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Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding

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Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding. / Boettcher, Michael; Covarrubias, Sergio; Biton, Anne; Blau, James; Wang, Haopeng; Zaitlen, Noah; McManus, Michael T.

In: BMC GENOMICS, Vol. 20, No. 1, 06.02.2019, p. 107.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Boettcher, M, Covarrubias, S, Biton, A, Blau, J, Wang, H, Zaitlen, N & McManus, MT 2019, 'Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding', BMC GENOMICS, vol. 20, no. 1, pp. 107. https://doi.org/10.1186/s12864-019-5480-0

APA

Boettcher, M., Covarrubias, S., Biton, A., Blau, J., Wang, H., Zaitlen, N., & McManus, M. T. (2019). Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding. BMC GENOMICS, 20(1), 107. https://doi.org/10.1186/s12864-019-5480-0

Vancouver

Boettcher M, Covarrubias S, Biton A, Blau J, Wang H, Zaitlen N et al. Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding. BMC GENOMICS. 2019 Feb 6;20(1):107. https://doi.org/10.1186/s12864-019-5480-0

Bibtex

@article{d993e644ba6844bbb8e5fe28e71937b3,
title = "Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding",
abstract = "BACKGROUND: While pooled loss- and gain-of-function CRISPR screening approaches have become increasingly popular to systematically investigate mammalian gene function, the large majority of them have thus far not investigated the influence of cellular heterogeneity on screen results. Instead most screens are analyzed by averaging the abundance of perturbed cells from a bulk population of cells.RESULTS: Here we developed multi-level barcoded sgRNA libraries to trace multiple clonal Cas9 cell lines exposed to the same environment. The first level of barcoding allows monitoring growth kinetics and treatment responses of multiplexed clonal cell lines under identical conditions while the second level enables in-sample replication and tracing of sub-clonal lineages of cells expressing the same sgRNA.CONCLUSION: Using our approach, we illustrate how heterogeneity in growth kinetics and treatment response of clonal cell lines impairs the results of pooled genetic screens.",
keywords = "CRISPR-Cas Systems, Gene Editing, Genetic Testing/methods, Humans, Jurkat Cells, Molecular Typing/methods, RNA, Guide",
author = "Michael Boettcher and Sergio Covarrubias and Anne Biton and James Blau and Haopeng Wang and Noah Zaitlen and McManus, {Michael T}",
year = "2019",
month = feb,
day = "6",
doi = "10.1186/s12864-019-5480-0",
language = "English",
volume = "20",
pages = "107",
journal = "BMC GENOMICS",
issn = "1471-2164",
publisher = "BioMed Central Ltd.",
number = "1",

}

RIS

TY - JOUR

T1 - Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding

AU - Boettcher, Michael

AU - Covarrubias, Sergio

AU - Biton, Anne

AU - Blau, James

AU - Wang, Haopeng

AU - Zaitlen, Noah

AU - McManus, Michael T

PY - 2019/2/6

Y1 - 2019/2/6

N2 - BACKGROUND: While pooled loss- and gain-of-function CRISPR screening approaches have become increasingly popular to systematically investigate mammalian gene function, the large majority of them have thus far not investigated the influence of cellular heterogeneity on screen results. Instead most screens are analyzed by averaging the abundance of perturbed cells from a bulk population of cells.RESULTS: Here we developed multi-level barcoded sgRNA libraries to trace multiple clonal Cas9 cell lines exposed to the same environment. The first level of barcoding allows monitoring growth kinetics and treatment responses of multiplexed clonal cell lines under identical conditions while the second level enables in-sample replication and tracing of sub-clonal lineages of cells expressing the same sgRNA.CONCLUSION: Using our approach, we illustrate how heterogeneity in growth kinetics and treatment response of clonal cell lines impairs the results of pooled genetic screens.

AB - BACKGROUND: While pooled loss- and gain-of-function CRISPR screening approaches have become increasingly popular to systematically investigate mammalian gene function, the large majority of them have thus far not investigated the influence of cellular heterogeneity on screen results. Instead most screens are analyzed by averaging the abundance of perturbed cells from a bulk population of cells.RESULTS: Here we developed multi-level barcoded sgRNA libraries to trace multiple clonal Cas9 cell lines exposed to the same environment. The first level of barcoding allows monitoring growth kinetics and treatment responses of multiplexed clonal cell lines under identical conditions while the second level enables in-sample replication and tracing of sub-clonal lineages of cells expressing the same sgRNA.CONCLUSION: Using our approach, we illustrate how heterogeneity in growth kinetics and treatment response of clonal cell lines impairs the results of pooled genetic screens.

KW - CRISPR-Cas Systems

KW - Gene Editing

KW - Genetic Testing/methods

KW - Humans

KW - Jurkat Cells

KW - Molecular Typing/methods

KW - RNA, Guide

U2 - 10.1186/s12864-019-5480-0

DO - 10.1186/s12864-019-5480-0

M3 - SCORING: Journal article

C2 - 30727954

VL - 20

SP - 107

JO - BMC GENOMICS

JF - BMC GENOMICS

SN - 1471-2164

IS - 1

ER -