{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Morabito A"],"funding":["Swiss National Science Foundation"],"pagination":["102603"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10522992"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["4(4)"],"pubmed_abstract":["Tissue autofluorescence poses significant challenges for RNA and protein analysis using fluorescence-based techniques. Here, we present a protocol that combines oxidation-mediated autofluorescence reduction with detergent-based tissue permeabilization for whole-mount RNA-fluorescence in situ hybridization (FISH) on mouse embryonic limb buds. We describe the steps for embryo collection, fixation, photochemical bleaching, permeabilization, and RNA-FISH, followed by optical clearing of RNA-FISH and immunofluorescence samples for imaging. The protocol alleviates the need for digital image post-processing to remove autofluorescence and is applicable to other tissues, organs, and vertebrate embryos."],"journal":["STAR protocols"],"pubmed_title":["Optimized protocol for whole-mount RNA fluorescent in situ hybridization using oxidation-mediated autofluorescence reduction on mouse embryos."],"pmcid":["PMC10522992"],"funding_grant_id":["207824","310030"],"pubmed_authors":["Sheth R","Zeller R","Malkmus J","Morabito A","Pancho A","Zuniga A"],"additional_accession":[]},"is_claimable":false,"name":"Optimized protocol for whole-mount RNA fluorescent in situ hybridization using oxidation-mediated autofluorescence reduction on mouse embryos.","description":"Tissue autofluorescence poses significant challenges for RNA and protein analysis using fluorescence-based techniques. Here, we present a protocol that combines oxidation-mediated autofluorescence reduction with detergent-based tissue permeabilization for whole-mount RNA-fluorescence in situ hybridization (FISH) on mouse embryonic limb buds. We describe the steps for embryo collection, fixation, photochemical bleaching, permeabilization, and RNA-FISH, followed by optical clearing of RNA-FISH and immunofluorescence samples for imaging. The protocol alleviates the need for digital image post-processing to remove autofluorescence and is applicable to other tissues, organs, and vertebrate embryos.","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Dec","modification":"2026-05-13T14:32:57.374Z","creation":"2025-02-19T04:08:50.239Z"},"accession":"S-EPMC10522992","cross_references":{"pubmed":["37742180"],"doi":["10.1016/j.xpro.2023.102603"]}}