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

We performed 10x Visium spatial transcriptomics on 16 adult human liver samples: eight from young, healthy, living donors (marked as 'M') and eight from patients with liver pathology, where we sampled ‘adjacent normal’ tissue (marked as 'P') to construct a spatial expression atlas of the adult human liver. To achieve higher spatial resolution, we also applied high-definition Visium HD measurements to two liver sections from young, healthy, living donors (M2 and M6).

To compare human liver zonation profiles with those of other mammals, we assembled a spatial transcriptomics dataset from three additional mammalian species with body sizes and metabolic rates more comparable to human: wild boar (n=2. marked as 'non+human_P'), cow (n=2. marked as 'non+human_C'), and domesticated pig (n=3. marked as 'non+human_PD'). 

For human Visium samples (n=16. M1, M2, M3, M4, M5, M6, M7, M8, P2, P3, P6, P7, P14, P17, P18 and P21) and non-human Visium samples (n=7. C1, C2, P1, P2, PD1, PD2 and PD3) the following files were uploaded:

Metadata:

Human samples metadata file.

Non-human metadata file.

For each Visium sample individually:

counts_ALL.csv

counts_UTT.csv

scalefactors_json.json

tissue_hires_image.png

tissue_positions_list.csv

cloupe file

filtered_feature_bc_matrix.h5

raw_feature_bc_matrix.h5

For M2 and M6 Visium HD samples:

cloupe file