{
  "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 highly concordant with CRISPRi, and induced comparable pathway-level responses albeit with distinct on-target and off-target effects between modalities. 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.",
  "abstract_shown": true,
  "affiliations": [
    "Cancer Research Horizons, Cambridge, United Kingdom"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "N. Gupta"
    },
    {
      "name": "A. Sayer"
    },
    {
      "name": "M. Prater"
    },
    {
      "name": "C. Mastrokalou"
    },
    {
      "name": "K. Saeed"
    },
    {
      "name": "C. Company"
    },
    {
      "name": "C. Hart"
    },
    {
      "name": "R. Miragaia"
    },
    {
      "name": "A. Trehan"
    },
    {
      "name": "Functional Genomics Centre"
    },
    {
      "name": "U. McDermott"
    },
    {
      "name": "M. E. Strauss"
    },
    {
      "name": "D. Ross-Thriepland"
    },
    {
      "name": "D. Walter"
    },
    {
      "name": "A. Kalinka"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/czmn7z6557vqe.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.08.26.747303",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.08.26.747303v2.full",
  "id": "czmn7z6557vqe",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.08.26.747303v2",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "genomics"
    ],
    [
      "openalex",
      "1312|CRISPR and Genetic Engineering"
    ]
  ],
  "openalex": "W7204456180",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.08.26.747303v2.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-26",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/czmn7z6557vqe.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:29:06Z",
      "native_id": "10.64898/2026.08.26.747303",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.08.26.747303v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genomics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Comparative Single-Cell Profiling of CRISPR Knockout and Interference Defines Modality-Specific Strengths in Functional Genomics",
  "title_text": "Comparative Single-Cell Profiling of CRISPR Knockout and Interference Defines Modality-Specific Strengths in Functional Genomics",
  "type": "preprint",
  "updated_at": "2026-10-30T12:29:06Z",
  "url": "https://research.draconitic.com/paper/czmn7z6557vqe",
  "venue": "bioRxiv",
  "versions": []
}