Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding
Standard
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, Jahrgang 20, Nr. 1, 06.02.2019, S. 107.Publikationen: SCORING: Beitrag in Fachzeitschrift/Zeitung › SCORING: Zeitschriftenaufsatz › Forschung › Begutachtung
Harvard
APA
Vancouver
Bibtex
}
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 -