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

UPDATED DEPOSITION - 30-Sep-2025Deposition of code for protocols paper. Summary: This protocol describes computational approaches to isolate mouse hippocampal neural stem cells from single-cell RNA-sequencing datasets, overcoming challenges distinguishing quiescent neural stem cells from astrocytes and proliferating neural stem cells from progenitor cells. We describe how to analyse whether a perturbation affects quiescence depth. Major steps include sequential reclustering, pseudotime trajectory analysis and statistical testing of distribution shifts from deep to shallow quiescence.