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Milena Musilova, Ph.D.

Milena Musilova, Ph.D.

Dr. Musilova uses the GS Junior System to research hematological malignancies. Her lab is a participant in the international IRON-II study to evaluate the usability of next-generation sequencing for the molecular characterization of different types of leukemia.

Department of Internal Medicine, Masaryk University | Czech Republic

Europe: Czech Republic

Milena Musilova, Ph.D.

Milena Musilova, Ph.D.

Dr. Musilova uses the GS Junior System to research hematological malignancies. Her lab is a participant in the international IRON-II study to evaluate the usability of next-generation sequencing for the molecular characterization of different types of leukemia

“We are primarily using the GS Junior System to study chronic myeloid leukemia, especially focusing on the analysis of the BCR-ABL1 fusion gene. We are also starting to detect mutations in DNMT3A gene in acute myeloid leukemia.”

The sensitivity of the GS Junior System has made a significant impact on our work. With the deep sequencing approach we can lower the limit of detection beyond traditional Sanger sequencing and achieve more exact analyses. We have been very interested to see what mutations fall below the detection limit of this classical method in the kinase domain of BCR-ABL1 fusion gene. Overall, we are very pleased with the system and performance in our lab.

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Fernando Chaves, M.D.

Fernando Chaves, M.D.

Dr. Chaves and his team use the GS Junior System to study bacterial outbreaks in the hospital setting.

Hospital Universitario 12 de Octubre| Spain

Europe: Spain

Fernando Chaves, M.D.

Fernando Chaves, M.D.

Dr. Chaves and his team use the GS Junior System to study bacterial outbreaks in the hospital setting.

“We are primarily using the GS Junior System to sequence whole bacterial genomes of different species, such as P. aeruginosa, S. aureus, and E. cloacae, which form part of our healthcare setting and can cause serious epidemiologic problems.”

Our goal is to understand what makes these bacterial species unique to allow their successful survival in the hospital setting. Overall, the GS Junior System has had a significant impact on our research and opened new application areas such as metagenomics.

We chose the GS Junior System because we needed a high-throughput sequencing system with long reads, a robust workflow, and protocols that were easy to follow. The platform allows our lab to perform studies that were simply not possible using standard methodologies due to technical, cost, and practicality reasons. We are very happy with the instrument in our lab so far and highly recommend the technology.

The team includes Esther Viedma Moreno, Laura Barrado Blanco, Jennifer Villa Garcia and Mª Mercedes Murcia Fernandez De Mera.

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Ana Osorio, Ph.D.

Ana Osorio, Ph.D.

Dr. Osorio and her team are using the GS Junior System in translational cancer genetics research.

Spanish National Cancer Research Centre| Spain

Europe: Spain

Ana Osorio, Ph.D.

Ana Osorio, Ph.D.

Dr. Osorio and her team are using the GS Junior System in translational cancer genetics research.

“We are using the GS Junior System in our translational research on cancer genetics, particularly for mutational screening for BRCA1 and BRCA1 breast cancer susceptibility genes.

Using the GS Junior System for next-generation sequencing has made a significant impact on our research. It has improved the sensitivity and time of response in specific studies, such as mutational screening of genes in hereditary cancer. It has also allowed us to design new studies focused in the sequencing of panel of genes that were impossible to approach with more conventional technologies.”

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Osamu Ohara, Ph.D.

Osamu Ohara, Ph.D.

Scientists at the Kazusa DNA Research Institute are using the GS Junior System for high-throughput amplicon sequencing.

Kazusa DNA Research Institute | Japan

Asia: Japan

Osamu Ohara, Ph.D.

Osamu Ohara, Ph.D.

Scientists at the Kazusa DNA Research Institute are using the GS Junior System for high-throughput amplicon sequencing.

“We are using the GS Junior System for resequencing of mammalian genes, mainly in clinical research applications. The increased throughput and reduction in the cost of DNA sequencing enabled by GS Junior has a tremendous impact on our work. We are very happy with the instrument in our laboratory so far.”

Publications

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Marie Yannick

Marie Yannick

Scientists at the ICM Institute at the Pitié Hospital in Paris, France are using the GS Junior System for amplicon resequencing in neurology and oncology research.

Pitié Hospital, ICM Brain & Spine Institute | France

Europe: France

Wansun Chantratita, Ph.D.

