FAQ

Planning an experiment

Q: Who can use the services offered by the facility?

A: Our services are open to all users from both internal and external labs, including industries.

Q: How much does a single-cell analysis experiment cost?

A: Different types of workflows have different prices. Please get in touch and we can discuss about the cost of your experiments.

Q: How long does a single-cell analysis experiment take?

A: Most workflows can be carried out over 1-3 days from cells/nuclei to libraries. Additional time can be necessary to optimise sample prep. We always try our best to accommodate user’s requests and timing when planning an experiment.

Q: Can both cells and nuclei be used as input for a scRNA-seq experiment?

A: Yes, both types of starting material can be used as input. Cells are more stable while nuclei are more delicate and require extra care.

Q: What kind of material do you require for a scRNA-seq experiment?

A: Ideally, we require a clean suspension of single cells with viability over 80% or nuclei, both resuspended at a concentration of about 1000/ul.

Q: Can you do scRNA-seq on fixed/frozen samples?

A: Potentially, but additional considerations must be made. Please get in touch to further discuss about this.

Q: Can I bring samples late in the afternoon/evening?

A: Yes. We always try our best to accommodate these requests when samples are not available at earlier times during the day.

Technical questions

Q: What buffer should I use to resuspend my samples?

A: 10X Genomics workflows are compatible with most buffers/media and their additives. However, buffers/media containing EDTA, MgCl₂ or surfactants should be avoided.

Q: How many cells or nuclei can you load in a scRNA-seq experiment?

A: The maximum number that can be loaded on a 10X Genomics 3’ V3.1 scRNA-seq workflow is 20,000. This experiment should yield less than 10,000 cells or nuclei during the analysis.

Q: Do you support other 10X Genomics workflows apart for scRNA-seq?

A: Yes, we have successfully used different workflows and we can easily implement those that we have not tried yet.

Q: How about spatial transcriptomics/Visium?

A: We have successfully processed a number of these samples.

Q: Can you do spatial transcriptomics on both fresh and fixed sections?

A: The 10X Genomics spatial transcriptomics/Visium workflow is compatible with both fresh/frozen and FFPE samples. However, the FFPE workflow can only be used with mouse or human samples.

Downstream processes

Q: Can you also sequence my libraries?

A: We currently don’t offer any sequencing service, but we are happy to put you in touch with sequencing labs and to help you during the sample submission process.

Q: How much does sequencing cost?

A: Sequencing costs depend on the workflow and on the type and number of input cells.

Q: Can you help me with bulk RNA-seq?

A: We do not offer this service, but most sequencing labs do and we are happy to put you in touch with sequencing labs for this.

Bioinformatic analysis

Q: Do you offer bioinformatic/data analysis support for single-cell experiments?

A: Yes. Please get in touch to further discuss about this.

Q: Can you analyse datasets generated elsewhere?

A: Our bioinformatic support service is primarily offered to users that also run their experiments with us. Occasionally we may have availability to accommodate external requests.