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 Zürich

1. Support and discussion for experimental design

2. Analysis of high-throughput data

  • RNAseq data analysis (raw data pre-processing, alignment, differential expression analysis, differential splicing analysis, pathway analysis)
  • Gene expression microarray data analysis (differential expression analysis, pathway analysis)
  • Methylation arrays/sequencing data analysis (differential methylation, allele-specific methylation)
  • Nanostring analysis (differential abundance analysis)
  • ChIPseq data analysis (differential binding)
  • CRISPR-Cas9 screening (targeted amplicon sequencing)
  • CyTOF analysis
  • PacBio sequencing analysis (targeted cDNA sequencing)
  • Submission of raw data to public repositories

Contact Information:

Dr. Helen Lindsay

Institute of Molecular Life Sciences
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich

E-Mail: helen.lindsay[at]uzh.ch
Phone: +41 44 635 4879

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:

Alain Scaiola

Institute of Molecular Biology & Biophysics
ETH Zürich
ETH-Hönggerberg, HPK H5
Otto-Stern-Weg 5
CH-8093 Zürich

E-Mail: scaiola[at]mol.biol.ethz.ch
Phone: +41 44 633 31 48

Crystallization

Infrastructure:

  • Sitting-drop crystallization robots at 4°C and 19°C supporting 96-well format
  • Formulator liquid handling/mixing robot at 19°C supporting 24 and 96-well format
  • Extensive commercial screen and stock solution libraries
  • Manual crystallization setup at multiple temperatures

Services provided:

  • Setup of crystallization screens for provided samples
  • Advice on sample preparation and inspection of crystals

Contact Information:

Tanja Schönhut

Institute of Molecular Biology & Biophysics
ETH Zürich
ETH-Hönggerberg, HPK H5
Otto-Stern-Weg 5
CH-8093 Zürich

E-Mail: tanja.schoenhut[at]mol.biol.ethz.ch
Phone: +41 44 633 29 24

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. Elodie Decuypere

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

E-Mail: elodie.decuypere[at]pharma.ethz.ch
Phone: +41 44 633 67 89