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RNA sequencing of control and TBXT-depleted human NMP-like axial progenitors

ABSTRACT: RNA sequencing of control and TBXT-depleted human NMP-like axial progenitors

PROVIDER: PRJNA765373 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16014112_1.fastq.gz	Fastqsanger.gz
	SRR16014112_2.fastq.gz	Fastqsanger.gz
	SRR16014113_1.fastq.gz	Fastqsanger.gz
	SRR16014113_2.fastq.gz	Fastqsanger.gz
	SRR16014114_1.fastq.gz	Fastqsanger.gz

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RNA sequencing of control and TBXT-depleted human NMP-like axial progenitors

Project description:A Tetracycline (Tet)-inducible TBXT shRNA human embryonic stem cell (hESC) line was treated with WNT and FGF agonists in the presence and absence of Tet for three days to generate NMP-like axial progenitors

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Single cell RNA sequencing of in vitro differentiation NMP protocols

Project description:The mammalian embryos Caudal Lateral Epiblast (CLE) harbours bipotent progenitors, called Neural Mesodermal Progenitors (NMPs), that contribute to the spinal cord and the paraxial mesoderm throughout axial elongation. Here we performed a single cell analysis of different in vitro NMPs populations produced either from embryonic stem cells (ESCs) or epiblast stem cells (EpiSCs) and compared them to E8.25 CLE mouse embryos. In our analysis of this region our findings challenge the notion that NMPs can be defined by the exclusive coexpression of Sox2 and T at mRNA level. We analyse the in vitro NMP-like populations using a purpose-built Support Vector Machine (SVM) based on the embryo CLE and use it as a classification model to compare the in vivo and in vitro populations. Our results show that NMP differentiation from ESCs, leads to heterogeneous progenitor populations with few NMP-like cells, as defined by the SVM algorithm, whereas starting with EpiSCs, yields a high proportion of cells with the embryo NMP signature. We find that the population from which the Epi-NMPs are derived in culture contains a node-like population, which leads to suggest that this population probably maintains the expression of T in vitro and thereby a source of NMPs. In conclusion, differentiation of EpiSCs into NMPs reproduces events in vivo and suggests a sequence of events for the emergence of the NMPs population.

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Project description:We analysed the transcriptomes of human embryonic stem cells (hESCs) and in vitro derived axial progenitors.

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Axial Elongation of Caudalized Human Pluripotent Stem Cell Organoids Mimics Neural Tube Development [RNA-Seq]

Project description:During mammalian embryogenesis, axial elongation of the neural tube is critical for establishing the anterior-posterior body axis, but is difficult to interrogate directly because it occurs post-implantation. Here we report an organoid model of neural tube extension using human pluripotent stem cell (hPSC) aggregates that recapitulates the morphologic and temporal gene expression patterns of neural tube development. Axially extending organoids consisted of longitudinally elongated epithelial compartments and contained TBXT(+)SOX2(+) neuromesodermal progenitors, PAX6(+) Nestin(+) neural progenitor populations, and MEOX1(+) paraxial mesoderm populations. Wnt agonism stimulated axial extensions in a dose-dependent manner and elongated organoids displayed regionalized rostral-caudal HOX gene expression, with hindbrain (HOXB1) expression distinct from brachial (HOXC6) and thoracic (HOXB9) expression. CRISPR interference-mediated silencing of BMP inhibitors induced elongation phenotypes that mimicked murine knockout models, and knock-down of the downstream Wnt target, TBXT, increased neuroepithelial compartmentalization and resulted in multiple extensions. These results indicate the potent morphogenic capacity of hPSC organoids to undergo axial elongation in a manner that can be used to dissect the cellular organization and patterning decisions that dictate early human nervous system development.

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Axial progenitors generate trunk neural crest cells in vitro

Project description:The in vitro generation of neural crest (NC) cells from human pluripotent stem cells (hPSCs) is a valuable approach to study human NC biology and isolate NC derivatives for disease modelling/regenerative medicine applications. However, conventional differentiation protocols induce only a modest yield of NC cells corresponding to the trunk level. Here we show that trunk NC cells and, their downstream derivatives, sympathoadrenal progenitors, can be produced at a high efficiency from hPSC-derived axial progenitors, the in vitro counterparts of the posteriorly-located drivers of embryonic axis elongation. Moreover, using transcriptome analysis, we define the molecular signatures associated with the emergence of human NC cells of distinct axial identities. Collectively, our findings indicate that a post-cranial NC state is achieved through two different routes: the birth of cardiac and vagal NC is facilitated by retinoic acid-induced posteriorisation of an anterior precursor whereas a trunk fate relies on a posterior axial progenitor intermediate.

2018-08-10 | GSE109267 | GEO

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Early anteroposterior regionalisation of human neural crest is shaped by a pro-mesodermal factor

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Proteomics analysis of plasma from radiographic axial spondyloarthritis patients.

Project description:Tandem mass spectrometry analysis of proteins from depleted plasma from radiographic axial spondyloarthritis patients pre- and post-treated with adalimumab.

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Axial progenitors generate trunk neural crest cells in vitro

Project description:Axial progenitors generate trunk neural crest cells in vitro

| PRJNA430261 | ENA