Service summary

• DNA extractions with Qiagen kits on QIAsymphony*
• QC check with Victor Nivo Multimode Microplate Reader
• Library preparation and sample indexing with Illumina kits
• Full automated library preparation on Hamilton NGS STAR
• Sequencing with NovaSeq 6000, 30x genome coverage
• Turnover time approx. 2 to 3 weeks**

(*) For unextracted samples.
(**) Turnover times are not guaranteed, may change according to your project.

Sample requirements

Accepted Sample Type	Recommended Amount	Shipment method
Whole Blood (Fresh or Frozen)	650μL-1ml	Blue ice for fresh blood Dry ice for frozen blood
Buccal Swab	Follow the kit manufacturer's instructions
Tissue	30 - 50 mg	Dry ice
FFPE Tissue	4-6 slices for 10µm, 8-10 slices for 5µm	Room temprature
Cell Pellet	≥10^6 cells (eukaryotic) ≥10^8 cells (microorganism)	Dry ice
Saliva	650μL-1mL	Dry ice or blue ice
Genomic DNA (RNA-free)	50μL, >20 ng/μL	Dry ice

How to evaluate the sample quality

We check your samples upon arrival however, we still require our users to do their own QC steps before sending samples.

Checking the concentration

Please use fluorometric measurements (e.g. Qubit, Quant-it), not absorbance measurements (Nanodrop, spectrophotometer).

Checking the quality and purity

The DNA should be in EB buffer (not EDTA or water), of high quality, and ideally have an A260/280: 1.8- 2.0 and A260/230: 2.0 – 2.2
If your samples are below the required thresholds, please get in touch.

What we do with your samples

Once your samples arrive at SZAOMICS, we start by performing a reception control step in which we make sure the samples meet our requirements.

If the samples fail this quality control step, we will contact you to discuss possible options. Should you choose to proceed with samples not fulfilling the criteria it will be at your own risk, SZAOMICS will only make one attempt at library preparation and if the prep does not work you will have to pay for the library preparation anyway.

If the samples pass reception control, we will inform you and the samples will be queued for library preparation.

Library preparation

Illumina’s new tagmentation-based DNA PCR-free library preparation is the method of choice for generating the highest quality DNA sequencing libraries. PCR-free libraries have better coverage of GC-rich regions compared to PCR-based methods and the reads are more evenly distributed over the genome.

This method is recommended when:

• Insert sizes approx. 350 bp are suitable for your application.
• You do not have enough DNA for the TruSeq PCR-free protocol.

Library QC and sequencing: We evaluate the concentration of the library and inform you of the QC status of each sample. Once the libraries have passed this QC step, they are normalized, pooled, and queued for sequencing.

Expected results

PCR-free libraries are well suited for deep sequencing to achieve high coverage genomes. The library preparation method shows a significantly better coverage of GC-rich regions compared to PCR-based methods and the reads are more evenly distributed over the genome.