May 25, 2007
Sanger miRBase microRNA Sequence Database Updated to Release 9.2
The study of microRNA (miRNA) is growing rapidly as researchers discover new miRNAs and uncover the importance of these small regulatory elements linked to a wide range of biological functions. As new miRNAs are discovered and experimentally verified, the data are deposited to the public database, miRBase. The miRBase sequence database1 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. http://microrna.sanger.ac.uk/.
The Sanger Institute released the latest version (9.2) of their miRBase sequence database for known miRNAs today (http://microrna.sanger.ac.uk/sequences/) This is the second update in 2007 and there have been 21 updates since the initial release in late 2002. Updates occur whenever a significant number of experimentally verified sequences are added to the database. For this update, 135 new hairpin sequences have been added, with 156 novel mature miRNA products including the first entries for Chlamydomonas, and HIV, HSV, RRV and MDV-2 viruses. Release 9.2 of the database contains 4584 entries representing hairpin precursor miRNAs, expressing 4430 mature miRNA products, in primates, rodents, birds, fish, worms, flies, plants and viruses.
The continued updating of the database can be problematic for researchers making use of pre-spotted glass slide microarrays for genome-wide miRNA expression profiling of miRNA transcripts as the probe content of the arrays immediately goes out of date whenever a new miRBase version is released. Existing spotted microarrays containing miRBase version as recent as 8.0 content are missing 18% of Human sequences, 30% of Mouse sequences, and 28% of plant sequences.
LC Sciences miRNA detection microarrays make use of a microfluidics on-chip synthesis platform, termed µParaflo®,versus a traditional spotted array based on pre-synthesized oligonucleotides. An on-chip synthesis platform solves the issue of out of date microarrays because made-to-order microarrays can be produced, delivering the most up-to-date research tools to researchers.
In addition to providing much more uniform and reproducible features than a spotted array, on-chip synthesis also permits the total customization of content on each individual microarray opening up additional applications such as the discovery of new miRNAs and other small non-coding RNAs.
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.
About LC Sciences
– LC Sciences offers specialty microarray services for nucleic acid/protein profiling and functional analysis, biomarker-discovery, and novel drug screening. Our array service products are based on the µParaflo® platform technologies that encompass advanced digital chemical synthesis, pico-liter scale biochemical assays, and microfluidic reaction devices containing high density individual 3D chambers.
More information about LC Sciences is available at http://www.lcsciences.com.
- Griffiths-Jones S, Grocock R, van Dongen S, Bateman A, Enright A. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34(Database issue), D140–D144. [abstract]