Next Generation Sequencer für Transkriptomanalysen

• Subject Area: Basic Research in Biology and Medicine
• Term: Funded in 2009
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 161267332

• Final Report Year: 2014

Final Report Abstract

Signaling networks control key decisions during development of organisms and are often mutated in cancer. We made use of recent technological advancements to systematically investigate signaling pathways. Next generation sequencing approaches was primarily used for transcriptome profiling to dissect the changes in transcriptional patterns after perturbing signaling pathway components. The next generation sequencer was primarily used in three large-scale projects: (1) we generated several hundred transcriptome profiles after perturbing signaling and transcription factors that are implicated in inflammatory and apoptotic pathways with the goal to understand how different signaling branches determine the transcriptional output in a time-dependent manner. Nested-effect modeling was used to establish models of pathway topology. (2) We analyzed the transcriptional effects of Wnt signaling pathways after stimulation with ligands and depletion of downstream pathway components, and (3) we used sequencing for a de novo assembly of the transcriptome of the planarian Schmidtea mediterranea. In addition, we established workflows to generate multiplexed RNAseq libraries in a semi-automated manner.

Publications

• The head-regeneration transcriptome of the planarian Schmidtea mediterranea. Genome Biology 12:R76
  Sandmann, T., Vogg, M.C., Owlarn, S., Boutros, M., Bartscherer, K.
  
• The Wnt secretion protein Evi/Gpr177 promotes glioma tumorigenesis. EMBO Molecular Medicine 4:38-51
  Augustin, I., Goidts, V., Bongers, A., Kerr, G., Vollert, G., Radlwimmer, B., Hartmann, C., Herold-Mende, C., Reifenberger, G., von Deimling, A., Boutros, M.
  
• Wnt secretion is required to maintain high levels of Wnt activity in colon cancer cells. Nature Communications 4:2610
  Voloshanenko, O., Erdmann, G., Dubash, T.D., Augustin, I., Metzig, M., Moffa, G., Hundsrucker, C., Kerr, G., Sandmann, T., Anchang, B., Demir, K., Boehm, C., Leible, S., Ball, C.R., Glimm, H., Spang, R., Boutros, M.