The dynamics of gene expression in vertebrate embryogenesis at single cell resolution

James A Briggs, Caleb Weinreb, Daniel E Wagner, Sean Megason, Leonid Peshkin, Marc W Kirschner*, Allon M Klein*‚Äč

Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
*Correspondence to:;


Time series of single cell transcriptome measurements can reveal dynamic features of cell differentiation pathways. From measurements of whole frog embryos spanning zygotic genome activation through early organogenesis we derived a detailed catalog of cell states in vertebrate development and a map of differentiation across all lineages over time. The inferred map recapitulates most if not all developmental relationships, and associates new regulators and marker genes with each cell state. We find that many embryonic cell states appear earlier than previously appreciated; we also assess conflicting models of neural crest development. Incorporating a matched time series of zebrafish development from a companion paper, we reveal conserved and divergent features of vertebrate early developmental gene expression programs.

Review of the Xenopus Jamboree
Lecture on single-cell transcriptomics in the Xenopus Embryo (James Briggs)
Overview of the single-cell field in light of embryology projects (Allon Klein)
Tutorial on using SPRING layout tool in the context of Xenopus embryology (Caleb Weinreb)

Reference SPRING plots

All stages

Tree view

Stage 8

Stage 10

Stage 11

Stage 12

Stage 13

Stage 14

Stage 16

Stage 18

Stage 20

Stage 22

Download data

Highly variable gene lists

IMPORTANT: All SPRING plots generated before 18/2/7 at 11AM

have been moved to a backup directory (HERE)

User generated SPRING plots

Sticky notes