SciLifeLab, Stockholm University

The in situ sequencing facility unit provides spatially resolved gene expression data for panels of genes at single cell resolution. The technique has been developed in the lab of Mats Nilsson who has pioneered the field of generating in situ gene expression (Ke, R., et al. 2013 Nature Methods 10, 857-860) and mutation (Grundberg, I., et al. 2013 Oncotarget 4, 2407-2418) profiles. In situ sequencing enables localisation and quantification of more than 100 transcripts simultaneously with subcellular resolution in a single tissue section in a single experiment. The method has been successfully demonstrated for a variety of applications such as mapping of molecularly defined cell types, RNA editing, mutational heterogeneity and splice-variants across different type of sections (fresh frozen, PFA-fixed and FFPE) in various tissues. The maps have been used to study molecular basis of different cancers including tumour stroma profiling and profiling of immune cell subsets.

Technical equipment and infrastructure

Two automated epifluorescence microscopes (Axio imager.Z2; Zeiss) equipped with multiwavelength LED light with 6 separate wavelengths.
Automated slide stainer (Autostainer 360; LAB Vision) which can process 36 slides at one go.


In situ Seq (RCA)

<span lang="EN-GB"><span><span>generating Rolling Circle Amplification products in the tissues</span></span></span>