- Dedicated service provider
We are the one-stop-shop for all single-cell sequencing projects.
- Continued support
We make sure to provide continuous support.
- Cost-effective services
We work with you to make sure you don't have to break the bank.
- Expert team
We have been running 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 two of those solutions as a complete service: Single Cell Gene Expression and Single Cell Immune Profiling.
Read more about these solutions below.
The two different 10x Genomics products we offer have different applications and uses.
SINGLE-CELL GENE EXPRESSION
The Single Cell Gene Expression solutions 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 sequencing solution is highly suitable for larger projects, that require data for a few thousand cells per sample.
What you can do with our 10x Genomics Single Cell Gene Expression service:
- Obtain 3’ single-cell transcriptomics data from cryopreserved and methanol-fixed samples
- Aim to target between 3,000 and 10,000 cells
- Choose your amount of reads per cell for the 3’ Gene Expression Library: between 30,000 and 80,000 reads per cell. 50,000 reads per cell is the most popular.
- Compatible with single cells or nuclei*
*Not applicable to all tissues, sample types, and projects: please contact us to discuss this option.
SINGLE-CELL IMMUNE PROFILING
The Single Cell Gene Expression 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.
What you can do with our 10x Genomics Single Cell Immune Profiling service:
- Obtain 5’ single-cell transcriptomics data and the immune repertoire
- Aim to target between 3,000 and 10,000 cells
- Choose the additional Immune Profiling Libraries: BCR, TCR and/or Cell Surface Library
- Choose your amount of reads per cell for the 5’ Gene Expression Library: between 30,000 and 80,000. 50,000 reads per cell is the most popular
- Choose your amount of reads per cell for the Immune Profiling Library: 5,000 reads per cell is recommended per Immune Profiling Library
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?
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.
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.
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.
Complete the form below and receive information on our pricing and services.
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.
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 SORT-seq, pricing starts at around €1100 per sample (excluding VAT) for academic customers.
For 10x Genomics, pricing typically starts at around €3000 per sample (excluding VAT) for academic customers.
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.