Marie Yannick

Scientists at the ICM Institute at the Pitié Hospital in Paris, France are using the GS Junior System for amplicon resequencing in neurology and oncology research.

“We chose the GS Junior System as an alternative to Sanger sequencing technology. Without any prior skills in pyrosequencing or high-throughput sequencing, we needed a machine that was easily accessible, quick to implement and did not require a large bioinformatics team. From the second week post installation, the GS Junior System gave very good results, with analysis that is still possible without intervention of bioinformaticians.”

We are primarily using the system for amplicon resequencing in neurology and oncology research. The system has opened to us new applications areas such as ultra-deep sequencing of rare mutant and whole free plasmid DNA, and sequencing of degraded or low quality DNA. Compared to Sanger sequencing, we can now analyze a large number of amplicons in several samples and see the results in individual reads, not just consensus sequences. This type of result is extremely powerful for our research.

After a short period of familiarization, the practicality of the system was really appreciated by the technical team. The workflow is easy, simple and robust and all users are delighted with this acquisition. We have just installed a second machine in another center within the institute. It is with enthusiasm that we continue our work on the GS Junior System to further improve its carry operation and explore new applications.

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David O’Connor, Ph.D.

David O’Connor, Ph.D.

Dr. O’Connor and his team study host and viral genetics in non-human primates infected with Simian immunodeficiency virus (SIV). This non-human primate model recapitulates many of the immunological and virological aspects of an HIV infection.

University of Wisconsin-Madison | United States

North America: United States

David O’Connor, Ph.D.

David O’Connor, Ph.D.

Dr. O’Connor and his team study host and viral genetics in non-human primates infected with Simian immunodeficiency virus (SIV). This non-human primate model recapitulates many of the immunological and virological aspects of an HIV infection.

“We are currently utilizing the GS Junior System to assess major histocompatibility complex genotypes of large cohorts of SIV infected non-human primates.”

The throughput of the platform has allowed us to study much larger cohorts, giving us greater statistical power, and the long read lengths allow accurate discrimination of haplotypes that would be difficult using reads shorter than 400 bp.

Additionally, we are sequencing SIV using both amplicon and full-genome approaches to monitor viral evolution over time in infected non-human primates. We have used the GS Junior’s sequencing depth to show that SIV escape from host immune responses is far more complex than previously appreciated, and that this escape occurs within the first 14 days of infection. We are now using similar methods to research drug resistance mutations in HIV infected individuals. Also, the GS Junior has allowed us to discover multiple novel RNA viruses in the blood plasma of non-human primates from Uganda.

The GS Junior has allowed us to begin thinking outside the box, with an emphasis on big picture science. Many of the old questions within the field are now new again, given the advancements in sequencing technologies. Indeed, we hope to significantly advance our understanding of HIV and SIV infection with the power of the GS Junior.

We were honored to be selected as a GS Junior beta-testing site. This was a unique experience and allowed us to construct an efficient next-generation sequencing workflow within our lab. We now run an average of 4 GS Junior runs per week, leading to enormous amounts of data that we are using to generate multiple manuscripts. Overall, we found the GS Junior was easily adaptable to a small academic lab setting.

Publications

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Wansun Chantratita, Ph.D.

Wansun Chantratita, Ph.D.

Dr. Chantratita and his team are focused on virology and pathology sequencing research applications, particularly emerging pathogen identification and viral drug resistance in HIV, HBV and HCV.

Mahidol University | Thailand

Asia: Thailand

Wansun Chantratita, Ph.D.

Wansun Chantratita, Ph.D.

Dr. Chantratita and his team are focused on virology and pathology sequencing research applications, particularly emerging pathogen identification and viral drug resistance in HIV, HBV and HCV.

“We are using the GS Junior System for a number of viral sequencing applications, including pathogen identification and deep sequencing for viral drug resistance research studies.”

The long reads and quick turn around time of the system have proven very powerful in detecting new emerging diseases, and allowed us to better fight known and unknown pathogens in real time. We have found that the approach is significantly more accurate than conventional real-time PCR and capillary sequencing.

We are particularly focused on deep sequencing in HIV-1, HBV and HCV. The deep sequencing approach with the GS Junior System allows us to detect many more point mutations at greater sensitivity than with conventional sequencing methods.

