Open Access

Single cell sequencing

Library preparation of up to 90 single cells using the smart-seq 2 protocol and subsequent sequencing on a HiSeq 2500 single read 50 bp lane. Analysis of results including separation and characterization of subpopulations.

Genomics / Next Generation Sequencing

Protein Quality Assessment Service 

A new service to evaluate the quality of protein samples for subsequent biophysical and biochemical experiments is provided. This service consists of a standard set of analysis techniques, analyzing protein purity, homogeneity and folding state. Introduction of this service should lead to a higher success rate of downstream experiments that require pure and homogeneous proteins.

Galaxy Workflow tool for NGS and imaging data analysis

Galaxy is a web-based easy-to-use bioinformatics analysis platform. We offer open access to the created installation including training of the involved scientists.

Data management solutions and making experimental data available through simple web interfaces for experimental labs

Open access to web applications LiteMol suite and ValTrendsDB. The application web pages contain interactive documentation, video guides and user support.

Motor function analysis with Motorater system

The MotoRater system by TSE-Systems allows for gold-standard gait analysis of mice as they walk across a runway or a ladder. Mice are briefly anesthetized, shaved and points of interest are marked with coloured pens such as the knee, ankle, elbow, etc.., and the mice are trained to walk across a runway or ladder while being videorecorded. Using SimiMotion software we can analyze the movement of each point in the 2D space, looking at the mouse from both sides and from below. The combination of movement and anatomical parameters (distances, angles during the movement, speed, gait pattern,..) is a valuable readout for  injury models and mouse models of e.g. Huntington’s or Parkinson’s disease or other neurodegenerative/neuromuscular disorders.

Pipeline for cognitive function

The Intellicage system by TSE-Systems allows for high-throughput screening of homecage behavior and cognitive performance (operant conditioning) in a social group (up to 16 mice simultaneously) with minimal handling by the experimenter. A multitude of conditioning protocols can be programmed using e.g. sucrose rewards or air puffs as negative feedback.

Pipeline for depression/anxiety-like behaviour

Using the Intellicage system by TSE-Systems (see also cognitive function pipeline), we can test for anxio-depressive-like behavior using a Vogel-water-lick conflict test in socially grouped mice by testing their reaction to punishment, which is often enhanced in anxio-depressive disorders.

Additionally, we can test the circadian rhythmicity (which often shows deviations in anxio-depressive disorders) by measuring the day and night activity and metabolic parameters in the PhenoMaster metabolic cages by TSE-Systems, and we can test for anhedonia in a sucrose preference test.

Functional imaging at high field

• Advanced processing of fMRI data
  (available at CEITEC MU/VBCF)

• Analysis of dynamic connectivity from both human and animal data
  (available at CEITEC MU/VBCF)

• Acquisition of functional MR images at ultra-high magnetic field strength 15.2 T
  (available at VBCF only)

• Acquisition of functional MR images with human scanners (3 T)
  (available at CEITEC MU only)

High-Resolution Imaging using cryo-electron microscopy

The Electron Microscopy Facility (EM) offers a variety of preparation techniques for biological samples of diverse origin. We examine the complex architecture of macromolecules, cells and tissues at nanometer resolution using state-of-the-art conventional and cryo-techniques for specimen preparation and visualization. Whether you are interested in quick sample screening or high resolution 2D or 3D imaging, we can help. Furthermore, we provide the processing of purified molecules for conventional and cryo-electron microscopy as well sample preparation for scanning electron microscopy.

The main objective of the Cryo-electron Microscopy & Tomography Core Facility is to establish a world-class facility for cryo-electron microscopy accessible also for external users. The centre will provide access to EM instrumentation set up for high-throughput image acquisition for single particle analysis as well as for the acquisition of cellular cryo-electron tomograms. Moreover, it will provide assistance to external users/collaborators in image processing (e.g. 3-D reconstruction, denoising, pattern recognition, segmentation, visualization). External user projects will be selected by peer review on the basis of scientific merit, technical suitability and feasibility. The centre will also offer training enabling non-specialists to develop the necessary skills. The high-end instrumentation and the team of experienced researchers will ensure expert services, user training and the cost-effective use of resources.

Improved in situ visualization of regions of interest in eukaryotic cells using HPF and cryo-FIB

This new service will allow researchers to examine the structure of a region of interest within a large biological samples - for example the nucleus of a eukaryotic cell - at high resolution and as close to the native state as possible today. Samples are rapidly frozen by High Pressure Freezing (HPF) and then a region of interest within this sample is "cut out" using a Focused Ion Beam (FIB). Finally the sample is transferred to a transmission electron microscope and the region of interest is examined by cryo-electron microscopy or -tomography to obtain unprecedented new 2D and 3D insights.

Custom made nanofabricated substrates for surface modified imaging/spectroscopy

TBD

High-resolution mechanical characterization of biological matter over various frequency regimes

We provide a correlative approach to obtain high resolution stiffness maps of biological samples under nearly physiological conditions. Mechanical approach given by atomic force microscopy (AFM) combined with optical microscopy (Brillouin microscopy, BFS) provides better view to distribution of elastic properties of living and biosamples.

Agar-plate screening system

Within the RIAT-CZ project, our PHENObox for side-view crop plant phenotyping was upgraded with a custom designed agar-plate sample holder facilitating semi-automated RGB screening of seedlings and root phenotyping. Corresponding image analysis algorithms were developed by using the LemnaTec software and are available at PlantS (VBCF). 

Environmental simulation and high-throughput plant phenotyping

Both Plant Sciences core facilities provide access to state-of-the-art and highly specialized plant growth chambers for environmental simulation and phenotyping analyses. 

At CEITEC MU, several chambers are capable of providing exceptional environmental conditions like low and high temperature stress, different light intensities and light spectra and different gas conditions (e.g. CO2 atmosphere). 

The VBCF PlantS Facility offers two of the completed pilot projects in one service. Their phytotrons are designed for simulation of complex global environments within the temperature limits of minus 15 °C and up to plus 30 °C.
In the framework of the RIAT-CZ project, several of the phytotrons were equipped with high-tech LED lights with adjustable light spectrum extending the simulation portfolio. Moreover, one of these phytotrons is equipped with a robotic high-throughput RGB plant phenotyping system. The subsequent analysis of the generated data including data visualization and statistics is done via the PHENOComp tool developed within RIAT-CZ.