This dataset contains spatial transcriptomics data from 181 mouse hypothalamus samples, 155 genes and a total of 1,027,080 cells. For running the vignettes, we subset the data by selecting total 6000 cells from only 3 samples - Animal 1 Bregma -0.09 (2080 cells) and Animal 7 Bregmas 0.16 (1936 cells) and -0.09 (1984 cells), excluding cells that were annotated as 'ambiguous', and removed 20 genes that were assessed using a different technology.
Usage
data(mHypothal)Format
mh_expr a gene expression matrix with normalised counts, where rows
indicate genes and columns indicate cells.
mh_data a data frame of cell metadata including cell IDs, sample IDs,
cell type annotations, and x-y coordinates of cells.
Source
Molecular, Spatial and Functional Single-Cell Profiling of the Hypothalamic Preoptic Region, Science, 2018. Webpage: https://www.science.org/doi/10.1126/science.aau5324