Roche Diagnostics and Applied Science has always been a great partner in our work and we continue to receive excellent service and technical support with the GS Junior System.

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Anne-Marte Bakken Kran, MD, Ph.D.

Anne-Marte Bakken Kran, MD, Ph.D.

Dr. Kran and her team are using the GS Junior System to study infectious diseases, such as HIV. In particular, the team is exploring the dynamics of HIV drug resistance.

University of Oslo | Norway

Europe: Norway

Anne-Marte Bakken Kran, MD, Ph.D.

Anne-Marte Bakken Kran, MD, Ph.D.

Dr. Kran and her team are using the GS Junior System to study infectious diseases, such as HIV. In particular, the team is exploring the dynamics of HIV drug resistance.

“We are using the GS Junior System for ultra-deep amplicon sequencing to study genetic variation of HIV and the impact of low-abundance HIV variants.”

Since each 454 sequencing read is a clone, we can accurately count how many individual virus variants in a large population contain mutations of interest. Ultimately, our research aims to better understand the dynamics of HIV drug resistance with the hope of developing individual antiretroviral drug resistance forecasts based on minority variant sequences.

The GS Junior System is a great fit for our lab. We needed a high-throughput sequencing platform with long reads and relatively low cost per run. We are very excited to have the instrument and to advance our understanding of HIV infection using state-of-the-art genomic technology.

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German GS Junior Community

German GS Junior Community

The first German GS Junior Applications Symposium took place on June 21st 2011 in Mannheim.

German GS Junior Community | Germany

Europe: Germany

German GS Junior Community

German GS Junior Community

The first German GS Junior Applications Symposium took place on June 21st 2011 in Mannheim.

“With over 80 GS Junior users and 10 scientific talks the 2011 GS Junior Applications Symposium was a huge success.”

Participants in the first GS Junior Applications Symposium highly appreciated the possibility for experience exchange within the growing German GS Junior community as well as the broad selection of scientific talks covering applications, studies, workflow options, methods and bioinformatics.

Across Germany the GS Junior System is successfully used for a wide range of applications such as targeted resequencing using amplicon sequencing and sequence capture, de novo sequencing, metagenomics and pathogen identification. The GS Junior enables groundbreaking research and supports applied studies in biotech companies, academic human genetics, oncology, pathology, immunology, virology, microbiology and ecology departments as well as genomics core facilities.

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Korinne Northwood

Korinne Northwood

Korinne Northwood and the team at the MRC Clinical Sciences Centre are using the GS Junior System for targeted gene sequencing on a wide variety of organisms.

Imperial College London | England

Europe: England

Korinne Northwood

Korinne Northwood

Korinne Northwood and the team at the MRC Clinical Sciences Centre are using the GS Junior System for targeted gene sequencing on a wide variety of organisms.

“We chose the GS Junior System to take advantage of the fast turnaround time and long reads for targeted gene sequencing in clinical research.”

Currently we are using the system for shotgun and amplicon sequencing on plasmids, bacterial viruses human and rat genomes. We can now perform high-throughput confirmatory screens by quickly sequencing target regions of interest. Previously, we used Sanger sequencing and were limited to single PCRs. With the GS Junior, we have been able transition to PCR on multiple samples in a single run.

Our experience has been very positive and we’ve found the system easy to use.

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Dr. Ralph Oehlmann, Director Business Development, IMGM Laboratories GmbH

Frances Brigg

Frances Brigg runs the sequencing service at the State Agricultural Biotechnology Centre in Western Australia. Researchers are using their GS Junior System in a wide range of applications – from nematode transcriptome sequencing to comparative sequencing of Xanthomonas bacterial pathovars responsible for citrus canker.

Murdoch University | Australia

Australia: Perth

Dr. Ralph Oehlmann, Director Business Development, IMGM Laboratories GmbH

Frances Brigg

Frances Brigg runs the sequencing service at the State Agricultural Biotechnology Centre in Western Australia. Researchers are using their GS Junior System in a wide range of applications – from nematode transcriptome sequencing to comparative sequencing of Xanthomonas bacterial pathovars responsible for citrus canker.

“The GS Junior System was an ideal entry-level next generation sequencer for our laboratory due to its small footprint and low cost.”

