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Single-cell Genomics

Working with us

Led by: Dr Iain Macaulay

Enquiries: If you are interested in working with the Earlham Institute (EI) single-cell genomics team on a project or research, please contact us.

Single-cell genomics can reveal previously unseen heterogeneity in living systems. Measuring cell-to-cell genetic, epigenetic and transcriptomic variation is key to understanding how multicellular organisms - or populations of single-cell organisms - develop, function and evolve.

As cells are a fundamental unit of all living systems, single-cell genomics approaches can be applied across a wide range of research activities. At EI, we apply single-cell genomics to:

  • Investigate evolution in bacterial populations
  • Study meiosis in plant pollen
  • Understand blood stem cell biology in health and under stress
  • Explore genomic and transcriptomic heterogeneity in cancer

Whether you are looking for research collaboration, contract research or training on single-cell platforms, our expert team - led by Technical Development Group Leader, Dr Iain Macaulay - provides access to cutting-edge cell sorting and single-cell genomics infrastructure and expertise.

To discuss a project or collaboration, get in touch with us today.

From cells to analysis

We can support all stages of a single-cell genomics analysis, from cell isolation, to library preparation, sequencing and analysis. If you are starting with tissue, sorted cells or even pre-made libraries, we have the platforms and expertise to support your project.

Image: A flowchart diagram explaining how to work with the single cell team

Our platforms for single-cell isolation

Housed in Biosafety Level 2 Labs, EI has a number of platforms for single-cell isolation for sequencing.

High-throughput single-cell sequencing.

The industry standard for single-cell analysis, the Chromium platform supports protocols for 3’ and 5’ RNA-sequencing (including V(D)J immune cell profiling) as well as ATAC-seq, CITE-seq and multi-omic profiling.

Simplified cell sorting with advanced capabilities.

Our instrument has a three laser configuration - Violet (405 nm), Blue (488 nM), Red (640 nm) and index sorting capability. We routinely use this for fast sorting of single-fluorophore samples (e.g. GFP+ cell selection) or multiparameter single-cell sorts into 96- and 384- well plates for downstream genomic or transcriptomic analysis. We also perform enrichment sorts before single-cell (or single nucleus) analysis on the 10X Genomics Chromium platform.

Advanced cell sorting enabling high parameter single-cell sorting.

Our advanced cell sorter has a five laser configuration - UV (355nm), Yellow-Green (561nm), Violet (405 nm), Blue (488 nM), Red (640 nm) and index sorting capability. Enabling up to 20-parameter sorts, the Fusion can be used to isolate extremely rare cells from complex populations, for example blood stem and progenitor cells or different immune cell populations. This instrument can sort into 96- and 384- well plates and can also be used for enrichment sorts before single-cell analysis on the 10X Genomics Chromium Instrument.

Isolation of single cells or microbiopsises from tissue sections.

Our laser microdissection platform can image and cut individual cells, or regions of interest, from tissue sections and collect them in tubes or 96-well plates for downstream analysis. The instrument is a fluorescence microscope, equipped with three fluorescence channels (DAPI, GFP and Cy3/RFP) and high magnification lenses (up to 150X) allowing fine dissection of regions or cells of interest.

Cell sorting and imaging in paralell.

Our cellenONE instrument is similar to FACS, but overcomes some of the challenges encountered when sorting larger, or more fragile cells. Using a glass capillary, individual cells are imaged and gently dispensed into an array of substrates, including 96- and 384- well plates. The instrument is also equipped with four fluorescence channels (DAPI, GFP, Cy3/RFP and Cy5) enabling live/dead cell selection and isolation of rare cell populations. As the instrument sorts, it images each cell, and so some information about cell phenotype can be associated with any downstream sequencing.

Our single-cell sequencing workflows

After cell isolation, we have a number of workflows to generate, sequence and analyse single-cell libraries.

Why work with us

Incorporating EI's single-cell genomics in your projects will provide:

  • Access to a wide range of platforms to support different sample types - whether it is a standard 10X Genomics RNA-seq experiment, or something more bespoke, we will be able to help
  • Experiments run by a dedicated team of experienced single-cell biologists - we have over ten years experience with cell sorting for single-cell and genomics applications, and have published a number of high impact papers and key technical developments in this field
  • Additional support and expertise from EI’s Genomics Pipelines team - from sample receipt to sequencing, all processing is taken care of under one roof. Advanced next-generation sequencing capability and expertise are on hand

Iain and the team at the Earlham Institute gave us great confidence. Our project involved sequencing of single cells to determine transcription profiles, which can be quite expensive, so we wanted to get it right the first time.

They are a great team to work with and were happy to go that bit further to give us the best possible service. We will do more work with the team and look forward to future projects.

Andrew Gane, Product Strategy and Technology Manager, Genomics and Diagnostics Solutions, Cytiva

Learn more about single-cell genomics at Earlham Institute