Spatial Transcriptomics Reveals Injured Cells, Signature Genes, and Communication Patterns in the Cyst Microenvironment of Polycystic Kidney Disease

This dataset contains a spatial transcriptomics AnnData object (spatial_processed.h5ad) with 8,149 spots and 17,628 genes, integrating gene expression, spatial coordinates, and image metadata. The dataset was used as input for all downstream analyses in the associated publication. Observations (.obs): Spot-level metadata, including spatial coordinates (array_row, array_col), tissue assignment (in_tissue), library identifiers, quality control metrics (mitochondrial, hemoglobin, ribosomal content), cell cycle scores, clustering assignments, and cell type annotations. Variables (.var): Gene information, genome annotations, feature categories, and per-gene QC metrics (counts, dropout rates, variability statistics). Unstructured data (.uns): Analysis metadata including clustering results, PCA/UMAP parameters, color maps, and the spatial field, which stores the tissue image(s) and spot-to-image coordinate transforms. Embeddings (.obsm): Low-dimensional representations (X_pca, X_umap) and spatial coordinates (spatial). Variable loadings (.varm): Principal component loadings. Layers (.layers): Log-normalized (LogNorm) and scaled expression matrices. Pairwise matrices (.obsp): Graph connectivities and distances among spots.