TY - JOUR T1 - A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics JF - bioRxiv DO - 10.1101/2022.09.06.506867 SP - 2022.09.06.506867 AU - Amitabh C. Pandey AU - Jon Bezney AU - Dante DeAscanis AU - Ethan Kirsch AU - Farin Ahmed AU - Austin Crinklaw AU - Kumari Sonal Choudhary AU - Tony Mandala AU - Jeffrey Deason AU - Jasmin Hamdi AU - Azeem Siddique AU - Sridhar Ranganathan AU - Phillip Ordoukhanian AU - Keith Brown AU - Jon Armstrong AU - Steven Head AU - Eric J. Topol Y1 - 2022/01/01 UR - http://biorxiv.org/content/early/2022/09/07/2022.09.06.506867.abstract N2 - Single-cell transcriptomics suffers from lapses in coverage of the full transcriptome, providing an incomplete gene expression profile of the cell. Here, we introduce single-cell CRISPRclean (scCLEAN), an in vitro molecular method that can be universally inserted into any single-cell RNA-seq workflow to improve the sensitivity of the assay. Utilizing CRISPR/Cas9, scCLEAN works to selectively remove highly abundant uninformative molecules, redistributing ~50% of reads to enrich for lowly expressed transcripts. Utilizing immune cells, we describe a validation of scCLEAN showing a 2.1-fold enrichment in library complexity with negligible off-target effects. Subsequently, applying scCLEAN to single-cell iso-seq samples results in a 4.6-fold improvement in unique isoform detection. Thus, demonstrating a benefit in short and long read sequencing applications. Finally, we illustrate the ability of scCLEAN to elucidate biological insights by applying it to two participant cohorts of cardiovascular samples, bringing to light novel molecular characteristics including inflammatory signatures.Competing Interest StatementDuring some point of manuscript preparation, J.B., D.D., A.C., K.C., J.D., A.S., S.R., K.B., and J.A. were employees of Jumpcode Genomics. ER -