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GT-Scan specifications

Information


Unique identifier OMICS_04721
Name GT-Scan
Alternative name Genome Target Scan
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Genome Target Scan

GT-Scan citations

 (8)
library_books

Generation and characterization of a hypothyroidism rat model with truncated thyroid stimulating hormone receptor

2018
Sci Rep
PMCID: 5838214
PMID: 29507327
DOI: 10.1038/s41598-018-22405-7

[…] we obtained five alleles which carry different deletions and/or insertions near the gRNA targeting site due to NHEJ. In order to evaluate off-target effect (OTE), we predicted the potential sites by GT-Scan. After examining 5 sites which OTE will most likely occur (Supplementary Table ), we found no detectable OTE. […]

library_books

CRISPR/Cas9 Mediated Genome Engineering for Improvement of Horticultural Crops

2017
Front Plant Sci
PMCID: 5609112
PMID: 28970844
DOI: 10.3389/fpls.2017.01635

[…] th gRNA sequence immediately followed by protospacer adjacent motif (PAM; ). The major concern is the off target cleavage by Cas9 that can be avoided by selecting unique target site. CRISPR-Plant (), GT-scan (), CRISPRdirect (), and many more tools are available that help select the unique target site. Among them, CRISPRdirect is an ideal platform for horticultural crops providing specificity chec […]

library_books

CRISPR/Cas9: A Practical Approach in Date Palm Genome Editing

2017
Front Plant Sci
PMCID: 5572371
PMID: 28878801
DOI: 10.3389/fpls.2017.01469

[…] scertain successful date palm genome engineering, several available web-based bioinformatics and data mining tools (like CCTop, ATUM, MIT CRISPR design, Alt-RTM CRISPR-Cas9 System, CHOPCHOP, CROP-IT, GT-Scan, sgRNA Designer, Cas-OFFinder, etc.) can impart very promising role. […]

library_books

Generation and quantitative proteomics analysis of CK2α/α’(−/−) cells

2017
Sci Rep
PMCID: 5314375
PMID: 28209983
DOI: 10.1038/srep42409

[…] A-3′ (CK2α), 5′-GTTCACCTCGGCGTAGACCC-3′ (CK2α′), and 5′-TCCTGGTTCTGTGGGCTCCG-3′ (CK2β). Sequence for CK2β have been chosen using the CRISPR MultiTargeter tool and off targets have been excluded using GT-Scan tools.C2C12 cells were cultured in six-well dishes to 70–80% confluence. Cells were co-transfected with 1 μg of sgRNA plasmid and Lipofectamine 3000 according to manufacturing instructions. Fo […]

library_books

Repurposing the CRISPR Cas9 system for targeted DNA methylation

2016
Nucleic Acids Res
PMCID: 4937303
PMID: 26969735
DOI: 10.1093/nar/gkw159

[…] nus of the dCas9-DNMT3A fusion to allow for either puromycin selection or EGFP screening of transfected cells.Guide sequences targeting the loci of interest were selected either manually or using the GT-Scan web-tool (http://gt-scan.braembl.org.au/gt-scan/) (). Sequences of the non-targeting (NT) control guide RNAs, without a target in the human genome, were taken from the Human GeCKOv2 Library () […]

library_books

Resources for the design of CRISPR gene editing experiments

2015
Genome Biol
PMCID: 4661947
PMID: 26612492
DOI: 10.1186/s13059-015-0823-x

[…] lign to a candidate sgRNA with fewer than n mismatches, provide flexibility for the user to determine their own criteria for utilizing mismatches in the prediction of potential OT sites (CCTop [] and GT-Scan []), for example, by specifying a core ‘seed’ sgRNA region within which mismatches are assumed to be effective at blocking activity. It is important to note that most of these tools discount a […]

Citations

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GT-Scan institution(s)
Genomics and Computational Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia

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