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 is a PCR-free genotyping workflow. The reagent kit contains everything you need to perform gene editing efficiency quantification. It includes: Probes, master mixes, enzymes, read-out consumables and software.
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 standard laboratory instrumentation. With GeneAbacus, you are able to bring extracted DNA to quantified data in under 5 hours, with no optimization and digital quantification precision.
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 light-weight analysis software that quantifies signals and computes editing efficiency.
GAIA is available for macOS and Windows and included in the purchase of GeneAbacus.
What does the kit consist of?
There are two boxes that come with the GeneAbacus kit shipment, one box containing the molecular assay components (-20°C) and another box containing the readout components (+4°C storage).
What is the shelf life of GeneAbacus?
The kits have a 6 months shelf life from date of delivery.
Please store the different components at their recommended temperatures, as specified in the kit documentation and on each box.
How many reactions are in the kit?
The kit is enough for running 32 reactions. We recommend running samples inat least duplicates to get statistical significance.
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
How long does it take to run the protocol?
We recommend planning for 5 hours with less than 1 hours hands-on time.
What are the assay steps in the protocol?
The protocol consists of 7 steps, starting with column-extracted genomic DNA, followed by probing, rolling circle amplification, fluorescence labeling, image acquisition and data analysis via GAIA.
Are there stopping points in the protocol?
Yes, the protocol contains several stopping points to offer flexibility.
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.
Can you run on crude DNA extracts?
The current version of GeneAbacus requires column purified DNA. Are you in need to run gene edit validation on crude DNA lysates? Get in touch with us at info@countagen.com or via the Contact Us form, and we are happy to discuss.
FAQ – Technology
How does your technology compare to NGS-based amplicon sequencing?
GeneAbacus has an excellent correlation of R^2=0.95 with amplicon sequencing (NGS + CRISPResso2).
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 kit, only a thermal cycler and an epifluorescence microscope are required.
For a complete list of required equipment and consumable for GeneAbacus, please contact info@countagen.com or via the Contact Us form.
What are the epifluorescence microscope requirements?
Standard epifluorescence microscopes can be used to read out GeneAbacus. A list of requirements can be found in the table below. Our team is happy to assist you with any questions you may have. Please contact info@countagen.com or via the Contact Us form.
| Microscope type | Epifluorescence |
| 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 |