Single-cell RNA sequencing of the ARC and MPOA across satiety and lactation states in female mice

These files accompany the single-cell RNA sequencing (scRNA-seq) portion of the research article "A hypothalamic circuit that modulates feeding and parenting behaviors" (Alcantara et al., 2025, Nature). In our study, we employed 10X Genomics scRNA-seq in two hypothalamic regions — the arcuate nucleus (ARC) and the medial preoptic area (MPOA) — of 4 groups of 14-week-old female C57BL/6 mice (n = 3 mice pooled per group): sated virgins (VS), fasted virgins (VF), sated mothers (MS), and fasted mothers (MF). The litter size for the lactating mother groups was 8 pups and pups were 13-15 days old at the time of sample collection. The fasted groups were food-deprived overnight for 16-18 hours. Raw sequencing data are in Gene Expression Omnibus (GEO) with the accession code GSE295610. allmetadata.csv contains our annotations of all cells. LoadProcDEGs.R loads scRNA-seq data and pre-annotated metadata (allmetadata.csv) for ARC and MPOA, filters for neurons with existing cluster labels, and performs SCTransform-based batch integration followed by PCA and UMAP visualization using those precomputed clusters. It then identifies conserved marker genes per cluster and runs pairwise differential expression analyses within each cluster across experimental conditions. ARC-Campbell-Compare.R and MPOA-Zhuang-Compare.R compare our ARC and MPOA neuronal clusters to those of previously published scRNA-seq datasets. ARC.clustermarks.xlsx and MPOA.clustermarks.xlsx contain the number of cells and marker genes for each neuronal cluster. ContributionPCA.R calculates the contribution of each neuronal cluster to the first n principal components (PCs) that explain ~85% of the variance between two experimental conditions (e.g. VF and VS). The other Excel files contain the differentially expressed genes (DEGs) for each ARC and MPOA neuronal cluster across pairs of experimental conditions. The direction of the fold changes (avg_log2FC) corresponds to the first condition in the file name relative to the second condition. For example, in ARC.VFvVS.xlsx, genes with positive fold changes are upregulated in VF compared to VS.