• Research

Single-cell sequencing at Earlham Institute

Developing and applying new technology to decode life at the single-cell level.

Project summary.

Led by: Macaulay Group

Duration: Ongoing

Multi-cellular organisms like plants, mice and humans contain many billions – often trillions - of cells, all of which originate from a single cell, or zygote, after fertilisation. As the organism develops from the zygote, cells make changes to their gene expression profiles, a process termed differentiation, allowing them to fulfil diverse and unique tasks throughout the organism.

Next generation sequencing (NGS) typically analyses pools of thousands, or even millions of single cells – and much of the detail and complexity of the cellular populations within these pools is lost. Single cell genomics approaches allow us to apply NGS technologies to the tiny amounts of DNA (genome) and RNA (transcriptome) that can be found in a single cell.

Currently, most single cell genomics work focuses on the transcriptome – to study the diversity of cell types arising during development and differentiation of the organism, as the cells make changes to the genes they express. By sequencing the transcriptomes of many individual cells, we can explore how many different cell types there are in an organism. We can also start to learn something about the function of those different cell types by looking at the kinds of genes they express.

By sequencing the genomes of single cells, we can learn about the mutations that that cell may have gained during development – this technology is particularly useful in teasing apart how cancer cells have ‘evolved’ within a patient. We can also use single cell sequencing approaches to study diversity in the epigenomes of single cells, by examining DNA methylation.

At EI, we are developing single cell approaches to apply across a wide range of species – from microbial populations to plants and mammals. One of the main technical focuses of single cell genomics research at EI is the integration of data types, so that we can, in parallel, understand gene expression and regulation within a single cell.



We have a number of commercial platforms for isolation and library preparation of single cells, including the Fluidigm C1 and the Chromium from 10x Genomics.

The C1 platform is capable of isolating 96 single cells and performing a diverse array of molecular biology protocols - including full-length mRNA-seq and ATAC-seq. The Chromium platform can isolate several thousand single cells in an experiment and rapidly generate 3’ mRNA sequencing libraries.


We have also implemented a number of single cell protocols, including Smart-seq2 for full-length mRNA-seq of single cells, as well as a range of protocols for whole genome amplification from single cell.

Technical Development

The technical development group is focussed on developing ‘multi-omics’ approaches for single cell (and low-input) samples - for example those which allow parallel analysis of the Genome and Transcriptome (G&T-seq) or the Methylome and Transcriptome (M&T-seq) of single cells. We aim to further expand the repertoire of single cell multi-omics approaches and develop methods that reveal a more detailed regulatory picture of biology at single cell resolution.


Single cell genomics: advances and future perspectives

Macaulay, I. C. & Voet, T., PLoS Genet 10, e1004126, doi:10.1371/journal.pgen.1004126 (2014).

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

Macaulay, I. C. et al., Nat Methods 12, 519-522, doi:10.1038/nmeth.3370 (2015).

Impact statement.

Single cell sequencing can reveal the complexity of the cell types that make up multicellular life - allowing us to understand how living systems develop and how they respond to disease.

Related reading.