Gene expression at single-cell resolution – Cancelled – Course and Conference Office

EMBL Course

Gene expression at single-cell resolution – Cancelled


We are sorry to inform you that we have to cancel this course, and apologise for the inconvenience.

Course overview

The goal of this course is to provide participants with both the theory and practical skills required to design, prepare, run and analyze high-throughput single cell transcriptomic experiments using the Chromium Single Cell Controller from 10x Genomics. We will begin with a general introduction on the topic, including the cell partitioning technology, fundamentals of NGS, and the library preparation workflow. The hands-on session starts with cell handling followed by the preparation of transcriptome libraries from single-cells with a focus on best practices. Finally, we will quantify and quality control the prepared libraries, before sequencing on a NextSeq instrument. The final day will be dedicated to single-cell data analysis with a mixture of theory and hands-on experience using the Loupe Cell Browser from 10x Genomics.


This course is directed towards biologists, scientists and technicians who want to apply single-cell transcriptome sequencing and learn the basics of library preparation. Knowledge of next generation sequencing technology and cell culture is desirable but not essential.


  • Preparation of high-quality single-cell suspensions, flow cytometry
  • Best practices and “tips and tricks” for preparation of 3’-tagged RNA-Seq libraries from single cells for whole transcriptome gene expression analysis
  • Best practices of sequencing library validation
  • Introduction to single cell transcriptome data analysis

Learning outcomes

After this course you should be able to:

  • Prepare libraries from cell cultures for single-cell whole transcriptome analysis
  • Apply quality controls and library quantification
  • Know the basics of single-cell transcriptome data analysis

Date: 25 - 29 Jul 2022

Location: Other

Venue: Copenhagen


  • Vladmir Benes
    EMBL Heidelberg, Germany
    • Malte Paulsen
      Novo Nordisk Foundation Center for Stem Cell, Denmark

EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

Corporate partners

Associate partners