Effective controls for gene editing

A CRISPR cheat sheet

Between choosing the right reagents and detecting changes at the genomic level, many factors need to be considered to create a well-designed CRISPR-Cas9 experiment. One of the most important considerations is the controls that will be included in the assay.

Whether this is a positive control to help achieve maximal gene editing, or a negative control to account for non-specific effects of a guide RNA on cells, each control has an important function. Don’t let your results get muddled by a lack of control data. This table will provide a brief explanation of the purpose of each, and help take the guess-work out of choosing the proper controls for your experiment.

If you still have questions or want to discuss the proper application of controls in gene editing experiments, please contact our technical support team.

Positive Control
Function Monitor gene editing efficiency and optimize delivery conditions to achieve maximum potential editing
Features Targets a housekeeping gene Editing efficiency is easy to assay using our Edit-R Positive Control Kits that include DNA mismatch detection primers Can also serve as a negative phenotypic control for screens where gene editing without a resulting phenotype is desired
Products Edit-R (Human, Mouse, Rat) Lentiviral Positive Controls Target DNMT3B or PPIB Edit-R (Human, Mouse, Rat) Synthetic crRNA Controls and Kits Target DNMT3B or PPIB
Non-targeting Control
Function Distinguishes between cellular responses to the general presence of guide RNA and the effects of gene-specific guide RNA
Features Bioinformatically designed not to target any known human, mouse or rat genes*
Products Edit-R Lentiviral sgRNA Non-Targeting Control Edit-R crRNA Non-targeting Control
Untransfected/Untransduced Control
Function Determine baseline cell viability and phenotype
Features Cells are cultured in the absence of Cas9 and guide RNA
HDR-specific Controls – HDR Plasmid/Oligo Donor Only
Function Controls for effects derived from the donor plasmid/oligo, including fluorescence
Features Cells are cultured in the presence of the donor template only (no Cas9 or guide RNA)
Products Edit-R HDR Plasmid Donor Kit For introduction of EGFP, mKate2 or a custom insert sequence ssDNA HDR Donor Oligo Custom-designed using the Edit-R HDR Donor Designer

Positive Control

Function

Monitor gene editing efficiency and optimize delivery conditions to achieve maximum potential editing

Features

Targets a housekeeping gene
Editing efficiency is easy to assay using our Edit-R Positive Control Kits that include DNA mismatch detection primers
Can also serve as a negative phenotypic control for screens where gene editing without a resulting phenotype is desired

Products

Edit-R (Human, Mouse, Rat) Lentiviral Positive Controls
- Target DNMT3B or PPIB
Edit-R (Human, Mouse, Rat) Synthetic crRNA Controls and Kits
- Target DNMT3B or PPIB

Non-targeting Control

Function

Distinguishes between cellular responses to the general presence of guide RNA and the effects of gene-specific guide RNA

Features

Bioinformatically designed not to target any known human, mouse or rat genes*

Products

Untransfected/Untransduced Control

Function

Determine baseline cell viability and phenotype

Features

Cells are cultured in the absence of Cas9 and guide RNA

HDR-specific Controls – HDR Plasmid/Oligo Donor Only

Function

Controls for effects derived from the donor plasmid/oligo, including fluorescence

Features

Cells are cultured in the presence of the donor template only (no Cas9 or guide RNA)

Products

Edit-R HDR Plasmid Donor Kit
For introduction of EGFP, mKate2 or a custom insert sequence
ssDNA HDR Donor Oligo
Custom-designed using the Edit-R HDR Donor Designer

* Recommended especially for experiments dependent on phenotypic measurement, see: Doing CRISPR-Cas9 gene editing experiments? Here are your negative controls!

Effective controls for gene editing

Positive Control

Function

Features

Products

Non-targeting Control

Function

Features

Products

Untransfected/Untransduced Control

Function

Features

HDR-specific Controls – HDR Plasmid/Oligo Donor Only

Function

Features

Products

Additional Resources