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 or watch our webinar with 10x Genomics .
As a Certified Service Provider, we are trained on 10x Genomics' best practices. Each year, we undergo a recertification process.
The two different 10x Genomics products we offer have different applications and uses. Find out if one of these products matches your project with our single-cell sequencing buying guide
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
Key benefits of 10x Genomics
- Analyze thousands of cells per sample
The 10x Genomic system allows us to target thousands of cells per sample, resulting in a low cost per cell for high-throughput projects.
- Obtain multi-dimensional single-cell data
If you choose the 5’ Single Cell Immune Profiling solution, you can analyze the transcriptome, the T-cell and/or B-cell receptor repertoire, cell surface proteins, and antigen-specificity, all at single-cell level.
- You’re in good company
Currently, the 10x Genomics single-cell platform has been used in more than 1,000 peer-reviewed publications, so you are far from alone in using this technique. Whatever your biological question, chances are that 10x Genomics services will have been used on similar tissue or species.
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, our team carefully prepares them, either by thawing cryopreserved samples or rehydrating MeOH fixed samples.
Then we wash, filter and count each sample to ensure we load a high-quality cell suspension that meets the 10x requirements. We also verify the quality of the sample as we count.
Next, we load the cell suspension on the chip according to 10x Genomics specifications, along with barcoded beads and reagents.
The chip is placed in the 10x controller and we start the run to initialize single-cell isolation, barcoding, and transcript amplification.
Once the 10x run is finished, 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.
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.
As with all of our services, we provide ongoing support from our single-cell sequencing specialists. For each 10x Genomics project, we provide the following:
- Regular email updates during sample processing
- Raw sequencing data (FASTQ files)
- A standard Cell Ranger QC report
- A standard Loupe Browser visualization file (cloupe)
- 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.
We accept cryopreserved and methanol-fixed samples for the 3’ Single Cell Gene Expression services.
For the 5’ Single Cell Immune Profiling service, we accept cryopreserved cells.
If you are located close to our lab in Utrecht, the Netherlands, then we can discuss receiving a fresh sample as well.
That depends on your biological question and sample type. Typically, our customers target between 3,000 and 8,000 cells per sample. Schedule a call with one of our specialists to discuss your specific project.
That depends on your biological question. Typically, we recommend a sequencing depth between 30,000 and 70,000 reads per cell for 10x Genomics projects. Schedule a call with one of our specialists to discuss your options.
Ideally, we require a cell suspension with at least 0.5 million cells per sample. If you are unable to achieve that, please contact us to discuss the possibilities.
Yes, before you send us your sample, you can perform a FACS sort to enrich for your cell type of interest. Please bear in mind that we need enough cells to start with (see previous question).
Not sure if 10x Genomics is right for your project? Explore our other services.
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