10X GENOMICS SINGLE CELL SEQUENCING
We offer 10x Genomics Single Cell Gene Expression, Single Cell Immune Profiling and Single Cell Gene Expression Flex as a service.
- Dedicated service provider
We focus on standard and custom (single-cell) RNA sequencing services.
- Personal approach
We like to get to know you and your project so we can aim for the best results together
- Continued support
We help you design your project and analyze your data with our (optional) data solutions
- Expertise
We’ve been running standard and out-of-the-box single-cell experiments since 2012
HIGH-THROUGHPUT SINGLE-CELL SEQUENCING
10x Genomics provides high-throughput microfluidics-based single-cell sequencing solutions. At Single Cell Discoveries, we offer three of those solutions as a complete service: Single Cell Gene Expression, Single Cell Immune Profiling and Single Cell Gene Expression Flex.
Read more about these solutions below.
AVAILABLE PRODUCTS
The two different 10x Genomics products we offer have different applications and uses.
SINGLE-CELL GENE EXPRESSION
The 10x Genomics Single Cell Gene Expression solution provides users with 3’ transcriptome gene expression at single-cell resolution. This allows you to perform molecular and cellular characterization of cells. This high-throughput single-cell RNA sequencing solution is highly suitable for larger projects, that require data for a few thousand cells per sample.
- Obtain 3’ single-cell transcriptomics data from your tissue of interest.
- Target between 3,000 and 10,000 cells and choose your amount of reads (30,000 – 80,000) per cell: The most popular is 50,000 reads per cell.
- Compatible with single cells or nuclei, depending on the project.
SINGLE-CELL IMMUNE PROFILING
The 10x Genomics Single Cell Immune Profiling solution provides users with 5’ transcriptome gene expression, combined with the T- and B-cell repertoire and antigen specificity. It allows you to, for example, explore the adaptive and innate immune cell diversity, and characterize the immune response to infection or treatment.
- Obtain 5’ single-cell transcriptomics data and the immune repertoire.
- Target between 3,000 and 10,000 cells and choose your amount of reads (30,000 – 80,000) per cell: The most popular is 50,000 reads per cell.
- Choose the additional Immune Profiling Libraries: BCR, TCR and/or Cell Surface Library and choose your amount of reads: 5,000 reads per cell is recommended.
SINGLE-CELL GENE EXPRESSION FLEX
The Single Cell Gene Expression Flex solution (Fixed RNA sequencing) enables single-cell 3’ transcriptome gene expression profiling of FFPE and fixed tissue. It allows for immediate preservation of samples on-site. This is highly convenient for biopsies and patient-derived xenograft tissue, time-course experiments, sensitive cell types, and cells of lower viability. Available for mouse and human tissue.
- Obtain 3’ single-cell transcriptomics data from FFPE and paraformaldehyde-fixed samples.
- Aim to target up to 1,024,000 fixed single cells simultaneously with a scalable multiplexing workflow that can be run on your schedule.
- Choose your amount of reads per cell for the Single Cell Gene Expression Flex Library: between 10,000 and 40,000 reads per cell. Discuss with our specialists to find your option.
Don't just believe our word, here's the word of one of our customers:
"Fantastic job made by a really professional and friendly team. I strongly recommend Single Cell Discoveries for sequencing services."
Samuel García Pérez
Galicia Sur Health Research Institute
How does it work?
Step 1:
Sample preparation
Create a single-cell suspension from your sample and either cryopreserve or methanol-fix the cells. Then send your samples to our lab on dry ice.
If you are based near our lab in Utrecht, the Netherlands, then it may be possible to use freshly dissociated samples. Contact us to discuss this.
Step 2:
Sample processing and library prep
After receiving your samples, we wash, filter and count each sample and verify the quality.
Next, we load the cell suspension on the 10x Genomics chip, along with barcoded beads and reagents.
The chip is placed in the 10x Genomics chromium controller to initialize single-cell isolation, barcoding, and transcript amplification.
After the run, we complete the NGS library preparation and send the sample out for sequencing.
Step 3:
Sequencing and data analysis
We send the finished NGS libraries to one of our sequencing partners for next-generation sequencing on the Illumina NovaSeq 6000.
When we've received the sequencing data, we map it to the appropriate reference transcriptome, perform a QC analysis, a preliminary clustering and differential gene expression analysis, done with a customized version of the Seurat analysis pipeline.
Mapping of sequencing data and initial quality control reports are done with the standard 10x Genomics Cell Ranger pipeline. You'll be provided with a cloupe data file for browsing the data with the 10x Genomics Loupe Browser.
We'll also provide you with a preliminary clustering and differential gene expression analysis, done with a customized version of the Seurat analysis pipeline.
Download pricing
Complete the form below and receive information on our pricing and services.
Deliverables
As with all of our services, we provide ongoing support from our single-cell sequencing specialists. For each single-cell sequencing project, we provide the following:
- Regular email updates during sample processing
- Raw sequencing data (FASTQ files)
- A QC report
- A standard Loupe Browser visualization file (for 10x Genomics projects)
- Mapped count tables for downstream analysis
- A preliminary clustering analysis, done with the Seurat pipeline
- A preliminary differential gene expression analysis
Once we have sent you the data, we'll invite you to schedule a call with one of our scientists to go over any additional questions you may have.
That's when we can discuss any additional data analysis you may need.
FAQ
The price for a single-cell sequencing project depends on multiple factors and is mostly influenced by the technology, the number of samples, the number of cells per sample that you want to target, and the number of required sequencing reads per cell.
- For 10x Genomics, pricing typically starts at around €3100 per sample (excluding VAT) for academic customers.
- For SORT-seq, pricing starts at around €1320 per sample (excluding VAT) for academic customers.
- For VASA-seq, pricing typically starts at around €2400 per sample (excluding VAT) for academic customers.
Complete the form on this page to receive a more detailed overview of our pricing, or schedule a call with one of our specialists to receive a more detailed offer for your project.
That depends on your biological question, sample type, and budget. Feel free to schedule a free intake meeting with us to discuss your project in more detail. We'll make sure to advise you on the best platform for your project.
We accept cryopreserved and methanol-fixed samples for the 10x Genomics 3’ Single Cell Gene Expression services.
For the 10x Genomics 5’ Single Cell Immune Profiling service, we accept cryopreserved cells.
If you choose SORT-seq, you send the filled cell-capture plates back to us on dry ice.
While this is possible in principle, it will likely require some batch effect correction. Different technologies will yield slightly different results due to technology-specific technical quirks and other biases. However, with batch effect correction and a clear biological difference between the different populations in your samples, it should be possible to mix with data from other platforms.
All our single-cell sequencing services include a preliminary data analysis. We map the data and perform a preliminary cluster analysis and differential gene expression analysis, so you can get started with your data right away.
If you need more help, we can discuss setting up a tailor-made data analysis project to make sure we answer your biological question.
Some of our customers
Not sure which technology to choose? Use our Single-cell Sequencing Buying Guide to get clear instant advice.
Bastiaan Bijl
Head of Business Development
Not sure what technology is right for you?
Contact us for advice.