Microsatellite markers: Development options

All our custom microsatellite marker development projects begin with enriching the genomic DNA for repeat motifs of your choice (e.g. CT and GT or GATA and GTAT). We then subject the repeat-enriched DNA fraction to next generation sequencing. Runs are scheduled every 5 to 6 weeks; please contact us to check for the dates of the runs.
ecogenics will use its well-proven bioinformatical pipeline to select a number of promising marker candidates and evaluate their PCR performance, polymorphy and interpretability by capillary electrophoresis. For genotyping projects involving larger numbers of samples and markers to be tested, it may be more cost-effective to establish the newly developed markers in PCR multiplex assays. If desired, ecogenics can establish multiplex assays to the needed degree of complexity.
We are dedicated to offer an optimal service to all our customers. You may select one of the following options.

A) The simplest way to profit from our marker development pipeline: sequencing only

As for all other development options, we subject your genomic DNA sample to our SSR enrichment protocol followed by next-gen sequencing. After sequencing, we will analyze the output with our well-proven bioinformatic pipeline to provide you with the best microsatellite candidates. You may directly order the respective primers and start with polymorphy tests on your population of interest.


B) The most cost-effective way to get your markers: polymorphy tested markers

This product includes functionality and polymorphy tests of 36 primer pairs identified by next-gen sequencing. The polymorphy of each locus is assayed in 7 individuals representing your population of interest.
Besides detailed assay description, customers receive 100 M stock solutions of the primers of each locus tested, the forward primers carrying a FAM label.


C) The most efficient way to speed up your lab work: guaranteed polymorphic markers

Guaranteed polymorphic markers, our prime product, are ready-to-use markers that exhibit at least 4 alleles among 15 samples of unrelated individuals representing the species of interest (assuming diploid species). Most customers choosing this option appreciate the unprecedented speed of this product from the time point of the order to delivery (6-10 weeks).
Most successful studies in population genetics involve 12 to 20 microsatellite markers of moderate polymorphy. ecogenics developed the required markers for numerous species, involving all kind of taxa. Editors of all relevant journals know ecogenics and trust our work.
Besides detailed assay description, customers receive 100 M stock solutions of the primers used for all loci, the forward primers carrying a FAM label.


D) Readymade genotyping assays: multiplex PCR establishment

For straight-forward use of the newly developed markers, ecogenics can establish ready-to-use multiplex PCR assays. Multiplex PCR assays are the most cost-effecive tool to reduce subsequent genotyping costs. Even for a moderate number of samples and markers, multiplexing is often more cost-effective compared to singleplex reactions.
Depending on the markers and population studied, we recommend to use 3 to 7-plex assays. By default we use the fluorescent dyes FAM, ATTO532, ATTO550 and ATTO565, compatible with ABIs standard filter set G5.
Besides detailed assay description, customers receive 100 M stock solutions of all primers used in the assay, including dye-labelled forward primers.




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