The hypothalamus controls essential social behaviors and homeostatic functions. However, the cellular architecture of hypothalamic nuclei, including the molecular identity, spatial organization, and function of distinct cell types, is poorly understood. Here, we developed an imaging-based cell type identification and mapping method and combined it with single-cell RNA-sequencing to create a molecularly annotated and spatially resolved cell atlas of the mouse hypothalamic preoptic region. We profiled ~1 million cells, identified ~70 neuronal populations characterized by distinct neuromodulatory signatures and spatial organizations, and defined specific neuronal populations activated during key social behaviors in male and female mice, providing a high-resolution framework for mechanistic investigation of behavior circuits. The approach described here opens a new avenue for the construction of cell atlases in diverse tissues and organisms.
Properties of cells measured with MERFISH
Properties of all cells measured with MERFISH provided as a csv file. “Cell ID” is a unique ID associated with each cell. “Animal ID” is a unique ID associated with animal. “Animal sex” is the gender of the animal in which the cell was imaged. “Behavior” describes the behavioral treatment of the animal. ‘Naïve’ indicates that no treatment was performed. “Bregma” indicates the approximate location of the slice in bregma coordinates. “Centroid X” is the x coordinate of the centroid position for the cell in µm. “Centroid Y” is the y coordinate of the centroid position for the cell in µm. “Cell class” lists the major cell class to which a cell was assigned. A value of 'Ambiguous' represents cells that were identified as putative doublets and were not further analyzed. “Neuron cluster_ID” represents the neuronal cluster to which a cell was assigned. This field is empty if the cell was not a neuron. Columns with a gene name, e.g. ‘Ace2’, contain the expression values for that gene in that cell. Expression values for the 135 genes measured in the combinatorial smFISH run were determined as the total counts per cell divided by the cell volume and scaled by 1000. Expression values for the 21 genes (including Fos) measured in the non-combinatorial, sequential FISH rounds were arbitrary fluorescence units per µm^3, but the same scale is used for all cells. A value of 'NaN' for Fos indicates that this gene was not measured in this animal. These 21 genes are the final genes in the listed genes. Genes named 'Blank-' represent the measurement of barcodes not assigned to any RNA and which serve as blank controls. There are five blank controls.
Moffitt_and_Bambah-Mukku_et_al_merfish_all_cells.csv
