MERFISH measurements of the mouse gastrointestinal tract in the presence and absence of the microbiome

The mammalian gastrointestinal tract is comprised of a diverse set of cell types, each responsive to a diversity of diet-, host-, and microbe-derived small molecules. These small molecules are sensed by a massive diversity of receptors and differential regional, spatial, and cellular expression of these receptors is a critical mode by which sensation is mediated. In parallel, the gut microbiome plays critical roles in modulating the homeostatic cellular, molecular, and spatial structure of the mammalian gut, including potential roles in shaping the receptors that are expressed and, thus, the molecular sensing capabilities of the gut. Here we provide a spatially resolved, single-cell atlas of gene expression across four regions of the murine gut in the presence and absence of the microbiome. These measurements provide a rich resource for understanding cell-type specific sensation capabilities, the way in which cells fine tune these capabilities across gut regions, and, on a smaller scale..., , # MERFISH measurements of the mouse gastrointestinal tract in the presence and absence of a microbiome

Rosalind J. Xu, Jeffrey R. Moffitt
Boston Children's Hospital, 2025

## Description

This repository contains a variety of data from a MERFISH study of the molecular and cellular organization of the murine gastrointestinal tract in the presence of a specific-pathogen-free (SPF) microbiota or no microbiota (germ-free [GF]).

The respository includes metadata associated with the identity and location of all imaged RNAs, a model used for cell segmentation, gene expression and metadata associated with identified cells, and other downstream analysis.

These data are organized in the following folders.

## transcripts

This folder contains files that describe metadata associated with all RNAs identified with MERFISH.
These metadata were derived either during the decoding of RNA barcodes or in the segmentation process.

#### transcript\_metadata\_raw\.csv

This file contains the location, id...,