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Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation [scRNASeq]

ABSTRACT: Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation [scRNASeq]

PROVIDER: PRJNA913169 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22779145.fastq.gz	Fastqsanger.gz
	SRR22779146.fastq.gz	Fastqsanger.gz
	SRR22779147.fastq.gz	Fastqsanger.gz
	SRR22779148.fastq.gz	Fastqsanger.gz
	SRR22779149.fastq.gz	Fastqsanger.gz

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Similar Datasets

Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation [scRNASeq]

Project description:The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like cells is obtained. We monitored transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. Here we show maintenance of pluripotency-signature (Nanog/Oct4-PouV/Klf4-positive) in undecided pan-ectodermal stem-cells spanning the entire ectoderm late during neurulation with ectodermal patterning completed only at the end of neurulation when the pluripotency-signature becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency-signature is found at all axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond “ectodermal-capacity” in chick and mouse embryos.

2023-03-02 | GSE221188 | GEO

Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation

Project description:Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation

| PRJNA971972 | ENA

Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation [bulk_RNASeq]

Project description:Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation [bulk_RNASeq]

| PRJNA913002 | ENA

Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation

Project description:The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like cells is obtained. We monitored transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. Unexpectedly, we find maintenance of undecided Nanog/Oct4-PouV/Klf4-positive pluripotent-like pan-ectodermal stem-cells spanning the entire ectoderm late in the neurulation process with ectodermal patterning completed only at the end of neurulation when pluripotency becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency is found at all axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond “ectodermal-capacity” in chick and mouse embryos.

2023-08-28 | GSE232432 | GEO

Maintenance of pluripotency in the entire ectoderm enables neural crest formation and challenges dogmatic viewpoints of gastrulation

Project description:Maintenance of pluripotency in the entire ectoderm enables neural crest formation and challenges dogmatic viewpoints of gastrulation

| PRJNA913168 | ENA

Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation [bulk_RNASeq]

2023-03-02 | GSE221125 | GEO

10x single cell RNAseq of chick ectoderm from stages HH5 to ss4

Project description:The vertebrate ectoderm gives rise to a variety of cell lineages, including neural, neural crest, placodal and non-neural cell fates. How cell fates are specified at the neural plate border (the region surrounding the neural plate) is not fully understood. We therefore carried out 10x scRNAseq of the chick epiblast to investigate cell fate specification at the neural plate border. Embryos were dissected and pooled according to stage. The tissue was then dissociated and FAC sorted to remove dead cells and remaining doublets before cells were stored in MeOH. Due to the time required to dissect embryos, multiple rounds of collections were carried out, with collections from the same stage pooled prior to 10x sequencing. Libraries were sequenced using an Illumina HiSeq 4000 at the Francis Crick Institute, London. This collection was a follow up to E-MTAB-10408.

2023-08-25 | E-MTAB-11444 | biostudies-arrayexpress

A Molecular Atlas of the Developing Ectoderm Defines Neural, Neural Crest, Placode and Non-Neural Progenitor Identity in Vertebrates.

Project description:During vertebrate neurulation, the embryonic ectoderm is patterned into lineage progenitors for neural plate, neural crest, placodes and epidermis. Here, we use Xenopus laevis embryos to analyze the spatial and temporal transcriptome of distinct ectodermal domains in the course of neurulation, during the establishment of cell lineages. In order to define the transcriptome of small groups of cells from a single germ layer, and to retain spatial information, dorsal and ventral ectoderm was subdivided along the anterior-posterior and medial-lateral axes by microdissections. Principal Component Analysis on the transcriptomes of these ectoderm fragments primarily identifies embryonic axes and temporal dynamics. This provides a genetic code to define positional information of any ectoderm sample along the anterior-posterior and dorsal-ventral axes, directly from its transcriptome. In parallel, we use Non-Negative Matrix Factorization to predict enhanced gene expression maps onto early and mid-neurula embryos, and specific signatures for each ectoderm area. The clustering of spatial and temporal datasets allowed detection of multiple biologically relevant groups (e.g. Wnt signaling, neural crest development, sensory placode specification, ciliogenesis, germ layer specification). We provide an interactive network interface, EctoMap, for exploring synexpression relationships among genes expressed in the neurula, and suggest several strategies to use this comprehensive dataset to address questions in developmental biology as well as stem cell or cancer research.

2017-10-25 | GSE103240 | GEO

From neural border epithelium to neural crest emigration: A comprehensive single cell roadmap of the timing and regulatory logic underlying cranial and vagal neural crest emergence [scRNAseq]

Project description:Neural crest cells exemplify cellular diversification from a multipotent progenitor population. However, the full sequence of molecular choices governing the emergence of neural crest heterogeneity from the ectoderm remains elusive. Gene regulatory networks govern these steps of embryonic development and cell specification towards definitive neural crest. Here, we combine ultra-dense single cell transcriptomes with machine-learning strategies and experimental validation to provide a comprehensive gene regulatory network driving vertebrate neural crest fate diversification, from induction to early migration stages. Transcription factor connectome and bifurcation analyses demonstrate emergence of early neural crest fates at the neural plate stage, alongside an unbiased multipotent neural crest lineage persisting until after epithelial-mesenchymal transition. We also define a new and transient neural border zone state, preceding choice between neural crest and placodes during gastrulation. Theis combination of experimental tests, with Machine Learning broadly applicable to single cell transcriptomics, deciphers the circuits driving cranial and vagal neural crest formation and provides a general model for investigating vertebrate GRNs in development, evolution and disease.

2024-03-29 | GSE198491 | GEO

Maintenance of pluripotency-like signature in the entire ectoderm leads to neural crest stem cell potential.

Project description:The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like derivatives is obtained. Here, we monitor transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. We show maintenance of pluripotency-like signature (Nanog, Oct4/PouV, Klf4-positive) in undecided pan-ectodermal stem-cells spanning the entire ectoderm late during neurulation with ectodermal patterning completed only at the end of neurulation when the pluripotency-like signature becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency-like signature is found at multiple axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond "ectodermal-capacity" in chick and mouse embryos.

| S-EPMC10518019 | biostudies-literature

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