysis identified 3,750 potential miRNA precursors. Probes for these candidate miRNAs in situ synthesized on a custom microfluidic microarray (3) (LC Sciences µParaflo® microfluidic platform) confirmed 354 of the candidates. Further microarray experiments profiled the expression level of these miRNAs at the various developmental stages of the silkworm (egg, larvae, pupa, and adult). QPCR (GenePharma, molecular beacon platform) validated several highly differentially expressed miRNAs, thought to be important for embryogenesis and metamorphosis.
It is well known that miRNAs are important players for regulation of cellular activities. Therefore, the establishment of miRNAs in traditional industrial or agriculturally important species such as the silkworm should lead to better understanding of the fundamentals of their growth, maturation, and disease-resistance.

1. The miRBase sequence database is a comprehensive database of miRNA sequence data, annotation, and predicted gene targets and is the primary public repository for these data. miRBase also provides a gene-naming service for assigning official miRNA names to novel miRNAs before they are published. It is freely available to all at http://microrna.sanger.ac.uk/.

2. Zhang Y, Zhou X, Ge X, Jiang J, Li M, Jia S, Yang X, Kan Y, Miao X, Zhao G, Li F, Huang Y. (2009) Insect-Specific microRNA Involved in the Development of the Silkworm Bombyx mori. PLoS ONE 4(3), e4677.

3. More information about LC Sciences miRNA discovery and analysis services is available at: http://www.lcsciences.com/mirna_discovery.html.

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March 2012 Update: The latest pig specific array is based on miRBase version 18 and features all 255 unique mature miRNAs.  You can download the full sequence list here: pig miRNA array probe content.

Houston, TX, – LC Sciences LLC., the worlds first miRNA array service provider, today anounced a new miRNA array layout focusing on researchers using pig animal models. With the recent update of the miRNA data base miRBase to version 12.0 the number of known and validated miRNA sequences for pig (Sus scrofa) doubled. Currently miRBase 12.0 lists 66 precurcor sequences which result in 64 mature pig miRNAs.

Of these 64 sequences 9 are unique for pig, 32 are identical to human, 16 to gorilla, 2 to pygmy chimpanzee, 2 to rat, 2 to platypus, and 1 is identical to common chimpanzee.

Depending on the goal of the experiment you can either chose a chip design with all 64 mature pig miRNA sequences (pig miRNA array chip) or based on the sequence conservation [click to continue…]

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