How tos and FAQs

Fragment analysis – Preparation of samples

Note: The term of fragment analysis covers a wide range of techniques with different methods of sample preparation (microsatellite analysis, AFLP, RFLP, MLPA, SNaPshot genotyping system, etc.). The following instructions are therefore only general. Should you have any specific questions or requests, please do not hesitate to contact us.


The sample is typically a PCR product or a mixture of PCR products which are fluorescently labelled. The PCR products do not have to be purified, you only need to send the aliquot of the PCR reaction.

Routinely we work using these combinations of dyes:

Dye set

Fluorescent dyes to label your products

Size standard and sizing range


Sample volume


6-FAM™, VIC®, NED™, PET®

GeneScan™-600 LIZ® (Life Technologies, PN 4408399), 20-600 bp or GeneScan™-1200 LIZ® (Life Technologies, PN 4379950), 20-1200 bp

We add the size standard free of charge

When ordering you can specify in the note the volume of the sample to be used (we typically use 1 μl).

PowerPlex® 5-Dyes

Fluorescein, JOE, TMR-ET, CXR-ET

Your choice, WEN-labelled (previously CC5, recently amended by the manufacturer)

You must provide the size standard

Please contact us before sending the first batch of samples


The PCR products should be labelled using an arbitrary combination of these fluorescent dyes. Note that you cannot combine dyes among dye sets, for example you cannot use VIC® and HEX dyes together.

We recommend 8-tube strips with individual caps (eg Eppendorf 0030124359) or 96-well plates. Do not use parafilm. Please mark the tubes preferably with a number indicating their order in the order form.

Download sample prep guide in pdf.


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