MouseColonIbdCadinu2024: MERFISH mouse colon IBD dataset from Cadinu et al., 2024

In ccb-hms/MerfishData: Collection of public MERFISH datasets

MERFISH mouse colon IBD dataset from Cadinu et al., 2024

Description

Obtain the MERFISH mouse colon IBD dataset from Cadinu et al., 2024

Usage

MouseColonIbdCadinu2024()

Details

Gut inflammation involves contributions from immune and non-immune cells, whose interactions are shaped by the spatial organization of the healthy gut and its remodeling during inflammation. The crosstalk between fibroblasts and immune cells is an important axis in this process, but our understanding has been challenged by incomplete cell-type definition and biogeography.

To address this challenge, Cadinu et al., 2024 used multiplexed error-robust fluorescence in situ hybridization (MERFISH) to profile the expression of 943 genes in 1.35 million cells imaged across the onset and recovery from a mouse colitis model. They identified diverse cell populations, charted their spatial organization, and revealed their polarization or recruitment in inflammation.

The barcoding scheme contained 990 possible barcodes; 943 of them were used to code the RNAs of the genes assayed via combinatorial smFISH across different stages of colitis in a mouse model; 47 of these barcodes were left unassigned ("blank"), providing a direct measure of the false-positive rate in MERFISH. Measurements for these 47 blank barcodes is stored in an altExp named "blank".

The dataset includes cell type labels with three levels of granularity. Data were collected at multiple time points: prior to the onset of colitis (sample_type="Healthy") and at intervals of 3 days, 9 days, and 21 days post-onset.

Value

An object of class SpatialExperiment.

Source

https://doi.org/10.5061/dryad.rjdfn2zh3

References

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

Examples

spe <- MouseColonIbdCadinu2024()

ccb-hms/MerfishData documentation built on June 30, 2024, 8:14 p.m.