Mouse speed congenics SNP genotyping
FIMM Technology Centre Genomics Unit offers Mouse speed congenics SNP genotyping service using a next generation sequencing panel, including 1447 SNPs annotated to the mouse genome build mm10 and dbSNP 1.37 database.
Current price for the speed congenics analysis is 300 € (0% VAT) per sample for University of Helsinki internal projects and 390.60 € (including 24% VAT) for other academic users. Both above mentioned prices require a set of 12 samples to be analyzed at the same time. If you are a non-academic user please contact Päivi Lahermo (email@example.com) or Kati Donner (firstname.lastname@example.org) for pricing.
The laboratory work is done by dedicated personnel years of experience in genotyping work. Our laboratory uses an electronic lab note book (ELN) for documentation of the laboratory workflow and an in-house made LIMS system for management of genotype and sample data.
Projects are managed and quality controlled by experienced specialists. The quality control includes visualizing and manually checking a selected set of results with Integrative Genomics Viewer based on read depths, heterozygosity etc. and utilizing in-house developed additional tools. In addition to the genotypes illustrative heterozygosity plots and reports are included in the release to help selection of the most suitable individuals for future crosses.
How to get started
If you are interested in mouse speed congenics SNP genotyping please contact Päivi Lahermo or Kati Donner. If necessary, a starting meeting can be organized, where all project details can be discussed.
A FIMM Service Agreement must be signed before the project can start in our laboratory. If your project is required by law to have an ethical permit you need to supply us with a copy of it.
2) Sample information
Provide the sample information using FIMM basic information form. Note! You need to enable the included macros. The filename should be FIMM_Perustietojen_luovutus_v2010.xlsm for the macros to work.
Fill up this sample submission form, print it and bring or send it to the lab together with the samples. Please also remember to submit the form electronically!
The gender information requested for in the FIMM basic information form is optional but central for detection of possible sample mix-ups in our quality control.
3) DNA samples
For the analysis we prefer good quality DNA in a concentration of 50 ng/µl in a minimum volume of 10 µl diluted 1 x TE (10m mM Tris-HCl, 1 mM EDTA, pH 8.0). In cases where DNA quality is high but amount is a limiting factor less may suffice, please enquire.
Note! We recommend that the concentration is measured with two independent methods, e.g. in addition to NanoDrop spectrophotometer with PicoGreen or Qubit fluorometric quantification. If only one method is used it should be PicoGreen, Qubit dsDNA assay or other similar method.
Notice that the analysis methods requires a set of 12 samples to be analyzed in each analysis run. If you have less samples please enquire if there is another project available to share the run.
DNA shipping instructions
DNA may be shipped in tightly capped tubes or on securely sealed 96-well plates. Note! If you send the plates frozen an adhesive foil seal should not be used. Use removable heat-seal or strip caps instead!
Mark the tubes or plates clearly with sample or plate name (the same name as in the FIMM basic information form), sample concentration and date information.
Frozen samples in tubes or on plates should be placed in the shipping container with enough dry ice/blocks to keep the samples frozen during shipment and any delays that may occur with the courier.
Whenever possible, please avoid shipping on Thursdays and Fridays to avoid the samples arriving over the weekend. Pack the samples so that the plates or seals are not damaged during shipment. If you stack multiple plates put cardboard or wadding layer between the plates.
Please ask us for instructions before sending the samples via air courier!
Mark the plate name (the same name as in the FIMM basic information form), sample concentration and date information clearly on the front side of the plate (see the image below for an example).
Frozen plates should be placed in the shipping container with enough dry ice/blocks to keep the samples frozen during shipment and any delays that may occur with the courier.
FIMM Genotyping Lab
FIMM Technology Centre