Protocol to analyse changes in hippocampal neural stem cell quiescence from single-cell RNA-sequencing data

Deposition of code for protocols paper. Summary: This protocol describes computational approaches to isolate hippocampal neural stem cells from single-cell RNA-sequencing datasets, overcoming challenges associated with distinguishing quiescent neural stem cells from astrocytes, as well as proliferating neural stem cells from other proliferative progenitor cells. We also describe how to analyse whether a perturbation has affected the depth of quiescence at a population level. Major steps include marker-based classification of neurogenic clusters, sequential reclustering, pseudotime trajectory analysis of quiescent neural stem cells, and statistical testing of differences in the distribution of these cells from deep to shallow quiescence.