Tissue Dissociation Workflows Influence Reactive Astrocyte Recovery in Single-Cell Transcriptomics

Single-cell RNA sequencing has advanced our understanding of glial diversity, yet tissue dissociation remains an important technical variable. We revealed that a widely used commercial dissociation protocol can underrepresent reactive astrocytes in an acute ischemic stroke model, with preliminary observations indicating a comparable trend in a chronic tauopathy model. Benchmarking against an optimized, low-shear workflow demonstrates that different tissue dissociation workflows can substantially alter the recovery and apparent transcriptomic profile of disease-associated astrocytes, selectively losing signatures of morphological remodeling. Our findings indicate that workflow-dependent recovery biases affecting reactive astrocytes may be more prevalent than recognized, underscoring the need for pathology-tailored, gentle isolation workflows to avoid distortions in downstream neuropathological interpretations and the prioritization of therapeutic targets.