Large-scale single-cell RNA-seq characterizes neural stem cells and progenitor cells in postnatal and young adult mouse hypothalamus

<strong> Background</strong> In recent years, studies have demonstrated that neurogenesis can also occur in the adult mammal hypothalamus. Although the hypothalamus is a critical brain region that plays a vital role in regulating homeostatic and survival-related behaviors, there is still limited knowledge about its intrinsic mechanisms of development. <br> <strong>Our Goal</strong> Our goal is to identify and extensively characterize the cell-type-specific features during neurogenesis in the hypothalamic region of mice, from postnatal to young adult stages. We processed and analyzed publicly available scRNA-seq transcriptomic data that were obtained from the hypothalamic regions of mice, using uniform and optimized informatics pipeline. <br> <strong>Methods</strong> We obtained 10 scRNA-seq datasets from independent studies using from the NCBI GEO, which were further processed using the Seurat package in R (v4.2.1). A standard informatics pipeline was applied to each dataset for pre-processing and cell clustering for cell-level metadata standardization (See R script). Further, Pseudotime trajectory using the Monocle3 Alpha package in R (v. 2.99.1) and slingshot package in R (v. 2.6.0) was performed to see developmental differentiation in the hypothalamus during ault neurogenesis. We also generated connect-seq-derived scRNA-seq dataset <strong>Validation.rds (barcodes.tsv.gz, </strong> <strong>features.tsv.gz, matrix.mtx.gz</strong>) of 1,533 cells from whole hypothalamus and the bed nucleus of the stria terminalis (BNST) for validation analysis of our integrated dataset, by performing anchor-based mapping and transferring of labels and merging both integrated and validation dataset(<strong>refquery.rds</strong>). <br> <strong>Result</strong> Our integrated dataset (<strong>final_hypo_ann.rds)</strong> has revealed 30 distinct cell types that encompass all major cell types found in the hypothalamic regions, including glial-like cells such as ependymal cells, tanycytes, astrocytes, oligodendrocytes, and intermediate progenitor cells (IPCs) and also explored gene expression and cellular differentiation in the hypothalamus across various stages of development.