Our clients are redesigning their experiments to take advantage of the possibilities this opens up, for example opting for shotgun sequencing of virus-infected plant material in a single run on the GS Junior over spending a year cloning and sequencing in the traditional Sanger method to obtain the virus sequence.

Researchers studying small genomes or amplicons can barcode multiple samples with MID tags and sequence them simultaneously in a single run to optimize data output and minimize redundant data.

For larger genomes and transcriptomes it offers an ideal testing platform for proof-of-concept and experimental optimization with minimal financial outlay that is directly portable to the GS FLX System for large-scale data acquisition.

As a small university sequencing service, teaching is vital and it is important for us not to outsource. Having the GS Junior enables us to provide students and researchers with invaluable hands-on experience with next generation sequencing from sample preparation to bioinformatics at a low price and with manageable computing requirements.

The GS Junior has made next generation sequencing, and the incredible expansion of research capacity that it offers, accessible to us at an affordable price.

Prof. Jacques Izopet, Ph.D.

Prof. Jacques Izopet, Ph.D.

Professor Jacques Izopet and his team are exploring the use of the GS Junior System to advance their study of minority variants in HIV and hepatitis viral domains.

Purpan IFB | France

Europe: France

Prof. Jacques Izopet, Ph.D.

Prof. Jacques Izopet, Ph.D.

Professor Jacques Izopet and his team are exploring the use of the GS Junior System to advance their study of minority variants in HIV and hepatitis viral domains.

“We chose the GS Junior System because of our interest in optimizing methodologies for HIV tropism determination using next-generation sequencing technology.”

We have found the system to be particularly powerful for our research on detection of viral quasispecies in HIV and hepatitis, and also for whole viral genome sequencing.

The GS Junior System allows our lab to pursue studies that were simply not possible using standard methodologies due to technical, cost and practicality reasons. Using this platform, we can answer specific scientific questions in a rapid, cost-effective manner. After a first period of optimization and familiarization, the utility of the system is truly appreciated by our team.

Publications

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Cedric Szpirer, Ph. D.

Cedric Szpirer, Ph. D.

Cedric Szpirer, CEO at Delphi Genetics, and the R&D team are using the GS Junior System to sequence the complete genomes of bacterial strains designed by the company for high-yield bioproduction.

Delphi Genetics SA | Belgium

Europe: Belgium

Cedric Szpirer, Ph. D.

Cedric Szpirer, Ph. D.

Cedric Szpirer, CEO at Delphi Genetics, and the R&D team are using the GS Junior System to sequence the complete genomes of bacterial strains designed by the company for high-yield bioproduction.

“The long reads of the GS Junior System have allowed us to identify repeat sequences and missing parts of the genome that are essential in microbial genetics. Even after a single sequencing run, we can produce assemblies with very few contigs and gaps.”

Delphi Genetics develops innovative technologies for the life science market and for large-scale biopharmaceutical production. In particular, we are developing new E. coli strains with modified genomes containing our StabyExpress technology, already licensed to Sanofi-Pasteur and GSK, which improves the yield of protein and DNA production without the use of antibiotics.

We are using the GS Junior System to perform complete genome sequencing of our uniquely designed bacterial strains, allowing for the first time the development of an antibiotic-free production process that uses completely characterized material. We are convinced that the genetic characterization of the microbial hosts in bioproduction will be increasingly important to regulatory agencies in the near future.

We are now able to completely characterize bacterial strains and then use that genome sequence to make the link between a specific phenotype and the genotype. We have already sequenced several E. coli strains and are impressed by the accuracy of the results.

The long reads of the GS Junior System have allowed us to identify repeat sequences and missing parts of the genome that are essential in microbial genetics. Even after a single sequencing run, we can produce assemblies with very few contigs and gaps. The subsequent work to identify junctions and complete the assembly is therefore much simpler and faster than with other sequencing technologies.

Dr. Ralph Oehlmann, Director Business Development, IMGM Laboratories GmbH

Dr. Ralph Oehlmann

Director Business Development

IMGM Laboratories is using the GS Junior System for targeted resequencing services.

IMGM Laboratories GmbH | Germany

Europe: Germany

Dr. Ralph Oehlmann, Director Business Development, IMGM Laboratories GmbH

Dr. Ralph Oehlmann

Director Business Development

IMGM Laboratories is using the GS Junior System for targeted resequencing services.

