MERFISH and snRNAseq analysis of healthy and disease human liver

Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of cell types and their heterogeneity within the human liver, but the spatial organization at single-cell resolution has not yet been described. Here we apply multiplexed error robust fluorescent in situ hybridization (MERFISH) to map the zonal distribution of hepatocytes, resolve subsets of macrophage and mesenchymal populations, and investigate the relationship between hepatocyte ploidy and gene expression within the healthy human liver. We next integrated spatial information from MERFISH with the more complete transcriptome produced by single- nucleus RNA sequencing (snRNA-seq), revealing zonally enriched receptor-ligand interactions. Finally, analysis of fibrotic liver samples identified two hepatocyte populations that are not restricted to zonal distribution and expand with injury. Together these spatial maps of the healthy and fibrotic liver provide a deeper understanding of the cellular and spatial remodeling t..., Two measurement modalities were used to generate these data, including multiplexed error robust fluorescence in situ hybridization (MERFISH) and single-nucleus RNA sequencing (snRNAseq)., , # MERFISH and snRNAseq data from Watson, Paul et al

This README file contains information on the data deposited for the manuscript \"Spatial transcriptomics of healthy and fibrotic human liver at single-cell resolution\" by Watson, Paul and colleagues.

## Anndata Structures

Multiple anndata structures are provide as h5ad files for different datasets.
These anndata structures were generated with the scanpy pipeline (v1.8.1) and can be loaded in python with the associated tools.
These include:
(1) adata_healthy_merfish.h5ad
(2) adata_healthy_diseased_merfish.h5ad
(3) adata_healthy_merfish_nucseq.h5ad
(4) adata_healthy_nucseq.h5ad

Each anndata frame contains distinctive values for the respective data set as follows:

(1) adata_healthy_merfish.h5ad
This structure contains data from healthy patient samples which were imaged with MERFISH.
Raw data is stored in the adata.raw.X while adata.X is normalized by the total counts per cell, scaled to a uniform value, and then converted to logarithm...