Tag Archives: uparaflo

Enabling microRNA Discoveries – 250th Peer-Reviewed Publication Made Possible By µparaflo Custom Microarray Technology

LC Sciences, a life sciences company leading the development of innovative microRNA (miRNA) analysis and discovery technologies, announced today the publication of over 250 peer-reviewed studies using the company’s microarray service for analyzing miRNA expression profiles. These studies, by leading researchers in the field, represent significant steps toward realizing these small regulatory RNA’s potential as biomarkers and therapeutic targets.

MiRNAs have proven to be an extremely important part of the gene expression regulation mechanism of a wide variety of cellular processes. This is evident in the amount of relevant findings by LC Sciences’ customers being translated into published reports and the diverse range of study areas that these publications encompass: cancer research, neuroscience, cardiovascular research, reproductive biology, plant science, microbiology, immunology and stem cell research. LC Sciences’ miRNA profiling service, powered by its µParaflo® custom microarray technology, provides quick, reliable, fully analyzed datasets enabling researchers to immediately move forward with groundbreaking research.

The miRNA field is still nascent, and it is advancing rapidly. The race to discovery has produced a continuous stream of new miRNA sequences as well as routine revisions of inaccurate or incomplete sequences. This fluidity has caused many microarrays with static content to fall away and has fueled reports of the wholesale replacement of microarrays by new methods such as RNA-Seq. But the nimble, customizable format of the µParaflo® array has given it staying power, not only by enabling it to keep current with all known miRNAs, but also by making use of data generated by RNA-Seq. These custom arrays have benefited from RNA-sequencing generating novel content that other arrays are unable to capture and take advantage of.

The 250th study, entitled “Wolbachia uses host microRNAs to manipulate host gene expression and facilitate colonization of the dengue vector Aedes aegypti.” appeared in the May 31st issue of PNAS and was one of a group of articles published recently by LC Sciences’ customers describing microarray expression analysis of miRNAs recently discovered through RNA Sequencing.

Researchers at the University of Queensland, Australia studied the underlying mechanisms of host manipulation by a widespread endosymbiont. Using microarrays, they show that the miRNA profile of the mosquito, Aedes aegypti, is significantly altered by a life-shortening strain of W. pipientis bacteria. This is extremely important work as introduction of Wolbachia into mosquitoes has been proposed as a method for malaria control. They found that a host miRNA (aae-miR-2940) is induced after W. pipientis infection in both mosquitoes and cell lines.

This study illustrates the versatility of µParaflo® from a couple of perspectives. First, mosquito, an important though non-model species was the target of interest here and mosquito arrays, as well as arrays from any of the 153 species listed in the miRBase public sequence database, are readily available from LC Sciences. Second, custom content (novel miRNA sequences from an earlier sequencing study on the same species) was quickly integrated into the content of the insect array providing an even richer expression dataset. Though all the previously described, known insect miRNAs were also present on the arrays, several custom sequences were significantly differentially expressed in infected mosquitoes and a custom sequence turned out to be one that became a focus of the investigation. Dr. Sassan Asgari, lead researcher for the study, commented that microarrays “…provided an affordable approach to the study of differential expression of small RNAs and miRNAs in particular.”

Via EPR Network
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LC Sciences Pairs Deep Sequencing with Customized Microarrays to Offer New Seq-Array Service for Discovery & Profiling Applications

LC Sciences today announced the launch of its new Seq-Array(SM) services designed to take full advantage of both the latest deep sequencing capabilities and the proven genomics tool – microarray. This combination of technologies advances microRNA research to the next level of depth and understanding that was not possible before with either of the technologies alone. LC Sciences has been a leading provider of microRNA discovery and profiling services since 2005.

LC Sciences Pairs Deep Sequencing with Customized Microarrays to Offer New Seq-Array Service for Discovery & Profiling Applications

microRNA is a young, dynamic field of study and though significant discoveries are being made every day, the very complex regulatory mechanisms of these small RNAs are still not fully understood. Continued advancement requires adaptable, even customizable research tools that can keep pace with the rapidly advancing research in this field. While deep sequencing yields results that broadly cover genome-wide miRNAs from samples of various origins, the relatively high cost and low throughput nature of sample handling, makes the systematic follow through of the sequencing discoveries for validation and/or profiling in a reproducible manner time consuming and expensive. Microarrays have achieved wide acceptance as the preferred tool to systematically profile and compare the gene expression of large numbers of samples rapidly, reproducibly, and cost effectively; however they are dependent on previously known sequence information. Seq-ArraySM is a combination of these technologies that maximizes the effectiveness of each method while overcoming the limitations of the other.

Seq-ArraySM for microRNA starts with exploratory small RNA deep sequencing of a single or mix of RNA samples to perform a broad search and generate a comprehensive atlas of all microRNAs within a given research study. Next, bioinformatics are employed to map the raw sequencing reads to a custom generated sequence database, classify and align all sequences and sequence variants, as well as to predict novel microRNAs. A custom SeqArrayâ„¢ microarray is designed based on the mapped novel microRNAs, the predicted novel microRNAs, and any previously described publicly available microRNA sequences. Finally, expression profiling of large numbers of samples on the custom array design together with additional bioinformatics work completes an efficient pathway to focused biological insights including: revealing regulatory target genes, defining gene expression pathways, and discovering biomarkers.

“We feel like this is a productive match of the two technologies,” says Dr. Christoph Eicken, Head of Technical Services at LC Sciences. “It’s something we have really already been doing for a while and thought it made sense to package together as a single service. Often times researchers come to us who are studying a non-typical species with very limited or no prior knowledge of microRNA sequences or function in their model system. By the end of the complete Seq-ArraySM project they have become the world authority on microRNA in their area of research. It’s been very exciting to be part of this.”

About microRNA – microRNAs are small non-protein-coding RNA molecules that function as negative regulators of gene expression by targeting specific mRNAs. This either inhibits translation or promotes mRNA degradation.

Via EPR Network
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