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SIB Swiss Institute of Bioinformatics

4 ARTICLES PUBLISHED IN JoVE

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Medicine

Improved Protocol For Laser Microdissection Of Human Pancreatic Islets From Surgical Specimens
Dorothée Sturm 1,2, Lorella Marselli 3, Florian Ehehalt 1,2, Daniela Richter 1, Marius Distler 2, Stephan Kersting 1,2, Robert Grützmann 2, Krister Bokvist 4, Philippe Froguel 5, Robin Liechti 6, Anne Jörns 7, Paolo Meda 8, Gustavo Bruno Baretton 9, Hans-Detlev Saeger 2, Anke M. Schulte 10, Piero Marchetti 3, Michele Solimena 1
1Molecular Diabetology, Paul Langerhans Institute Dresden, 2Department of GI-, Thoracic- and Vascular Surgery, University Hospital Carl Gustav Carus, University of Technology Dresden, 3Department of Endocrinology and Metabolism, Metabolic Unit University of Pisa, 4Labs DC0522, Lilly Corporate Center, 5Genomics, Faculty of Medicine Imperial College London, 6Vital-IT, SIB Swiss Institute of Bioinformatics, 7Clinical Biochemistry, Hannover Medical School, 8Cell Physiology and Metabolism, Medical School, University of Geneva, 9Department of Pathology, University Hospital Carl Gustav Carus, University of Technology Dresden, 10R&D DIAB Division / Translational Medicine, Sanofi-Aventis

Laser microdissection is a technique that allows the recovery of selected cells from minute amounts of parenchyma. Here we describe a protocol for acquiring human pancreatic islets from surgical specimens to be used for transcriptomic studies. Our protocol improves the intrinsic autofluorescence of human beta cells, thus facilitating their collection.

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Cancer Research

Micromanipulation of Circulating Tumor Cells for Downstream Molecular Analysis and Metastatic Potential Assessment
Cinzia Donato *1, Barbara M. Szczerba *1, Manuel C. Scheidmann *1, Francesc Castro-Giner 1,2, Nicola Aceto 1
1Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 2SIB Swiss Institute of Bioinformatics

Here, we present an integrated workflow to identify phenotypic and molecular features that characterize circulating tumor cells (CTCs). We combine live immunostaining and robotic micromanipulation of single and clustered CTCs with single cell-based techniques for downstream analysis and assessment of metastasis-seeding ability.

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Biology

Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV
Sara Cristinelli 1, Paolo Angelino 2, Angela Ciuffi 1
1Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 2Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics

The role of RNA modifications in viral infections is just starting to be explored and could highlight new viral-host interaction mechanisms. In this work, we provide a pipeline to investigate m6A and m5C RNA modifications in the context of viral infections.

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Biology

Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions
Frédérique Lisacek 1,2,3
1Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 2Computer Science Department, University of Geneva, 3Section of Biology, University of Geneva

This protocol illustrates how to explore, compare, and interpret human protein glycomes with online resources.

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