MERFISH data from the murine hypothalamus in health and under induced sickness states

In natural environments, animals encounter diverse pathogens that engage specific peripheral host defense programs and elicit sickness behavior – a set of stereotyped physiological and behavioral changes thought to promote host fitness. So far, most studies have relied on one or few mouse models of infection, limiting insights into pathogen-specific neuroimmune interactions that generate sickness.
We hypothesized that different pathogens may elicit distinct sickness states and engage various brain circuits. Using different models of infection and inflammation representing bacterial, viral, allergic, parasitic and colitis conditions, we assessed sickness across scales: organismal – behavior and physiology; cellular – brain-wide neural activity; and molecular – single-cell in situ transcriptomics in the hypothalamus, associated with social and homeostatic functions affected during sickness. Remarkably, immune challenges each elicited unique repertoires of changes across all scales. Our fi..., , # MERFISH data from the murine hypothalamus in health and under induced sickness states

Bertrand J. Wong, Jeffrey R. Moffitt

Boston Children's Hospital, 2025

## File Organization

### molecules.zip

This folder contains csv files that describe the properties of all identified RNAs with MERFISH. Each csv file is named 'processed_barcodes_*name*.csv', where *name* represents the unique name assigned to each animal. The name describes the sickness condition (PBS: control; DSS, PIC, PLA, LPS, or STAG) and the mouse number (m#). Each csv file has the following fields:

* gene_name: The name of the gene from which the RNA was transcribed
* fov: A unique ID for the field-of-view in which the RNA was imaged
* section: A unique ID for the section in which the RNA was imaged
* cell: A unique ID for the cell to which the RNA was assigned
* cell_detailed: A name for each cell that is unique across the entire dataset
* x: The x position of the RNA in microns
* y: The y position of the RNA in micr...,