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

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. 136,966 single cell transcriptomes were profiled from whole Xenopus tropicalis embryos at ten timepoints during the first 24 hours of its embryonic development. The data includes 75 total single cell RNA sequencing libraries, collected in 2 replicate timeseries. 4 of the 75 libraries focussed on dissected neural plate border tissue. The counts data for all pass filter cells are available in a single matrix (see "Corrected_combined.annotated_counts.tsv.gz" and "Raw_combined.annotated_counts.tsv.gz"). Alternatively, raw FASTQ or unfiltered counts files are also available for each individual library.