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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. 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The experiments involving C57BL\/6J mice were approved by the ethical committee of the Institute of Experimental Medicine of the Czech Academy of Sciences under project No: 50\/2020, 112\/2023 and 146\/2024. The experiments involving Tg(Thy1\u00adMAPT*P301S)2541GODT mice followed the ARRIVE guidelines (\n                      \n                      ) and were approved under project No: 7848\/2022 and performed in accordance with Law No. 77\/2004 of the Czech Republic.","order":1,"name":"Ethics","label":"Ethics Approval and Consent to Participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent for Publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"974"}}