CRISPRroots: On-and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells

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

Standard

CRISPRroots : On-and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells. / Corsi, Giulia I.; Gadekar, Veerendra P.; Gorodkin, Jan; Seemann, Stefan E.

In: Nucleic Acids Research, Vol. 50, No. 4, E20, 2022.

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

Harvard

Corsi, GI, Gadekar, VP, Gorodkin, J & Seemann, SE 2022, 'CRISPRroots: On-and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells', Nucleic Acids Research, vol. 50, no. 4, E20. https://doi.org/10.1093/nar/gkab1131

APA

Corsi, G. I., Gadekar, V. P., Gorodkin, J., & Seemann, S. E. (2022). CRISPRroots: On-and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells. Nucleic Acids Research, 50(4), [E20]. https://doi.org/10.1093/nar/gkab1131

Vancouver

Corsi GI, Gadekar VP, Gorodkin J, Seemann SE. CRISPRroots: On-and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells. Nucleic Acids Research. 2022;50(4). E20. https://doi.org/10.1093/nar/gkab1131

Author

Corsi, Giulia I. ; Gadekar, Veerendra P. ; Gorodkin, Jan ; Seemann, Stefan E. / CRISPRroots : On-and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells. In: Nucleic Acids Research. 2022 ; Vol. 50, No. 4.

Bibtex

@article{1b0abab26da44a318dd00ab831f93090,
title = "CRISPRroots: On-and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells",
abstract = "The CRISPR-Cas9 genome editing tool is used to study genomic variants and gene knockouts, and can be combined with transcriptomic analyses to measure the effects of such alterations on gene expression. But how can one be sure that differential gene expression is due to a successful intended edit and not to an off-target event, without performing an often resource-demanding genome-wide sequencing of the edited cell or strain? To address this question we developed CRISPRroots: CRISPR-Cas9-mediated edits with accompanying RNA-seq data assessed for on-target and off-target sites. Our method combines Cas9 and guide RNA binding properties, gene expression changes, and sequence variants between edited and non-edited cells to discover potential off-targets. Applied on seven public datasets, CRISPRroots identified critical off-target candidates that were overlooked in all of the corresponding previous studies. CRISPRroots is available via https://rth.dk/resources/crispr.",
author = "Corsi, {Giulia I.} and Gadekar, {Veerendra P.} and Jan Gorodkin and Seemann, {Stefan E.}",
note = "Publisher Copyright: {\textcopyright} 2022 The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.",
year = "2022",
doi = "10.1093/nar/gkab1131",
language = "English",
volume = "50",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "4",

}

RIS

TY - JOUR

T1 - CRISPRroots

T2 - On-and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells

AU - Corsi, Giulia I.

AU - Gadekar, Veerendra P.

AU - Gorodkin, Jan

AU - Seemann, Stefan E.

N1 - Publisher Copyright: © 2022 The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2022

Y1 - 2022

N2 - The CRISPR-Cas9 genome editing tool is used to study genomic variants and gene knockouts, and can be combined with transcriptomic analyses to measure the effects of such alterations on gene expression. But how can one be sure that differential gene expression is due to a successful intended edit and not to an off-target event, without performing an often resource-demanding genome-wide sequencing of the edited cell or strain? To address this question we developed CRISPRroots: CRISPR-Cas9-mediated edits with accompanying RNA-seq data assessed for on-target and off-target sites. Our method combines Cas9 and guide RNA binding properties, gene expression changes, and sequence variants between edited and non-edited cells to discover potential off-targets. Applied on seven public datasets, CRISPRroots identified critical off-target candidates that were overlooked in all of the corresponding previous studies. CRISPRroots is available via https://rth.dk/resources/crispr.

AB - The CRISPR-Cas9 genome editing tool is used to study genomic variants and gene knockouts, and can be combined with transcriptomic analyses to measure the effects of such alterations on gene expression. But how can one be sure that differential gene expression is due to a successful intended edit and not to an off-target event, without performing an often resource-demanding genome-wide sequencing of the edited cell or strain? To address this question we developed CRISPRroots: CRISPR-Cas9-mediated edits with accompanying RNA-seq data assessed for on-target and off-target sites. Our method combines Cas9 and guide RNA binding properties, gene expression changes, and sequence variants between edited and non-edited cells to discover potential off-targets. Applied on seven public datasets, CRISPRroots identified critical off-target candidates that were overlooked in all of the corresponding previous studies. CRISPRroots is available via https://rth.dk/resources/crispr.

U2 - 10.1093/nar/gkab1131

DO - 10.1093/nar/gkab1131

M3 - Journal article

C2 - 34850137

AN - SCOPUS:85125431123

VL - 50

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 4

M1 - E20

ER -

ID: 306685079