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

UPDATED DEPOSITION - 03-OCT-2025 > updating minor error in one line in each of scripts 03, 04, and 05 where the RunUMAP function did not appropriately call the integrated dimensional reductionDeposition 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.