SCID interactive workshop on scRNAseq


From 9:15 am to 14:30 pm


ENS de Lyon, Salle Condorcet "Place de l'Ecole", 1 place de l'Ecole, LYON 69007

Spatial-Cell-ID is starting a series of interactive workshops for troubleshooting technical/analysis barriers in spatial transcriptomics. These workshops are meant to generate ample discussion and troubleshoot within the local community of Spatial-Cell-ID.

The first workshop dedicated to scRNAseq will be held on June 12, 2023.

We chose two topics highlighted by your feedbacks during the SCID day:

1: Cells vs Nuclei? 

2: Clustering my dataset

As a starting point, members of spatial Cell ID working groups will make short presentations illustrating methodological choices with their own data. These short presentations are only aimed at initiating discussions. Most of the time will be devoted to discussion and we will invite participants to provide their own feedback and answer the numerous questions which should come in the discussion.

We will also dedicate two hours to troubleshooting at the bench and in data analysis, again based on participant's questions and feedback. For the bench part, we will focus on nuclei preparation, and as a starting point, we will welcome a short presentation by the 10x Genomics Application Field scientist specialized in nuclei. For the data analysis part, we will follow up on pitfalls and tricks in clustering datasets.

Participants will finally be invited to further discuss while eating pizzas, kindly offered by 10x Genomics, and drinking coffee until 14:30.


Registration is free but mandatory before June, 5.



9:15 Welcome coffee

9:30 Introduction: welcome to this interactive workshop!

9:35 - 10:15 Users’ feedback on a methodological choice: using cells vs. nuclei 

  • Short presentation by Elodie Babina or Olivier Raineteau (SBRI): cell types sensitivity to cell vs. nuclei extraction and drawbacks of nuclei preparation
  • Short presentation by Philippe Bertolino (CRCL): single cells vs single nuclei analysis, results vs practicality.
  • Feedbacks and questions from the room 

10:15 - 11:15 Bench troubleshooting 

  • Preparing nuclei:
  • Short presentation by Cecilia Korol, Field Application scientist at 10x Genomics: Tricks for nuclei preparation 
  • Questions and answers from the room 
  • Open bench troubleshooting: hot questions and answers from participants (any subject)

11:15 - 11:35 Coffee break (20min)

11:35 - 12:15 Users’ feedback on methodological choices in dataset clustering 

  • Short presentation by Elodie Babina/Olivier Raineteau: Clustering the “biased” way… then subclustering or identifying lineages based on combination of markers
  • Short presentation by Quentin Cavallini-Speisser (RDP): Finding an optimal number of clusters with the tool MultiK
  • Feedbacks and questions from the room 

12h15-13h15: Data analysis troubleshooting 

  • Clustering your cells or nuclei: 
  • Short presentation by Océane Chanel/Sophie Pantalacci (LBMC): Two effects that may blur your clustering (contamination and proliferation status)
  • Questions and answers from the room on clustering your cells or nuclei
  • Open data analysis troubleshooting: hot questions and answers from participants (any subject)

13:10 - 14:30 Ongoing discussions with pizzas offered by 10x Genomics and Coffee