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TIDE

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 by Victor Dillard

Description

TIDE is a web tool which rapidly analyses genome editing efficiency based on Saner sequencing results.

TIDE is the first and most widely cited tool used to assess genome editing of a target locus by CRISPR-Cas9. Based on the quantitative sequence trace data from two standard capillary (Sanger) sequencing reactions, the TIDE software quantifies editing efficacy and identifies the predominant types of insertions and deletions (indels) in the DNA of a targeted cell pool.

TIDE was developed by the van Steensel lab at the Netherlands Cancer Institute (NKI).
See Brinkman et al. 2014 Nucl. Acids Res. for a detailed explanation and examples.

Discussion

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Victor Dillard
Desktop Genetics
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Victor Dillard

Desktop Genetics

Why should I use TIDE? Oval 17

To assess the efficiency of a genome editing experiment (with CRISPR, TALEN, ZFNs or others), the standard has alwasy been to use a mismatch cleavage assay. Quick and cheap, this assay provides little quantitative or qualitative information about the population of insertion and deletions ("indels") present in your clones. It only effectively answers the question "did something happen?", and has been demonstrated to have a poor limit of detection and poor reproducibility.

From Sanger sequencing results, TIDE provides an in depth understanding of your clonal population, with details of which indels are present. For example, by decomposing the Sanger trace signals, TIDE will tell you how much of your clonal population has a 1 insertion, as well as the nature of these insertions.

TIDE, developed and launched in 2014 by the van Steensel lab at the Netherlands Cancer Institute (NKI). It is the most widely cited and used Sanger decomposition tool for assessing genome editing. With its advanced parameters, users are able to precisely control the analysis, particularly helpful when the ab1 trace files are tricky or of poor quality.

Try it now at tide.deskgen.com

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Posted: 2 years ago
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