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Comprehensive single cell transcriptome lineages of a proto-vertebrate

ABSTRACT: Comprehensive single cell transcriptome lineages of a proto-vertebrate

PROVIDER: PRJNA542748 | ENA |

REPOSITORIES: ENA

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Comprehensive single cell transcriptome lineages of a proto-vertebrate

Project description:Studies of ascidian (sea squirt) embryos have highlighted the importance of cell lineages in animal development for over 100 years. As simple proto-vertebrates, they are also used to explore the evolutionary origins of novel cell types, such as cranial placodes and neural crest in vertebrates. To build upon these efforts we have determined comprehensive single cell transcriptomes of Ciona intestinalis throughout embryogenesis. More than 90,000 cells from 10 different developmental stages were examined, spanning the entirety of morphogenesis, from the onset of gastrulation at the 110-cell stage to the hatching of swimming tadpoles. This represents an average of over 12-fold coverage for every cell at every stage of development, owing to the small cell numbers that are a hallmark property of ascidian embryogenesis. Single cell transcriptome trajectories were used to construct “virtual” cell lineage maps, which confirm and extend those determined by conventional labeling methods. These datasets were also used to reconstruct regulatory cascades and provisional gene networks for a variety of cell types, including nearly 40 different neuronal subtypes comprising the larval nervous system. We summarize several applications of these datasets, including the identification of individual transcriptomes within the complete synaptome of swimming tadpoles, visualizing dynamic changes in gene expression during the birth, migration, and axogenesis of defined neurons, and the evolution of novel cell types such as the vertebrate telencephalon.

2019-07-08 | GSE131155 | GEO

Comprehensive single-cell transcriptome lineages of a proto-vertebrate.

Project description: Not available

| S-EPMC6978789 | biostudies-literature

Reprogramming the CNS of the Proto-Vertebrate Ciona intestinalis Using Single-Cell Transcriptomics

Project description:Reprogramming the CNS of the Proto-Vertebrate Ciona intestinalis Using Single-Cell Transcriptomics

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Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

Project description:Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

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An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution

Project description:Neural crest cells (NCCs) are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here, we utilized single-cell transcriptomic analyses to delineate NCC-derivatives along the posterior developing vertebrate, zebrafish, during the late embryonic to early larval stage, a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC-derived cell-types including mesenchyme, neural crest, neural, neuronal, glial, and pigment, from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages, mesenchyme subtypes, and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes, with distinct profiles within neuronal cells. From these analyses, we present a comprehensive cell-type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation.

2021-02-16 | GSE152906 | GEO

Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding

Project description:A fundamental interest in developmental neuroscience is to map the complete single-cell lineages within the brain. We developed a CRISPR editing-based lineage specific tracing (CREST) method for clonal tracing in Cre mice. We combined two complementary strategies to map the comprehensive single-cell lineage landscape in developing mouse brain. Applying snapCREST (snapshotting CREST) in mouse ventral midbrain (vMB), we constructed a spatiotemporal lineage landscape spanning the major developmental stage of vMB. Specifically, we identified six progenitor archetypes that could represent principal clonal fate of individual vMB progenitors, whose progenies showed restricted and graded distribution along the dorsal-ventral axis. We uncovered subregion-specific relationship between glutamatergic and GABAergic neurons and identified three distinct clonal lineages in the floor plate that specified glutamatergic neurons, dopaminergic neurons, or both neuronal types. We further created pandaCREST (progenitor and derivative associating CREST) by combining CREST, ex vivo organoid culture, and clonal splitting strategy to associate the transcriptome of progenitor cells in vivo with their differentiation potentials. Using pandaCREST, we identified multiple developmental origins of dopaminergic neurons and demonstrated that the fate potential of a transcriptome-defined progenitor type reflects the composite potentials of individual progenitors, each with distinct clonal fate and molecular signatures. Thus, the CREST method and strategies allow comprehensive single-cell lineage analysis that could offer new insights into the molecular programs underlying neural specification.

2023-05-01 | GSE210139 | GEO

Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution.

Project description: Not available

| S-EPMC8302630 | biostudies-literature

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

Project description: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.

2018-04-28 | GSE113074 | GEO

vertebrate gut metagenome

Project description:vertebrate gut metagenome Metagenome

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Single-cell RNA-seq transcriptome profiling of Prdm1+ lineages in E9.5 mouse placenta

Project description:Our goal was to transcriptionally profile Prdm1+ cell lineages of maternal and embryonic origin in mid-gestation mouse placenta in order to study vascular mimicry and additional processes in the placenta. Profiling of 61 single cells and 17 clusters of 2 or 3 cells chosen based on expression of Prdm1, a paternally inherited Prdm1-Venus fluorescent reporter, progenitor trophoblast marker Gjb3 and spiral artery trophoblast giant cell marker Prl7b1.

2016-03-14 | E-GEOD-74406 | biostudies-arrayexpress

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