next-gen sequencing

somagenics_logoSANTA CRUZ, Calif., April 28, 2015 /PRNewswire/ — SomaGenics has been awarded a two-year NIH grant to develop its novel RealSeq™–T technology for targeted next-generation sequencing (NGS) of small RNAs such as microRNA.

There is increasing interest in using NGS for miRNA biomarker discovery from biofluids such as blood plasma as well as for miRNA expression profiling and diagnostic purposes. There are many advantages to using NGS, including unlimited multiplexing, high sensitivity, sequence specificity and ability to detect miRNA sequence editing.  Targeted NGS brings these advantages to the quantification of any specific group of sequences of interest.  However, sequence bias in the construction of the small RNA libraries used in sequencing has so far limited the utility of NGS, both targeted and non-targeted. This bias gives distorted small RNA profiles and renders some species of RNA that might be good biomarkers unavailable for accurate quantification.

“RealSeq–T improves the accuracy and sensitivity of targeted NGS compared to current methods and provides accurate quantification of all miRNA species of interest,” said Dr. Brian Johnston, CEO of SomaGenics.  “We are excited [click to continue…]


Novel Biomarkers for Drug-induced Liver Injury

by Christoph on December 12, 2014

in Publications

MicroRNAs have emerged as promising biomarkers of organ damage including injury of the liver. In this study the new generation of high-throughput sequencing technology was applied to detect circulating  miRNAs in serum from patients with accidental acetaminophen overdose and identified a set of 33 known miRNAs and 3 novel miRNA-like small RNAs that are functionally associated with liver-specific biological processes and relevant to acetaminophen toxic mechanisms. The study suggests a profile of circulating miRNAs in human serum that might provide additional biomarker candidates for drug-induced liver injury and possibly adds mechanistic information relevant to liver injury.


circulating miRNAs of drug-induced liver injury Figure: Serum levels of liver-associated miRNAs after acetaminophen overdose. The liver associated miRNAs miR-122 and miR-192 were detected in serum from acetaminophen-overdosed patients. The graph represents serum levels, based on normalized sequencing reads, of the liver-associated miRNA hsa-miR-122 (A) and hsa-miR-192 (B) in control and acetaminophen-overdosed samples.


For the full article:

Krauskopf J, Caiment F, Claessen SM, Johnson KJ, Warner RL, Schomaker SJ, Burt DA, Aubrecht J, Kleinjans JC. Application of High-Throughput Sequencing to Circulating microRNAs Reveals Novel Biomarkers for Drug-induced Liver Injury. Toxicol Sci. 2014 Oct 29. pii: kfu232. [Epub ahead of print] PubMed PMID: 25359176.


The UEA sRNA workbench was developed by the Moulton group at the University of East Anglia and is a new simple to use, downloadable, Java based sRNA software package. It is based on algorithms developed for the 2008 released original UEA sRNA Toolkit. The software will perform a complete analysis of single or multiple-sample sRNA datasets from both plants and animals to identify interesting landmarks (such as detection of novel miRNA sequences) in genetic data. The latest Version 2.3.1 (Released: March 9th 2012) includes now the PAREsnip tool which allows to find targets of small RNAs using the degradome. For more see the PAREsnip page.

Currently, the downloadable version of the UEA sRNA workbench contains a subset of the web-based sRNA toolkit functionality. The later is still available for animal as well as plant and both version can be accessed from the main UEA sRNA toolkit site.

The UEA sRNA workbench is available for download at:

citation for the original version:
S. Moxon, F. Schwach, D. MacLean, T. Dalmay, D. J Studholme, and V. Moulton
A toolkit for analysing large-scale plant small RNA datasets. 


Outsourcing your RNA

by Chris on September 30, 2010

in Publications

RNA expression analysis can be acomplished by microarrays, next-gen sequencing, in situ hybridization or qRT-PCR, but not all investigators have these capabilities in their own labs. Whether constrained by space, infrastructure, know-how, or time, many have no choice but to outsource these types of analyses to others. Often, that means employing a university core facility. But some elect to go off campus altogether, enlisting commercial service providers instead.  Here are some accounts of outsourcing experiences by a few RNA researchers. (read more… )


MicroRNA Expression Analysis

by Chris on June 3, 2010

in News

Biocompare – Featured Article

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… )

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