Course overview

Understanding the cellular complexity of the nervous system is a key endeavor in the pursuit to reveal the biological underpinnings of brain function. The recent methodological development of high-throughput single-cell profiling techniques and analysis has emerged as an essential tool for characterizing cellular diversity in the brain offering data sets that hold the promise of being complete, accurate and permanent. This course will teach central ideas, methods, and practices of single cell profiling and hands-on computational analysis through a combination of lectures from prominent international faculty speakers, experimental projects and data analysis workshops.

We encourage both applicants from experimental and computational backgrounds. Students who do not have experience with bioinformatic analysis will receive information on preparatory web courses to take before coming to course.

Course partner

Course directors

Jens Hjerling

Course Director

Department of Medical Biochemistry and Biophysics,  Karolinska Institute,  Sweden

Peter Karchenko


Biomedical Informatics, Harvard Medical School, USA

Alexandre Favereaux


CNRS – IINS, University of Bordeaux, France

Keynote Speakers

Naomi Habib – The Edmond and Lily Safra Center  (ELSC), Israel

Kenneth Harris – University College London, UK

Ed Lein – Allen Institute for Brain Science, USA

Sten Linnarsson – Karolinska Institute, Sweden

John Marioni – European Bioinformatics Institute (EMBL-EBI), UK

Ana Martin-Villalba – German Cancer Research Center, Germany

Rahul Satija – New York Genome Center (NYGC), USA

Kun Zhang – Department of Bioengineering, University of California, USA


Please note this list is subject to change


Song Chen – UC San Diego, USA

Martin Häring – University of Vienna, Austria

Markus Hilscher – SciLifeLab, Stockholm University, Sweden

Danny Kitsberg – The Edmond and Lily Safra Center (ELSC), Israel

Gioele La Manno – Brain Mind Institute, EPFL, Switzerland

Romain Lopez – UC Berkeley, USA

Malte Lücken – Institute of Computational Biology, Munich, Germany

Christian Mayer – Max Planck Institute of Neurobiology, Germany

Fatima Memic – Karolinska Institute, Sweden

Ana Munoz Manchado – University of Cádiz, Spain

Viktor Petukhov – University of Copenhagen, Denmark

Xiaoyan Qian – Cartana, Sweden

Please note this list is subject to change

Course content

                         Topics & Techniques

During this course, students will get hands-on experience with entire single-cell transcriptomic projects from tissue dissociation to publishable figures. We will teach the use of different kinds of starting material, three different sequencing techniques, how to treat the raw sequencing data and a multitude of analytical tools. After attending the course, our goal is that the students should be able to go back to their institute and have enough knowledge and understanding to initiate well-designed single-cell sequencing projects to tackle important questions in Neuroscience..


For more information on projects download the “Programme info”.

– Project 1: Visualization and quantification of cellular complexity of the CA1 region of the
mouse brain

– Project 2: Understanding cellular maturation during the development of the embryonic
nervous system by whole-cell RNA seq

– Project 3: GABAergic neuronal diversity across different forebrain structures

– Project 4: Single whole cells analysis of an Alzheimer’s disease mouse model

– Project 5: Single nuclei analysis of an Alzheimer’s disease mouse model

– Project 6: Single nuclei analysis of GABAergic cells in the dorsal horn in a Chronic pain

– Project 7: Single whole cells analysis of GABAergic cells in the dorsal horn in a Chronic pain model

– Project 8: Large scale single-cell RNA-sequencing of brain tissue using SPLiT-Seq 

– Computational Projects: state-of-the-art approaches for computational analysis and interpretation of single-cell RNA-seq data. 

Bordeaux School of Neuroscience, France

The Bordeaux School of Neuroscience is part of Bordeaux Neurocampus, the Neuroscience Department of the University of Bordeaux. Christophe Mulle, its current director, founded it in 2015. Throughout the year, renowned scientists, promising young researchers and many students from any geographical horizon come to the School.
The school works on this principle: training in neuroscience research through experimental practice, within the framework of a real research laboratory.

Their dedicated laboratory (500m2), available for about 20 trainees, is equipped with a wet lab, an in vitro and in vivo electrophysiology room, IT facilities, a standard cellular imaging room, an animal facility equipped for behavior studies and surgery and catering/meeting spaces. They also have access to high-level core facilities within the University of Bordeaux. They offer their services to international training teams who wish to organize courses in all fields of neuroscience thanks to a dedicated staff for the full logistics (travels, accommodation, on-site catering, social events) and administration and 2 scientific managers in support of the experimentation.


Fee : 3.500 € (includes tuition fee, accommodation and meals)

The CAJAL programme offers 4 stipends per course (waived registration fee, not including travel expenses). Please apply through the course online application form. In order to identify candidates in real need of a stipend, any grant applicant is encouraged to first request funds from their lab, institution or government.

Kindly note that if you benefited from a Cajal stipend in the past, you are no longer eligible to receive this kind of funding. However other types of funding (such as partial travel grants from sponsors) might be made available after the participants selection pro- cess, depending on the course.