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

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

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.