This Summer school is 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 will cover all the stages of a scRNAseq project in plants. Through a combination of lectures and practical work, the many specific features of plant models will be 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 will:
–    Have an overview of the different scRNAseq technologies and understand their pros and cons.
–    Be able to design experiments depending on the biological question. 
–    Be trained on sample preparation techniques for single cell and single nuclei
–    Understand the different steps of bioinformatics and statistical analysis
–    Have a better biological interpretation of results
–    Have facilitated exchanges with technology platforms, bioinformaticians, and biostatisticians in order to successfully complete their scRNAseq project

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

Program and speakers

Download the provisional 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 will include:

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

Each participant will give a short “get to know me” flash talk at the beginning of the Summer School. The poster session will be organized to allow each participant to discuss their poster and to see all posters. It will finish 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 will give lectures and lead 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 will allow 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

Practical information

This SPS Summer School is limited to 20 participants.
It is open to PhD students and young post-docs.
Prerequisites: Basic use of RStudio (editing and running scripts)

ATTENTION: For administrative and financial reasons, only applicants with a formal attachment to a research laboratory at the time of the Summer School will be considered. This Summer School is not open to applicants with a permanent position in their host institution.

There is no registration fee for this Summer School.

> For successful applicants, the Summer School WILL cover the following costs:
   - The scientific program
   - Housing from Sunday June 28 to Friday July 3 (5 nights) at the hotel “Le Bout du Parc”
   - Coffee-breaks from Sunday June 28 (2 PM) to Friday July 3 (6 PM)
   - Lunches from Monday June 29 to Friday July 3
   - Welcome cocktail on Sunday June 28 (during the poster session)
   - Dinners on Monday June 29, Wednesday July 1 and Thursday July 3.

> The Summer School WILL NOT cover the following costs:
   - Transport costs to and from the Summer School location
   - Lunch on Sunday June 28
   - Dinners on Sunday June 28, Tuesday June 30 and Friday July 3.

During the Summer School, the successful participants will have to present themselves and their research:
- In a flash-talk (not more than 3 Powerpoint slides, 5 min maximum).
- In a poster (portrait format, approximately A0 size).

Every participant is expected to bring a laptop.

Application

Application deadline: March 12, 2026 (midnight)
Answers will be sent mid-April at the latest.

For your application, you will have to provide a single PDF file containing four documents:

1. A motivation letter explaining your research interests and the expected benefits from attending the summer school. This letter must also highlight your experience in R use.

2. A curriculum vitae

3. An abstract detailing your research project (250 words, with title, author(s), institution(s)). This abstract must correspond to the poster and the flash-talk presentations of your research that you will prepare for the Summer School.
ATTENTION: Your abstract will be included in the Summer School booklet, which will be distributed to all participants and made public on the Summer School web page.

4. A letter of support from your supervisor or a senior coworker indicating that your host laboratory will finance your transport and any additional costs you could have during your stay, according to the downloadable model.

Only applications written in English are accepted.
Only complete applications will be taken into account.

Contact

sps-summer-school@inrae.fr
Please precise [SPS Summer School 2026] in the object of your email.

Sponsors

If you wish to sponsor the SPS Summer School 2026, do not hesitate to contact us.