Jul

21

microRNA Discovery & Profiling

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Jul

16

Small RNA Sequencing – Sample Data

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InDepth Data Analysis Report Includes:

Map to Reference Sequence

  • Includes custom construction of reference database(s) for mapping – miRBase, genome, etc
  • Sequence data can be aligned to any publicly available small RNA databases for annotation of known small RNA
  • Unknown small RNAs can be aligned with reference genomes

Additional Bioinformatics Analysis

  • Classification of all mapped reads
  • Length distribution of mapped sequences
  • Annotation documentation of mapped sequences
  • Alignment of sequence variants such as isomirs
  • Genomic and chromosomal location of sequence clusters
  • Prediction of new possible miRs
  • Detailed explanation of miRNA analysis results and their context

 

Download the PDF of the summary report here.  Please contact us to obtain a complete set of sample data files.

Jul

14

Featured Article – MicroRNAome of Porcine Pre- and Postnatal Development

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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

Jul

9

New Sample Submission Form – microRNA Microarray Service

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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

Jun

30

Featured Publication – Costimulation-Dependent Expression of MicroRNA-214 Increases the Ability of T Cells To Proliferate by Targeting Pten

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T cell activation requires signaling through the TCR and costimulatory molecules, such as CD28. MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression posttranscriptionally and are also known to be involved in lymphocyte development and function. In this paper, we set out to examine potential roles of miRNAs in T cell activation, using genome-wide expression profiling to identify miRNAs differentially regulated following T cell activation. One of the miRNAs upregulated after T cell activation, miR-214, was predicted to be capable of targeting Pten based on bioinformatics and reports suggesting that it targets Pten in ovarian tumor cells. Upregulation of miR-214 in T cells inversely correlated with levels of phosphatase and tensin homolog deleted on chromosome 10. In vivo, transcripts containing the 3′ untranslated region of Pten, including the miR-214 target sequence, were negatively regulated after T cell activation, and forced expression of miR-214 in T cells led to increased proliferation after stimulation. Blocking CD28 signaling in vivo prevented miR-214 upregulation in alloreactive T cells. Stimulation of T cells through the TCR alone was not sufficient to result in upregulation of miR-214. Thus, costimulation-dependent upregulation of miR-214 promotes T cell activation by targeting the negative regulator Pten. Thus, the requirement for T cell costimulation is, in part, related to its ability to regulate expression of miRNAs that control T cell activation.

Jindra PT, Bagley J, Godwin JG, Iacomini J. (2010) Costimulation-Dependent Expression of MicroRNA-214 Increases the Ability of T Cells To Proliferate by Targeting Pten. J Immunol [Epub ahead of print]. [abstract]

Jun

22

MicroRNA-378, a Novel Regulator of Heat Shock Transcription Factor-1, Involves Development of Cardiac Hypertrophy

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Oral Presentations From the
WORLD CONGRESS OF CARDIOLOGY
Scientific Sessions
Beijing, China
16–19 June 2010

MicroRNA-378, a Novel Regulator of Heat Shock Transcription Factor-1, Involves Development of Cardiac Hypertrophy

Jie Yuan1, Hong Ma1, Hui Gong1, Ning Zhou1, Yanyan Liang1, Yuhong Niu1, Yunzeng Zou1,2 1-Shanghai Institute of Cardivascular Diseases, 2- Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University (Shanghai, China)

Introduction: HSF1, as a protective factor, plays an important role in the development of pressure overload cardiac hypertrophy. However, the exact mechanisms of its regulation are less known. MicroRNAs, one of key regulators for post-transcriptional gene control, have been suggested to involve in the development of cardiac hypertrophy. Aim of our study was to investigate the potential role of microRNA in regulating HSF1 in the development of cardiac hypertrophy.

