The first PROTrEIN winter school will take place between the 3rd and 11th of February 2022 at the Functional Genomics Center Zurich, Switzerland and is composed of the following two modules:

3rd – 5th of February: Consortium Meeting

7th – 11th of February: Integrative Omics Course

Description Integrative Omics Course

Functional genomics aims to identify the function of genes in a given organism by combining an array of different -omics techniques such as transcriptomics and proteomics. As a joint state-of-the-art research and training facility of the ETH and of the University of Zurich, the Functional Genomics Center Zurich (FGCZ) offers a five-day course with hands-on practicals. The aim of this course is to help scientists interested in transcriptomics and proteomics technologies and their data integration to gain a better understanding, not only on the techniques available and their applications, but also to help in the interpretation of these – omics data. The transcriptome and proteome of yeast grown either with glucose or a nonfermentable substrate will be analyzed, using Next-generation sequencing (NGS) technologies and labelfree quantitative proteomics using high-resolution mass spectrometry (MS) respectively. The correlation and integration of the resulting data will be addressed. This course is not meant to replace any manufacturers’ training normally supplied with any instrument. The hands-on sessions for data analysis does neither require a pre-existing knowledge of Unix nor the command line environment. This course is not intended to be a training course for those solely interested in bioinformatics either.

Transcriptomics

Short lectures will cover present NGS technologies, their applications and the principles of downstream data analysis. The practical consists of a complete transcriptomics workflow. This involves, the library preparation and sequencing run, followed by processing of the data for transcript expression quantification and differential expression analysis.

Proteomics

The theoretical part covers the complete proteomics workflow from experimental design, samples preparation, data acquisition, towards data analysis. The practical part will allow the participants to perform sample preparation in proteomics from protein extract to the purified peptide sample ready for MS analysis. The students will be introduced to nanoLC– MS/MS analysis and data analysis using data base search algorithm.

-Omics Data Integration

The results of the transcriptomics part and the proteomics part will be integrated together in several aspects. The integrated data analysis consists of direct feature and functional overlap as well as a joint pathway analysis. Most of the tools that we will use are open source/(free to use) and considered as ‘state of the art’.

Instructors

Dr. Jonas Grossmann, Dr. Bernd Roschitzki, Dr. Lucy Poveda, Lennart Optitz