FIMM Genomics NGS sample delivery

Make sure your project has been approved via iLAB before sending or bringing your samples to the core.
General gDNA requirements
  • Samples must be normalized before delivery. Normalization as well as nucleic acid extraction can be ordered as a service from HiPrep Core.
  • Recommended buffer used for diluting samples is Tris-HCl (less than 10 mM) or Qiagen EB buffer. If you use buffers containing EDTA (TE buffer etc.). Make sure the EDTA content of the solution doesn’t exceed 0.1 mM. ATE-buffer is not recommended since sodium-azide inhibits the enzymatic reactions.
  • We do not recommend diluting the samples in water. Diluting the samples in water can affect DNA integrity when large dilutions are made. The salt concentration is needed in the process.
  • It is important to remove all cations and chelators from the gDNA sample. The presence of cations and chelators may affect the initial fragmentation reaction.
  • The samples should be free of organic contaminants
  • RNAse treatment is highly recommended as RNA contamination will interfere with the DNA quantification
  • For DNA quantitation we recommend Qubit, PicoGreen or other fluorescence-based method

We have no capacity for long time storage so delivered gDNA samples are for one-time use only.

Samples should be delivered in fully skirted 96-well PCR-plates column wise (A1, B1, C1…). Mark the project name (sample batch ID in iLab) on the skirt of the plate.

Full reaction cost will be charged for the empty wells in the middle of the plate.

Plates must be properly sealed with PCR plate seal.

Recommended plates:

Skirted Eppendorf™ twin.tec™ 96 Well LoBind PCR Plates (Catalog no. 0030129512)

FrameStar® 96 Well Skirted PCR Plates (4ti-0960)
Application specific requirements

WES and Targeted Custom Panels

Twist Library Prep kit
  • All samples need to be in the same concentration and volume
  • Concentration 1.25 ng/µl (+-30%) dsDNA
  • Volume min 50 µl, optimal 100 µl

Human WGS

Illumina PCR free prep kit
  • Recommended concentration 20 ng/µl (+-30%) dsDNA
  • Optimal volume 30 µl, all samples need to be in the same volume
  • >300ng recommended input
  • Processing can be started with less starting material (please consult our experts in this case)
  • Protocol is not suitable for fragmented FFPE samples
  • A260/280: 1.8–2
    A260/230 2–2.2

Enzymatic Methyl-seq

NEBNext Enzymatic Methyl-seq (EM-seq)
  • Recommended concentration 4 ng/µl (+-30%) dsDNA, all samples in the same concentration
  • Optimal volume 60 µl (min. 55µl), all samples in the same volume
  • Processing can be started with less starting material (please consult our experts in this case)
  • cfDNA is also an option (at least 1ng): cfDNA samples should be delivered frozen. Keep freeze-thaw cycles into a minimum.

cfDNA WGS/Targeted Sequencing

QIASeq
  • Samples should be delivered frozen. Keep freeze-thaw cycles into a minimum.
  • Requested volume 50µl (min 40µl), 1-100ng
  • Fragment size distribution can be provided on customer request
Sample delivery

When your project has been approved via iLAB you can bring your sample plate to the freezer which is located in Biomedicum 2U, room F216a (”gDNA samples for NGS workflow" or "Sequencing ready libraries for NovaSeq run")

You can also send samples by mail or courier service. Contact core personnel before sending the samples using the address below:

FIMM Technology Centre
Genomics NGS Sequencing
Biomedicum 2U, 2nd floor, F-wing
Tukholmankatu 8
00290 Helsinki

DNA samples can be shipped at room temperature without compromising results when the samples are free of contaminants and the duration of transport is not long. Seal the plates securely using PCR seal. Make sure to attach the seals properly.