Home Services Single Cell Genomics: DropSeq

The Princess Margaret Genomics Centre is proud to announce we are now offering single cell RNA-seq services using the DropSeq protocol. We have assembled our own DropSeq system following the instructions from the McCarroll lab.

Pricing: Please inquire

Contact: Troy Ketela ( )

PMGC DropSeq System
  • The PMGC has built a DropSeq system based on the protocols published by the McCarroll laboratory
  • We have used the system to profile a diverse range of cell types.

FlowJEM DropSeq Flow Cell
  • The PMGC obtains flow cells for running DropSeq from a local Toronto company FlowJEM.
  • The chips contain 26 discrete DropSeq flow cells - each for one time use.

How many cells do I need to use the DropSeq system?

We typically capture between 1,000 and 5,000 cells with our DropSeq system. Unlike the 10X Genomics Chromium, DropSeq uses a double Poisson distribution and as such is not as efficient at capturing cells. We generally ask customers to have at least 200,000 cells to start with.

Does the DropSeq protocol cover the entire transcript or only the 3' ends?

The DropSeq 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 DropSeq 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. Please contact us for more accurate pricing.

Do you provide training to use your DropSeq system?

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.