Tag Archives: Science

LC Sciences First miRNA Microarray Service Provider to Offer Plant MicroRNA Database (PMRD) Probe Content

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 Researchintroducing the public database 1 . 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.

LC Sciences miRNA microarrays make use of a microfluidics on-chip synthesis platform, termed µParaflo®, versus a traditional spotted array based on pre-synthesized oligonucleotides. This on-chip synthesis platform means made-to-order microarrays can be produced, delivering the most up-to-date research tools to researchers; in this case, the PMRD content.

In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, the possible target genes for each miRNA with a predicted interaction site are included in the database. This represents a significant increase in content vs plant miRNA microarrays based solely on the miRBase content.

The public miRBase sequence database 2 serves as the primary probe content for many commercially available miRNA profiling microarrays (http://microrna.sanger.ac.uk/sequences/). Detection of miRNAs using a microarray offers the opportunity for genome-wide miRNA expression profiling by examining all known miRNA transcripts in a single experiment. However, in a rapidly evolving field such as miRNA research, it is important to have a flexible system that can keep up with all the newly discovered and predicted sequences. Pre-spotted glass slide arrays immediately go out of date whenever new miRNA database versions are released. LC Sciences’ microarrays ensure scientists have the most complete picture of miRNAs expressed in their experimental samples.

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Enabling microRNA Discoveries – LC Sciences Tops 100th Customer Publication

LC Sciences announced today the publication of the 100th peer-reviewed study by one of its customers using the company’s microarray service for analyzing microRNA (miRNA) expression profiles and for discovery of novel small RNAs. These studies, by leading researchers in the field, contribute to a fast growing body of knowledge defining this recently discovered class of regulatory RNAs.

To date, miRNAs have proven to be extremely important part of the gene expression regulation mechanism. Expression profiling and functional studies conducted so far indicate that miRNAs participate in the regulation of almost every cellular process investigated and this is evident in the amount of relevant findings being translating into published reports.

The publications to date by LC Sciences’ customers span a diverse range of study areas, including cancer research, neuroscience, cardiovascular research, MicroRNA Publications reproductive biology, plant science, virology, stem cell research, immunology, and small RNA discovery. Their miRNA profiling service has provided a tool for many researchers to explore and examine a wide assortment of miRNA cellular networks and the resulting publications are often the first description of miRNA activity in these systems.

LC Sciences’ miRNA profiling service, powered by its µParaflo® microfluidic technology, provides quick, reliable, fully analyzed data enabling researchers to immediately move forward with innovative research, and publish their results faster. Microarray results require extensive validation prior to publication. The speed with which researchers using this miRNA profiling service have published their discoveries demonstrates the high-quality and reliability of these results.

The 100th study, entitled “MicroRNA-146a feedback inhibits RIG-I-dependent Type I IFN production in macrophages by targeting TRAF6, IRAK1, and IRAK2” appeared in the September issue of The Journal of Immunology and was one of a group of articles published recently by LC Sciences’ customers describing miRNA involvement in the immune system. Researchers at the National Key Laboratory of Medical Immunology, China studied the fine tuning effect that miRNA has on inflammatory response to viral infection and even propose a new mechanism for the evasion of innate immune control by viruses. MiRNA microarray data revealed, and real-time quantitative PCR confirmed, many up-regulated miRNAs in vesicular stomatitis virus (VSV) infected mouse macrophages. Specifically miR-146a expression was significantly up-regulated. Further studies revealed that miR-146a negatively regulated VSV-triggered interferon production (which is necessary to exert feedback control over inflammation) promoting VSV replication in macrophages. The identification of miRNAs and a better understanding of their expression in response to various stimuli/pathogens may reveal that miRNAs offer multiple new therapeutic targets/strategies for fine tuning the immune response to treat and prevent of a number of inflammatory diseases.

“We are very excited about the announcement of the 100th peer-viewed publication by one of our customers,” says Chris Hebel, VP of Business Development at LC Sciences. “MiRNA has become a very hot area of research and many scientists would like to be the first to describe the mechanism of miRNA as it relates to their field of study. We are happy to provide a first look into this exciting new field for them and are proud that our technology has been a part of such groundbreaking work”.

About µParaflo® Technology – The µParaflo® technology is a microfluidic platform for in situ parallel synthesis of biomolecular chips and miniaturization of bioassays including binding and enzymatic reactions. This unique platform technology is based on a new class of three-dimensional pico-liter microfluidic reaction devices, and a digital light controlled synthesis method that employs conventional oligonucleotide or peptide synthesis chemistry; a completely programmable process. The seamless integration of these multidisciplinary technologies enables a significant advance in parallelization, miniaturization, customization, and automation.

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LC Sciences’ Versatile Microfluidics Chip Technology Extended to Target Selection Applications

LC Sciences has announced the availability of a custom target enrichment service for next-generation sequencing applications. LC Sciences now provides a service for Target-Specific Selection of a defined genomic region (such as Mbp region at a specific location, suspected cancer regions, SNP regions, regions for genomic comparisons) or RNA sequences (such as sets of transcriptome sequences known f r o m previous screening experiments, mRNAs, and miRNAs). This new service enables researchers to take full advantage of new “next-generation” high throughput sequencing technologies.

It is clear that these new sequencing technologies can be more effectively utilized for systematic studies of genetic variation by targeting certain specific regions (subsets) of complex genomes. Essentially, our service achieves more coverage and deeper sequencing by reducing sample complexity and focusing reads on the areas of interest.

LC Sciences µParaflo® technology’s unique combination of advanced microfluidics and innovative synthesis chemistry provides a robust synthesis process which is necessary to achieve high quality selection and the flexibility to handle almost any target selection project. This technology has been used to produce custom sequence microarrays [Nucleic Acids Res. 2004,32,5409] and custom designed oligonucleotide mixture libraries (OligoMix®) [Nature. 2004,432,1050] since 2003 and is now particularly well suited to providing target selection solutions. The versatility of the technology makes it a good fit for the diverse needs of researchers embarking on new high-throughput sequencing projects.

“It’s really the flexibility of the technology that sets it apart f r o m others”, says Dr. Christoph Eicken, Head of Technical Services, Microarrays. “First, this is a completely custom synthesis technology, meaning almost any selected genomic region of any species and all known RNA transcripts can be targeted. Second, target selection may be achieved by hybridization using complementary capture probes immobilized on surface or by in-solution hybridization. By altering the target selection approach we take, we can address the widely varied needs of each individual sequencing project. With our help, researchers can tailor design the target selection process based on the specificity, coverage, selection resolution and throughput requirements of their particular project.”

LC Sciences’ microarray based approach utilizes thousands of custom oligonucleotide sequences which are synthesized in situ on a programmable high density microfluidics chip as capture probes designed to target specific regions of interest in any genome (or transcriptome). Samples are hybridized to the chip, undesired sequences are washed off and the captured target sequences are recovered by eluting them f r o m the chip. The selected target sequences are ready for high-throughput sequencing or further processing.

When target selection in-solution makes sense, this flexible chemistry can directly synthesize biotinylated or phosphorylated oligonucleotides (capture probes) that are designed to target specific genomic/sequence regions of interest. After hybridization with a sample, magnetic beads are added and the capture probes are affinity linked to the beads. The captured target sequences are separated f r o m other sequences by washing the beads after which the target sequences can be recovered. Alternatively, the oligonucleotides (OligoMix®) may be immobilized on beads prior to target selection, again depending on the needs of the particular project.

LC Sciences currently offers its Target-Specific Selection application as a service, as it has successfully done with other applications of the µParaflo® technology such as miRNA profiling, small RNA discovery, kinase profiling and epitope mapping with peptide arrays, and others.

“We find that researchers would prefer to spend their valuable time focusing on their research, not figuring out how to make successful use of someone else’s new technology”, says Chris Hebel, Director of Business Development. “We offer a comprehensive solution: customers tell us their experiment goals, send us their samples and we provide the material ready for sequencing. There is no reason they need to become target selection experts to keep their research moving forward. We have already developed methods to design optimized hybridization probes and suitable experimental procedures and conditions for different sample types, such as miRNA, small RNA, or genomic DNA samples, on different sequencing platforms. We can even perform the high-throughput sequencing and deliver the results, as not all labs have access to next-generation sequencers yet.”

