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.
The course will include practical training in small groups of students on single cell methodologies and computational and statistical data analysis needed to interpret large data sets. This integration of data analysis with hands-on experiments will allow the students to gain knowledge in technical performance as well as biological interpretation of single cell data sets.
Will be announced soon.
Will be announced soon.
Topics & Techniques
The course will include practical training in small groups of students on single cell methodologies and computational and statistical data analysis needed to interpret large data sets. This integration of data analysis with hands-on experiments will allow the students to gain knowledge in technical performance as well as biological interpretation of single cell data sets. Single cell transcriptomics and analysis will cover following topics:
- Cell classification in the nervous system and its implication on how we do neuroscience
- Discrete versus continuous variability in gene expression
- Single-cell transcriptomics and analysis of disease
- Advantages and disadvantages of different techniques; RNA amplification, Smartseq, Dropseq, 10X genomics,
- What type of biological insights can be gained from single cell transcriptomics
- Multimodal analysis of single cell biology where transcriptomics is coupled with other biological parameters such as a cell’s morphology, tissue localization, epigenome, proteome and/or function
- Preparation and isolation of single cell, nuclei isolation, RNA isolation, single cell RNA amplification procedures, library construction for sequence analysis and RNA sequencing.
- Experimental design considerations, data processing, data handling, quality control of the sequencing data, understanding the variances of the data, clustering of cell types
- Nervous system development and other dynamical processes including lineage tracing including RNA-Velocity and pseudotime analysis
This advanced course is aimed for graduate students from a variety of disciplines, including neuroscience, physics, computer science and applied mathematics. Students are expected to have a keen interest and basic background in neurobiology, and to fully benefit from the data analysis it is expected that the students have at least a basic knowledge in programming.
Students (25 max) will follow theoretical and methodology lectures by leading scientists from the field in the mornings and hands-on training in groups of 2-3 students per project in the afternoons. The projects will be performed in the Neuroscience Training Lab at the Neurocampus. The labs are equipped with a wet lab for molecular and cellular biology, cell culture room, and computers for analyses. The core facilities at the Bordeaux Imaging Center and the Functional Genomics facility and are available as well. The methodology and expertise to perform the projects will be provided by external instructors from research groups all over the world, and they will be present throughout the projects to guide and assist the students.
- Single cell/nuclei sequencing (a few different chemistries)
- Mouse embryos, across developmental stages – allow for RNA Velocity analysis, pseudotime analysis.
- Adult mouse, different brain areas – allow for comparative and batch effect reduction analysis.
- Single-cell ATAQ-seq
- Spatial transcriptomics: PCI-seq (in situ hybridization-based spatial transcriptomics approach)
- Lineage tracing of cell fates in the developing nervous system
- Single cell cut&tag for epigenetic analysis
- Activity dependent programs (hippocampus, Cortex)
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 : 3.950 € (includes tuition fee, accommodation and meals)
Applications will open soon.
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.