Comparing 10x Visium spatial transcriptomic technologies

Spatial transcriptomics facilitates the understanding of gene expression within complex tissue contexts. Among the array of spatial capture technologies available is 10x Genomics' Visium which provides whole tissue section profiling, enabling whole transcriptome spatial analysis. Our dataset comprises spleen tissue from mice infected with malaria, spanning multiple experiments and sample preparation protocols for tissue preservation, either as fresh frozen at optimal cutting temperature (OCT) or formalin-fixed paraffin-embedded (FFPE). Tissue placement was also considered, comparing direct tissue placement on the slide with the use of CytAssist (CA), which expands the Visium platform's capabilities by allowing for the pre-selection of tissue sections and genes through a set of probes. We also include a matching scRNA-seq dataset that can be integrated with the spatial data. Overall design: Samples were captured over 5 10x Genomics Visium fresh-frozen (FF) slides and 3 formalin-fixed paraffin-embedded (FFPE) slides and sequenced over 6 Illumina runs. A matching scRNA-seq sample of the 3 mouse spleens (708, 709, 713): 10x scRNA-seq with the large BioLegend panel of antibody derived tags (ADTs) was captured over 1 GEM wells and GEX, ADT, and HTO were sequenced over 1 Illumina run.