Jun
3
Wednesday June 02, 2010 – by Jeffrey M. Perkel
If you want an inkling of how hot the microRNA field is, just look at miRBase.
In April, the University of Manchester’s miRNA database updated to version 15 with the addition of some 4,000 new sequences, including 300 or so new human miRNAs. The database now contains 14,197 records from some 130-plus organisms and viruses, up from 10,883 in September 2009’s version 14.
“It was unexpected that there would suddenly be such a sudden jump in known human miRNAs,” says Christoph Eicken, head of microarray technical services at LC Sciences, a microRNA service provider. “It was almost stable for one to one-and-a-half years, which is a long time in the microRNA field.” (read more… )
May
25
miRBase Updates Keep Coming
Filed Under Technical Article | Leave a Comment
After couple of years with nominal growth in the number of database entries, miRBase growth has turned to exponential over the last four to five updates. The latest deep sequencing technologies have palyed a key role in the discovery of new miRNAs. A full 30% increase in the number of entries and a 48% increase in the number of experimentally verified functional mature sequences in the single most recent miRBase update gives little doubt that there are many more as yet undiscovered miRNAs.
Apr
26
miRBase Version 15.0 Arrives
Filed Under miRNA News | Leave a Comment
April 26th, 2010 – miRBase microRNA Sequence Database Updated to Release 15.0
The latest version (15.0) of the miRBase sequence database for known miRNAs was released today.
miRBase 15 is freely available at http://www.mirbase.org/. You can find a quick summary for the new release at ftp://mirbase.org/pub/mirbase/CURRENT/README.
Highlights of the new release:
- Release 15 represents a major update to the database increasing the number of mature miRNA sequences by a full 48% over release 14.0.
- This latest release features a total of 15,632 mature miRNA sequences.
- The number of verified microRNAs has increased from 10,883 to 14,197 hairpin precursor miRNAs.
- 18 new species have been added bringing the total to 133 species.
- Many sequences have been updated or revised.
- New sequences have been added to important model species – Human (219), Mouse (11), Rat (1), Drosophila (218), Nematode sp. (311), Arabidopsis (9).
- New sequences have been added to important agricultural species – Cow (50), Pig (98), Silkworm (396), Peanut (23), Cotton sp.(24), Orange sp.(25), Rice (33), Sorghum (8), Corn (61).
- A total of 526 new plant sequences and 53 new virus sequences
- Other important new species include – Zebra Finch, Japanese Killifish, Yellow Fever & West Nile Mosquitos, Castor Oil Plant
This updated probe content is currently available on all of our standard or custom microRNA microarrays.
Jan
8
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
Filed Under Events | Leave a Comment
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
15
LC 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 |
Dec
2
UNLOCKING THE SECRETS OF microRNA
Filed Under Review Article | Leave a Comment
By 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)
Oct
16
The most current probe content available delivering the most complete microRNA expression profile of your samples
miRBase Sequence Database Content – Release 14.0 – September 2009
The miRBase database provides a searchable online repository for published microRNA sequences and associated annotation.
miRBase 14 Probe content is available now at LC Sciences!
- 10883 entries representing hairpin precursor miRNAs
- 10581 mature miRNA products
- Verified miRNAs for 115 species
Plant MicroRNA Database (PMRD) Content – Release 1 – October 2009
The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated by the database organizers. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser.
PMRD Probe content is available now at LC Sciences!
- 8433 miRNAs
- 121 plant species
- Includes model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc in this first edition of the database.
Customer Defined Content
These are not spotted arrays. Each microarray is custom synthesized when ordered. That means we can add custom content to any of our standard microRNA microarrays with no delay in data delivery. There is no charge for addition of up to 100 of your custom sequences. Furthermore, the entire contents of the arrays are completely customizable according to the customer’s design at a very affordable price. Customers may add up to 3,918 sequences of their own selection for various applications.
- Screen for new microRNAs by adding predicted mature microRNA sequences or performing tiling along a certain section of genome.
- Combine microRNA sequences of different species to identify cross-species conservations.
- Add controls of customer’s choice for the detection of customer-added spiking RNA sequences and use as customer-selected internal controls.
- Add probes for the detection of siRNAs and/or other small non-coding RNAs.
Oct
15
Press Release – LC Sciences First miRNA Microarray Service Provider to Offer Plant MicroRNA Database (PMRD) Probe Content
Filed Under Press Release | Leave a Comment
Houston, TX – October 15, 2009 – Taking full advantage of its flexible µParaflo® Biochip Technology, Houston based LC Sciences today announced immediate availability of probe content from the newly created Plant MicroRNA Database (PMRD) for their microRNA (miRNA) microarray customers. This announcement comes immediately following a publication in Nucleic Acids Research introducing the public database1. The PMRD integrates available plant miRNA data deposited in other public databases, gleaned from the recent literature, and data generated by the database organizers. It is freely available at http://bioinformatics.cau.edu.cn/PMRD. Read more
Sep
21
microRNA Microarray Service
Filed Under Information | Leave a Comment
LC Sciences provides a genome-wide microRNA (miRNA) expression profiling service using µParaflo®technology and proprietary probe design, which enable highly sensitive and specific direct detection of miRNAs. We have standard arrays for mature miRNA of all species available in the latest version of the miRBase database (Release 14.0). Our service is comprehensive and includes small RNA enrichment from your total RNA sample, single or dual color labeling, hybridization, image data processing and in-depth data analysis. Two-three weeks after receiving your total RNA samples, we send you the analyzed data, representative and original images of the array, and raw data. We offer additional products and services including arrays containing miRNA*, walk/tiling arrays, custom arrays (first 100 probes free of charge), and in-depth analysis for multiple data sets. The in-depth data analysis may include multi-array normalization, t-test, ANOVA, False Discovery Rate calculator, and/or clustering analysis.
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LC Sciences in the News- microRNA News
- Scientists on path to new treatments for Parkinson's July 30, 2010
- Macro Roles of microRNAs in Rett Syndrome? - rettsyndrome.org July 29, 2010
- Rosetta Genomics Names Genekor S.A Exclusive Distributor for Three ... July 29, 2010
- Alimta Mesothelioma | Rosetta Genomics Names Genekor S.A Exclusive ... July 29, 2010
- Live Cell Monitoring of hiPSC Generation and Differentiation Using ... July 29, 2010
- Thinking In Genes » Cancer Cells Show Rewired, Fragmented microRNA ... July 29, 2010
