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Towards Single Cell Genomics

Integration of multilayer soft lithography with next-generation sequencing in order to achieve transcriptome analysis of single cells.

Project Leaders Marco Marra , Carl Hansen
Project Co-Investigators Steven Jones , Martin Hirst , Sam Aparicio , Robert Holt
Involved Organizations
Funding Agencies

Empty chip



Microfluidic Chip Prototype

Coloured reagents being mixed within the microfluidic chip.

The technology we are developing will enable the application of next-generation DNA sequencing to the characterization of the transcriptomes of single cells. Our project represents a timely integration of multilayer soft lithography and next generation sequencing, which together have the potential to revolutionize genomics and the types of studies that use genomic approaches. While our long-term objective is to implement methods for genomic analysis of thousands of cells in parallel, our first and critical near term objective is to demonstrate that robust next generation sequencing libraries for transcriptome analysis can be made reproducibly from RNA extracted from single cells. To achieve our near-term objective, we have identified four specific aims that address separate outstanding technological challenges in single cell transcriptome analysis.


    These are:
  1. Construction and sequencing microRNA libraries prepared from RNA purified from single cells
  2. Construction and sequencing of SAGE libraries from RNA purified from single cells
  3. Construction and sequencing of whole transcriptome sequencing libraries from RNA purified from single cells
  4. Development of multiplexing strategies for high-throughput single cell profiling

Expected deliverables of this project are microfluidic devices designed to perform single cell manipulations in formats capable of interfacing with next generation sequencing devices. We will also produce protocols to allow replication of our procedures in other laboratories. We anticipate that translation of our technologies to the scientific, biotechnology and pharmaceutical industries will have profound consequences for several fields including biomarker discovery, drug development, environmental genomics, metagenomics and personalized medicine.

For all project related inquires please contact us.



Robyn Roscoe, Projects Leader
Genome Sciences Centre, BC Cancer Agency
Phone: (604)707-5900 x 5963
Fax: (604)876-3561