Across all biological sciences, technological advances result in more ambitious projects and larger data sets. Launched in 2016, this practical, laboratory-based course will demonstrate how to take common immunological techniques to the next level by combining them with semi-automated and automated analysis methods and using appropriate statistical analysis pipelines. The course is aimed at PhD students and postdocs who would like to get more out of the experiments they perform and make sure their data analysis has a sound basis.

This course is conducted in collaboration with the Wellcome Trust Sanger Institute Mouse Genetics Project (MGP) and the Infection and Immunity Immunophenotyping (3i) consortium.

Participants will receive training in immunological phenotyping and will gain hands-on experience in a number of immunological techniques suitable for large-scale phenotyping. Using the data generated during the course, we will explore manual, semi-automated and automated analysis approaches and relevant statistics for different data sets and discuss benefits and challenges. All experiments will be conducted on samples from a knockout mouse strain which the participants will identify at the end of the course.

The programme will cover a number of tests that are conducted routinely by 3i under high-throughput conditions and discuss the best way to analyse and interpret the data.

Feedback from the inaugural 2016 course

  • Read one participant's course blog here.
  • Extremely well organized course!
  • This was an excellent course and I am happy I had the opportunity to attend!
  • Thanks to all instructors and course organisers. The course exceeded my expectations - I learned a lot.
  • Thank you to all the organisers, instructors and speakers for a fantastic experience.
  • Overall, the course was a fantastic experience and was very interesting and scientifically useful. Considering the course was in its first year I was impressed by the level of organisation.
  • The course was really well organised and I profited a lot from it, especially due to the interactions with other people, both with participants and instructors!

Scientific and collaborative background to the course
MGP generates and phenotypes knockout mice, most of which were generated by the International Knockout Mouse Consortium. For each mutant line, groups of seven male and seven female mice move through a standard analysis pipeline aimed at detecting traits that differ from healthy C57BL/6N mice. The pipeline collects many measurements of viability, fertility, body weight, infection, hearing, morphology, haematology, behaviour, blood chemistry and immunity and compares them to wild type controls. An overview over the first 250 lines has been published in Cell by White and al. ( Currently, MGP phenotypes 160 knockout lines a year.

Given the large number of immune-related phenotypes, it was decided to subject these 160 knockout lines to an immunological phenotyping and the 3i consortium was formed to this end in 2013. 3i conducts an in-depth immunological screen in the steady state and under challenge. The consortium analyses the immune cell compartments of spleen, mesenteric lymph nodes, bone marrow, blood and serum in order to identify genes regulating the immune system in the absence of challenge. Furthermore 3i investigates responses to chemical stress (DSS colitis) and to viral, bacterial and nematode infections (Salmonella, influenza and Trichuris muris).
Data from both the MGP and the 3i screen are open-access and are publicly available on the 3i website ( and the website of the International Mouse Phenotyping Consortium (, an overarching international initiative.

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