10X Genomics Single Cell RNA-seq
Home Services Single Cell Genomics: 10X Genomics

The Princess Margaret Genomics Centre is proud to announce we are now offering single cell RNA-seq services using the 10X Genomics Chromium system. The 10X system is ideally suited to the 3'-end gene expression profiling of thousands of cells (1,000-6,000 typically). Due to the ability to assay a large number of cells this is an excellent platform for the analysis of complex tissues and heterogeneous collections of cells.

Pricing: Please inquire

Contact: Neil Winegarden ( )

Service Includes:

  • Determination of cell viability and density by Countess
  • Cell washing and resuspension
  • Capture and encapsulation of cells (1,000 to 6,000 cells as specified by customer
  • cDNA amplfication
  • Illumina sequencing library preparation and quality check
  • Deep sequencing on the Illumina NextSeq 500 (depth determined by customer; typically 60,000 reads per cell)
  • Delivery of FASTQ files and QC results
We also offer an optional data analysis service for scRNA-seq.

Sample Requirements:

Ideally we request customers supply 50,000+ fresh cells with >90% viability. As such, it is critical that customers coordinate with the PMGC to arrange times for which we can receive samples so that they are processed immediately.

Single Cell RNA-seq is a lengthy process. Library construction takes 2-4 days, cluster generation and sequencing reads can take up to 2 weeks and pipeline processing and QC checks add at least another 2-3 days. Please plan your experiments with the expectation of at least one month lag time from sample submission to results acquisition. Delays exceeding this level will be reported at the onset of your project, or as soon as they arise.

How many cells do I need to use the 10X Genomics Chromium system?

The 10X Chromium single cell solution is optimised to work with between 1,000 and 6,000 cells. Typically you will want at least 50,000 to allow for efficient sample handling, washing and processing. Ultimately 2,000 to 12,000 cells are loaded on the device in order to capture 1,000 to 6,000 cells. We belive that as we become more familiar with the system that we will be able to reduce the sample requirement (and we will update this when we do).

Does the 10X single cell RNA-seq protocol cover the entire transcript or only the 3' ends?

The 10X Genomics Chromium system analyses the 3'-ends of transcripts. This leads to a more cost effective analysis of gene expression from thousands of cells.

How many genes are typically detected per cell in single cell RNA-seq?

The average number of genes detected per cell really depends on the cell type. Large, fast growing cells like those from culture or from tumours will often have 5,000 or more genes detected per cell on average. Primary immune cells that are smaller, and less transcriptionally active may only have 1,000 to 3,000 genes detected per cell.

What does a 10X single cell RNA experiment cost?

The cost depends on a lot of factors. For that reason we prefer to talk customers to understand exactly what they need. The number of cells analysed per sample and the number of sequencing reads per cell will greatly affect the cost. However due to the amount of data generated these experiments are indeed more costly than traditional RNA-seq. A "typical" experiment may cost between $4,000 and $10,000 per sample (academic customers). Please contact us for more accurate pricing.

Do you offer training to use your 10X Chromium machine?

Unfortunately due to the specialised nature of these instruments as well as the importance of them to our operation we do not allow researchers outside our core to operate the instruments themselves. If you would like to see the instruments to better understand how the techniques work we'd be happy to have you come by for a visit.

Can I talk to someone to get some help in setting up my experiment?

Absolutely, in fact we would prefer it. We offer free consultation to any potential customer. We are here to help. Please contact us and we'd be happy to meet in person, by phone or by Skype.