A spatial transcriptomics atlas of live donors reveals unique zonation patterns in the healthy human liver

Samples description The dataset includes the following human & non-human samples: Human samples: -Live healthy donors (LHD; n = 8), labeled as M -Patients with liver pathology (adjacent normal tissue sampled; n = 8), labeled as P Non-human samples: -Wild boar (n = 2), labeled as non_human_P -Cow (n = 2), labeled as non_human_C -Domesticated pig (n = 3), labeled as non_human_PD Visium: LHDs and adjacent normal samples: Human loupe files: This folder includes the Loupe Browser-compatible files (16 total) corresponding to the human samples (M1–M8, P2, P3, P6, P7, P14, P17, P18, P21) for downstream visualization and exploration. Human_h5_files This folder contains .h5 formatted output files from Space Ranger for the 16 human samples. Human_Spatial_transcriptomics_data: This folder contains spatial transcriptomics data from 16 human samples.For each sample the following files are included: counts_ALL.csv – full gene expression matrix counts_UTT.csv – filtered matrix (UTT: under the tissue) tissue_positions_list.csv – spatial barcode coordinates scalefactors_json.json – image scaling information tissue_hires_image.png – high-resolution histology image Non Human Loupe files: This folder contains Loupe Browser-compatible files for the 7 non-human samples (C1, C2, P1, P2, PD1, PD2, PD3). Non_human_h5_files This folder contains.h5 formatted output files from Space Ranger for the 7 non-human samples Non_Human_Spatial_transcriptomics_data: This folder includes spatial transcriptomics data from 7 non-human samples (C1, C2, P1,P2, PD1, PD2, PD3). counts_ALL.csv – full gene expression matrix counts_UTT.csv – filtered matrix (UTT: under the tissue) tissue_positions_list.csv – spatial barcode coordinates scalefactors_json.json – image scaling information tissue_hires_image.png – high-resolution histology image VisumHD: This folder contains spatial transcriptomics data from 10x Genomics Visium HD for human liver samples: M1_VisiumHD.cloupe – Loupe Browser visualization file for patient M1, showing spatial transcriptomics data at 8 μm bin resolution. M2_VisiumHD.cloupe – Loupe Browser visualization file for patient M2, showing spatial transcriptomics data at 8 μm bin resolution. M6_VisiumHD.cloupe – Loupe Browser file for a Visium HD slide that includes two tissue sections. The tissue at the bottom of the slide corresponds to patient M6, which is the one analyzed in the downstream dataset (marked under ‘patients’ as ‘M6-high quality’). Data is shown at 8 μm bin resolution. visiumHD_data_M2_M6.h5ad – A filtered and integrated .h5ad file containing single-cell–resolved spatial gene expression data from both M2 and M6 samples. -Resolution: Cells. Based on single-cell segmentation (see “Liver Cell Atlas using Visium HD” method). -Cell filtering: Only cells detected via segmentation and that have passed quality filters were included. -UMI threshold: Cells with fewer than 200 UMIs were excluded. -Batch correction: Harmony was applied to correct sample-specific effects prior to UMAP visualization. -Format: .h5ad (AnnData format, compatible with Scanpy). -Includes: Single-cell expression matrix, spatial coordinates, Harmony-corrected UMAP, cluster identity, and metadata. M1, M2, M6 These folders contains the full, unmodified output of the 10x Genomics Visium HD Space Ranger for the M1,M2 and M6 liver tissue sample (2X2 and 8X8 um resolution). Sample M6M2 covers two samples, only M6 was used in the analysis.A list of bins from M6 is included. filtered_feature_bc_matrix_8um.h5 filtered_feature_bc_matrix_2um.h5 raw_feature_bc_matrix_8um.h5raw_feature_bc_matrix_2um.h5 scalefactors_json.json Images: tissue_hires_image.tif / tissue_lowres_image.tif/fullres_image.tif tissue_positions_orig.csv - snRNAseq: This folder contains single-nucleus RNA-seq (snRNA-seq) data from four human liver samples (M5, M6, M7, M8). Data was generated using Cell Ranger multi. single_nuc_RNAseq.cloupe - Output from Cell Ranger multi. data from all four samples. snRNAseq.h5ad - Processed and filtered .h5ad file containing single-nucleus expression data from M5–M8, integrated into one dataset. -Filtering includes standard QC (e.g., low-gene/UMI exclusion, mitochondrial content, etc.) -Batch correction: Harmony was applied to correct sample-specific effects prior to UMAP visualization. -Format: .h5ad (AnnData format, compatible with Scanpy). -Includes: expression matrix, spatial coordinates, Harmony-corrected UMAP, cluster identity and metadata. M5, M6, M7, M8 Each sample folder contains raw and filtered matrices generated by Cell Ranger: -sample_filtered_feature_bc_matrix -sample_raw_feature_bc_matrix MERFISH: For both samples- M5 and M8, each sample folder contains: -cell_by_gene.csv -cell_metadata.csv -detected_transcripts.csv As an additional validation step, we performed highly multiplexed immunofluorescence (PhenoCycler™) using a panel of 48 antibodies targeting a broad range of parenchymal and non-parenchymal cell types in 2 live-donor livers (LHDs) and 4 adjacent-normal liver samples (Supplementary Table 5 in the linked dataset). This data can be found at: https://zenodo.org/records/17730820