A protocol for Targeted Perturb (TAP)-seq and targeted single-cell RNA-seq

doi:10.21203/rs.3.pex-864/v1

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Method Article

Daniel Schraivogel, Lars Velten, Andreas R. Gschwind, Lars M. Steinmetz

Daniel Schraivogel

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany

ORCiD: https://orcid.org/0000-0002-5734-6980

Lars Velten

Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain

ORCiD: https://orcid.org/0000-0002-1233-5874

Andreas R. Gschwind

Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA

ORCiD: https://orcid.org/0000-0002-0769-6907

Lars M. Steinmetz

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; Stanford Genome Technology Center, Palo Alto, California 94304, USA

Corresponding Author

ORCiD: https://orcid.org/0000-0002-3962-2865

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Here we provide a step-by-step protocol for targeted single-cell RNA-seq and targeted Perturb-seq, as reported in the linked publication Schraivogel et al. Nat Meth 2020. The protocol describes cell preparation using flow cytometry, single-cell droplet formation with 10X Genomics, and targeted 3’ single-cell RNA-seq library preparation for Illumina sequencing.

Keywords

single-cell, CRISPR, Cas9, CRISPRi, functional genomics, genetic screens, RNA sequencing

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The authors declare no competing financial interests.

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10.1038/s41592-020-0837-5

An open repository of community-contributed protocols sponsored by Nature Research.

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Method Article

Daniel Schraivogel, Lars Velten, Andreas R. Gschwind, Lars M. Steinmetz

Daniel Schraivogel

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany

ORCiD: https://orcid.org/0000-0002-5734-6980

Lars Velten

Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain

ORCiD: https://orcid.org/0000-0002-1233-5874

Andreas R. Gschwind

Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA

ORCiD: https://orcid.org/0000-0002-0769-6907

Lars M. Steinmetz

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; Stanford Genome Technology Center, Palo Alto, California 94304, USA

Corresponding Author

ORCiD: https://orcid.org/0000-0002-3962-2865

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DOI:

10.21203/rs.3.pex-864/v1

Download PDF

The full text of this article is available to read as a PDF.

License:

This work is licensed under a CC BY 4.0 License. Read Full License

Figure 1

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Figure 3

The authors declare no competing financial interests.

Associated Publications

10.1038/s41592-020-0837-5

An open repository of community-contributed protocols sponsored by Nature Research.

Learn more about Protocol Exchange

Method Article

Daniel Schraivogel, Lars Velten, Andreas R. Gschwind, Lars M. Steinmetz

Daniel Schraivogel

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany

ORCiD: https://orcid.org/0000-0002-5734-6980

Lars Velten

Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain

ORCiD: https://orcid.org/0000-0002-1233-5874

Andreas R. Gschwind

Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA

ORCiD: https://orcid.org/0000-0002-0769-6907

Lars M. Steinmetz

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; Stanford Genome Technology Center, Palo Alto, California 94304, USA

Corresponding Author

ORCiD: https://orcid.org/0000-0002-3962-2865

DOI:

10.21203/rs.3.pex-864/v1

Download PDF

License:

This work is licensed under a CC BY 4.0 License. Read Full License

Abstract

Keywords

single-cell, CRISPR, Cas9, CRISPRi, functional genomics, genetic screens, RNA sequencing

Figures

Introduction

Reagents

Equipment

Procedure

Time Taken

Anticipated Results

References

Acknowledgements

Competing Interests

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Associated Publications

10.1038/s41592-020-0837-5

An open repository of community-contributed protocols sponsored by Nature Research.

Learn more about Protocol Exchange

Method Article

Daniel Schraivogel, Lars Velten, Andreas R. Gschwind, Lars M. Steinmetz

Daniel Schraivogel

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany

ORCiD: https://orcid.org/0000-0002-5734-6980

Lars Velten

Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain

ORCiD: https://orcid.org/0000-0002-1233-5874

Andreas R. Gschwind

Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA

ORCiD: https://orcid.org/0000-0002-0769-6907

Lars M. Steinmetz

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; Stanford Genome Technology Center, Palo Alto, California 94304, USA

Corresponding Author

ORCiD: https://orcid.org/0000-0002-3962-2865

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