Quantify transgenes

The gene Editing-digital PCR (Ed-digital) test directly informs on the presence and number of transgenes inserted in the genome of CRISPR-edited cells.

The Ed-digital PCR test
Cell types

Any cells


Gene editing


- gDNA
- Cell pellet
- Cells in fresh culture media
(or in cell culture supernatant)


- Room temperature
- Dry ice
- Room temperature




2-3 days
after sample reception

Stem Genomics Ed-digital test offers

Thanks to its flexibility and ability to achieve precise targeting, the CRISPR system is a powerful gene editing tool for various molecular biology applications. The Ed-digital test allows the detection of the number of transgene copies present in the genome of gene-edited cells using digital PCR.

Transgene copy number determination: puromycin, neomycin, EGFP or mCherry
Our test has been designed for the detection of common resistance cassettes (puromycin or neomycin) or fluorescent reporter genes (EGFP or mCherry).
It provides precise information on:
• The actual presence or absence of the transgene
• The number of integrated transgenes
• Off-target genomic integration (see below)

If transgene copy number = 2
1. The on-target insertion is homozygous: absence of off-target insertion (A)
2. The zygosity of the on-target insertion is unknown:
- The insertion is homozygous and on-target (A)
- There is one on-target and one off-target insertion (B)

If transgene copy number > 2
In this case, there is at least one off-target insertion.
Example with copy number = 3:
1. If the on-target insertion is homozygous, there is only one off-target insertion (C)
2. The zygosity of the on-target insertion is unknown:
- The insertion is homozygous; there is one off-target insertion (C)
- There is one on-target and two off-target insertions (D)

Custom assays for the detection of a specific transgene
Custom assays can be developed on request. Please, contact us.

Different scenarios of transgene insertions

• If copy number values are different from a whole number, the population is not clonal (mosaicism).
• For off-target insertions, the Ed-digital test cannot provide information on their genome position.

Stem Genomics offers a fast and precise method to quantify transgene copy number in gene-edited cells.


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