Zentrum für Quantitative Biologie

Services

Next Generation Sequencing (DNA/RNA)

  • Library preparation (including quality control and validation)
    • Genomic libraries with different insert lengths or PCR free
    • RNA-Seq libraries
    • Chip-Seq libraries
  • DNA/RNA sequencing using Illumina MiSeq, HiSeq 2500, HiSeq 3000 and NovaSeq platforms, as well as PacBio Sequel and Oxford Nanopore sequencing.

Proteomics

  • Sample preparation for proteomics
    • Enzymatic digest
    • Fractionation of proteins (1D-PAGE) and peptides (isoelectric focussing (IEF))
  • Quantitative shotgun proteomics assays
    • Stable isotope labeling of aminoc acids in cell culture (SILAC)
    • Label-free quantification
  • LC-MS/MS measurements on high resolution platforms
    • Thermo Fisher LTQ-Orbitrap XL
    • Thermo Fisher LTQ-Orbitrap Elite
    • Thermo Fisher Q-Exactive plus
  • Quantitative targeted proteomics
    • Targeted MS2 assays using Thermo Fisher q-Exactive plus
  • Analysis of postranslational modifications (PTM)
  • Routine analysis of phosporylated proteins via TiO2 enrichment of peptides

Metabolomics

  • Metabolomics profiling of metabolites (untargeted Metabolomics)
    • Waters Synapt G2
  • Targeted metabolomics
    • Absolute quantification using Biocrates chemistry
    • Quantification using multiple reaction monitoring (MRM)

Data Management & IT

  • Transfer, storage and user-authorized access to large OMICS data
    • OpenBIS is used as a central data management facility. Data moving is done using Rsync routines as part of the OpenBIS data mover
  • Web-portal-based data access to data and analysis pipelines
    • Liferay is used as Portal solution
    • gUSE is in use a production workflow system and as an interface the high-performance-computing (HPC) cluster

Bioinformatics Analysis

Structural Biology

  • Small-Angle X-ray Scattering (SAXS)
    • Structure of materials (crystalline, amorphous, or porous)
    • Solution structure of nanoparticles, colloids, surfactant, polymer or biomacromolecules (protein or DNA)
    • Kinetics of phase transition, self-assembly, etc.

Small-Angle X-ray Scattering is a powerful technique to study the structure and interactions of various systems with a typical size on the order of 1 nm to 100 nm. Particularly the properties of biological macromolecules such as DNA and proteins can be determined by SAXS. For more information about SAXS/WAXS please visit the following website:

http://www.soft-matter.uni-tuebingen.de/index.html?saxs.html