Applications for pilot facility


The Spatial Transcriptomics pilot facility provides spatially resolved RNA-seq data, and includes data analysis and bioinformatics support. The facility also conducts research for the continual improvement of this technology. The pilot facility can only accommodate Swedish researchers at the present time.



  • Creation of spatial libraries from tissue samples
  • Bioinformatic analysis of spatial libraries – from raw FASTQ to spatial data
  • Assistance with bioinformatic analysis of spatial libraries – for users performing their own analysis
  • Tutorials and workshops

Currently the spatial transcriptomics method only supports polyadenylated RNA.



  • High resolution microscopes
  • Low resolution scanner for quick feedback
  • Cryostat for tissue sectioning
  • Fully equipped laboratory for preparation of samples



Facility supported tissues:

  • Human
    • Breast cancer
    • Prostate cancer
    • Brain cancer
    • Heart
    • Lymph
    •  Mouse
    • Brain



  • Annelie Mollbrink (Head of the pilot facility)
  • Ludvig Larsson (Bioinformatics)
  • Sidra Manzoor (Experimental)
  • Sami Saarenpää (Experimental)




Application Form

Spatial Transcriptomics application form