Methods and Results: Firstly, to identify some microRNAs that may be related to HSF1 expression under pressure overload, we performed miR microarray analysis (LC Sciences _Paraflo™ microRNA chips) on RNA isolated from the hearts of wild-type (C57B/L6) and HSF1 knockout mice subjected to transverse aortic constriction (TAC) or a sham operation for 14 days. After TAC, twenty miRNAs were up-regulated and thirty-five were down-regulated (p_0.05) in wild-type group, and seven miRNAs were up-regulated and ten were downregulated (p_0.05) in HSF1 knockout group compared to sham operated groups. Of these miRNAs, miR-378 expression decreased (0.69 fold) in heart of wild-type group while no change in HSF1 knockout mice, which was confirmed by Northern blot analysis and Real-time PCR. Northern analysis of adult mouse heart tissues revealed that miR-378 is highly expressed in the heart, as well as specific expression in cardiomyocytes. Secondly, to test the potential role of miR-378 in regulating HSF1, we observed HSF1 was up-regulated in wild-type mice after 14-day TAC, together with down-regulation of miR-378. In vitro, the upregulation of HSF1 is also associated with a downregulation of miR-378 by mechanical stretching cardiomyocytes. It seemed that miR-378 functioned as a suppressor of HSF1 protein. To confirm this, cardiomyocytes were transiently transfected with miR-378 mimics and inhibitors in vitro. Our data showed that over-expression of miR-378 inhibited endogenous HSF1 protein synthesis, and down-regulation of miR-378 made HSF1 expression increased. In addition, the miRBase Target database (http: //microrna.sanger.ac.uk/) suggested that a potential target sequence of miR-378 was found in the 3’ UTR of HSF1 in both mouse and human. To determine targeting by miR-378, we inserted a fragment of the HSF1 3’ UTR containing the target sequence, or the fragment whose target site was mutated, into a luciferase reporter vector. Luciferase activity was significantly repressed in the construct harboring the miR-378 target sequence, compared with the control vector harboring a nonrelated fragment or the mutated sequence. Taken together, the negative relationship between miR-378 level and HSF1 indicates that miR-378 is an essential regulator for HSF1 by targeting HSF1 3’UTR.

Conclusion: MiR-378 is a critical factor regulating HSF1 by targeting the HSF1 3’UTR. It suggests that miR-378 may participate in the development of cardiac hypertrophy by inhibiting HSF1 expression.

Jun

10

Tooth, Tail, & Hair – Where would we be without microRNA?

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  1. Cao H, Wang J, Li X, Florez S, Huang Z, Venugopalan SR, Elangovan S, Skobe Z, Margolis HC, Martin JF, Amendt BA. (2010) MicroRNAs Play a Critical Role in Tooth Development. J Dent Res [Epub ahead of print]. [abstract]
  2. Sehm T, Sachse C, Frenzel C, Echeverri K. (2009) miR-196 is an essential early-stage regulator of tail regeneration, upstream of key spinal cord patterning events. Dev Biol 334(2), 468-80.  [abstract]
  3. Mardaryev AN, Ahmed MI, Vlahov NV, Fessing MY, Gill JH, Sharov AA, Botchkareva NV. (2010) Micro-RNA-31 controls hair cycle-associated changes in gene expression programs of the skin and hair follicle. FASEB J [Epub ahead of print]. [abstract]

Jun

3

MicroRNA Expression Analysis – Biocompare Featured Article

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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

28

microRNA Study in Non-Model Species

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LC Sciences’ custom microRNA microarray service is based on the flexible µParaflo® microfluidic chip technology which enables us to produce custom synthesized microarrays when ordered. (vs. an off-the-shelf spotted array)  Therefore, researchers are not limited to the species (and sequences) listed in miRBase.  They can add any sequence of their design to the standard miRBase probe content.

Customizable features include – sequence design, varying chain lengths, chip layout, synthesis chemistry, and more.   Each µParaflo® microfluidic chip has room for thousands of sequences of your design.  Add sequences for various applications:

  • Screen for new microRNAs by adding predicted mature microRNA sequences or perform sequence tiling along certain sequences sections.
  • Combine microRNA sequences of different species to identify cross-species conservations or host-parasite interaction.
  • 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.
  1. Liu G, Fang Y, Zhang H, Li Y, Li X, Yu J, Wang X. (2010) Computational identification and microarray-based validation of microRNAs in Oryctolagus cuniculus.  Mol Biol Rep [Epub ahead of print]  [abstract]
  2. Legeai F, Rizk G, Walsh T, Edwards O, Gordon K, Lavenier D, Leterme N, Mereau A, Nicolas J, Tagu D, Jaubert-Possamai S. (2010) Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum. BMC Genomics 11(1), 281.  [abstract]
  3. Gundersen-Rindal DE, Pedroni MJ. (2010) Larval stage Lymantria dispar microRNAs differentially expressed in response to parasitization by Glyptapanteles flavicoxis parasitoid. Arch Virol (5), 783-87.  [abstract]
  4. Dongdong L, Yusheng Zheng, Li Wan, Xiaoming Zhu and Zhekui Wang. (2009) Differentially expressed microRNAs during solid endosperm development in coconut (Cocos nucifera L.). Scientia Horticulturae 122(4), 666-69.  [abstract]
  5. Sehm T, Sachse C, Frenzel C, Echeverri K. (2009) miR-196 is an essential early-stage regulator of tail regeneration, upstream of key spinal cord patterning events. Dev Biol 334(2), 468-80.  [abstract]

May

26

Seq-Array: microRNA Discovery and Profiling Using a Customizable Workflow

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Seq-ArraySM provides an efficient pathway from an initial broad search to focused biological insights.

Seq-ArraySM 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.

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