PT - JOURNAL ARTICLE AU - Villacampa, Eva Gracia AU - Larsson, Ludvig AU - Kvastad, Linda AU - Andersson, Alma AU - Carlson, Joseph AU - Lundeberg, Joakim TI - Genome-wide Spatial Expression Profiling in FFPE Tissues AID - 10.1101/2020.07.24.219758 DP - 2020 Jan 01 TA - bioRxiv PG - 2020.07.24.219758 4099 - http://biorxiv.org/content/early/2020/07/25/2020.07.24.219758.short 4100 - http://biorxiv.org/content/early/2020/07/25/2020.07.24.219758.full AB - Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here we present a procedure to perform genome-wide spatial analysis of mRNA in FFPE tissue sections. The procedure takes advantage of 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. First, we conducted 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. Second, we explored the spatial composition of transcriptomic signatures in ovarian carcinosarcoma samples using data driven analysis methods, exemplifying the method’s potential to elucidate molecular mechanisms in heterogeneous clinical samples.Competing Interest StatementJL, EVG, LL, LK, AA are scientific advisors to 10x Genomics Inc, which holds IP rights to the ST technology.