Single-cell RNA sequencing (scRNA-seq) experiments come in many shapes and sizes, and a 10x Genomics price may differ significantly per project.
Here, we explore the four factors determining the pricing of your 10x Genomics project: the technology you need, the number of samples, the number of cells per sample, and the sequencing depth.
1. The technology you need
10x Genomics' single-cell sequencing technologies (often called solutions) are performed on the Chromium Instrument. This instrument can run various technologies that enable analyzing the transcriptome, chromatin accessibility, or T and B cell receptors of individual cells.
We offer two scRNA-seq solutions by 10x Genomics as a service: Single Cell Gene Expression and Single Cell Immune Profiling.
- Single Cell Gene Expression analyzes the whole transcriptome at the single-cell level.
- Single Cell Immune Profiling allows you to study the transcriptome and the immune receptors. This is done by sequencing the full-length V(D)J sequences for B and T cells. In addition, we combine RNA sequencing with the CITE-seq technology TotalSeq to include T or B cell receptor sequencing and get data on the cell surface proteins.
As you can imagine, the multiplex nature of Immune Profiling raises the price of this technology over that of Single Cell Gene Expression.
2. How the number of samples affects 10x Genomics pricing
10x Genomics pricing increases per sample, which is relatively straightforward. However, the Chromium Instrument can run up to eight samples simultaneously. This is because the microfluidics chip used for sequencing has room for eight samples. As a result, a ninth sample increases prices more than a sixth sample because it requires a second run.
The optimal price-per-sample of 10x Genomics is usually when you have (a multiple of) eight samples.
This suggests that it is wise to look critically at your experimental setup. Then, determine if there is a real need to include all samples to answer your biological question or if some samples can be omitted or combined.
The cost per 10x Genomics sample also varies depending on the number of targeted cells and the sequencing depth.
3. How the number of cells affects
10x Genomics pricing
The number of cells you want to target in each sample influences your price. As with the number of samples, the 10x Genomics price increases with the number of cells you target. Of course, the number of cells you need to target depends on your biological question.
With 10x Genomics, you can aim to target between 3,000 and 10,000 cells per sample. Its minimal target of 3,000 cells can make the starting experiment relatively expensive. When you expect to require fewer cells, plate-based technologies like SORT-seq and VASA-seq may be the better choice.
One can think of methods to reduce the number of cells and costs by selecting the cells of interest. For example, you can enrich for cells of interest by FACS-sorting, laser capture microdissection, or chromatography—although you will need to test how this affects cell viability and cell number.
On the other hand, it can be recommended to aim for high cell numbers depending on the research question. For example, if you aim to study a rare cell type, it is often best to target many cells. It can be helpful to study literature employing 10x Genomics solutions in your field and try to gauge the number of cells your peers' target. This often provides the right direction for the number of cells to target.
4. How sequencing depth affects
10x Genomics pricing
Depending on your biological question, you might want to increase the 10x Genomics sequencing depth, which means you include more transcripts in your analysis. As a result, you can get a higher-resolution picture of the gene expression profile of each cell, potentially catching lowly expressed genes that you would otherwise miss. Increasing the sequencing depth has many potential benefits, such as more precisely resolving pathways activated in disease or therapy, or finding novel biomarkers for complex disease states.
Sequencing depth in 10x Genomics solutions usually ranges between a minimum of 20,000 and recommended 40,000–80,000 reads per cell. For Single Cell Gene Expression Flex, the minimum is 10,000 and 40,000–80,000 reads per cell is recommended. As can be expected, 10x Genomics pricing increases with the sequencing depth.
How can you find out what sequencing depth you need?
- As with the number of cells, literature research can help you make a reasonable estimate.
- Moreover, the advised sequencing depth varies depending on the amount of RNA expected in the sample, which differs per tissue and sample type. In RNA-rich cells such as cell lines, 50,000 reads per cell may only supply 30-50% sequencing saturation, 10x Genomics notes.
- Finally, we can gauge the optimal read depth by looking at the sequencing saturation (i.e., a computed percentage of transcripts sequenced compared to what was expected) during data analysis. The results of a first experiment can thus inform later experiments. It is one of the reasons why we advise starting small with a pilot experiment before expanding into larger 10x Genomics projects.
How to get a price for your experiment
The only way to get an exact price for a 10x Genomics project is to discuss the project's ins and outs with one of our specialists. In a consultation, we can help guide you through some of the complex decisions you have to make on the above factors.
For example, more reads can significantly reduce the effects of technical noise in generating single-cell transcriptional profiles, but with a limited budget, this might affect how many cells you can sequence. Yet, more cells can give you a broader view of the biological variability in the cell population, which might be crucial for certain research questions. Which factor has your priority, and is there a 'sweet spot' between sequencing depth and cell number?
For questions like these, you can schedule a virtual meeting with one of our specialists and find out how your 10x Genomics project can best fit your budget.
