{"doi":"10.1089/zeb.2024.0175","title":"An Improved, High-Yield Method for Isolating Nuclei from Individual Zebrafish Embryos for Single-Nucleus RNA Sequencing","abstract":"Zebrafish is an ideal system to study the effect(s) of chemical, genetic, and environmental perturbations on development due to their high fecundity and fast growth. Recently, single-cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole-embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here, we report a method for efficiently isolating high-quality nuclei from zebrafish embryos in a 96-well plate format by bead homogenization in a lysis buffer. Through head-to-head single-cell combinatorial indexing RNAseq experiments, we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.","journal":"Zebrafish","year":2025,"id":562783,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9365,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":159308,"name":"Heidi Lee","orcid":null,"position":1,"is_corresponding":false},{"id":268501,"name":"Amy Tresenrider","orcid":"0000-0002-0819-9187","position":2,"is_corresponding":false},{"id":36581,"name":"Riza M. Daza","orcid":"0000-0003-1635-8675","position":3,"is_corresponding":false},{"id":417213,"name":"Andrew R. Mullen","orcid":null,"position":4,"is_corresponding":false},{"id":36510,"name":"Jay Shendure","orcid":"0000-0002-1516-1865","position":5,"is_corresponding":false},{"id":492444,"name":"David Kimelman","orcid":"0000-0002-9261-4506","position":6,"is_corresponding":false},{"id":19437,"name":"Cole Trapnell","orcid":"0000-0002-8105-4347","position":7,"is_corresponding":false},{"id":109709,"name":"Clifford Rostomily","orcid":"0000-0001-9550-6538","position":0,"is_corresponding":true}],"reference_count":7,"raw_metadata":null,"created_at":"2026-07-19T02:56:09.638214Z","pmid":"40040474","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}