Spatial transcriptomics Chowdhury et al

Data is spatial transcriptomics from Pancreatic Cancer PDX tissue. The mice were treated with Control or fibrinogen ASOs and tumors were collected at week 4 post-implant. Raw FASTQ files and accompanying H&E images were processed with SpaceRanger (10x Genomics). Reads were aligned to a dual-species reference (GRCh37 + mm10), after which unique molecular indices (UMIs) were assigned to individual Visium spots to generate spot-level gene-expression matrices. Because a matched single-cell reference was unavailable, initial compartment identification used the unsupervised spatial deconvolution tool stDeconvolve. For each inferred “topic,” we inspected the top-ranked genes, classified them as human- or mouse-specific, and labelled the corresponding spots as cancer (human) or stromal (mouse). Topic-wise proportions were then aggregated to yield the total cancer and stromal fractions per slide.