Technology Platforms

Bioinformatics Basel

Bioinformatics Basel

Contact Information:

Dr. Aleksei Mironov

University of Basel

Email: aleksei.mironov@unibas.ch

Bioinformatics Bern

Bioinformatics Bern

Contact Information:

Dr. Puneet Sharma

University of Bern
Department of Chemistry and Biochemistry
Room N427
Freiestrasse 3
CH-3012 Bern

Email: puneet.sharmawhatever@dcb.unibe.ch
Phone: +41 31 631 42 84

Bioinformatics Lausanne

Bioinformatics Lausanne

Contact Information:

Dr. Lies Chikhaoui

University of Lausanne

Email: lies.chikhaouiwhatever@unil.ch

 

Cryo-EM

Cryo-EM

Contact Information:

Dr. Daniel Böhringer

Head of the ETHZ Cryo-EM Knowledge Hub
ETH Zürich
ETH-Hönggerberg, HPM C51
Otto-Stern-Weg 3
CH-8093 Zürich

Email: boehringerwhatever@mol.biol.ethz.ch
Phone: +41 44 633 39 85

Website Cryo-EM Knowledge Hub

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.xtalwhatever@bioc.uzh

Website Protein Crystallization Center

Website Jinek Lab


mRNA Synthesis Platform

mRNA Synthesis Platform

Contact Information:

PD Dr. Steve Pascolo

Head mRNA Platform
University of Zürich URPP Translational Cancer Research
Department of Dermatology
University Hospital Zürich
Rämistrasse 100
CH-8091 Zürich

Email: steve.pascolowhatever@usz.ch

Website UZH URPP Tranlsational Cancer Research mRNA Platform

Next Generation Sequencing

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:

Dr. Pamela Nicholson

Institute of Genetics
Vetsuisse Faculty University of Bern
Bremgartenstrasse 109a
3001 Bern

E-Mail: pamela.nicholsonwhatever@vetsuisse.unibe.ch
Phone: +41 31 631 22 85

Website NGS Platform University of Bern

Nuclear Magnetic Resonance

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

ETH Zurich
Institute of Biochemistry
Biochemie II
HPP L15
Hönggerbergring 64
CH-8093 Zürich

E-Mail: antoine.clerywhatever@bc.biol.ethz.ch
Phone: +41 44 633 07 04

Website BNSP ETH Zürich

 

Proteomics

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.hellerwhatever@dbmr.unibe.ch
Phone: +41 31 632 84 04

Website PMSCF University of Bern

RNA Synthesis

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:

Moravcík Štefan

Institute of Pharmaceutical Sciences
ETH Zürich
ETH-Hönggerberg, HCI H 436
Vladimir-Prelog-Weg 1-5/10
CH-8093 Zürich

E-Mail: stefan.moravcikwhatever@pharma.ethz.ch

RNA Mass Spectrometry Platform

RNA Mass Spectrometry Platform

More info coming soon.

Contact
Prof. Dr. Sebastian Leidel
DCBP, University of Bern

sebastian.leidelwhatever@unibe.ch

Structural Mass Spectrometry Platform

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: leitnerwhatever@imsb.biol.ethz.ch
Phone: +41 44 633 2698

Website Structural Mass Spectrometry Platform