During the initial part of the course we will provide a general description of different methods related to the "omics" field. The presented techniques will be discussed in terms of their rationale, applicability and limitations. During the second part of the course, students will take part in hands-on rotations in participating technological platforms allowing them to put the theory into practice inside a laboratory environment.

The following topics will be covered during the theoretical and practical parts of the course:

General introduction to Omics

From genes to proteins

- Strategy of cloning for protein expression, production of proteins in different cellular settings.

- Purification of proteins by diverse methods.

- Quantity and quality controls of final protein samples by biophysical techniques.

Flow cytometry and cell sorting

- Basics of flow cytometry and cytometer subsystems.

- Principles of Multicolour flow cytometry including fluorescence and fluorochromes and appropriate experimental controls.

- Principles on cell sorting: why and how, technological principle, basic parts of a cell sorter.

Genomics and transcriptomics

Broad overview of genomics/transcriptomics techniques to investigate, at bulk and single cell levels:

- Gene expression (RNA-seq, qPCR).

- Epigenetic control of gene expression (ChIP-seq, ATAC-seq).

- Spatial organization of gene expression (spatial transcriptomics).

Proteomics

- Introduction to proteomics and mass spectrometry.

- Mass spectrometry-based proteomics workflows.

- Data analysis (search engines and databases, statistics, data visualization and result interpretation).

Bioinformatics

- Experimental design and sample nomenclature.

- Data clustering and its applications: theory and practice.

- Data formats and handling.

- Data quality control, analysis and visualization, mapping on reference genomes.

- Variant calling, peak calling, quantification, GSEA.

- Protein and transcript reference databases, nomenclature.

- Biological function knowledge, domains, structures, annotations and visualization.

- Evaluation of genetic mutation impact.

Omics (including single cell omics)

Bioinformatics

Quality control

Data analysis

Data interpretation

• Choose appropriate Omics technique(s) to design relevant experiment
• Apply the concept of data quality control
• Interpret the generated data
• Contextualise theoretical and technical concepts of the covered Omics techniques

• Use a work methodology appropriate to the task.
• Collect data.
• Plan and carry out activities in a way which makes optimal use of available time and other resources.
• Evaluate one's own performance in the team, receive and respond appropriately to feedback.

3 weeks of common theoretical lectures

11 weeks of practical rotation sessions in small groups in scientific platforms: Protein Production and Structure, Flow Cytometry, Gene Expression, Proteomics and Bioinformatics.

In-person attendance is expected for all practical rotation sessions

Lectures

Hands-on practical work during practical rotation sessions in scientific platforms

Reading articles

Project presentation

Written reports or oral presentations for rotation sessions during the semester.

Written exam during exam session.

• https://www.epfl.ch/research/facilities/ptpsp/https://www.epfl.ch/research/facilities/ptpsp/
• https://www.epfl.ch/research/facilities/cytometry/https://www.epfl.ch/research/facilities/cytometry/
• https://www.epfl.ch/research/facilities/gene-expression-core-facility/https://www.epfl.ch/research/facilities/gene-expression-core-facility/
• https://www.epfl.ch/research/facilities/proteomics-core-facility/https://www.epfl.ch/research/facilities/proteomics-core-facility/
• https://www.epfl.ch/research/facilities/ptbicc/https://www.epfl.ch/research/facilities/ptbicc/

• https://go.epfl.ch/BIOENG-519https://go.epfl.ch/BIOENG-519