title: Pooled CRISPR screening with single-cell transcriptome readout.
abstract: 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.
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Paul
authors.initials: P
authors.lastname: Datlinger
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: André F
authors.initials: AF
authors.lastname: Rendeiro
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Schmidl
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Krausgruber
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Peter
authors.initials: P
authors.lastname: Traxler
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Johanna
authors.initials: J
authors.lastname: Klughammer
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Linda C
authors.initials: LC
authors.lastname: Schuster
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Amelie
authors.initials: A
authors.lastname: Kuchler
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Donat
authors.initials: D
authors.lastname: Alpar
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.|Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.|Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Bock
mesh_terms: D002460:Cell Line; D049109:Cell Proliferation; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D057809:HEK293 Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D000094704:RNA, Guide, CRISPR-Cas Systems / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods; D059467:Transcriptome / Q000235:genetics*
chemical_list: D000094704:RNA, Guide, CRISPR-Cas Systems