Frequently asked questions

    Q: How much does it cost?

    A: Our prices are based on actual costs that are calculated according to University’s regulations. The prices depend on the type of service and number of samples processed.

    Q: Is the price lower for research collaboration projects?

    A: Our prices are based on actual costs that are calculated according to University’s regulations. Therefore, the prices are same for routine services and collaborative research projects.

    Q: Why should I sequence a single cell?

    A: While seuquencing one single cell can be informative in some cases, in a typical experiment, thousands of individual cells are analysed with a goal of capturing cellular heterogeneity in a sample.

    Q: How many single cells should I study?

    A: This depends on the experimental design. In general, the more heterogeneous your sample is, the more you will benefit from a large number of cells. In a single experiment, typically 1000-10,000 cells are analyzed from a single sample. The number of cells does not influence library preparation costs, but it does influence the costs of sequencing.

    Q: How much does sequencing cost?

    A: It depends on the total number of cells in your experiment. 10X Genomics recommends 20 000 reads per cell as the sequencing depth for 3’-scRNAseq.

    Please contact for a more precise cost estimation.

    Q: How many replicate samples do I need to analyse?

    A: This depends on your experimental design and variability between samples. In some cases it is also possible to validate the most important results by more cost efficient methods such as flow cytometry or immunohistochemistry.

    Q: How do I analyse the data? Do you provide bioinformatics services?

    A: Our unit does not provide data analysis services. The data can be analysed in R using packages such as Seurat, or interactive tools such as 10x Genomics Loupe, Chipster, or Cellenics.

    Q: Can you isolate a specific cell type of interest during the cell capture?

    A: No. Any cell enrichment steps must be done before delivering the sample to us.

    Q: What is the minimum cell number I need?

    A: For routine 3´/5´-scRNA-seq, we recommend preparing at least 50 000 cells. In some cases, smaller sample sizes are also possible, but this should be discussed in advance.

    Q: What kind of buffer should the cells be in?

    A: We recommend 0.04% ultrapure BSA in PBS (which we can provide on request). The following buffers are also compatible:

    • Dulbecco’s Phosphate-Buffered Saline (DPBS)
    • Hank’s Balanced Salt Solution (HBSS)
    • Eagle’s Minimum Essential Medium (EMEM) + max. 10% FBS
    • Dulbecco’s Modified Eagle Medium (DMEM) + max. 10% FBS
    • Iscove’s Modified Eagle Medium (IMEM) + max. 10% FBS
    • Roswell Park Memorial Institute (RPMI) + max. 10% FBS
    • Ham’s F12 + max. 10% FBS
    • 1:1 DMEM/F12 + max. 10% FBS
    • M199

    Q: Can I use EDTA?

    A: Media should not contain excessive amounts of EDTA (>0.1mM) or magnesium (>3mM) as those components will inhibit the reverse transcription reaction.

    Q: Can I use heparin or EDTA when collecting blood samples?

    A: Yes, Sodium Heparin, Sodium Citrate, K2EDTA, and ACD-A anticoagulants can be used.

    Q: Do the cells need to be viable?

    A: No data can be recorded from dead cells. We recommend at least 70% viability for routine samples, and at least 90% for samples for multiplexed analyses (CellPlex).

    Q: Can I study frozen or fixed cells?

    A: Viable frozen cells can be studied, providing that viability remains high after thawing. Human cells can be fixed and studied using 10x genomics Fixed RNA reagents.

    Link to 10X genomics FAQ