Pooled CRISPR screening with single-cell transcriptome readout

Nat Methods. 2017 Mar;14(3):297-301. doi: 10.1038/nmeth.4177. Epub 2017 Jan 18.


CRISPR-based genetic screens are accelerating biological discovery, but current methods have inherent limitations. Widely used pooled screens are restricted to simple readouts including cell proliferation and sortable marker proteins. Arrayed screens allow for comprehensive molecular readouts such as transcriptome profiling, but at much lower throughput. Here we combine pooled CRISPR screening with single-cell RNA sequencing into a broadly applicable workflow, directly linking guide RNA expression to transcriptome responses in thousands of individual cells. Our method for CRISPR droplet sequencing (CROP-seq) enables pooled CRISPR screens with single-cell transcriptome resolution, which will facilitate high-throughput functional dissection of complex regulatory mechanisms and heterogeneous cell populations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • Cell Proliferation
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics*
  • Gene Expression Profiling / methods*
  • HEK293 Cells
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • RNA, Guide, CRISPR-Cas Systems / genetics
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods
  • Transcriptome / genetics*


  • RNA, Guide, CRISPR-Cas Systems