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The Megaruptor® was designed to provide researchers with a simple, automated, and reproducible device for the fragmentation of DNA from 2 kb - 75 kb. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly software allows for two samples to be processed sequentially without additional user input and without cross-contamination. Just set the desired parameters and the automated system takes care of the rest. Clogging issues are eliminated in this design. 


At the VIB Department of Molecular Genetics we strive to implement the best technologies in our workflows. Recent advances in long read sequencing using Oxford Nanopore technology have made the investigation of complex genomic variation in the human genome possible. A crucial step in the beginning of the library preparation is the shearing of genomic DNA, and this is where we implement the Megaruptor. The straightforward protocol is efficient, requires minimal sample handling and results in very reproducible fragment sizes. Another advantage is the consumable cost, which is lower than alternative technologies. For our applications we prefer shearing to lengths of 10 to 40kb, and for this the Megaruptor is the optimal solution.

Wouter de Coster and the Genomic Service Facility, VIB Department of Molecular Genetics, Antwerp, Belgium

The Megaruptor® shows a more dense size distribution of sheared fragments, and a higher and more reproducible yield.

Sylke Winkler, Sylvia Clausing, Nicola Gscheidel, Yannick Duport, Eugene Myers and Andreas Dahl, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany, and Deep Sequencing Group, BIOTEC, TU Dresden, Germany
  • Reproducible and narrow DNA size distribution with Megaruptor® using short fragment size Hydropores
    Validation using two different DNA sources and two different methods of analysis. A: Shearing of lambda phage genomic DNA (20 ng/μl; 150 μl/sample) sheared at different speed settings and analyzed on 1% agarose gel. B: Fragment Analyzer profiles of human genomic DNA (25 ng/μl; 200 μl/sample) sheared at different software settings of 2, 3, 5 and 8 kb. (Standard Sensitivity Large Fragment Analysis Kit ; Advanced Analytical Technologies, Inc. was used for separation and fragment sizing).
  •  Testimonials

    The Norwegian sequencing centre (NSC) is a national core facility fully equipped to handle a diverse set of sequencing projects. We see an increased interest in long read technologies, in which our PacBio Single Molecule sequencing service is important. PacBio, (or SMRT) sequencing, like any other single molecule system, starts with a critical library preparation step to generate long fragment libraries of 10-20kb length. Even longer libraries can be made, but common to all library types is to start with good quality DNA of high molecular weight. Physical shearing of the DNA, targeting the desired library length, is the first critical step in the procedure. NSC has experience with different methods to fragment DNA like nebulization, enzymatic, tagmentation, covaris AFA, g-tubes (also covaris), custom syringe/needle protocols and hydroshearing. The best fragmentation method should produce a sharp fragmentation pattern close to the target length as defined by the protocol settings, with as little “smear like” pattern of lower molecular length as possible. The final step of PacBio library preparation is to size select only the longest fragments (> 7kb) as this increases the overall success rate of only sequencing the longest library fragments. It is not uncommon to loose a lot of material during this step. However, if the initial fragmentation yields sharp fragmentation patterns with minimal smear, more of the total DNA is retained in the final library. This is perhaps most important on samples were DNA amounts are limited. The optimal fragmentation method has to produce similar fragmentation pattern each time, with little deviation with sample type and input amount. We have found the new Megaruptor from Diagenode to be one of the best instruments for routine shearing of DNA to lengths of 2-40kb. It is easy to use, with walk away shearing, and the instrument does all the washes before, in between samples and after shearing without user intervention. Disposable hydropores is beneficial for lowering the contamination risk. The fact that it is so easy to use make it a good choice for laboratories with multiple users and/or when training new staff.

    Morten Skage and Dr Ave Tooming-Klunderud, Norwegian Sequencing Centre, Oslo, Norway

    We will use  the Megaruptor® within our PacBio® Single Molecule Sequencing workflows, especially for the construction of very big insert  (>20kb) libraries.

    Andrea Patrignani, Anna Bratus and Ralph Schlapbach, Functional Genomics Center Zurich (ETHZ/UZH), Switzerland
  •  Documents
    Improvements in Hydrodynamic Shearing Facilitates 20-50 kb True Mate Pair Library Construction POSTER
    The Megaruptor® has been used by several sequencing centers to produce high-quality small ins...
    Megaruptor® DNA Shearing System User Manual v2 MANUAL
    The Megaruptor® was designed to provide researchers with a simple, automated, and repro...
  •  Publications

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    Complete Genome Sequence of the Type Strain Pectobacterium punjabenseSS95, Isolated from a Potato Plant with Blackleg Symptoms.
    Sarfraz, S and Oulghazi, S and Cigna, J and Sahi, ST and Riaz, K andTufail, MR and Fayyaz, A and Naveed, K and Hameed, A and Lopez-Roques, Cand Vandecasteele, C and Faure, D
    Pectobacterium punjabense is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of P. punjabense SS95T, which contains a circular chromosome of 4.793 Mb wi...

