Macro photo focusing on a 96-plate in blue-teal tones

Single-cell and Spatial analysis

Platform Leads:

Iain Macaulay, Group Leader

Andrew Goldson, Platform Manager

Our single-cell platforms are strategically supported by BBSRC, part of UKRI, through the Transformative Genomics NBRI.

From isolation through to analysis

We can support all stages of a single- or multi-cell 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. 

Working with us

Whether you are looking for collaboration, contract research or training, our expert team provides access to cutting-edge cell sorting and single-cell genomics infrastructure and expertise.

Dr Sonia Fonseca in the single-cell labs demonstrating the Vizgen technology platform
Dr Iain Macaulay, Group Leader at the Earlham Institute and single-cell lead
Close up of the BD S8 Flow Cytometer

Our platforms for single-cell isolation

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

Spatial Transcriptomics

The Merscope is a state-of-the-art spatial genomics platform that enables the visualization and mapping of hundreds to tens of thousands of RNA species.

The instrument utilises the MERFISH (Multiplexed Error Robust Fluorescence In Situ Hydridization) technology to quantify and map the transcriptome of whole tissues down to a sub cellular level.

The Vizgen MERSCOPE equipment


High-throughput single-cell sequencing.

The latest in advanced single-cell analysis technology, the Chromium X 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. Chromium X has increased the capacity of the 10X system to enable loading of 16 samples and up to 20,000 cells per sample. The platform also has improved user interface and overall system stability.

Chromium X equipment

Cutting edge spectral imaging cell sorter.

We are one of the earliest adopters of this groundbreaking platform. Six imaging parameters enable pictures of each cell sorted to be captured in addition to the spectral 78 fluorescence channel detection from 5 lasers. Laser configuration - UV (355nm), Violet (405 nm), Blue (488 nM), Yellow-Green (561nm), Red (640 nm) and index sorting capability.

Imaging parameters captured can now isolate cells based on the morphology of specific cell types. The spectral capabilities facilitate autofluorescence exclusion and multiparameter analysis not previously possible on conventional flow cytometers.

This instrument can sort into 96- and 384- well plates as well as up to 6 population simultaneous sorting.

The BD S8 Discover

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.


Close up photo of the BDFACS Aria Fusion equipment

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.


The study presents an approach for single bacterial genomic analysis using FACS isolation of individual bacteria followed by whole-genome amplification and sequencing.

Cell sorting and imaging in parallel.

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.


Photo of the Cellenion equipment

Isolation of single cells or micro biopsies 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.

Close up on the eyepiece of the Leica microscope with a blurred out background

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