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SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression

ABSTRACT: SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression

PROVIDER: PRJNA1061516 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27430847.fastq.gz	Fastqsanger.gz
	SRR27430848.fastq.gz	Fastqsanger.gz
	SRR27430849.fastq.gz	Fastqsanger.gz
	SRR27430850.fastq.gz	Fastqsanger.gz
	SRR27430851.fastq.gz	Fastqsanger.gz

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SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression [ChIP-seq]

Project description:Here we investigate a functional role for SoxB1 transcription factors, Sox2 and Sox3, on the transient embryonic cell population, the neural plate border. We find through gain/loss-of-function studies necessary for neural plate border cells to become neural crest cells. and genomics experiments (ChIP-seq and RNA-seq) that SoxB1 transcription factors directly promote neural plate border formation. and that down-regulation of SoxB1 expression is

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SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression [RNA-seq]

Project description:SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression [RNA-seq]

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SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression [ChIP-seq]

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SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression

Project description:This SuperSeries is composed of the SubSeries listed below.

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Segregation of neural crest specific lineage trajectories from a heterogeneous neural plate border territory only emerges at neurulation

Project description:The epiblast of vertebrate embryos is comprised of neural and non-neural ectoderm, with the border territory at their intersection harbouring neural crest and cranial placode progenitors. Here we profile avian epiblast cells as a function of time using single-cell RNA-seq to define transcriptional changes in the emerging ‘neural plate border’. The results reveal gradual establishment of heterogeneous neural plate border signatures, including novel genes that we validate by fluorescent in situ hybridization. Developmental trajectory analysis shows that segregation of neural plate border lineages only commences at early neurulation, rather than at gastrulation as previously predicted. We find that cells expressing the prospective neural crest marker Pax7 contribute to multiple lineages, and a subset of premigratory neural crest cells shares a transcriptional signature with their border precursors. Together, our results suggest that cells at the neural plate border remain heterogeneous until early neurulation, at which time progenitors become progressively allocated toward defined lineages.

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Single cell RNA-sequencing of induced Neural Plate Border Stem Cells

Project description:We describe a so far uncharacterized, embryonic and self-renewing Neural Plate Border Stem Cell (NBSC) population with the capacity to differentiate into central nervous and neural crest lineages. NBSCs can be obtained by neural transcription factor-mediated reprogramming (BRN2, SOX2, KLF4 and ZIC3) of human adult dermal fibroblasts and peripheral blood cells (induced Neural Plate Border Stem Cells, iNBSCs) or by directed differentiation from human induced pluripotent stem cells (NBSCs). Moreover, human (i)NBSCs share molecular and functional features with an endogenous NBSC population isolated from neural folds of E8.5 mouse embryos. Upon differentiation, iNBSCs give rise to either (1) radial glia-type stem cells, dopaminergic and serotonergic neurons, motoneurons, astrocytes, and oligodendrocytes or (2) cells from the neural crest lineage. Here we provide single cell RNA-sequencing data of six iNBSC lines (310 cells total). iNBSCs were single-cell-sorted and RNA sequencing was performed following the Smart-seq2 protocol. This dataset further supports the notion that iNBSC cultures mainly consist of stem cells with a molecular and functional neural plate border-like identity and a minor fraction of cells that show signs of some spontaneous differentiation towards sensory neurons.

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Single cell RNA-sequencing of primary mouse Neural Plate Border Stem Cells

Project description:We describe a so far uncharacterized, embryonic and self-renewing Neural Plate Border Stem Cell (NBSC) population with the capacity to differentiate into central nervous and neural crest lineages. NBSCs can be obtained by neural transcription factor-mediated reprogramming (BRN2, SOX2, KLF4, and ZIC3) of human adult dermal fibroblasts and peripheral blood cells (induced Neural Plate Border Stem Cells, iNBSCs) or by directed differentiation from human induced pluripotent stem cells (NBSCs). Moreover, human (i)NBSCs share molecular and functional features with an endogenous NBSC population isolated from neural folds of E8.5 mouse embryos. Upon differentiation, iNBSCs give rise to either (1) radial glia-type stem cells, dopaminergic and serotonergic neurons, motoneurons, astrocytes, and oligodendrocytes or (2) cells from the neural crest lineage. Here we provide single cell RNA-sequencing data of two primary mouse Neural Plate Border Stem Cell Lines (pNBSCs). pNBSCs were single cell sorted and RNA sequencing was performed following the Smart-seq2 protocol. In sum, pNBSCs and iNBSCs share a similar regional identity, expression signature and analogous differentiation dynamics on the single-cell-level, suggesting the presence of a transient, NBSC-like progenitor during the neurulation stage of mouse and likely also human embryos.

2018-12-20 | E-MTAB-6925 | biostudies-arrayexpress

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Project description:We describe a so far uncharacterized, embryonic and self-renewing Neural Plate Border Stem Cell (NBSC) population with the capacity to differentiate into central nervous and neural crest lineages. NBSCs can be obtained by neural transcription factor-mediated reprogramming (BRN2, SOX2, KLF4, and ZIC3) of human adult dermal fibroblasts and peripheral blood cells (induced Neural Plate Border Stem Cells, iNBSCs) or by directed differentiation from human induced pluripotent stem cells (NBSCs). Moreover, human (i)NBSCs share molecular and functional features with an endogenous NBSC population isolated from neural folds of E8.5 mouse embryos. Upon differentiation, iNBSCs give rise to either (1) radial glia-type stem cells, dopaminergic and serotonergic neurons, motoneurons, astrocytes, and oligodendrocytes or (2) cells from the neural crest lineage. Here we provide array-based expression data of (i)NBSCs and CNS- and neural crest progeny derived thereof. The former comprise radial glia-type stem cells, while the latter are neural crest and mesenchymal stem cell-like cells. The data provided reveal that (i)NBSCs can be directed into defined neural lineages and that iNBSCs pass through successive developmental stages. These data support the notion that it is possible to reprogram human adult cells into expandable, multipotent NBSCs that define a novel embryonic neural stem cell population in human and mouse.

2018-12-20 | E-MTAB-5804 | biostudies-arrayexpress

RNA Expression profiling of primary mouse Neural Plate Border Stem Cells, differentiated progeny and biological controls

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