Do you perform DNA extraction?

Yes, we offer DNA extraction service for isolating the total environmental DNA from any type of sample. We use commercial DNA isolation kits from QIAGEN. The price is 50 € / sample.

Which sample types are accepted?

Any type of samples, such as but not limited to soil, sediment, sludge, manure, stool, meat, tissue, swabs, river, lake, wastewater or seawater.

What are the required volume and concentration of the liquid samples?

For liquid samples: we recommend to filter about 1 liter of water samples from river, lake and seawater and for wastewater, 100 mL from influent and 250 mL from effluent. The water sample should be filtered/concentrated using hydrophilic membrane filter with minimum pore size 0.2 µm. The concentrated water-filters are stored in Falcon tube and delivered on dry ice to our facility in Helsinki, Finland.

What are the required volume and concentration of the solid samples?

For solid samples: we recommend 100 g of dry/wet weight. The solid samples are stored in zip lock plastic bags or 1,5 mL tube and delivered on dry ice to our facility in Helsinki, Finland.

We have the DNA samples ready, what are the required volume and concentration
of the DNA samples?

For DNA samples: we recommend 10 ng/µL and 100 µl of volume, with the DNA quality of 260/280 between 1.8-2.0 +/- 0.1. If you have samples with low amounts of DNA, the minimum DNA concentration and volume are 3 ng/µL and 100 µL, respectively.

Which genes are measured?

We measure up to 384 genes, including 16S rRNA gene (positive control); antibiotic resistance genes (ARGs) targeting aminoglycoside, amphenicol, beta lactam, florfenicol, multidrug efflux-pump, macrolide-lincosamide-streptogramin B (MLSB), trimethoprim, tetracycline, vancomycin; genes targeting other antibacterials such as nisin, bacitracin, antiseptic, mercury; genes targeting bacteriophage, CrAssphage; and genes that associated with mobile genetic elements (MGEs) and integrons.

How the hundreds of genes are measured?

The ARG 1.0 and ARG 2.0 primer sets were used to detect and quantify up to 384 genes in parallel in one measurement using the smartChip real-time PCR.

How do you account variation in the genes in the primer design?

Each primer set was designed to target a specific region in antibiotic resistance gene (ARG). For ARG variations more primers have been designed to cover all known ARG variations.

Do you detect pathogens?

No, at the moment we only detect the antibiotic resistance genes. However, in the ARG2.0 eight primer sets were designed to target certain taxonomy group of bacteria: A. baumannii, Bacteroidetes, Campylobacter, Enterococci, Firmicutes , K. pneumoniae, P. aeruginosa and Staphylococci.

Is the quantification absolute or relative?

The quantification is based on abundance of the genes relative to the amount of 16S rRNA gene in each sample.

How is the relative quantification performed?

We use the delta Ct calculation (reference). Delta Ct = Ct of genes – Ct of 16S rRNA gene. The relative quantification is calculated with formula: 2^-delta Ct.

How long is the analysis process?

We deliver the result of analysis within 10 working days.

Can you add custom targets to the SmartChip?

Yes, if the primer sets are already validated and have annealing temperature of 60 °C in quantitative PCR.

How quickly do you add new genes to your offering?

It requires at least 2 – 3 months to optimize and validate assays for new genes.

Can you provide additional analyses from the SmartChip measurement results?

Yes, we have extra analysis service which costs 200 € / analysis such as ordination, fold change and gene network.

Can you perform analysis from the SmartChip measurement results?

Yes, for industry the service costs 2300€* and includes the analysis service.  For academia, we have both the SmartChip service (measurement only) which costs 1200 € *and the SmartChip with analysis service which costs 1800 €* / SmartChip. The analysis report includes an interactive heatmap, table of detected genes in each sample and their relative abundance values and a two pages summary report in pdf.

* All the prices are not include 24% VAT