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Humboldt-Universität zu Berlin - SYSTHER

Methods


Transcriptomics

We use DNA microarrays to measure of the activity (= expression) of thousands of genes simultaneously to create a global picture of cellular status with respect to the mRNA profile. Comparison of these gene expression profiles (e.g. normal vs disease) allows the identification of genes that are differentially expressed in between the investigated stages or conditions.
 

 

Illumina Arrays

Metabolomics

The metabolome is the entirety of small molecules present in an organism and can be regarded as the ultimate expression of its genotype in response to environmental changes. Metabolomics is the comprehensive analysis of the small molecules that compose an organism's metabolism. Metabolite profiling is performed in collaborations with experts from the MPIMP in Potsdam/Golm and metanomics. We focus on mass spectrometry in combination with several separation techniques such as gas chromatography or liquid chromatography.

 Metabolite Profile
 

Peptide Arrays

Proteins play key roles in essentially all cellular processes. In many cases, the biological activities of the proteins can be recapitulated by shorter peptides that are taken from the primary sequences. We use arrays representing synthetic peptide libraries as a tools for identifying biologically interesting patterns and for profiling cellular activities.
 

 

 peptideArrays
 

Phenotypical Characterization of Cells

To monitor the behaviour of our experimental systems, a broad range of phenotypical parameters is tested for their potential to  describe the system. Appropriate markers and assays are selected and constantly measured and applied to characterize the system phenotypically. This includes for instance the characterization of cells based on suitable markers, as well as migration, differentiation and proliferation assays.   

spheroidsMigration
 

Bioinformatics / Informatics

A tremendeous amount of high-thoughput data representing different data types is generated in the project. These data needs to be stored, integrated and analyzed. We developed a database for the storage and analysis of the SYSTHER data that is accessible for all partners within the consortium. Gene expression data is analyzed to identify genes that differentially expressed and pathways that are influenced in the conditions that are investigated. We apply standard analysis approaches and develop new algorithms e.g. to integrate data of different sources and derive biologically meaningful hypotheses out of the analysis. 
 Heatmap
 

Systems Biology

Systems Biology focusses on the systematic study of complex interactions in biological systems. Based on the data generated from our experimental systems, selected parts and modules will be identified that will be studied and described in detail to develop a model.
eryModel