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Pooled CRISPR screening with single-cell transcriptome read-out

Paul Datlinger, Christian Schmidl, André F Rendeiro, Peter Traxler, Johanna Klughammer, Linda Schuster, Christoph Bock
doi: https://doi.org/10.1101/083774
Paul Datlinger
1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Christian Schmidl
1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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André F Rendeiro
1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Peter Traxler
1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Johanna Klughammer
1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Linda Schuster
1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Christoph Bock
1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
2Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
3Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
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  • For correspondence: cbock@cemm.oeaw.ac.at
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Abstract

CRISPR-based genetic screens have revolutionized the search for new gene functions and biological mechanisms. However, widely used pooled screens are limited to simple read-outs of cell proliferation or the production of a selectable marker protein. Arrayed screens allow for more complex molecular read-outs such as transcriptome profiling, but they provide much lower throughput. Here we demonstrate CRISPR genome editing together with single-cell RNA sequencing as a new screening paradigm that combines key advantages of pooled and arrayed screens. This approach allowed us to link guide-RNA expression to the associated transcriptome responses in thousands of single cells using a straightforward and broadly applicable screening workflow.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted October 27, 2016.
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Pooled CRISPR screening with single-cell transcriptome read-out
Paul Datlinger, Christian Schmidl, André F Rendeiro, Peter Traxler, Johanna Klughammer, Linda Schuster, Christoph Bock
bioRxiv 083774; doi: https://doi.org/10.1101/083774
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Pooled CRISPR screening with single-cell transcriptome read-out
Paul Datlinger, Christian Schmidl, André F Rendeiro, Peter Traxler, Johanna Klughammer, Linda Schuster, Christoph Bock
bioRxiv 083774; doi: https://doi.org/10.1101/083774

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