Frequently Asked Questions
Below you will find answers to some of the most common questions from our clients.
How do I get started?
Getting a project started is easy. CONTACT US to share a few details about your project. We will reach out to you to review your experiment, desired nuclei and sequencing output, and pricing options.
How much time will it take for me to get single-cell cDNA libraries or data back?
Libraries and data are generated in 4-8 weeks, depending on the service contracted (scBASIC, scPLUS or scPREMIUM). We dedicate the first 2 weeks after samples are received to Process Development, when the conditions for nuclei isolation are optimized. Nuclei isolation and cDNA libraries are prepared in the Production phase – completed up to 4 weeks after samples are received. For the scPLUS and scPREMIUM services (including next-generation DNA sequencing and basic bioinformatic analysis), an additional 4 weeks are required.
How many cells will I get data from?
For standard projects, we generate data for 5,000-10,000 nuclei per sample. If data for a greater number of cells is desired, we will review approaches to generate them in our onboarding call.
Do you generate single-cell RNA sequencing data from nuclei?
Yes, we generate data from nuclei isolated from individual cells. The use of nuclei enables the analysis of all cells, without biases caused by differences in the dissociation of distinct cell types. Also, by avoiding long and harsh enzymatic treatments that are required for cell isolation, we limit cell stress responses often seen when these treatments are applied. These and other reasons have resulted in single-cell genomic analysis of nuclei becoming the standard in studies of plants, animals, and fungi.
How much tissue do I need to send, and how? Does it have to be frozen?
Typically, less than 1 gram of tissue is sufficient. A specific tissue amount determination, as well as the collection and shipping instructions, are reviewed in the onboarding call with our team. For material from species and tissues that require the optimization of nuclei isolation, larger amounts of sample may be required for the Process Development phase. Samples need to be flash-frozen immediately upon collection and sent in dry ice.
What type of bioinformatic analysis (scPLUS Service) can you do with my single-cell RNA sequencing data?
The analysis includes quality control, identification of doublets (when two or more cells are given the same nuclei barcode), and discovery of the optimal number of clusters in your datasets. Clusters will be assigned to cell types based on our SolusCell Annotator™ database of markers derived from models and non-model organisms. These markers may not represent all existing cell types in your sample and species. Thus, our annotation is designed to provide a robust yet preliminary annotation to be further validated by the client. Advanced analyses such as integrating multiple samples, pseudotime and trajectory inference, and gene regulatory network analysis can be contracted, in addition to our standard pipeline. The availability of these analyses is decided on a case-by-case basis, depending on your sample(s) and experimental design. If your sample(s) qualify and you choose this option, our bioinformatics team will work with you to maximize the information obtained from your dataset.
What method do you use to make the single-cell RNA sequencing libraries?
Our method uses commercial platforms adapted by us to the analysis of difficult to dissociated tissues, such as many from plants and animal species, and fungi.
Do I need to know the genome sequence of the species I want to do single-cell RNA sequencing?
For analysis of single-cell data, DNA sequencing reads are aligned to an annotated genome sequence, or a transcriptome assembly from the same or a related species. Thus, this information is required for completion of a project.
What species and tissues have you isolated nuclei and made single-cell libraries from?
We have generated single-cell genomics data from a wide range of plants, including monocots and dicots, and material sources ranging from roots to leaves, stems, and reproductive tissues, as well as animal and fungi. However, each sample is unique. For that reason, we allocated the first 2 weeks (the Process Development phase) of each project to testing and optimizing the methods required for nuclei isolation and data generation. If further development is required for nuclei isolation, our team will reach out to discuss options and timelines.
What happens if you can’t get good-quality nuclei from my sample?
If we fail to obtain high-quality nuclei, we reach out to review and discuss alternatives. Failure to obtain high-quality nuclei for single-cell analysis has occurred in fewer than 5% of the samples that we have analyzed.
Where will be my data stored and for how long?
All your data will be stored on highly secured, vetted, third-party servers located in the United States, from the time of the data generation, and up to 60 days following the completion of your project. Longer-term storage and access to data visualization and mining tools can be contracted using the service scPREMIUM.
Where is SolusCell located?
The SolusCell sample processing facility and headquarters are located in Alachua, Florida.
