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 findings reveal specific pathogen-specific sickness states encoded by the brain across scales, thereby broadening our understanding of how infections make us sick. This repository contains MERFISH-related data associated with these studies. Namely it contains the merfish_adata.h5ad file. This file was created from the scanpy package and can be loaded with tools from that package. It contains the following items: * X: The matrix of expression for all cells and all genes. This matrix was divided by total counts per cell then log1p-transformed.* obs: A dataframe with the following properties for all cells The index of each row in this data frame is a unique name for each cell * batch: A unique name for each MERFISH dataset * x: The centroid of that cell in x, in microns * y: The centroid of that cell in y, in microns * z: The average position of that cell in z-stacks, in microns * cellType: The cell type label associated with that cell * condition: The treatment condition for the mouse in which the cell was imaged * section: An index for the section in which the cell was imaged * ignoreCell: A flag that indicates that the cell was not included in subsequent analysis