DOI: 10.5061/dryad.v6wwpzh98
title: MERFISH data from the murine hypothalamus in health and under induced sickness states

description: 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 all MERFISH-related data
 associated with these studies. 
description: # 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 microns * z: The z position of the RNA
 in microns * xf: The x position of the RNA within the fov in microns * yf:
 The y position of the RNA within the fov in microns * zi: The index of the
 z-slice in which the RNA was imaged * brightness: The normalized
 brightness of the RNA * area: The number of pixels associated with the RNA
 * weighted_distance: The distance between the measured intensity profile
 for the RNA and that predicted for the matching barcode * xgb_raw: The
 normalized quality score of the RNA (distinguishing it from a blank
 barcode) * mir: The misidentification rate of the RNA * concordance: Is
 the RNA correctly within a region where both libraries are overlapping *
 isBlank: Is the RNA associated with a blank barcode * library: The name of
 the library in which the RNA was identified ### merfish_adata.h5ad 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