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 closed

Important dates

Application open from December 17, 2019

Application deadline: February 10, 2020

Confirmation to accepted participants: February 12, 2020

Responsible teachers: Claudia Bergin, Anna-Maria Divne and Johan Ankarklev

If you don’t receive information about your application by February 14, 2020, contact claudia.bergin@icm.uu.seanna-maria.divne@icm.uu.se or johan.ankarklev@icm.uu.se

Social program

Coffee/tea will be served during breaks in the mornings and afternoons. Lunches are not included.

Course content

The purpose of this course is to give theoretical and practical insight into microbial single cell genomics. This will include all steps from experiment planning, sample preparation, single cell sorting/sampling, as well as whole genome amplification and single cell transcriptomics. The participants will get hands-on experience on the different methods and learn about recent advances in the field of single cell genomics and scRNAseq. There will also be time to discuss projects. The downstream bioinformatics will be covered briefly. More extended bioinformatics is offered by other SciLifeLab courses.

  • Single cell genomics for microbial diversity and population genetics in theory and practice
  • Single cell transcriptomics related to infectious diseases and non-pathogenic host-microbe associations
  • Computational aspects of single cell data analyses

Each participant is 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.

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.