RNA Next Generation Sequencing

Course Description

This five day practical course consists of a library preparation starting from total RNA, followed by a sequencing run on a bench top sequencer. An introduction to the analyses of the resulting data and some exercises will be offered too. The lectures cover existing and upcoming NGS technologies, their applications and the principles of downstream data analysis

The data analysis part starts off from the raw reads, as generated by the instrument, and cover pre-processing, alignment, several quality control checkpoints, transcripts expression quantification and differential expression analysis, and comparison of bulk RNA-seq versus single cell RNA-seq.

By the end of the course participants should be able to make informed decisions about which technology and workflow to apply to solve specific research questions.

Course Programme

Library Prep

• PolyA RNA-seq
  library generation: principles and types

Sequencing

• Detailed description of available 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)
• Introduction to single cell RNA-seq data analysis 
• IT and awareness of the data storage and its size

Didactical approach

The course is conceived as highly interactive which includes:

• Theoretical inputs (lectures)
• Interactive discussions on case studies (group discussions)
• Pair and group work in the laboratory
• Instrument handling for the practical part
• Hands-on activities for data analysis (computer sessions)
• Q&A sessions, feedback and discussions with other participants and instructors
• Flash presentations by means of whiteboards or slides

Learning outcomes

At the end of the course, participants will be able to:
1. Demonstrate an understanding of NGS technologies;

2. Assess the challenges involved in investigating the transcriptome;

3. Perform library preparation and sequencing procedures in the laboratory;

4. Assess the quality of the library as well as the data obtained;

5. Perform basic data analysis using the Sushi pipeline;

6. Compare bulk RNA-seq and single cell RNA-seq workflow and data;

7. Apply NGS 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
   c. presenting their strategy to the class

Important facts and how to apply

Costs Transcriptomics Course (Practical Part and Data Analysis)

PhD Students UZH or ETHZ CHF 300

Postgraduate Member UZH or ETHZ CHF 500

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

Other academics (non-UZH, non-ETHZ) CHF 1200

Industrial delegates CHF 1500

An invoice will be issued. Those participants that register will be sent an email with an ‘Application Form’ to be signed by their correspondent supervisor and e-mailed back to the FGCZ as PDF. Upon receiving the signed ‘Application Form’, the participant will be considered and their place in the course will be confirmed.

Cancellation policy

Please note that due to the high demand for this course any change related to your participation should be informed as soon as possible, but not later than ten (10) working days prior to the course start date. The notice must be e-mailed to .

If the cancellation of the course occurs after this time period, the tuition fee will not be refunded.