Spatial scRNAseq

Optimized tool for transcriptome analysis of a large number of individual cells based on a large spectrum of fluorophores, with excellent sensitivity, resolution, and speed. Spatiotemporal context is computationally reconstructed a posteriori.


  • Sophie Pantalacci (LBMC)
  • Yad Ghavi-Helm, Camille Guillermin and Romain Guyot (IGFL)
  • Olivier Raineteau (SBRI)
  • Sébastien Dussurgey and Estelle Devevre (ANIRA Cytometry)
  • Sandrine Hughes and Benjamin Gillet (IGFL Sequencing Platform)
  • Thibault Andrieu and Christophe Vanbelle (Cytometry Lyon Est)
  • Marie Monniaux (RDP)
  • Cyril Dégletagne and Philippe Bertolino (CRCL)
  • Sergio Sarnataro (Spatial-Cell-ID)


  • Equipment bought by Spatial-Cell-ID:

- 10X Chromium Controller at the IGFL Sequencing Platform (PSI)

  • Equipment currently tested by Spatial-Cell-ID:

- Spectral Flow Cytometer (Aurora CS Cell Sorter) at the cytometry platform of SFR-Santé Lyon Est / CRCL

- Robot to construct libraries for sequencing at the IGFL Sequencing Platform (PSI)

  • scOMICS-friendly equipment available in the different units (non exhaustive list):

- At the cytometry platform of SFR-Santé Lyon Est / CRCL: BD Aria III (cell sorter with lasers 355/405/488/561/633 for bulk or single cell sorting, in tube or plates), BD Accuri (cytometer and absolute counter for cells in suspension with lasers 488/633)

- At the ANIRA cytometry platform of SFR-Biosciences: BD Accuri C6+ (2 lasers, to count cells and check viability), Cytek Aurora 5L (5 lasers, spectral cytometer, compatible for plates, to count cells and check viability), Luminex ImageStream X Mark II (PHENOCAN, cytometer with cell/nuclei imaging, 5 lasers, high-throughput)

- At the Cancer Genomics Platform (CRCL): LUNA-FL (cell counter with double fluorescence), 10X Chromium iX (cell encapsulation for 10X, compatible with flex kits), 10X Visium CytAssist (compatible with the 10X v2 Visium slides)

- At ProfilXpert: 10X Chromium Controller

- At the IGFL Sequencing Platform (PSI): MinION sequencer

Facilities hosting the equipment: