Microbial single cell genomics workshop – from environment to infection


National course. The course is open for current and potential facility users such as PhD students, postdocs, group leaders and core facility staff within all Swedish universities, with an interest in single cell genomics. The course includes both theoretical and practical components.

This course is supported by SciLifeLab and run by the SciLifeLab Microbial Single Cell Genomics facility in Uppsala.

Application form

Important dates

Application open: June 27

Application deadline: September 16

Confirmation to accepted participants: September 20

Course responsible: Claudia Bergin, Anna-Maria Divne and Johan Ankarklev

If you don’t receive information according to the dates above, contact education@scilifelab.uu.se

Course content

This course will cover theoretical and practical aspects of single cell analysis with focus on microbial single cell genomics and host-pathogen interactions in the practical part. We include lectures that cover both pro- and eukaryotic single cell omics. The course will cover recent advances in single-cell genomics and transcriptomics of eukaryotic pathogens, and includes methods for cell isolation and sample prep. We will further discuss single cell applications targeting host-pathogen interactions both in circulation and in tissues.
Topics covered will include:

  • Single cell genomics for microbial cells in theory and practice
  • Single cell transcriptomics related to infectious diseases
  • Computational aspects of single cell data analyses
  • Single cell techniques, e.g. droplet microfluidics, in situ hybridization

Each participant is also required to give a short presentation about their work/project.

Please note that SciLifeLab training courses do not provide any formal university credits.
The course content is estimated to correspond to 
a certain number of credits, however the estimated credits are just guidelines.
If formal credits are crucial, the student needs to confer with the home department before course application, whether the course is valid for formal credits or not.

Social program

The course contains a voluntary social program for networking purposes (including coffee, lunches and one course dinner with teaching experts). A course fee of 1300 SEK will be invoiced to accepted participants that attend the social program, after completion of the course. NOTE – Uppsala University cannot invoice individuals.

Entry requirements

To attend, the course participants must have experience in molecular work and preferably an ongoing or planned research project that involves single cell applications. Participants with strong interest in single cell work are welcome as well.

Due to limited space for the practical laboratory work, there are a maximum number of participants. If we receive more applications, participants will be selected based on several criteria including correct entry requirements, motivation to attend the course as well as gender and geographical balance.