Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Briggs JA

PROVIDER: S-EPMC6038144 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Briggs James A JA Weinreb Caleb C Wagner Daniel E DE Megason Sean S Peshkin Leonid L Kirschner Marc W MW Klein Allon M AM

Science (New York, N.Y.) 20180426 6392

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 fi ...[more]

PMID: 29700227

Similar Datasets

Project description:This study presents statistical analyses of gene expression during all 40 developmental stages in the teleost Fundulus heteroclitus using four biological replicates per stage. Patterns of gene expression for 7,000 genes appear to be important as they recapitulate developmental timing. Among the 45% of genes with significant expression differences between pairs of temporally adjacent stages, significant differences in gene expression vary from as few as five to more than 660. Five adjacent stages have disproportionately more significant changes in gene expression (>200 genes) relative to other stages: four to eight and eight to sixteen cell stages, onset of circulation, pre- and post-hatch, and during complete yolk absorption. The fewest differences among adjacent stages occur during gastrulation. Yet, at stage 16 (pre-mid-gastrulation), the largest number of genes has peak expression. This stage has an over-representation of genes in oxidative respiration and protein expression (ribosomes, translational genes and proteases). Unexpectedly, among all ribosomal genes, both strong positive and negative correlations occur. Similar correlated patterns of expression occur among all significant genes. These data provide statistical support for the temporal dynamics of developmental gene expression during all stages of vertebrate development. A double-loop design was used for the microarray hybridizations, where each sample is hybridized to 2 arrays using both Cy3- and Cy5-labelled fluorophores (Kerr and Churchill 2001a; Kerr and Churchill 2001b). The loop consisted of Cy3- and Cy5-labelled embryo aRNAs from 4 biological pools for each of 40 stages (S). In total, 160 biological pools were hybridized to 80 microarrays. Each array had different combinations of biological pools (Altman and Hua 2006). The double loop formed was S1M-bM-^FM-^R S2 M-bM-^FM-^R S3M-bM-^FM-^R M-bM-^@M-& S40M-bM-^FM-^R S1 and S40M-bM-^FM-^R S39M-bM-^FM-^R S38M-bM-^FM-^R M-bM-^@M-& S2M-bM-^FM-^R S1 M-bM-^FM-^R S40, where each arrow represents a separate hybridization (array) with the biological pool at the base of the arrow labeled with Cy3 and the biological pool at the head of the arrow labelled with Cy5.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets