Genome-wide detection and analysis of CRISPR-Cas off-targets
Copyright © 2021 Elsevier Inc. All rights reserved..
The clustered, regularly interspersed, short palindromic repeats (CRISPR) technology is revolutionizing biological studies and holds tremendous promise for treating human diseases. However, a significant limitation of this technology is that modifications can occur on off-target sites lacking perfect complementarity to the single guide RNA (sgRNA) or canonical protospacer-adjacent motif (PAM) sequence. Several in vivo and in vitro genome-wide off-target profiling approaches have been developed to inform on the fidelity of gene editing. Of these, GUIDE-seq has become one of the most widely adopted and reproducible methods. To allow users to easily analyze GUIDE-seq data generated on any sequencing platform, we developed an open-source pipeline, GS-Preprocess, that takes standard base-call output in bcl format and generate all required input data for off-target identification using bioconductor package GUIDEseq for off-target identification. Furthermore, we created a Docker image with GS-Proprocess, GUIDE-seq, and all its R and system dependencies already installed. The bundled pipeline will empower end users to streamline the analysis of GUIDE-seq data and motivate their use of higher throughput sequencing with increased multiplexing for GUIDE-seq experiments.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2021 |
|---|---|
| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:181 |
|---|---|
| Enthalten in: |
Progress in molecular biology and translational science - 181(2021) vom: 07., Seite 31-43 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Rodríguez, Tomás C [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
CRISPR |
|---|
| Anmerkungen: |
Date Completed 25.11.2021 Date Revised 04.01.2024 published: Print-Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1016/bs.pmbts.2021.01.012 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM326749799 |
|---|
| LEADER | 01000caa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM326749799 | ||
| 003 | DE-627 | ||
| 005 | 20240108141527.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231225s2021 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1016/bs.pmbts.2021.01.012 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1248.xml |
| 035 | |a (DE-627)NLM326749799 | ||
| 035 | |a (NLM)34127199 | ||
| 035 | |a (PII)S1877-1173(21)00023-5 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Rodríguez, Tomás C |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Genome-wide detection and analysis of CRISPR-Cas off-targets |
| 264 | 1 | |c 2021 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 25.11.2021 | ||
| 500 | |a Date Revised 04.01.2024 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2021 Elsevier Inc. All rights reserved. | ||
| 520 | |a The clustered, regularly interspersed, short palindromic repeats (CRISPR) technology is revolutionizing biological studies and holds tremendous promise for treating human diseases. However, a significant limitation of this technology is that modifications can occur on off-target sites lacking perfect complementarity to the single guide RNA (sgRNA) or canonical protospacer-adjacent motif (PAM) sequence. Several in vivo and in vitro genome-wide off-target profiling approaches have been developed to inform on the fidelity of gene editing. Of these, GUIDE-seq has become one of the most widely adopted and reproducible methods. To allow users to easily analyze GUIDE-seq data generated on any sequencing platform, we developed an open-source pipeline, GS-Preprocess, that takes standard base-call output in bcl format and generate all required input data for off-target identification using bioconductor package GUIDEseq for off-target identification. Furthermore, we created a Docker image with GS-Proprocess, GUIDE-seq, and all its R and system dependencies already installed. The bundled pipeline will empower end users to streamline the analysis of GUIDE-seq data and motivate their use of higher throughput sequencing with increased multiplexing for GUIDE-seq experiments | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a CRISPR | |
| 650 | 4 | |a GUIDE-seq | |
| 650 | 4 | |a Genome editing | |
| 650 | 4 | |a Off-targets analysis | |
| 650 | 4 | |a Software | |
| 650 | 7 | |a RNA, Guide, CRISPR-Cas Systems |2 NLM | |
| 700 | 1 | |a Dadafarin, Sina |e verfasserin |4 aut | |
| 700 | 1 | |a Pratt, Henry E |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, PengPeng |e verfasserin |4 aut | |
| 700 | 1 | |a Amrani, Nadia |e verfasserin |4 aut | |
| 700 | 1 | |a Zhu, Lihua Julie |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Progress in molecular biology and translational science |d 2008 |g 181(2021) vom: 07., Seite 31-43 |w (DE-627)NLM18554178X |x 1878-0814 |7 nnns |
| 773 | 1 | 8 | |g volume:181 |g year:2021 |g day:07 |g pages:31-43 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1016/bs.pmbts.2021.01.012 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 181 |j 2021 |b 07 |h 31-43 | ||