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MERFISH Colitis Reference (Healthy) Spatial Dataset

Source: R/dataDocumentation.R
merfish_reference_data.Rd

This dataset contains a downsampled reference (Day 0, healthy colon) subset of the Cadinu et al. (2024) mouse colitis MERFISH dataset. It is a SpatialExperiment on a 943-gene targeted panel, preprocessed to include log-normalized counts, a cell-type column, and PCA results, restricted to 5 shared cell types (including fibroblasts).

Usage

merfish_reference_data

Format

An object of class SpatialExperiment with 943 rows and 1100 columns.

Source

Cadinu CA, et al. (2024), processed and hosted at https://doi.org/10.5281/zenodo.18274942.

Details

This dataset underwent the following steps:

  • Downloads the processed reference (Day 0) object from Zenodo (https://doi.org/10.5281/zenodo.18274942), itself derived from the Cadinu et al. (2024) MERFISH mouse colitis dataset (MerfishData package).

  • Collapses inflammation-associated variants of a cell state (e.g. "Inflamed Fibroblast", present only in the query) into their parent lineage for a shared cell_type_merged column, while retaining the original fine-grained tier2_merged label.

  • Restricts to 5 shared cell types (Fibroblast, Smooth Muscle, Epithelial, Other Immune, Endothelial).

  • Downsamples to at most 220 cells per cell type.

  • Performs Principal Component Analysis (PCA) using the function runPCA from the scater package on the full 943-gene panel.

References

Cadinu CA, et al. (2024). Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling. Cell 187(8):2010-2028.

See also

Use data("merfish_reference_data") to load and access the resulting reference dataset, and data("merfish_query_data") for the corresponding query (Day 9 colitis) dataset.

Examples

# Load and explore the MERFISH reference dataset
data("merfish_reference_data")