How to characterize your sample and start testing
This section provides information on how to process less common sample materials, if no validated QIAsprint Connect protocol is available. These materials cannot be easily classified under the standard human, animal, plant or microbial categories and require case-by-case optimization.
The following are examples of sample types that may require optimization:
- Processed food (fermented food, chocolate, gummy matrices)
- Unusual biological samples (fish scales, feathers, nails, earwax, mucus or old degraded tissue)
- Inhibitor-rich natural material (woody plants, pine needles, fungi or algae)
- Biotechnological samples and advanced cellular samples (bioreactors, cell culture supernatant, organoids, 3D cultures, isolated extracellular vesicles)
- Environmental or industrial samples (sediment slurry, air filters, wastewater)
If you want to process samples like this, first characterize the sample.
1. Classify the sample.
Answer the following questions to determine the most suitable PrepSet for lysis.
| Question | Why this matters? | Recommended QIAsprint PrepSet (starting point) |
|---|---|---|
| What biological category does the sample most resemble? For example, does it resemble human/animal or plant material? |
When the origin of the biological sample is not clear, establishing the closest biological match allows selection of the correct lysis chemistry. |
|
| Is the sample liquid, semi-solid or solid? |
The physical state of the sample affects lysis efficiency and the degree of homogenization. |
|
| Does the sample contain high levels of inhibitors such as polyphenols, humic acids, heme or fats? |
Inhibitors may compromise binding efficiency or be carried over into eluates, resulting in failure of downstream applications such as PCR or NGS. |
|
| Is the sample difficult to lyse? | Hard-to-lyse material can vary in size from wood or bone fragments to Gram-positive bacteria or spores. In this case, mechanical disruption is required for full nucleic acid release. |
For hard-to-lyse samples: PrepSets intended for tissue or stool (if microbial) or a plan that includes mechanical disruption in the protocol. |
| Does the sample contain a cell wall or rigid structure (plant, fungi, yeast, bacteria, viruses)? |
Requires stringent lysis conditions, often with mechanical disruption. |
|
| Are the samples processed or mixed food samples, liquid food samples (e.g., milk, juice, wine, beer, broth)? |
Mixed matrices may include plant, animal and microbial material and should be classified based on the dominant material. |
|
2. Select an Essential Kit
After sample classification, you then need to select the appropriate Essential Kit, which contains reagents for the bind, wash and elute steps of the workflow.
There are four Essential Kits for QIAsprint Connect. Each kit has a unique chemistry, but all kits contain magnetic beads and are designed for highly efficient magnetic-bead purification. In practice, it is often difficult to predict which Essential Kit will be the ideal choice for a new or unusual sample type. For this reason, it is helpful to test more than one Essential Kit in combination with the selected PrepSet during the initial evaluation phase.
Below is a short overview to support your choice of starting point.
| Components | Recommended in combination with the following PrepSets or applications |
Comparable to chemistry used with the following manual kits |
|
|---|---|---|---|
| Essential A | Buffer AW1, Buffer AW2, RNase-free water MagG bead suspension |
gDNA from blood, pathogen nucleic acids from body fluids, DNA from plants |
QIAamp Virus Kit; DNeasy Plant Kit |
| Essential B |
Buffer RPE, RNase-free water MagG bead suspension |
RNA, including miRNA from tissue and cells, RNA, including miRNA from plants |
RNeasy; AllPrep |
| Essential C | Buffer MW1, RNase-free water MagG bead suspension |
Microbial nucleic acids from stool, gDNA from tissues, cells and swabs, nucleic acids from wastewater |
MagAttract HMW Kit |
| Essential D | Buffer PE, Buffer EB MagG bead suspension |
Plasmid DNA from bacterial cultures | QIAGEN Plasmid Plus Kits |
If you are unsure which Essential Kit to use:
- Select the PrepSet based on the sample type.
- Start with the QIAGEN-validated combination shown in the table above.
- Compare yield, purity and downstream performance. Continue protocol development.
How to test compatibility with specific sample storage reagents
When working with samples stored in stabilization or transport reagents, it is important to assess whether the storage solution interferes with the purification chemistry. First, check whether the reagent can be removed prior to lysis, for example by centrifugation, washing or transferring the sample into a fresh tube. If this is possible, it is usually the simplest and most reliable solution. When in doubt, and if the sample allows it, we recommend removing the storage solution in line with QIAGEN stabilization reagents such as RNAprotect Tissue Reagent or Allprotect Tissue Reagent.
If it is not possible to remove the storage reagent e.g., as you have liquid samples like blood, test the sample using the standard workflow recommended for the respective PrepSet and Essential Kit combination. Should performance issues arise (e.g., low yield, poor purity, precipitation or viscosity problems), it may be helpful to obtain detailed information about the composition and nature of the storage reagent or tube from the manufacturer.