Dataset summary

Original publication DOI: https://doi.org/10.1101/2023.01.26.525195
Specific data link: https://figshare.scilifelab.se/articles/dataset/Spatial_Multimodal_Analysis_SMA_-_Spatial_Transcriptomics/22778920
Original abstract: Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here, we report a procedure to perform genome-wide spatial analysis of mRNA in FFPE-fixed tissue sections, using well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3′ end of mRNA molecules in tissue sections. We applied this method for expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method’s capability to delineate anatomical regions from a molecular perspective. We also profiled the spatial composition of transcriptomic signatures in two ovarian carcinosarcoma samples, exemplifying the method’s potential to elucidate molecular mechanisms in heterogeneous clinical samples. Finally, we demonstrate the applicability of the assay to characterize human lung and kidney organoids and a human lung biopsy specimen infected with SARS-CoV-2. We anticipate that genome-wide spatial gene expression profiling in FFPE biospecimens will be used for retrospective analysis of biobank samples, which will facilitate longitudinal studies of biological processes and biomarker discovery.

Summary statistics

Slides: 14
Patients: 4
Spots: 43804

How to use

                    
                        # Import spared library
                        import spared 
                        from spared import datasets
                        # Dataset
                        dataset = datasets.get_dataset("vicari_mouse_brain", visualize=True)