Fluidigm C1 Single Cell RNA-seq
Home Services Single Cell Genomics: Fluidigm RNA-seq

The Princess Margaret Genomics Centre is proud to announce we are now offering single cell RNA-seq services using the Fluidigm C1 system. The C1 system is ideally suited to the full length gene expression profiling of dozens of cells (up to 96 cells per sample. The C1 is an excellent platform for the analysis of morphologically homogeneous collections of cells. The full length transcript profiling allows for gene expression and alternative splicing information to be gathered.

Pricing: Please inquire

Contact: Neil Winegarden ( )

How many cells do I need to use the Fluidigm C1 system?

The Fluidgim C1 single cell solution is optimised to capture up to 96 cells currently. Typically you will want at least 50,000 to allow for efficient sample handling, washing and processing. Ultimately ~1,000 cells are loaded on the device in order to capture up to 96 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 Fluidigm C1 single cell RNA-seq protocol cover the entire transcript or only the 3' ends?

The Fluidgim C1 solution uses the Clontech SMARTer chemistry and as such provides full-length transcript information.

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 Fluidigm C1 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 $5,000 and $9,000 per sample (academic customers). Please contact us for more accurate pricing.

Can I get trained up to use your Fluidigm C1 instrument?

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.