Location & dates EMBL Heidelberg, Germany 15 - 18 May 2018
Deadlines Application closed

EMBL Courses and Conferences during the Coronavirus pandemic

With the onsite programme paused, many of our events are now being offered in virtual formats.

Registration is open as usual for many events, with back-up plans in place to move further courses and conferences online as necessary. Registration fees for any events affected by the COVID-19 disruption are fully refundable.

More information for participants of events at EMBL Heidelberg can be found here.

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.


During this course we will focus on the following aspects:

  • Preparation of high-qualithy single-cell suspensions
  • 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

This course is co-organized with 10x Genomics.


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

Founder partners

  • Leica logo
  • Olympus logo

Corporate partners

  • 10x Genomics_120x82
  • Becton Dickinson logo
  • Bio-Rad logo
  • Boehringer Ingelheim logo
  • Eppendorf logo
  • GSK logo
  • Milteniy Biotec logo
  • NetApp logo
  • Stilla logo
  • ThermoFisher logo

Associate partners

  • Merck logo
  • New England Biolabs logo
  • Nikon logo
  • Promega logo
  • Roche logo
  • Sanofi logo
  • Sartorius logo