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Early transcriptional similarities between two distinct neural lineages during ascidian embryogenesis

ABSTRACT: Early transcriptional similarities between two distinct neural lineages during ascidian embryogenesis

PROVIDER: PRJNA1023890 | ENA |

REPOSITORIES: ENA

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Early transcriptional similarities between two distinct neural lineages during ascidian embryogenesis

Project description:In chordates, the central nervous system arises from precursors that have distinct developmental and transcriptional trajectories. Anterior nervous system is ontogenically associated with ectoderm lineages while posterior nervous systems are associated with mesoderm. Taking advantage of the well-documented cell lineage of ascidian embryos, we addressed how early similarities in the transcriptional states of the different neural lineages become apparent. We performed single-cell RNA sequencing (scRNA-seq) analyses of hand-dissected neural precursor cells of these lineages, together with those of their sister cell lineages, with a high temporal resolution covering five successive cell cycles from 16-cell to neural plate stages. A transcription factor binding site enrichment analysis of neural specific genes at the neural plate stage revealed limited evidence for shared transcriptional control between the two neural lineages, consistent with their different ontogenies. Nevertheless, PCA analysis and hierarchical clustering showed that, by neural plate stages, the two neural lineages cluster together. Consistent with this, we identified a set of genes enriched in both neural lineages at the neural plate stage.

2025-01-29 | GSE244615 | GEO

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

Lipidomics Reveals Cell Specific Changes During Pluripotent Differentiation to Neural and Mesodermal Lineages

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COMMD10 is essential for neural plate development during embryogenesis

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Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages

Project description:Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages

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Identification of Setdb1 interaction proteins in neural stem cells

Project description:Setdb1 is an epigenetic factors catalyzing modification of H3K9me3. Expression of its gene is localized to embryonic neural cells during vertebrate embryogenesis, suggesting its role in regulating neural stemness. The project is to identify the interaction partners of Setdb1, by which Setdb1 regulates neural stemness in neural stem cells.

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Single-cell transcriptomic analysis of Sox17-expressing lineages reveals dynamic developmental trajectories and distinct gene regulatory networks during embryogenesis

Project description:As Sox17 plays a critical role in the development of multiple cell types during early embryogenesis, we utilized a dual-color lineage-tracing strategy in combination with single-cell RNA sequencing (scRNAseq) to capture and analyze Sox17-expressing lineages. GFP production from Sox17GFPCre allele marks cells that currently express Sox17 or short-term progeny of Sox17 expressing progenitors. TdTomato production from R26LSL.TdTomato reporter allele in the presence of Sox17GFPCre marks long-term progeny of Sox17-expressing progenitors. In brief, GFP and Tdtomato positive cells were isolated from E9.5 embryos of specific genotypes to generate two separate scRNAseq datasets, referred to in the manuscript as the GFP and TdTomato datasets, respectively.

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Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages [scRNA-seq]

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