    Sizing, stabilising, and cloning repeat-expansions for gene targeting constructs.
    Nair RR, Tibbit C, Thompson D, McLeod R, Nakhuda A, Simon MM, Baloh RH, Fisher EMC, Isaacs AM, Cunningham TJ
    Aberrant microsatellite repeat-expansions at specific loci within the human genome cause several distinct, heritable, and predominantly neurological, disorders. Creating models for these diseases poses a challenge, due to the instability of such repeats in bacterial vectors, especially with large repeat expansions. ...

    Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants.
    Xu Z, Pu X, Gao R, Demurtas OC, Fleck SJ, Richter M, He C, Ji A, Sun W, Kong J, Hu K, Ren F, Song J, Wang Z, Gao T, Xiong C, Yu H, Xin T, Albert VA, Giuliano G, Chen S, Song J
    BACKGROUND: Plants have evolved a panoply of specialized metabolites that increase their environmental fitness. Two examples are caffeine, a purine psychotropic alkaloid, and crocins, a group of glycosylated apocarotenoid pigments. Both classes of compounds are found in a handful of distantly related plant genera (C...

    Nanopore Sequencing and Its Clinical Applications.
    Sun X, Song L, Yang W, Zhang L, Liu M, Li X, Tian G, Wang W
    Nanopore sequencing is a method for determining the order and modifications of DNA/RNA nucleotides by detecting the electric current variations when DNA/RNA oligonucleotides pass through the nanometer-sized hole (nanopore). Nanopore-based DNA analysis techniques have been commercialized by Oxford Nanopore Techn...

    Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum
    Massonnet M. et al.
    The ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood-infecting fungus and a serious threat to grape production worldwide. The capability of colonizing woody tissue combined with the secretion of phytotoxic compounds is thought to underlie its pathogenicity an...

    Complete genome of Staphylococcus aureus Tager 104 provides evidence of its relation to modern systemic hospital-acquired strains
    Richard W. DavisIV, Andrew D. Brannen, Mohammad J. Hossain, Scott Monsma, Paul E. Bock, Matthias Nahrendorf, David Mead, Michael Lodes, Mark R. Liles and Peter Panizzi
    Background Staphylococcus aureus (S. aureus) infections range in severity due to expression of certain virulence factors encoded on mobile genetic elements (MGE). As such, characterization of these MGE, as well as single nucleotide polymorphisms, is of high clinical and microbiological importance. To und...

    Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections
    Craig M. Stephens, Jeffrey M. Skerker, Manraj S. Sekhon, Adam P. Arkin, Lee W. Rileyd
    Finished genome sequences are presented for four Escherichia coli strains isolated from bloodstream infections at San Francisco General Hospital. These strains provide reference sequences for four major fimH-identified sublineages within the multilocus sequence type (MLST) ST95 group, and provide insights into patho...

    Diversification of bacterial genome content through distinct mechanisms over different timescales.
    Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WP
    Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled genomes, we show that Streptococcus pneumoniae lineages are typically characterized by combinations ...

    Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance
    Mark R Davies, Matthew T Holden, Paul Coupland, Jonathan H K Chen, Carola Venturini, Timothy C Barnett, Nouri L Ben Zakour, Herman Tse, Gordon Dougan, Kwok-Yung Yuen & Mark J Walker
    A scarlet fever outbreak began in mainland China and Hong Kong in 2011 (refs. 1–6). Macrolide- and tetracycline-resistant Streptococcus pyogenes emm12 isolates represent the majority of clinical cases. Recently, we identified two mobile genetic elements that were closely associated with emm12 ou...

    Microevolution of Burkholderia pseudomallei during an acute infection.
    Limmathurotsakul D, Holden MT, Coupland P, Price EP, Chantratita N, Wuthiekanun V, Amornchai P, Parkhill J, Peacock SJ
    We used whole-genome sequencing to evaluate 69 independent colonies of Burkholderia pseudomallei isolated from seven body sites of a patient with acute disseminated melioidosis. Fourteen closely related genotypes were found, providing evidence for the rapid in vivo diversification of B. pseudomallei after inoculatio...

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