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The domestic pig is of enormous agricultural significance and valuable models for many human diseases. Information concerning the pig microRNAome (miRNAome) has been long overdue and elucidation of this information will permit an atlas of microRNA (miRNA) regulation functions and networks to be constructed. Here we performed a comprehensive search for porcine miRNAs on ten small RNA sequencing libraries prepared from a mixture of tissues obtained during the entire pig lifetime, from the fetal period through adulthood. The sequencing results were analyzed using mammalian miRNAs, the precursor hairpins (pre-miRNAs) and the first release of the high-coverage porcine genome assembly (Sscrofa9, April 2009) and the available expressed sequence tag (EST) sequences. Read more

Please nte that the sample submission form for microRNA Microarray Service has been updated due to the update of miRBase to version 15.  If you have a previous version of the form saved locally, please replace with this new form.  Click the link below or visit www.lcsciences.com to download the form.

Thank You

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… )

Seq-Array^SM provides an efficient pathway from an initial broad search to focused biological insights.

Seq-Array^SM offers a customized solution to high-throughput genome-wide microRNA discovery and profiling, especially in species with limited or no microRNA 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.

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.

Cancer Research Tech Guide – From Genome Technology

Download Your Copy Here

Letter from the Editor

Cancer is tricky. But equipped with a vast arsenal of tools, investigators are on the offensive against the duplicitous disease. Still, even the most robust cancer research techniques come with their own sets of challenges. From sequencing to interrogating microRNAs, this technical guide aims to give you a fresh look at what a number of cancer researchers are doing to improve their day-to-day results at the bench in an effort to supply optimal diagnostics and care at the bedside.

The following pages contain tips for genome sequence analysis, optimizing qRT-PCR procedures for the investigation of miRNAs, the merits of various methylation interrogation techniques, isolating RNA from paraffin-embedded tissues, and what to do when gene expression microarray data is inconsistent with the clinical presentation in diagnosing cancers of unknown primary site. Be sure to consult the list of resources at the end of this guide for citations to the methods and research papers our experts have referred to in their responses.

— Tracy Vence

Phloem small RNAs, nutrient stress responses, and systemic mobility

The authors used LC Sciences’ custom miRNA microarrays containing all known plant miRNAs and a set of unknown small (s) RNAs earlier cloned from Brassica phloem sap, to comprehensively analyze the phloem response to nutrient deficiency by removing sulfate, copper or iron, respectively, from the growth medium. They show that phloem sap contains a specific set of sRNAs that is distinct from leaves and roots, and that the phloem also responds specifically to stress. They further demonstrate that under nutrient starvation miR399 and miR395 can be translocated through graft unions from wild type scions to rootstocks of the miRNA processing hen1-1 mutant. In contrast, miR171 was not transported. Translocation of miR395 led to a down-regulation of one of its targets in rootstocks, suggesting that this transport is of functional relevance, and that miR395, in addition to the well characterized miR399, could potentially act as a long-distance information transmitter.

Buhtz A, Pieritz J, Springer F, Kehr J. (2010) Phloem small RNAs, nutrient stress responses, and systemic mobility. BMC Plant Biol 10(1), 64. [Article]

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.

Book Series	Methods in Molecular Biology
ISSN	1064-3745 (Print) 1940-6029 (Online)
Volume	Volume 592
Book	Plant MicroRNAs
Publisher	Humana Press
DOI	10.1007/978-1-60327-005-2
Copyright	2010
ISBN	978-1-60327-004-5 (Print) 978-1-60327-005-2 (Online)
DOI	10.1007/978-1-60327-005-2_8
Pages	107-125
Subject Collection	Biomedical and Life Sciences
SpringerLink Date	Saturday, October 03, 2009

By: Cheng Lu¹, Frédéric Souret²

miRNAs have emerged as key regulators of gene expression in both plants and animals. These small (generally 21–22 nt) RNA molecules, originated from primary “hairpin” transcripts, can induce translational suppression or direct mRNA cleavage. Similar to regular mRNAs, the expression of miRNAs is highly regulated. Their expression pattern could provide critical clues to understanding miRNA functions. However, many previously identified miRNA families have multiple paralogous loci. Within each family, different members are often closely related and sometimes give rise to identical miRNAs. This poses critical challenges in the analysis of individual miRNA genes. This chapter describes several methods that are commonly used for miRNA expression analysis, including high-throughput sequencing, microarrays, and briefly discusses qRT-PCR, northern blotting, and other approaches used for data validation.

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