BIO 675 RNA Next Generation Sequencing

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.

Allgemeine Informationen

The aim is to help students, researchers and medical professionals master fast developing NGS techniques.
The practical consists of a library preparation starting from total RNA, enrichment of polyA RNA and a sequencing run on a bench top sequencer, together with an introduction to the analyses of the resulting data and exercises. The lectures cover NGS technologies, their applications and data analysis principles.

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
This course is for PhD students accepted to one of the PhD programs of the Life Science Zurich Graduate School. Basic biology and lab techniques knowledge is required. As the places in this course are very limited we give priority to students who are in the beginning of their PhD studies.
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
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
PhD students of the Life Science Zurich Graduate School have priority. External students can register to the waiting list and will be accepted if the course is not fully booked.
ECTS: 2.0

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