More information about LC Sciences’ Targeted Sequencing Sample Enrichment Service and the µParaflo® technology is available at:http://www.lcsciences.com/targeted_sequencing.html.

About LC Sciences – LC Sciences is a genomics and proteomics products company offering a comprehensive line of DNA, RNA, and peptide microarrays for nucleic acid/protein profiling and functional analysis, biomarker-discovery, novel drug screening, and the custom development of miniaturized assay devices for diagnostics and biosensing applications. Based on the µParaflo® microfluidics technology, LC Sciences’ innovative products and services offer significant flexibility and customization capability for rapidly evolving, diverse customer needs. In an era of rapid technological advancement, LC Sciences offers service products which enable efficient one-stop solution for assays of DNA, RNA, protein, enzymes, antibodies, or small molecules. LC Sciences also provides unique synthetic DNA and RNA products such as OligoMix®, generated using their microfluidic biochip synthesizer. These innovative products drive synthetic biology, systems biology and sequencing applications by reducing the cost and increasing the speed of highly multiplexing large-scale nucleic acid and protein engineering experiments.

More information about LC Sciences is available at www.lcsciences.com.

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LC Sciences announced the availability of probe content miRBase 10.0 for their microRNA (miRNA) microarray customers

Taking advantage of its flexible µParaflo™ Chip Technology, Houston based LC Sciences today announced immediate availability of probe content miRBase 10.0 for their microRNA (miRNA) microarray customers. This announcement comes less than a week after Sanger Institute’s update of their sequence database for known miRNAs (miRBase) 1 to version 10.0 (http://microrna.sanger.ac.uk/sequences). As the jump in

version numbers from 9.2 to 10.0 suggests, this update marks a major milestone and features significant changes: 489 new hairpin sequences and 971 novel mature miR and miR* experimentally verified products have been added.

These numbers represent an increase of unique miRNA sequences by 42%. “This exciting increase in data means that researchers using pre-spotted glass arrays with probe content based on versions as recent as 9.1 are missing 49% of mouse, and more than 50% of human sequences, just to give two examples. The other important point is that these sequences are experimentally verified and publicly available data. Unlike with proprietary probe content the researcher has full access and control over the results.” said Chris Hebel, Director of Business Development at LC Sciences.

The importance of this update is emphasized by another aspect of the release: many human, mouse and rat mature miRNAs were renamed and the sequence boundaries changed to reflect the predominant forms identified in recent large-scale cloning studies. The public miRBase sequence database serves as the primary probe content for many commercially available miRNA profiling microarrays. Detection of miRNAs using a microarray offers the opportunity for genome-wide miRNA expression profiling by examining all known miRNA transcripts in a single experiment. However, the continued updating of the database can be problematic for researchers using pre-spotted glass slide arrays as the probe content of the arrays immediately goes out of date whenever a new miRBase version is released. Especially, in a rapidly evolving field as miRNA research it is important to scientists to have the most complete picture of miRNAs expressed in their experimental samples.

LC Sciences miRNA microarrays make use of a microfluidics on-chip synthesis platform, termed µParaFlo™, versus a traditional spotted array based on pre-synthesized oligonucleotides. This 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 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.

About microRNA (miRNA)
miRNAs are small non-protein-coding RNA molecules that function as negative regulators of gene expression by base pairing with specific mRNAs. This either inhibits translation or promotes mRNA degradation. About miRBase – 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. Release 10.0 of the database contains 5071 entries representing hairpin precursor miRNAs, expressing 4922 maturemiRNA products, in primates, rodents, birds, fish, worms, flies, plants and viruses (miRBase release summary). miRBase also provides a gene-naming service for assigning official miRNA names to novel miRNAs before they are published. It is freely available to all at http://microrna.sanger.ac.uk/.

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 Atactic Technologies’ µParaflo™ platform technologies that encompass advanced digital chemical synthesis, pico-liter scale biochemical assays, and microfluidic reaction devices containing high density individual 3D chambers.

 

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