Spatial transcriptomics using Visium FFPE technology
FFPE tissue sections were placed on Visium slides and prepared according to the 10x Genomics protocols. After H&E staining, imaging and de-crosslinking steps, tissue sections were incubated with human-specific probes targeting 17,943 genes (10x Genomics, Visium Human Transcriptome Probe Set v.1.0). Probes hybridized on mRNA were captured on Visium slides and a gene xpression library prepared following the provided protocol and sequenced on an Illumina NovaSeq 6000 with 50,000 reads per spot targeted sequencing depth.For each FFPE section, FASTQ files and histology images were processed using 10x Space Ranger v.2.0 to obtain the gene expression matrix associated with each spot.Seurat v.4 (