Location

Targeted methylation

Targeted methylation analysis is available at our genomics facility with AgenaBiosciences EpiTyper method. One or several amplicons can be analyzed in 384-well format.

Pricing

Examples of analysis prices per run:

Number of runs /

costs per run

University of Helsinki

(includes 0% VAT)

Other academic

(includes 24% VAT)

1 run (384 wells)

3665.22 €

4772.12 €

4 runs (384 wells)

2711.50 €

3530.37 €

One run can include different combinations of samples / amplicons in a 384-well plate, inquire us about details.

Oligo order, bilsulphite conversion and plate handling cost shall be added to the run costs listed above.

For more information about pricing or if you are a non-academic user please contact Päivi Lahermo or Kati Donner.

Service description

The laboratory work is done by dedicated personnel with nearly 15 years of experience in Agena Biosciences/Sequenom analysis methods. 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 manual checking of results with AgenaBiosciences EpiTyper analysis software. Routine data release includes quality metrices as well as epigrams and numerical methylation values from EpiTyper.

All received and produced data is stored in a database at FIMM. FIMM guarantees the storage of your data for 5 years.

How to get started

If you are interested in targeted methylation analysis please contact Päivi Lahermo or Kati Donner. A meeting can be organized, where all project details can be discussed.

 

 

Customer provides

1) Documentation

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) Sequence information

You need to provide us with information on the genomic regions to be analyzed. We shall design the amplicons with EpiDesigner software, or you may do the design yourself. For detailed instructions please contact us.

 

4) DNA samples

For the analysis we need 1000 ng of good quality DNA in a concentration of 50 ng/ul in nuclease-free water.

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 you use only one method it should be PicoGreen, Qubit dsDNA assay or other similar method.

For quality control reasons we recommend that the samples would be run as triplicates. In addition we add an internal control sample and a water sample per each amplicon. We recommend that the groups deliver a suitable pair of methylated and non-methylated samples as controls for analysis with the project samples.

 

DNA shipping instructions

Ship the DNA samples on 96-well plates.

Seal the plates securely using either an adhesive seal, strip caps or a removable heat-sealed lid. Use Adhesive PCR foil (e.g Cat. # AB-0626, Thermo Fisher Scientific Abgene) only for shipments at room temperature. Make sure to attach the foil seal properly to each well by rubbing the surface with soft cloth or lab wipe. Make sure to protect the seals from punches. If you stack multiple plates, put cardboard or wadding layer between the plates. 

Note! If you send the plates on dry ice an adhesive foil seal should not be used. Use strip caps instead! 

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!

Plate naming:

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 samples:

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.

Shipping address:

FIMM Genotyping Lab
FIMM Technology Centre
Room: F215a
Biomedicum 2U
Tukholmankatu 8
00290 HELSINKI
FINLAND

Last updated: 14.05.2018 - 13:28