TIDE is a simple and accurate assay to precisely determine the spectrum and frequency of targeted mutations generated in a pool of cells by genome editing tools such as CRISPR/Cas9, TALENs and ZFNs. TIDE requires only standard molecular biology reagents and involves three simple steps: 1. One pair of standard PCR reactions. 2. One pair of standard capillary ("Sanger") sequencing reactions. 3. Analysis of the two resulting raw sequencing files using the TIDE web tool. The algorithm accurately reconstructs the spectrum of indels from the sequence traces. The web tool reports the identity of the detected indels and their frequencies. TIDE cannot detect ‘designer’ mutations generated by homologous recombination using a donor template. For this, please use TIDER.
TIDER is a modified version of TIDE that estimates the frequency of targeted small nucleotide changes introduced by CRISPR in combination with homology-directed repair using a donor template. In addition, it determines the spectrum and frequency of non-templated indels. Compared to TIDE, TIDER requires one additional sequencing trace (i.e., three instead of two). Preparation of this third “reference” DNA can be done with a simple two-step PCR protocol. The web tool reports the estimated frequencies of the templated mutation and of all non-templated indels. If you are only interested in quantifying non-templated indels, we recommend the simpler TIDE method.
