Frequently Asked Questions
Welcome to our FAQ section! Here, you’ll find answers to the most commonly asked questions about our product, protocol and more. If you can’t find an answer, feel free to contact us below.
FAQ – Product
What is GeneAbacus?
GeneAbacus (GA) is a PCR-free genotyping product line. The products adapt to the edit validation needs whether it is low throughput (GA 32), high throughput (GA 96) or limited starting material (CellBoost). All the GeneAbacus assays contain everything you need to perform gene editing efficiency quantification.
What makes GeneAbacus unique compared to other technologies?
GeneAbacus utilizes the unique combination of padlock probes and rolling circle amplification to speed up and simplify genotyping for gene-editing efficiency quantification. It is a PCR-free assay that can be performed completely in-house with a standard workflow.
How can I order a GeneAbacus kit?
You can request a quote directly on our website (https://countagen.com/quotation-form/) or email info@countagen.com and we will contact you.
How do I analyze the GeneAbacus output images?
GAIA, short for GeneAbacus Image Analyzer, is a cloud-based software that quantifies signals and computes editing efficiency. GAIA is included with the first purchase of GeneAbacus.
What gene editing modalities can GeneAbacus validate?
GeneAbacus is a genotyping platform and supports validation of any gene editing modalities, such as TALEN, CRISPR/Cas9, /Cas12, base and prime editing and programmable genomic integration (PGI). The GeneAbacus probes precisely target any DNA sequence of interest independently of the editor technology used.
FAQ – Protocol
Are there any controls included in the kit?
Two types of controls included in the kit. The first is a control of genomic DNA that that is used to confirm correct execution of the protocol and stability of reagents. The other, control is an control probe included in the custom probe mix to account for differences in the amount of genomic DNA input between samples and allow for data normalization.
What type of external controls do you recommend?
It is always recommended to include control samples in the experimental design. Besides the edited samples, a wildtype sample has to be included in the analysis. Other controls might include non-sense sgRNA or lack of Cas.
What is the minimum genomic DNA input?
100 ng of DNA (column extracted) is recommended for each reaction. The DNA concentration of the sample should be equal or above 10 ng/µL.
What sample type can you run on?
GeneAbacus currently supports column purified DNA from human cell lines and mouse cells, tissue or model organism. The purity of the DNA should be that the 260/280 ratio is >1.7 and 260/230 ratio between 1.8 and 2.2.
For further details or questions, please contact info@countagen.com or via the Contact Us form.
FAQ – Technology
Can GeneAbacus detect high GC content regions?
Yes, in general, the GeneAbacus workflow is more robust to high and low GC content target regions than PCR-based assays. Contact us and we are happy to discuss your tricky targets.
Can it distinguish point mutations and base edits?
Yes, it is a perfect match for the validation of precision edits as it relies on padlock probe chemistry.
What is the lowest editing efficiency that GeneAbacus can quantify accurately?
GeneAbacus can quantify gene editing efficiency accurately above 10%.
What is the specificity of the technology?
Single mismatch discrimination accuracy of >95%.
FAQ – Instrument
What instruments do I need to run GeneAbacus?
To run the GeneAbacus 32, only a thermal cycler and an epifluorescence microscope are required.
GeneAbacus 96 requires a thermal cycler, an oven at 37 ºC, a high content imager and in its absence, an epifluorescence microscope.
For a complete list of required equipment and consumable for GeneAbacus, please contact info@countagen.com or via the Contact Us form, and we will be happy to get you all set for experiencing GeneAbacus.
What are the epifluorescence microscope requirements?
A list of requirements can be found in the table below. Our team is happy to assist you with any questions you may have, and of course get you up to speed to experience GeneAbacus. To get in touch with us, write us at info@countagen.com or use the Contact Us form and we will get back to you right away.
| Microscope type | Epifluorescence or high content imager |
| Fluorescence filter channels | FITC, Cy3, Cy5 |
| Microscope objective | 20x, NA>0.5, WD>0.6 mm |
| Field of view | 0.65 mm^2 |
| Resolution | 1024×1024 minimum |
| Pixel size | 0.66 µm/pixel |
| Light source | LED |
| System | Upright or inverted |