Type: Practical with Student Seminar

Date: 30.04.-18.05.2012

Location: TP3 (INF 580)

Hosts/Supervisors: Martina Schnölzer, Tore Kempf, Christoph Rösli; Ulrike Korf, Stefan Wiemann; Ruprecht Kuner, Holger Sültmann (contact: r.kuner@dkfz.de, u.korf@dkfz.de, s.wiemann@dkfz.de)

Topics:

Functional genomic research collects qualitative and quantitative genomic as well as proteomic data and translates this into information about the dynamics, interactions and functions of macromolecules within biological networks. This practical presents an overview of up-to-date genomic and proteomic technologies and their application in high-throughput biology and cancer research.

Content:

Module 1 – Qualitative and quantitative proteomics
(supervisors: Martina Schnölzer, Tore Kempf, Christoph Rösli):
Protein separation of cancer cell line samples by gel electrophoresis, in-gel and in-silico digestion of proteins, protein identification, peptide fragmentation and sequencing by mass spectrometry, comparison of gel-based and mass spectrometry-based techniques for protein quantitation.

Module 2 – Quantitative analysis of gene and protein expression in cellular signaling
(supervisors: Ulrike Korf, Daniela Berg, Christian Quack, Stefan Wiemann):
Targeting of protein kinases using siRNA or miRNA knockdown, validation by quantitative RT-PCR, Western-Blot, and quantitative protein arrays (RPPA); analysis of phenotypes by luciferase assay and high-content screening microscopy assays; data analysis tools.

Module 3 – Comprehensive gene and microRNA analysis in cancer, validation and bioinformatics
(supervisors: Ruprecht Kuner, Stephan Gade, Holger Sültmann):
Extraction, quantification and quality control of total RNA and microRNA; activation and inhibition of specific microRNAs in cancer cell lines; validation of microRNA and gene expression by qRT-PCR; microarray analysis of genes and microRNAs; statistical analyses of microarrays (LIMMA, classification); data mining (gene ontology, gene interaction networks, target gene prediction)