Indel Spectrum Analysis of RGN Edits

PCR mixtures containing amplicons spanning RGN target sequences were purified using SureClean Plus (Bioline) according to the manufacturer's recommendations. Next, the purified PCR amplicons were subjected to Sanger sequencing (BaseClear, Leiden, the Netherlands). The indel spectra were obtained through the online TIDE tool (http://tide.nki.nl) (40 (link)) by using as input the PCR product chromatograms derived from edited and unedited DNA as indicated. The indel size ranges were set to 20 nucleotides upstream and downstream of the RGN target sequences.

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Maggio I., Stefanucci L., Janssen J.M., Liu J., Chen X., Mouly V, & Gonçalves M.A. (2016). Selection-free gene repair after adenoviral vector transduction of designer nucleases: rescue of dystrophin synthesis in DMD muscle cell populations. Nucleic Acids Research, 44(3), 1449-1470.

Publication 2016

SureClean Plus

Indel Nucleotides

Corresponding Organization :

Other organizations : Leiden University Medical Center, University of Rome Tor Vergata, Inserm, Sorbonne Université, Centre de Recherche en Myologie, Centre National de la Recherche Scientifique

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Variable analysis

independent variables

RGN target sequences

dependent variables

Indel spectra
Indel size ranges

control variables

PCR mixtures containing amplicons spanning RGN target sequences
Purified PCR amplicons
Sanger sequencing
PCR product chromatograms derived from edited and unedited DNA

positive controls

Unedited DNA

negative controls

Not explicitly mentioned

Annotations

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