CHOPCHOP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CHOPCHOP
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Tool usage distribution map

This map represents all the scientific publications referring to CHOPCHOP per scientific context
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Associated diseases

This word cloud represents CHOPCHOP usage per disease context
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Popular tool citations

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Protocols

CHOPCHOP specifications

Information


Unique identifier OMICS_04700
Name CHOPCHOP
Interface Web user interface
Restrictions to use None
Input data Gene, target region sequence
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Tessa G. Montague

Publications for CHOPCHOP

CHOPCHOP citations

 (82)
library_books

Genome wide and high density CRISPR Cas9 screens identify point mutations in PARP1 causing PARP inhibitor resistance

2018
Nat Commun
PMCID: 5945626
PMID: 29748565
DOI: 10.1038/s41467-018-03917-2

[…] In all, 29 sgRNAs were designed using the ChopChop algorithm. The guides were synthesised and cloned in an array format into pLentiGuide-puro by Eurofins genomics. A single colony for each vector was used to inoculate a pooled culture for pla […]

library_books

Chromatin accessibility is associated with CRISPR Cas9 efficiency in the zebrafish (Danio rerio)

2018
PLoS One
PMCID: 5912780
PMID: 29684067
DOI: 10.1371/journal.pone.0196238

[…] Altogether, we have designed 86 sgRNAs using the crispr.mit.edu, ChopChop (V1 and V2) and CRISPRscan softwares [,,]. Of these sgRNAs, 30% showed detectable in vivo activity (). As GC-content (%) has been suggested to influence the effectiveness of CRISPR-Cas9 mutag […]

library_books

Orientation dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome

2018
Nat Commun
PMCID: 5899087
PMID: 29654302
DOI: 10.1038/s41467-018-03694-y

[…] ersions were induced using pairs of small guide RNAs (sgRNAs) that flank either most of the hinge region or only some of its elements (Supplementary Table ). The allele-specific sgRNAs designed using CHOPCHOP, were selected to include BL6 SNPs at the PAM site if available (Supplementary Fig. ; Supplementary Table ). Patski cells were transfected using Ultracruz transfection reagents (Santa Cruz). […]

library_books

Multiple sgRNAs with overlapping sequences enhance CRISPR/Cas9 mediated knock in efficiency

2018
PMCID: 5938013
PMID: 29622782
DOI: 10.1038/s12276-018-0037-x

[…] Cas9 mRNAs were purchased from Toolgen (Seoul, Korea). sgRNAs for each gene were designed using CHOPCHOP and synthesized using an in vitro RNA-synthesis kit (Thermo Fisher Scientific, MA, USA) following PCR amplification. ssODNs were commercially designed and synthesized (IDT, CA, USA). The 3′ e […]

library_books

CRISPR/Cas9 Mediated Gene Disruption Reveals the Importance of Zinc Metabolism for Fitness of the Dimorphic Fungal Pathogen Blastomyces dermatitidis

2018
MBio
PMCID: 5885028
PMID: 29615501
DOI: 10.1128/mBio.00412-18

[…] nd Biolabs, Ipswich, MA), and the sgRNA/protospacer regions of all targeting constructs were confirmed by Sanger DNA sequencing.Candidate protospacer sequences in the targeted genes were generated by CHOPCHOP (, ), and high-scoring candidates near the N-terminal region of the protein coding sequence were searched against the B. dermatitidis genome by using BLAST to eliminate candidates with obviou […]

library_books

Small molecules promote CRISPR Cpf1 mediated genome editing in human pluripotent stem cells

2018
Nat Commun
PMCID: 5880812
PMID: 29610531
DOI: 10.1038/s41467-018-03760-5

[…] ALKBH1 has recently been identified as a tRNA demethylase. CLEC16A plays important roles in the development of diabetes. To construct gene-specific crRNA plasmids, we used an online software (http://chopchop.cbu.uib.no) to design a panel of crRNAs specifically targeting these genes (Fig.  and Supplementary Table ). We tested the genome editing capacity of these crRNAs in 293T cells and observed 2 […]


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CHOPCHOP institution(s)
Computational Biology Unit, Department of Informatics, University of Bergen, Norway; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA; Sars International Centre for Marine Molecular Biology, University of Bergen, Norway
CHOPCHOP funding source(s)
Bergen Research Foundation; University of Bergen core funding; National Defense Science and Engineering Graduate Fellowship; American Cancer Society

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