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 in publications

 (76)
PMCID: 5945626
PMID: 29748565
DOI: 10.1038/s41467-018-03917-2

[…] the end of the assay with sulforhodamine b. when plotting survival curves, the surviving fraction was calculated relative to dmso (solvent)-exposed cells., 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 […]

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

[…] in more detail with all our sgrnas. we were able to detect mutagenesis activity at 1hpf (roughly corresponding to 4-cell stage)., 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 […]

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

[…] 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). […]

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

[…] national university and yonsei university and was conducted in accordance with approved guidelines., 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′ […]

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

[…] 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 […]


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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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