“As a genomic service provider, we decided on the GS Junior system because we needed a robust and powerful work horse for our professional targeted resequencing services.”

The combination of GS Junior, Fluidigm Access Array platform and our professional assay design pipeline enables us to offer our customers a fast, flexible and cost effective targeted resequencing service.

Currently, we are successfully developing and validating resequencing assays for single genes or gene panels, which can readily be used as plug-in applications.

The GS Junior’s long reads, high data quality and short turn-around-times are the features we love most - therefore, we give it a thumbs-up!

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Prof. Neil Hall

Prof. Neil Hall

Professor Neil Hall, Director of the Centre for Genomic Research at Liverpool, is using the GS Junior System for metagenomic analysis of complex environmental samples.

University of Liverpool | England

Europe: England

Prof. Neil Hall

Prof. Neil Hall

Professor Neil Hall, Director of the Centre for Genomic Research at Liverpool, is using the GS Junior System for metagenomic analysis of complex environmental samples.

“We are using the GS Junior System to investigate diversity within microbial communities isolated from a range of environments.”

The instrument provides us not only with the longer read length required for accurate species determination, but also allows us to quickly and efficiently process samples that only require comparatively fewer numbers of reads.

We chose the system in our laboratory because we needed a benchtop instrument for smaller projects to complement our larger next-generation sequencing platforms.

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Janelle Noble, Ph.D.

Janelle Noble, Ph.D.

Dr. Janelle Noble and her team are researching the genetic basis of susceptibility to complex diseases and conditions, with a particular emphasis on type 1 diabetes in underserved populations, including African American and Hispanic children.

Children’s Hospital Oakland Research Institute | United States

North America: United States

Janelle Noble, Ph.D.

Janelle Noble, Ph.D.

Dr. Janelle Noble and her team are researching the genetic basis of susceptibility to complex diseases and conditions, with a particular emphasis on type 1 diabetes in underserved populations, including African American and Hispanic children.

“The focus of our lab is on understanding the role of genes, particularly HLA, in complex, autoimmune diseases such as type 1 diabetes.”

Our previous experience with the GS FLX System revealed to us that the long reads produced by 454 systems are critical for high-resolution, high-throughput genotyping of this highly variable genomic region. Now that we have access to this technology in our lab with the GS Junior System, we are in control of our own scheduling and can manage multiple projects simultaneously. The system allows us to generate data with significantly higher resolution than we were able to get with our previous genotyping system, allowing us to generate more accurate data for our own projects and those of our collaborators.

Our research has demonstrated that one must consider the combination of all of HLA-encoding genes on both chromosomes to fully understand how HLA is associated with T1D susceptibility. Studying a single gene is not sufficient to understand risk for complex diseases. The GS Junior System affords the flexibility to obtain a high-resolution picture of a variety of genes in a single run, or to generate single-locus data on many samples. With the system, we can quickly generate data that allow us to compare populations and individuals, which is essential to understanding both the disease itself and the way genes influence disease risk.

Ultimately, the ways in which our genes confer susceptibility to disease is a complicated web, which we are beginning to unravel with the aid of cutting edge DNA sequencing technology like the GS Junior System.

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Simon Lee, Ph.D.

Simon Lee, Ph.D.

Dr. Lee and his team are using the GS Junior System for a range of sequencing applications, including metagenomics, transcriptome sequencing and whole genome sequencing.

University of Macau | China

Asia: China

Simon Lee, Ph.D.

Simon Lee, Ph.D.

Associate Professor, Institute of Chinese Medical Sciences, University of Macau

Dr. Lee and his team are using the GS Junior System for a range of sequencing applications, including metagenomics, transcriptome sequencing and whole genome sequencing.

“The GS Junior System has been a great fit for our lab due to the long read lengths and affordable price per run. We are using the system for a wide variety of projects, including metagenomics, transcriptome sequencing and viral genome sequencing.”

Since receiving the instrument, we’ve already initiated quite a lot of projects in our laboratory. The system has been particularly useful in speeding up the discovery of novel genes and microbial identification.

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Prof. Marcus Frohme

Prof. Marcus Frohme

Prof. Marcus Frohme and the sequencing specialist Markus Grohme are using the GS Junior System in various projects, such as bacterial genome sequencing or de novo micro-satellite discovery in various genomes for ecological studies.

University of Applied Sciences Wildhau (FH) | Germany

Europe: Germany

Prof. Marcus Frohme

Prof. Marcus Frohme

Prof. Marcus Frohme and the sequencing specialist Markus Grohme are using the GS Junior System in various projects, such as bacterial genome sequencing or de novo micro-satellite discovery in various genomes for ecological studies.

“We chose the GS Junior System because of its long reads and the flexibility of its broad application range.”

At the moment we are using the GS Junior mainly for shotgun sequencing projects and the long and accurate reads have allowed us to identify many potential micro-satellite marker sequences in a single run. Therefore, in a few days we can go from DNA sample to the first micro-satellite candidates with minimal effort at a very low cost.

The flexibility of the GS Junior format makes it ideal for many applications in our laboratory and it seamlessly integrates into our existing projects. We are already planning amplicon sequencing projects to take advantage of the haplotype resolution the read length has to offer. We are very happy with the performance of the GS Junior System and had sequencing runs outperforming its specifications.

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Jon Warner, Ph.D.

Jon Warner, Ph.D.

Jon Warner and his team at the South East Scotland Genetics Service are using the GS Junior System to perform deep sequencing research on large sets of tumor samples.

South East Scotland Genetics Service | Scotland

Europe: Scotland

Jon Warner, Ph.D.

Jon Warner, Ph.D.

Jon Warner and his team at the South East Scotland Genetics Service are using the GS Junior System to perform deep sequencing research on large sets of tumor samples.

“The GS Junior was ranked #1 on our competitive tender, and had the ability to deliver long reads straight out of the box.”

We are using the GS Junior System to perform deep sequencing on tumor samples and we can now perform much larger scale oncology experiments than before. In an instrument with such a small footprint, we can sequence large numbers of sample in a single experiment.

We were able to get up and running very quickly. The protocols were very easy to follow and the GS Junior System met its specifications with ease.

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John Lester

John Lester

John Lester and his team at the Cambridge University Department of Biochemistry Sequencing Facility added a GS Junior System alongside their GS FLX System in order to accommodate the needs of customers with smaller sequencing projects.

Cambridge University | England

Europe: England

John Lester

John Lester

John Lester and his team at the Cambridge University Department of Biochemistry Sequencing Facility added a GS Junior System alongside their GS FLX System in order to accommodate the needs of customers with smaller sequencing projects.

“As a core facility using the GS Junior System we can now accommodate smaller projects at competitive pricing, and we can now turn around projects in a shorter time frame.”

The primary driver for the purchase of our GS Junior System was to be able to provide rapid delivery of results to our customers. As an existing GS FLX owner, the smaller capacity of the GS Junior System eliminates the need to wait for projects to fill the larger GS FLX plates.

Overall we have been very pleased with the GS Junior System. We were up and running very quickly and the whole process was very plug-and-play.

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Uwe John, Ph.D.

Uwe John, Ph.D.

Dr. Uwe John and his team use the GS Junior System to study both functional genomics and environmental diversity of marine microalgae. In particular, his team is exploring processes such as species’ interactions and the related environmental impact on natural communities.

Alfred Wegener Institute for Polar and Marine Research | Germany

Europe: Germany

Uwe John, Ph.D.

Uwe John, Ph.D.

Dr. Uwe John and his team use the GS Junior System to study both functional genomics and environmental diversity of marine microalgae. In particular, his team is exploring processes such as species’ interactions and the related environmental impact on natural communities.

“The GS Junior System is a great asset to our working group. Due to its physical compactness, we are able to exploit this system both in our laboratory, as well as on research cruises.”

Our general aims are to understand the underlying principles in how microbial eukaryotes cope with the changing marine environment, how/if they adapt, and why some groups are able to dominate the community. Thus, the use of a high-throughput sequencing platform enables us to generate the required data both quickly and flexibly.

The length of 454 Sequencing reads plays an important role in our research, as we need longer reads and flexibility in order to perform shotgun and amplicon analysis, as well as cDNA library sequencing. As we work with non-model organisms, it is crucial to have a high-throughput sequencing platform with long reads, and furthermore, one that is cost-efficient.

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Peer-reviewed Publications Using GS Junior

View the complete list of 454 Sequencing publications >