Technology Platforms

Bioinformatics Basel

1. Support and discussion for experimental design

2. Functional genomics analyses

  • Genomic data pre-processing and alignment
  • RNA-seq - focus on differential expression analysis
  • small RNA-seq
  • ChIP-seq normalization, peak finding and profiling
  • RNA IP-seq (CLIP, RIP, etc.)
  • Ribosomal footprinting
  • Motif finding
  • Enrichment analyses (GO terms, genomic features)
  • Integration of publicly available datasets

Much of my work involves integrating different types of datasets, including publicly available data. In the past I have also done evolutionary and phylogenetic analyses, and I am generally happy to work with any type of genomic data!

Contact Information:

Dr. Sarah Carl

FMI Basel
Maulbeerstrasse 66
P.O. Box 3775
CH-4002 Basel

E-Mail: sarah.carl[at]fmi.ch
Phone: +41 61 69 75172

Bioinformatics Bern

1. Support and discussion for experimental design

2. Analysis of High-Throughput Sequencing Data (Application RNA-Seq)

3. Phylogenetic analysis and gene evolution

  • Aligning sequences
  • Estimating evolutionary distances
  • Detection of fixed mutations during gene evolution
  • Measuring the evolutionary rate of gene - Mutation accumulation likelihood
  • Building phylogenetic gene trees based on gene homology between species

Contact Information:

Dr. Walid Gharib

Interfaculty Bioinformatics Unit
University of Bern
Baltzerstrasse 6
CH-3012 Bern

E-Mail: walid.gharib[at]sib.swiss
Phone: +41 31 631 84 46

Bioinformatics Lausanne

More information to follow.

Contact Information:

Dr. Rene Dreos

University of Lausanne

Email: rene.dreos[at]unil.ch

Cryo-EM

Infrastructure:

  • FEI Vitrobot Vitrification device
  • FEI Morgagni Electron Microscope equipped with a CCD camera (100 kV)
  • FEI Tecnai F20 Cryo-electron Microscope equipped with a Gatan 4k CCD camera (200 kV)

Services provided:

  • Preparation and/or visualization of provided samples using negative stain techniques
  • Cryo-preparation of provided samples for cryo-electron microscopy
  • Eventual data collection and low resolution reconstruction from negative stained sample subject to negotiation
  • Advice on sample preparation and data collection for negative stain and cryo-electron microscopy

Contact Information:

Armin Picenoni

Institute of Molecular Biology & Biophysics
ETH Zürich
ETH-Hönggerberg, HPK H10.1
Otto-Stern-Weg 5
CH-8093 Zürich

E-Mail: armin.picenoni[at]mol.biol.ethz.ch

Crystallization

Workflow:

Infrastructure:

  • Robots for setting up crystallization experiments at 4°C and 20°C
  • Formulatrix RockImagers 1000 at 4°C and 20°C allowing for remote inspection
  • Formulator liquid handling/mixing robot
  • Extensive commercial screen and stock solution libraries
  • Manual crystallization setup at multiple temperatures
  • Access to the Swiss Light Source

Services provided:

  • Advice on sample preparation and inspection of crystals
  • Setup of crystallization screens for provided samples
  • Initial data collection at the Swiss Light Source
  • Full crystal optimization and data collection with subsequent structure determination possible on a collaborative basis with the Jinek lab

Contact Information:

Beat Blattmann, Dr. Marcello Clerici, Dr.Carmela Garcia Doval and Caroline Simmen

Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich

E-Mail: rna.xtal[at]bioc.uzh

Website Protein Crystallization Center

Website Jinek Lab

Next Generation Sequencing

Infrastructure:

  • Illumina HiSeq3000
  • Illumina MiSeq

Services provided:

  • Library Generation
  • Illumina sequencing
  • Additional types of sequencing experiments (e.g. Pacific Biosciences, IonTorrent, etc.) subject to negotiation

Contact Information:

Prof. Tosso Leeb

Institute of Genetics
Vetsuisse Faculty University of Bern
Bremgartenstrasse 109a
P.O. Box 8466
3001 Bern

E-Mail: tosso.leeb[at]vetsuisse.unibe.ch
Phone: +41 31 631 23 26

Website NGS Platform University of Bern

Nuclear Magnetic Resonance

Infrastructure:

  • 5 spectrometers with cryoprobe: 500MHz, 2x600MHz, 700MHz, 900MHz
  • 1 spectrometer without cryoprobe: 750MHz
  • Measurable nuclei: 1H, 13C, 31P, 2H, 19F and 15N (direct detection not recommended)

Services provided:

  • Expertise on production (e.g. isotope labeling) and preparation of NMR samples
  • Expertise on acquisition and analysis of NMR data

Contact Information:

Dr. Antoine Cléry

Institute of Molecular Biology & Biophysics
ETH Zürich
ETH-Hönggerberg, HPP L23
Otto-Stern-Weg 5
CH-8093 Zürich

E-Mail: aclery[at]mol.biol.ethz.ch
Phone: +41 44 633 07 04

Website BNSP ETH Zürich

Proteomics

Infrastructure:

  • 3 nanoLC-MS systems from Thermo (Fusion Lumos ETD, QExactive HF, QExactive)

Services provided:

  • Standard sample preparation for LC-MS
  • Protein identification
  • PTM analysis
  • Relative protein quantification (SILAC or label-free)
  • Basic results evaluation of proteomics data
  • Please enquire if you intend to do something that is not listed above

Contact Information:

PD Manfred Heller

KiKl D 841
PF 37, Inselspital
CH-3010 Bern

E-Mail: manfred.heller[at]dbmr.unibe.ch
Phone: +41 31 632 84 04

Website PMSCF University of Bern

RNA Synthesis

Infrastructure:

  • Two oligonucleotide synthesizers (phosphoramidite method)
  • Semi-preparative and preparative HPLC for purification
  • Quadrupole LC-coupled MS

Services provided:

  • Synthesis of new phosphoramidite building blocks
  • Preparation of modified oligonucleotides (Synthesis scale 50 nmol to 0.5 µmol)
  • Preparation of selected modified oligonucleotides in 96-well format for screening

Contact Information:

Dr. Pascal Röthlisberger

Institute of Pharmaceutical Sciences
ETH Zürich
ETH-Hönggerberg, HCI H 423
Vladimir-Prelog-Weg 1-5/10
CH-8093 Zürich

E-Mail: pascal.roethlisberger[at]pharma.ethz.ch

Structural Mass Spectrometry Platform

Services provided:

  • Crosslinking of segmentally isotope-labeled RNA and tandem mass spectrometry (CLIR-MS/MS) method (G. Dorn, A. Leitner et al. (2017) Structural modeling of protein-RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS Nature Methods, 14(5):487-490 Pubmed)
  • Cross-linking of protein-protein complexes mass spectrometry (XL-MS) 

Contact information:

Dr. Alexander Leitner

Institute of Molecular Systems Biology
ETH Zurich
ETH Hönggerberg, HPT E53
Auguste-Piccard Hof 1
CH-8093 Zurich

Email: leitner[at]imsb.biol.ethz.ch
Phone: +41 44 633 2698