Protocol to analyze changes in hippocampal neural stem cell quiescence from single-cell RNA sequencing data
Year: 2025
Type: article
Abstract: Here, we present a protocol to isolate mouse hippocampal neural stem cells from single-cell RNA sequencing datasets using a computational approach. We describe steps to analyze whether a perturbation affects quiescence depth. Specifically, we detail procedures for sequential reclustering, pseudotime trajectory analysis, and statistical testing of distribution shifts from deep to shallow quiescence. This protocol overcomes challenges in distinguishing quiescent neural stem cells from astrocytes and proliferating neural stem cells from progenitor cells. For complete details on the use and execution of this protocol, please refer to Rigo et al. 1 • Instructions for isolating quiescent stem cells from mouse hippocampal scRNA-seq • Steps for separating quiescent neural stem cells from astrocytes • Guidance on separating proliferating neural stem cells from progenitors • Procedures for ordering quiescence of neural stem cells via trajectory inference Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Here, we present a protocol to isolate mouse hippocampal neural stem cells from single-cell RNA sequencing datasets using a computational approach. We describe steps to analyze whether a perturbation affects quiescence depth. Specifically, we detail procedures for sequential reclustering, pseudotime trajectory analysis, and statistical testing of distribution shifts from deep to shallow quiescence. This protocol overcomes challenges in distinguishing quiescent neural stem cells from astrocytes and proliferating neural stem cells from progenitor cells.
Source: STAR Protocols
Authors: Jessica Hart, Lachlan Harris
Language: English
Subfield: Developmental Neuroscience
Field: Neuroscience
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,550
OpenAlex ID: W4416738420