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Anatomy of a decision: mapping early development

last modified Nov 21, 2016 02:36 PM

A new atlas of gene expression during the earliest stages of life boosts studies of development - new study published in Nature led by CSCI researchers from the Gottgens Lab and the European Bioinformatics Institute (EMBL-EBI).

In the first genome-scale experiment of its kind, researchers have gained new insights into how a mouse embryo first begins to transform from a ball of unfocussed cells into a small, structured entity.

Gastrulation is the point when an animal’s whole body plan is set, just before individual organs start to develop. Understanding this point in very early development is vital to understanding how animals develop and how things go wrong. One of the biggest challenges in studying gastrulation is the very small number of cells that make up an embryo at this stage.

“If we want to better understand the natural world around us, one of the fundamental questions is, how do animals develop?” says Bertie Gottgens, Research Group Leader at the Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute. “How do you turn from an egg into an animal, with all sorts of tissues? Many of the things that go wrong, like birth defects, are caused by problems in early development. We need to have an atlas of normal development for comparison when things go wrong.”

Today, thanks to advances in single-cell sequencing, the team was able to analyse over 1000 individual cells of gastrulating mouse embryos. The result is an atlas of gene expression during very early, healthy mammalian development.

The study was made possible by a Wellcome Trust Strategic Award to study Gastrulation and by the Sanger/EBI Single Cell Genomics Centre.

Read moreEBI, University of Cambridge


RNAseq data are available in Array Express under accession numbers E-MTAB-4079 and E-MTAB-4026. Processed RNAseq data are also available at

Publication details:

Scialdone A, Tanaka Y, Jawaid W, Moignard V, Wilson NK, Macauly IC, Marioni JC, Gottgens B (2016). Resolving early mesoderm diversification through single-cell expression profilingNature (in press); published online 6 July. DOI: 10.1038/nature18633. Url: