{"doi":"10.17504/protocols.io.3byl4z7drvo5/v1","title":"Mapping Enhancer–Gene Interactions with Direct-Capture Targeted Perturb-seq (DC-TAP-seq) v1","abstract":"Mapping enhancer-gene (E-G) connections is critical for dissecting the functional impact of noncoding variants in the human genome. Single-cell CRISPRi screens offer a powerful approach to identify these regulatory interactions, but existing methods such as Perturb-seq are limited by high sequencing costs and inefficient guide RNA capture across diverse cell types. Here, we decribe a detailed protocol for Direct-Capture Targeted Perturb-seq (DC-TAP-seq) — a cost-effective and scalable approach that integrates TAP-seq1 with direct capture of Pol III-derived guide RNAs2 to sensitively screen thousands of E-G connections across the genome. This protocols describes pooled cloning of gRNAs into an sgOpti-CS vector, high MOI lentiviral transduction, cell preparation for single-cell RNA-seq, and targeted amplification of both transcripts and guide RNAs. DC-TAP-seq enables large-scale mapping of E-G interactions with reduced cost and improved sensitivity, and is broadly applicable for studying E-G regulation in diverse human cell types.","journal":null,"year":2025,"id":557500,"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":0.945,"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":75056,"name":"Evelyn Jagoda","orcid":null,"position":1,"is_corresponding":false},{"id":268408,"name":"Dulguun Amgalan","orcid":"0000-0001-6398-3372","position":2,"is_corresponding":false},{"id":1453332,"name":"James Galante","orcid":null,"position":3,"is_corresponding":false},{"id":931895,"name":"Chad J. Munger","orcid":"0000-0003-1906-1164","position":4,"is_corresponding":false},{"id":75052,"name":"Andreas R. Gschwind","orcid":"0000-0002-0769-6907","position":5,"is_corresponding":false},{"id":75055,"name":"Maya U. Sheth","orcid":"0000-0003-1466-8899","position":6,"is_corresponding":false},{"id":1457684,"name":"Jacob Huang","orcid":null,"position":7,"is_corresponding":false},{"id":54720,"name":"Glen Munson","orcid":null,"position":8,"is_corresponding":false},{"id":714437,"name":"Madeleine Murphy","orcid":"0000-0002-9052-702X","position":9,"is_corresponding":false},{"id":805526,"name":"Timothy Barry","orcid":"0000-0002-4356-627X","position":10,"is_corresponding":false},{"id":1457380,"name":"Vasundhara Singh","orcid":"0000-0001-8639-2313","position":11,"is_corresponding":false},{"id":1457685,"name":"A. Baskaran","orcid":null,"position":12,"is_corresponding":false},{"id":815298,"name":"Helen Kang","orcid":"0000-0001-9522-1911","position":13,"is_corresponding":false},{"id":805527,"name":"Eugene Katsevich","orcid":"0000-0003-0598-2050","position":14,"is_corresponding":false},{"id":4994,"name":"Lars M. Steinmetz","orcid":"0000-0002-3962-2865","position":15,"is_corresponding":false},{"id":3038,"name":"Jesse M. Engreitz","orcid":"0000-0002-5754-1719","position":16,"is_corresponding":false},{"id":513577,"name":"Judhajeet Ray","orcid":"0000-0003-1524-2603","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-19T02:55:17.435961Z","pmid":null,"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":[]}