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bioRxiv · 10.64898/2026.08.26.747303

Comparative Single-Cell Profiling of CRISPR Knockout and Interference Defines Modality-Specific Strengths in Functional Genomics

Gupta, N.·Sayer, A.·Prater, M.·Mastrokalou, C.·Saeed, K.·Company, C.·Hart, C.·Miragaia, R.·Trehan, A.·Functional Genomics Centre,·McDermott, U.·Strauss, M. E.·Ross-Thriepland, D.·Walter, D.·Kalinka, A.
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Abstract

Pooled CRISPR screens coupled with single-cell RNA sequencing enable high-throughput functional interrogation of gene regulatory networks, yet systematic comparisons of CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) remain limited. We established a single-cell CRISPRko workflow and benchmarked it against CRISPRi using 87 sgRNAs targeting 29 unfolded protein response genes. CRISPRko generated transcriptional phenotypes are highly concordant with CRISPRi, and induced comparable pathway-level responses. While CRISPRi allows direct assessment of target gene repression, CRISPRko provides an effective complementary approach for complete loss-of-function studies, expanding the toolkit for single-cell functional genomics.

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Gupta, N., Sayer, A., Prater, M., Mastrokalou, C., Saeed, K., Company, C., Hart, C., Miragaia, R., Trehan, A., Functional Genomics Centre,, McDermott, U., Strauss, M. E., Ross-Thriepland, D., Walter, D., Kalinka, A.. 2026-08-27. Comparative Single-Cell Profiling of CRISPR Knockout and Interference Defines Modality-Specific Strengths in Functional Genomics. https://doi.org/10.64898/2026.08.26.747303

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