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Schraivogel D, Gschwind AR, Milbank JH, et al. Targeted Perturb-seq enables genome-scale genetic screens in single cells. Nat Methods. 2020;17(6):629-635doi: 10.1038/s41592-020-0837-5.
Schraivogel, D., Gschwind, A. R., Milbank, J. H., Leonce, D. R., Jakob, P., Mathur, L., Korbel, J. O., Merten, C. A., Velten, L., & Steinmetz, L. M. (2020). Targeted Perturb-seq enables genome-scale genetic screens in single cells. Nature methods, 17(6), 629-635. https://doi.org/10.1038/s41592-020-0837-5
Schraivogel, Daniel, et al. "Targeted Perturb-seq enables genome-scale genetic screens in single cells." Nature methods vol. 17,6 (2020): 629-635. doi: https://doi.org/10.1038/s41592-020-0837-5
Schraivogel D, Gschwind AR, Milbank JH, Leonce DR, Jakob P, Mathur L, Korbel JO, Merten CA, Velten L, Steinmetz LM. Targeted Perturb-seq enables genome-scale genetic screens in single cells. Nat Methods. 2020 Jun;17(6):629-635. doi: 10.1038/s41592-020-0837-5. Epub 2020 Jun 01. PMID: 32483332; PMCID: PMC7610614.
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Nat Methods. 2020 Jun;17(6):629-635. doi: 10.1038/s41592-020-0837-5. Epub 2020 Jun 01.

Targeted Perturb-seq enables genome-scale genetic screens in single cells.

Nature methods

Daniel Schraivogel, Andreas R Gschwind, Jennifer H Milbank, Daniel R Leonce, Petra Jakob, Lukas Mathur, Jan O Korbel, Christoph A Merten, Lars Velten, Lars M Steinmetz

Affiliations

  1. European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
  2. Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
  3. European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany. [email protected].
  4. Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain. [email protected].
  5. European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany. [email protected].
  6. Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. [email protected].
  7. Stanford Genome Technology Center, Palo Alto, CA, USA. [email protected].

PMID: 32483332 PMCID: PMC7610614 DOI: 10.1038/s41592-020-0837-5

Abstract

The transcriptome contains rich information on molecular, cellular and organismal phenotypes. However, experimental and statistical limitations constrain sensitivity and throughput of genetic screening with single-cell transcriptomics readout. To overcome these limitations, we introduce targeted Perturb-seq (TAP-seq), a sensitive, inexpensive and platform-independent method focusing single-cell RNA-seq coverage on genes of interest, thereby increasing the sensitivity and scale of genetic screens by orders of magnitude. TAP-seq permits routine analysis of thousands of CRISPR-mediated perturbations within a single experiment, detects weak effects and lowly expressed genes, and decreases sequencing requirements by up to 50-fold. We apply TAP-seq to generate perturbation-based enhancer-target gene maps for 1,778 enhancers within 2.5% of the human genome. We thereby show that enhancer-target association is jointly determined by three-dimensional contact frequency and epigenetic states, allowing accurate prediction of enhancer targets throughout the genome. In addition, we demonstrate that TAP-seq can identify cell subtypes with only 100 sequencing reads per cell.

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