Spatial gene expression in the mouse colon during experimental colitis measured with MERFISH|基因表达分析数据集|炎症研究数据集

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 stromal 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, we used MERFISH to profile the expression of 940 genes in 1.35 million cells in colon slices collected across the onset and recovery from a mouse colitis model. We identified a large diversity of cell populations; charted their spatial organization; and revealed their polarization or recruitment in inflammation. We found a staged progression of inflammation-associated tissue neighborhoods orchestrated, in part, by multiple inflammation-associated fibroblasts, with unique expression profiles, spatial localization, cell-cell interactions, and healthy fibroblast origins. Similar signatures in ulcera..., This dataset was collected using multiplexed error robust fluorescence in situ hybridization (MERFISH) as described in the methods of the supporting paper. The methods section of this paper also describes the approaches used to analyze the data, which include the use of publicly available pipelines for the analysis of raw MERFISH images (github.com/ZhuangLab/MERFISH_analysis), RNA assignment to cells (github.com/kharchenkolab/Baysor), and single-cell analysis (github.com/scverse/scanpy). The organization of the provided files is described in the included README.md. , We have provided the output of our single-cell analysis in the AnnData format utilized by scanpy and saved in hdf5. Consult the scanpy documentation for instructions on loading this file. To facilitate additional access to these data, we have also provided the key elements included in the AnnData format in CSV format. All other information is provided in CSV format. We have also provided AnnData format for our reanalysis of published scRNA-seq data relevant to comparisons in our manuscript., # Spatial gene expression in the mouse colon during experimental colitis measured with MERFISH

Jeffrey R. Moffitt
Paolo Cadinu
Boston Children's Hospital, 2024

## File organization

### Anndata structure for Day 0 - Day 21 MERFISH data

#### adata.h5ad

This file was generated with the scanpy pipeline and can be loaded in Python with the tools associated with this pipeline.

The adata object contains a measure of the normalized counts observed in each cell for each of the genes measured with MERFISH.
The values stored in the X matrix are normalized by the total counts per cell, scaled to a uniform value, and then converted to logarithmic space by adding a pseudo count and applying a log10 transform.

The adata object contains an obs field that contains a data frame that describes the properties of each field.
The fields of this data frame are defined as follows:

* x: This field describes the x position of the centroid of the cell in microns
* y: This field describes the y positio...