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ERK signalling orchestrates neural differentiation by promoting the polycomb repressive complex [dataset 1]

ABSTRACT: In this experiment patterns of chromatin accessibility were compared in (H9) human ES cell derived neuromesodermal progenitors (NMP-L)s and derived neural progenitors (NP)s at different days during the neural differentiation procedure (day 5, day 6 and day 8) and also in NPs at day 5 and 6 exposed to carrier control with DMSO or the MEK inhibitor PD184352.

ORGANISM(S): Homo sapiens

PROVIDER: GSE121126 | GEO | 2022/09/16

REPOSITORIES: GEO

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Transcriptomic profiling of human neuromesodermal-like cells and spinal cord progenitors derived in vitro from H9 ES cell line

Project description:Human ES (H9) cells were directed towards a neuromesodermal progenitor-like cell state and these cells were then subsequently differentiated towards a neural cell fate. Human ES cells (H9) were differentiated into neuromesodermal progenitor-like cells by culturing in Neurobasal/1x N2/1x B27 medium (N2/B27) supplemented with 20 ng/ml bFgf and 3 μM CHIR99021 for 3 days and exposure to dual SMAD inhibition (dSMADi) (Noggin 50 ng/ml and the TGFb receptor type 1 inhibitor SB431542 10 μM) during day 3 (D3). Transcriptome analysis was then carried out following a selection procedure to enrich for NMP-like cells (sD3/NMP-like). This involved use of a hES (H9) cell line engineered with CRISPR-Cas9 to express GFP under the control of the endogenous Nkx1.2 promoter. At the end of day 3 cells were selected for high GFP expression, as high Nkx1.2 transcription is characteristic of NMP cell populations in mouse and chick embryos. These cells were then lysed and RNA extracted for RNASeq. Humans ES cells (H9) differentiated into NMP-like cells as above (without selection) were also allowed to develop further on day 4 (in the presence of dSMADi and Retinoic acid (RA) 100nM, in N2/B27) and then in RA alone until end of day 8 (D8). These cells were then lysed and RNA extracted for RNASeq.

2018-07-04 | E-MTAB-6680 | biostudies-arrayexpress

ERK signalling orchestrates neural differentiation by promoting the polycomb repressive complex [dataset 2]

Project description:In this experiment, Ring1b occupancy was examined in human neuromesodermal progenitors derived from embryonic stem cells (H9)

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ERK signalling orchestrates neural differentiation by promoting the polycomb repressive complex [dataset 3]

Project description:mRNAseq was examined in human embryonic stem cells (H9) and neuromesodermal progenitors differentiated from these cells in vitro

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Generation and characterisation of pre-neural progenitors and neural crest from human embryonic stem cells.

Project description:The spinal cord emerges from a niche of neuromesodermal progenitors (NMPs) formed and maintained by Wnt/FGF signals in the posterior end of the embryo. NMP-like cells can be generated from human pluripotent stem cells providing a promising source for spinal cord replacement therapies. However, these progenitors are often transient and unable to produce the full range of rostrocaudal spinal cord identities in vitro. Here we report the generation of NMP-derived pre-neural progenitors (PNPs). These PNPs maintain pre-spinal cord identity by co-expressing the transcription factors SOX2 and CDX2, while losing the mesodermal potential of NMPs by downregulating TBXT. They gradually adopt more posterior identity by activating collinear HOX gene expression, and in parallel undergo an epithelial-to-mesenchymal transition to give rise to neural crest (NC) cells with corresponding rostrocaudal identity.

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Sustained experimental activation of FGF8/ERK in the developing chicken spinal cord reproducibly models early events in ERK-mediated tumorigenesis

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Project description:Posterior embryonic axis develops from neuromesodermal progenitors which differentiate into neural tube and paraxial mesoderm

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

Project description:We employed ATAC-seq to interrogate the chromatin accessibility landscape in neuromesodermal progenitor (NMP)-like cells derived from a human embryonic stem cell (hESC) line engineered to exhibit shRNA-mediated, tetracycline (Tet)-inducible knockdown of TBXT expression. TBXT shRNA hESCs were differentiated toward NMPs following a three day treatment in the presence of WNT and FGF agonists in the presence or absence of tetracycline and +/-Tet treated samples were harvested and analysed by ATAC-seq.

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Differential Gene Expression in Daphnia magna Suggests Distinct Modes of Action and Bioavailability for ZnO nanoparticles and Zn ions

Project description:Zinc Oxide nanoparticles (ZnO NPs) are being rapidly developed for use in consumer products, wastewater treatment and chemotherapy providing several possible routes for ZnO NP exposure to humans and aquatic organisms. Recent studies have shown that ZnO NPs undergo rapid dissolution to Zn+2, but the relative contribution of Zn+2 to ZnO NP bioavailability and toxicity is not clear. Gene expression profiling of D. magna exposed to ZnO NPs or ZnSO4 at equitoxic concentrations demonstrated that the particles cause toxicity through a distinct mechanism compared with Zn+2. D. magna were also exposed to a SiO NPs as a particle control at equimolar concentrations. The SiO NPs resulted in few differentially expressed genes and there was very little overlap between the genes affected by the ZnO NPs and the SiO NPs, suggesting that ZnO NPs cause a distinct pattern of differentially expressed genes. In the ZnO NP exposures, effects were observed to genes involved in cytoskeletal transport, cellular respiration and reproduction. Three biomarker genes including a multi-cystatin, ferritin and a C1q containing gene were confirmed as differentially expressed in a specific pattern by ZnO NP and provide a suite of biomarkers for identifying environmental exposure to ZnO NP and differentiating between NP and ionic exposure.

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