SnCED-seq: high-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues.

ABSTRACT: Recent advances have shown that single-nucleus RNA sequencing (snRNA-seq) can be applied to formalin-fixed, paraffin-embedded (FFPE) tissues, opening avenues for transcriptomic analysis of archived specimens. Yet, isolating intact nuclei remains difficult due to RNA cross-linking. Here, we introduce a cryogenic enzymatic dissociation (CED) strategy for rapid, high-yield and fidelity nuclei extraction from FFPE samples and validate its utility with snRandom-seq (snCED-seq) using male C57/BL6 mice. Compared with conventional approaches, CED delivers a tenfold increase in nuclei yield with significantly reduced hands-on time, while minimizing secondary RNA degradation and preserving intranuclear transcripts. snCED-seq enhances gene detection sensitivity, lowers mitochondrial and ribosomal con

SUBMITTER: Guo Y 

PROVIDER: S-EPMC12048618 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature