Modelling Inflammation with iPS-Macrophages and Microglia


A two-part course in applying human Pluripotent Stem cell models for inflammation and neuroscience research.

  • Four-week online course (no attendance at Oxford required)
  • Hands-on training day in Oxford (optional)

The course uses a combination of Video Podules, Standard Operating Procedures, Discussion Forums, Self-evaluation Tests and Hands-on options to provide practical training in the use of human induced Pluripotent Stem Cell-Macrophages and Microglia for modelling innate immunity, neuro-inflammation and host-pathogen interactions.

The course has been designed by leading experts in the field at the James Martin Stem Cell Facility and the Oxford Stem Cell Institute at the University of Oxford to offer training in stem cell technology of the very highest quality.

It comprises innovative interactive online training materials, with the option to attend an additional intensive, hands-on, one-day practical course at the University of Oxford.

The course is intended for scientists in both academic labs and in industry, who will be applying the techniques learnt back in their own laboratories.

Is this course right for you? Watch our video to find out:

Programme details

Four-week Online Course

The online course modules require a time commitment of approximately 4 hours per week:

Week 1 (commencing 24 February 2020)

  • Standard human iPS cell culture methods
  • Automated, high-throughput culture of iPS cells
  • CRISPR/Cas9-mediated gene editing of iPS cells
  • Moderated discussion
  • Self-evaluation test (required to move to next module)

Week 2 (commencing 2 March 2020)

  • Differentiation of macrophages from iPS cells
  • Differentiation of microglia-like cells from iPS cells
  • Moderated discussion
  • Self-evaluation test (required to move to next module)

Week 3 (commencing 9 March 2020)

  • Differentiation of cortical neurons from iPS cells
  • Differentiation of astrocytes from iPS cells
  • Co-culture of microglia, neurons and astrocytes from iPS-derived precursors
  • Moderated discussion
  • Self-evaluation test (required to move to next module)

Week 4 (commencing 16 March 2020)

  • Live cell imaging methodologies for studying cellular dynamics
  • Phagocytosis assays
  • Profiling cytokine production
  • Approaches to developing screens using iPS cells
  • Moderated discussion
  • Self-evaluation test

The course material will be available online for a four further weeks after the finish date.

There is also the opportunity to undertake an additional optional assignment, should you wish, which will receive feedback from the course tutor.

Practical Course (optional day - limited places available)

Wednesday 25 March 2020 at the Sir William Dunn School of Pathology, University of Oxford

By the end of the optional intensive one-day practical course, which takes place in Oxford, you will have gained hands-on experience of:

  • Differentiation of macrophages from iPS cells
  • Co-culture of microglia, neurons and astrocytes from iPS-derived precursors
  • Downstream assays
  • Imaging microglia


example of a practical day on the courseExample of practical day


Participants who complete the full online course will receive a University of Oxford certificate of completion.

Those attending the full Practical Course (optional day) will receive an additional certificate of attendance.

The certificate(s) will show your name, the course title and the dates of the course you attended.


Description Costs
Online course £595.00
Online course AND optional practical course £990.00


All courses are VAT exempt.

Fees include course materials, access to the online course materials throughout the course and tuition.

Practical course

If you also enrol on the optional practical course, the fee will include additional course materials, tuition, refreshments and lunch on 25 March 2020. The price does not include accommodation.


Dr Sally Cowley

Head, James Martin Stem Cell Facility, University of Oxford

A graduate of Natural Sciences at Cambridge, Sally began her research career working on host-pathogen interactions (Ph.D 1990 University of London, and later at AHRI, Ethiopia). Her post-doctoral work (New England Deaconess Hospital, Harvard, Boston, and Institute of Cancer Research, London) centred around signal transduction pathways involved in differentiation: She identified and cloned a novel tyrosine kinase, MATK, implicated in megakaryocyte differentiation; and was the first to demonstrate that the protein kinase MEK (/MKK) is critical for signal transduction pathways leading to differentiation and to tumorigenic transformation.

Following a career break to raise children, she obtained a Wellcome Trust Career Re-entry fellowship and joined the Sir William Dunn School of Pathology in 2007, where, with Professor William James, she established and Heads the James Martin Stem Cell Facility (JMSCF). The Facility has expertise in human induced Pluripotent Stem (iPS) cell derivation, culture, genetic modification and differentiation. iPS cells derived from patients with genetic disease offers a new, hugely exciting opportunity to model human diseases ‘in a dish’. The lab has pioneered methods for differentiation of iPSC to macrophages for modelling innate immunity and infection pathways, thereby overcoming the limitations of blood-derived macrophages. The JMSCF has generated a world-class panel of iPS cells from Parkinson’s patients as part of a large scale Oxford Parkinson’s Disease Centre research programme funded by Parkinson’s UK (in collaboration with Professor Richard Wade-Martins). Sally has been a key member of StemBANCC, leading the development of iPSC gene-editing technologies in this EU-wide collaborative programme focussed on developing iPSc disease models as drug-screening platforms. She is also a Co-Investigator in the MRC DPUK Experimental Medicine Dementia Stem Cell Network, using iPSC-microglia to study neuroinflammation in neurodegenerative disease.  

Professor William James

Professor of Virology, Sir William Dunn School of Pathology, University of Oxford

Tutor in Medical Sciences, Brasenose College Oxford

A graduate of the University of Birmingham, William obtained his DPhil in Biochemistry in 1984 at the University of Oxford studying the genetic control of cellular differentiation and respiration in bacteria, during which he cloned the genes for the master transcriptional regulator, gerE, and haem A synthase, CtaA. He was appointed to an academic position at the Dunn School in Oxford on graduation, where he has studied the processes of cellular infection by viruses including HIV-1 and Dengue virus, particularly their adaptations to macrophages. His group were the first to report inhibition of HIV-1 replication by endogenous antisense RNA and by synthetic RNA aptamers, and elucidated the endocytic pathway of HIV-1 infection in macrophages. In order to provide a genetically tractable but physiologically authentic model for human macrophages in vitro, his group developed the pluripotent stem cell model for macrophage differentiation. The Oxford Stem Cell Facility in the James Lab was joined by Dr Cowley in 2007, and with sponsorship from  the James Martin foundation and many others has developed an internationally recognized pipeline in hiPS cell generation, mutagenesis and differentiation.

In addition to research, William has served as Head of Department at the Sir William Dunn School of Pathology, Deputy Head of the University’s Medical Sciences Division, and, between 2011 and 2017, was the Oxford University Pro-Vice Chancellor for Planning and Resources. He currently combines the full-time roles of Professor of Virology in the Dunn School and lead Tutor for Medicine at Brasenose College.

Learning outcomes

Four-week Online Course

By the end of the online course you will have gained:

  • an in depth understanding of the rationale for using human iPS cells to model innate immunity, neuro-inflammation and host-pathogen interactions
  • the ability to design strategies for gene knockouts and targeted gene edits in human iPS cells, protocols for carrying out the wet lab work, and an appreciation of potential pitfalls
  • an in depth understanding of the practical aspects of culturing human iPS cells at different scales and their differentiation to macrophages, microglia, astrocytes and neurons for monoculture and co-culture
  • in depth knowledge of downstream assays relevant to studying macrophage and microglial biology

Practical Course (optional day)

By the end of the practical day in Oxford, you will have gained hands-on experience of:

  • handling human iPS cells
  • the key manipulations required to make Embryoid Bodies from iPS cells, set Embryoid Bodies up for myelopoiesis differentiation, and harvest of cells from those cultures to plate as macrophages
  • setting up iPS-microglia in monoculture and in co-culture for various downstream assays
  • imaging iPS-microglia



How to apply:

  1. complete the pre-application questionnaire 
    • provide a copy of your CV
    • to include the optional practical course, provide a letter from your supervisor confirming your competence in mammalian cell culture.
  2. send a completed application form to the course administrator by email or post and await your invoice.

If you would like to discuss your application or any part of the application process before applying for this course, please get in touch. 

Please note:

The practical course is presently fully-booked. If you would be interested in this option, please apply as normal and we will add you to the waiting list and contact you should any space become available. 

The online course remains open for applications as normal. 

Level and demands

The course is intended for scientists in both Academic labs and in Industry, who will be applying the techniques learnt back in their own laboratories.

Four-week Online Course 

Before you start the online course, you should have some experience in basic mammalian cell culture techniques. It is also helpful if you have any prior experience of working with pluripotent stem cells.

Practical Course (optional day)

If you are hoping to register for the intensive hands-on one-day practical course at Oxford, it is essential that you are competent in basic mammalian cell culture techniques.


Practical Course Only (optional day):

Although not included in the course fee, accommodation may be available at our on-site Rewley House Residential Centre. All bedrooms are en suite and decorated to a high standard, and come with tea- and coffee-making facilities, free Wi-Fi access and Freeview TV. Guests can take advantage of the excellent dining facilities and common room bar, where they may relax and network with others on the programme.

To check prices, availability and to book rooms please visit the Rewley House Residential Centre website.