Integrative-Omics practical course: From the transcriptome to the proteome

Course Description

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 label-free 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’.

Course Program

Transcriptomics

Library Prep

• PolyA RNA-seq library generation: principles and types

Sequencing

• Sequencing technologies platforms

• Hands-on laboratory work: preparing and performing sequencing runs

Data analysis

• Run QC: Criteria for run performance and quality of data

• Preprocessing of the raw data

• Mapping the data to a reference,

• Mapping quality control for RNA-seq data

• Transcripts expression quantification and tests for differential expression

• Set-based analysis (e.g., pathways, GO-categories)

• IT and awareness of the data storage and its size

Proteomics

Sample preparation

• Protein reduction, alkylation, and enzymatic digestion

• Peptide clean-up

MS analysis

• Handling of high-resolution nanoLC-MS/MS system

Data analysis

• Performance and quality control of nanoLC-MS/MS system

• Data base search algorithm for protein identification

• Quantitative data quality control

• Differential protein expression

• IT and awareness of the data storage and its size

-Omics Data Integration

• Feature overlap of differential expression

• Functional categorization and characterization of the different levels

• Joint pathway analysis

Learning outcomes

At the end of the course, participants will be able to:
1. Demonstrate an understanding of NGS and MS technologies;
2. Assess the challenges involved in investigating the transcriptome and the proteome;
3. Perform sample preparation in the laboratory;
5. Assess the quality of the sample as well as the data obtained
6. Perform basic data analysis 
7. Apply NGS and MS into a research-based context by:
a. formulating a meaningful research question
b. designing an experimental setup (based on the analytical techniques learned during the course) to address this specific question on transcriptomics and proteomics
c. presenting their strategy to the class

Participants

The course is limited to 8 participants only.

Target audience and prerequisites

Applicants should be postdoctoral scientists, PhD students or masters students actively engaged in or soon to commence research involving next generation sequencing technology and mass spectrometry.

Please note, that the above prices can only be applied if the tuition fee is paid through an internal, i.e. University of Zurich or ETHZ, account (valid Kostenstelle/PSP-Element).

An invoice will be issued upon registration. Registered participants will receive an email containing an “Application Form”, which must be signed by their respective supervisor.

The signed form should then be returned to the FGCZ via email as a PDF. Only upon receipt of the signed “Application Form”, will the participant’s registration be considered complete, and their place in the course officially confirmed.

Cancellation Policy

Please note that, due to the high demand for this course, any change  related to your participation must be communicated as soon as possible, but not later than twenty (20) working days prior to the course start date. The notice must be sent via email to . If the cancellation of the course occurs after this time period, the tuition fee will not be refunded. 

Changes to the course dates

The FGCZ reserves the right to postpone the course to a later date should the number of applicants be lower than six.