{"doi":"10.1101/2025.05.27.656468","title":"MIC-Drop-seq: Scalable single-cell phenotyping of mutant vertebrate embryos","abstract":"Advances in genome engineering and single-cell RNA sequencing (scRNAseq) have revolutionized the ability to precisely map gene functions, yet scaling these techniques for large-scale genetic screens in animals remains challenging. We combined high-throughput gene disruption in zebrafish embryos via Multiplexed Intermixed CRISPR Droplets with phenotyping by multiplexed scRNAseq (MIC-Drop-seq). In one MIC-Drop-seq experiment, we intermixed and injected droplets targeting 50 transcriptional regulators into 1,000 zebrafish embryos, followed by pooled scRNAseq. Tissue-specific gene expression and cell abundance analysis of demultiplexed mutant cells recapitulated many known phenotypes, while also uncovering novel functions in brain and mesoderm development. We observed pervasive cell-extrinsic effects among these phenotypes, highlighting how whole-embryo sequencing captures complex developmental interactions. Thus, MIC-Drop-seq provides a powerful and scalable platform for mapping gene functions in vertebrate development with cellular resolution.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":558083,"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":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9401,"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":644023,"name":"Saba Parvez","orcid":"0000-0001-8608-1494","position":1,"is_corresponding":false},{"id":382796,"name":"Zachary J. Brandt","orcid":"0000-0002-7710-2959","position":2,"is_corresponding":false},{"id":493769,"name":"Brent W. Bisgrove","orcid":"0000-0002-0665-6401","position":3,"is_corresponding":false},{"id":1458076,"name":"Christopher J. Yates","orcid":"0000-0003-4559-4482","position":4,"is_corresponding":false},{"id":268421,"name":"Randall T. Peterson","orcid":"0000-0003-0727-3469","position":5,"is_corresponding":false},{"id":460961,"name":"James A. Gagnon","orcid":"0000-0003-3978-6058","position":6,"is_corresponding":false},{"id":772539,"name":"Clayton M. Carey","orcid":"0000-0002-9458-649X","position":0,"is_corresponding":true}],"reference_count":60,"raw_metadata":null,"created_at":"2026-07-19T02:55:21.727661Z","pmid":"40502104","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":[]}