This Summer school was organized by the Saclay Plant Sciences (SPS) network, one of the largest European plant sciences communities.

scRNAseq approaches have revolutionized the way biologists approach their research subjects, by making it possible to dissect molecular mechanisms at the single-cell level. But although technological developments have recently made these approaches more accessible, their expensive use still requires significant technical training, including the good conception of experimental designs, the preparation of samples as well as their bioinformatics analyses. In addition, different protocols and various bioinformatics and statistical analyzes are available, and it can be difficult to choose the most relevant ones for the biological question at hand.

Over five days, the SPS Summer School 2026 covered all the stages of a scRNAseq project in plants. Through a combination of lectures and practical work, the many specific features of plant models were highlighted by experts from the Saclay Plant Sciences network (CNRS and INRAE), the ViB in Ghent and the Pasteur Institute.

After this international school, participants:
–    had an overview of the different scRNAseq technologies and understand their pros and cons.
–    were able to design experiments depending on the biological question. 
–    were trained on sample preparation techniques for single cell and single nuclei
–    could understand the different steps of bioinformatics and statistical analysis
–    has a better biological interpretation of results
–    had facilitated exchanges with technology platforms, bioinformaticians, and biostatisticians in order to successfully complete their scRNAseq project

The summer school brought together outstanding and enthusiastic young scientists (PhD students and post-docs) from all over the world in order to exchange knowledge and ideas. It was limited to a small group of participants (20 maximum) to privilege informal interactions and scientific discussions.

Program and speakers

Download the program of the Summer School:

Start of the school: Sunday June 28, 2026 at 2pm.
End of the school: Friday July 3, 2026 at the end of the day.

The Summer School included:

              > Participant flash-talks and poster session (~5 hours)

Each participant gave a short “get to know me” flash talk at the beginning of the Summer School. The poster session was organized to allow each participant to discuss their poster and to see all posters. It finished with a general discussion.

              > Theoretical and practical modules (~27.5 hours):

Global overview of Single-cell RNA-seq approaches
–    Single-cell RNA-seq: what for? Overview of the main biological questions addressed using scRNAseq (Theory: 1h30)
–    Single-cell RNA-seq technologies pros and cons: a review of the main scRNAseq technologies single cells vs single nuclei (Theory: 1h30) 

Sample preparation and data generation
–    Preparation of plant nuclei for scRNAseq (Theory: 1h30 / Practice: 7h)
–    Loading the nuclei in the Chromium (10X Genomics), Rhapsody (BD Bioscience) (Practice: 1h30) 

Data analysis
–    From reads to count matrices: Bioinformatic processing of sequencing data: QC, mapping, counting (Theory: 1h30)
–    From raw count matrices to high quality data (Theory: 1h30 / Practice: 1h)
          o    Removing low quality cells
          o    Normalization
          o    Removing batch and sampling effects
–    From normalized counts to cell types (Theory: 1h30 / Practice: 1h)
          o    Selecting informative genes and reducing dimensionality
          o    Clustering cells
          o    Annotation of clusters
–    Cell trajectories (Theory: 1h / Practice: 30min)
–    Revealing mechanisms (Theory: 3h / Practice: 1h30)
          o    Differential gene expression
          o    Functional enrichment analysis
          o    Changes in cell composition
          o    Others

Perspectives
–    What’s next?  Experimental validation of scRNAseq results. Spatial transcriptomics (Theory: 2h)

Scientists gave lectures and led discussions, giving the participants an insight into the latest research findings and identifying key open questions in the field.

              > Discussions (~6h)

              > Social activities
- A pétanque tournament (https://www.wikihow.com/Play-Petanque)
- Dinner at a local restaurant
- Visit of the Versailles Palace

This intensive and varied one-week program allowed many opportunities to discuss with speakers and fellow participants.

Organizers

Bruno Guillotin¹ (Coordinator)
Etienne Delannoy¹
Julien Lang¹
Marie-Laure Martin¹
Clément Pichot²

¹ Institute of Plant Sciences Paris Saclay – IPS2 (Gif-sur-Yvette, France)
² Jean-Pierre Bourgin Institute for Plant Sciences / IJPB (Versailles, France)

Invited experts

- Nathalie Lehmann, Institut Pasteur, France
- Freya Persyn, ViB Ghent, Belgium

Teaching language

English

Venue

INRAE Centre Île-de-France Versailles-Saclay
Route de St-Cyr (RD 10)
78026 Versailles Cedex France

Sponsors