{"doi":"10.1101/2022.10.25.513758","title":"A contamination focused approach for optimizing the single-cell RNA-seq experiment","abstract":"Abstract Achieving high data quality in single-cell RNA-seq (scRNA-seq) experiments has always been a significant challenge stemming from minute signal that can be detected in individual cells. Droplet-based scRNA-seq additionally suffers from ambient contamination, comprising nucleic acid materials released by dead cells into the loading buffer and co-encapsulated with real cells, which further washes out real biological signals. Here, we developed quantitative, ambient contamination-based metrics and an associated software package that can both evaluate current datasets and guide new experimental optimizations. We performed a series of experimental optimizations using the inDrops platform to address the mechanical and microfluidic cell encapsulation aspect of an scRNA-seq experiment, with a focus on minimizing ambient contamination. We report improvements that can be achieved via cell fixation, microfluidic loading, microfluidic dilution, and nuclei versus cell preparation; many of these parameters are inaccessible on commercial platforms. We provide insights into previously obscured factors that can affect scRNA-seq data quality and suggest mitigation strategies that can guide future experiments.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":304662,"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":0.9486,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":991896,"name":"Zhengyi Chen","orcid":"0000-0003-4774-945X","position":1,"is_corresponding":false},{"id":86827,"name":"Alan J. Simmons","orcid":"0000-0002-3412-5819","position":2,"is_corresponding":false},{"id":86831,"name":"Cody N. Heiser","orcid":"0000-0002-1299-1628","position":3,"is_corresponding":false},{"id":86837,"name":"Austin N. Southard-Smith","orcid":"0000-0003-0022-6897","position":4,"is_corresponding":false},{"id":998075,"name":"Michael J. Brenan","orcid":null,"position":5,"is_corresponding":false},{"id":997590,"name":"Yilin Yang","orcid":"0009-0000-9869-4044","position":6,"is_corresponding":false},{"id":31816,"name":"Bob Chen","orcid":"0000-0003-1508-1758","position":7,"is_corresponding":false},{"id":86838,"name":"Yanwen Xu","orcid":"0000-0002-8308-9383","position":8,"is_corresponding":false},{"id":364433,"name":"Eunyoung Choi","orcid":"0000-0002-1501-1568","position":9,"is_corresponding":false},{"id":225132,"name":"Joshua D. Campbell","orcid":"0000-0003-0780-8662","position":10,"is_corresponding":false},{"id":307313,"name":"Qi Liu","orcid":"0000-0003-2578-1221","position":11,"is_corresponding":false},{"id":60556,"name":"Ken S. Lau","orcid":"0000-0001-8438-0319","position":12,"is_corresponding":false},{"id":997589,"name":"Deronisha Arceneaux","orcid":"0000-0003-4008-0415","position":0,"is_corresponding":true}],"reference_count":39,"raw_metadata":null,"created_at":"2026-07-19T00:32:32.651796Z","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":[]}