{"doi":"10.1101/2023.08.16.553527","title":"Highly multiplexed mRNA quantitation with CRISPR-Cas13","abstract":"Abstract RNA quantitation tools are often either high-throughput or cost-effective, but rarely are they both. Existing methods can profile the transcriptome at great expense or are limited to quantifying a handful of genes by labor constraints. A technique that permits more throughput at a reduced cost could enable multi-gene kinetic studies, gene regulatory network analysis, and combinatorial genetic screens. Here, we introduce q uantitative C ombinatorial A rrayed R eactions for M ultiplexed E valuation of N ucleic acids (qCARMEN): an RNA quantitation technique which leverages the programmable RNA-targeting capabilities of CRISPR-Cas13 to address this challenge by quantifying over 4,500 gene-sample pairs in a single experiment. Using qCARMEN, we studied the response profiles of interferon-stimulated genes (ISGs) during interferon (IFN) stimulation and flavivirus infection. Additionally, we observed isoform switching kinetics during epithelial-mesenchymal transition. qCARMEN is a simple and inexpensive technique that greatly enhances the scalability of RNA quantitation for novel applications with performance similar to gold-standard methods.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":394974,"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":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9575,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1169797,"name":"Jiayu Zhang","orcid":"0000-0001-6035-479X","position":1,"is_corresponding":false},{"id":404677,"name":"Michael P. Schwoerer","orcid":"0000-0001-8068-0509","position":2,"is_corresponding":false},{"id":1169798,"name":"Amy N. Nelson","orcid":"0000-0002-3654-163X","position":3,"is_corresponding":false},{"id":1170327,"name":"Emily Schoeman","orcid":null,"position":4,"is_corresponding":false},{"id":915857,"name":"Andrew Guo","orcid":null,"position":5,"is_corresponding":false},{"id":418557,"name":"Alexander Ploß","orcid":"0000-0001-9322-7252","position":6,"is_corresponding":false},{"id":35849,"name":"Cameron Myhrvold","orcid":"0000-0002-8971-184X","position":7,"is_corresponding":false},{"id":363007,"name":"Brian Kang","orcid":"0009-0002-1594-6264","position":0,"is_corresponding":true}],"reference_count":35,"raw_metadata":null,"created_at":"2026-07-19T01:19:18.686170Z","pmid":"37645785","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":[]}