Making single-cell biology work

New collaboration between EMBL-EBI, the Wellcome Trust Sanger Institute and Fluidigm keeps research and technology on the cutting-edge of single-cell genomics

Luis Saraiva, EMBL-EBI
Single olfactory sensory neuron cell captured in the Fluidigm C1 system

A formal collaboration was announced today between the Wellcome Trust Sanger Institute, the European Bioinformatics Institute (EMBL-EBI) and Fluidigm Corporation to accelerate the development of new methods for the analysis of single-cell genomics data.

The Single Cell Genomics Centre (SCGC) on the Wellcome Trust Genome Campus will work with onsite Fluidigm senior staff to ensure that the centre has early access to the latest equipment, workflows and methods for genomics and proteomics research.

“Because we have early access to the most advanced technology, we can develop new experimental and computational methods that help us understand what is happening in each of our cells, at different points in the cell cycle. This is really a new frontier – we hope the work we do will help the technology mature more quickly, so that it can help more people find answers to complex biological questions.”

Dr Sarah Teichmann of EMBL-EBI and the Sanger Institute

In addition to technology advancements The collaboration will make single-cell research more accessible to the greater research community by developing and disseminating new workflows, bioinformatics tools, and data sets.

The collaboration builds on previous work between Fluidigm and founding members of the SCGC. For example, the Teichmann group discovered that immune cells produce steroids to regulate themselves – knowledge based on mRNA-seq data from single cells prepared by Fluidigm technology. Using single-cell gene expression data from Fluidigm’s C1TM Single-Cell Auto Prep system and sequencing technology, John Marioni’s group at EMBL-EBI developed a novel statistical method that shows how single-cell mRNA sequencing can be used to pinpoint true differences between cells in apparently homogeneous samples. Thierry Voet, based at KU Leuven and an associate member of Faculty at the Sanger Institute, uses DNA sequencing at the single-cell level to understand how spontaneous variations in DNA can arise as cells divide.

“Our work with the SCGC is about co-creating a solid foundation for a revolution in biological understanding that will come from single-cell analysis. Together, we can build better informatics tools to extract relevant biology from the massive amounts of single-cell RNA expression data that our systems generate. We’ll also find innovative ways to determine the DNA, protein, RNA, and epigenetic state of each cell and to scale the process up to perform across thousands and millions of cells.”

Robert C Jones, Fluidigm Executive Vice President of Research and Development

These high-throughput techniques allow researchers to explore cellular heterogeneity in normal development and in disease at the single-cell level, offering a vast improvement over the current practice of investigating millions of cells in bulk. Until now, scientists have been limited in their ability to identify functionally distinct subpopulations of cells and understand their contribution into the development of diseases such as cancer. DNA-seq and RNA-seq techniques are opening up new opportunities to discover and explore the diverse nature of cells at the highest possible resolution.

More information

Fluidigm Technology

The Single-Cell Genomics Centre employs Fluidigm’s C1 Single-Cell Auto Prep and BiomarkTM HD systems, and has access to Fluidigm’s CyTOF® mass spectrometry technology as well.


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Selected websites

  • EMBL- European Bioinformatics Institute

    The European Bioinformatics Institute is part of EMBL, Europe’s flagship laboratory for the life sciences. EMBL-EBI provides freely available data from life science experiments covering the full spectrum of molecular biology. While we are best known for our provision of bioinformatics services, about 20 per cent of our institute is devoted to basic research. Our extensive training programme helps researchers in academia and industry to make the most of the incredible amount of data being produced every day in life science experiments. We are a non-profit, intergovernmental organisation funded by EMBL member states. Our 540 staff represent 55 nationalities, and we welcome a regular stream of visiting scientists throughout the year.

  • Fluidigm

    Fluidigm (NASDAQ:FLDM) develops, manufactures, and markets life science analytical and preparatory systems for growth markets such as single-cell biology and production genomics. We sell to leading academic institutions, clinical laboratories, and pharmaceutical, biotechnology, and agricultural biotechnology companies worldwide. Our systems are based on proprietary microfluidics and multi-parameter mass cytometry technology, and are designed to significantly simplify experimental workflow, increase throughput, and reduce costs, while providing excellent data quality. Fluidigm products are provided for Research Use Only. Not for use in diagnostic procedures.

  • The Wellcome Trust Sanger Institute

    The Wellcome Trust Sanger Institute is one of the world’s leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease.

  • The Wellcome Trust

    The Wellcome Trust is a global charitable foundation dedicated to achieving extraordinary improvements in human and animal health. We support the brightest minds in biomedical research and the medical humanities. Our breadth of support includes public engagement, education and the application of research to improve health. We are independent of both political and commercial interests.