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Effect of SOX9 dosage changes on chromatin accessibility in hESC-derived cranial neural crest cells [ATAC-seq]

ABSTRACT: Effect of SOX9 dosage changes on chromatin accessibility in hESC-derived cranial neural crest cells [ATAC-seq]

PROVIDER: PRJNA848207 | ENA |

REPOSITORIES: ENA

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Effect of SOX9 dosage changes on gene expression in hESC-derived cranial neural crest cells [RNA-seq]

Project description:To assess the effects of quantitative SOX9 dosage changes on gene expression in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of differing concentrations of the degrader molecule dTAGV-1 results in different SOX9 concentrations, as measured by flow cytometry. We then profiled gene expression profiling in each of these SOX9 concentrations

2022-07-04 | GSE205902 | GEO

Effect of SOX9 dosage changes on chromatin accessibility in hESC-derived cranial neural crest cells [ATAC-seq]

Project description:To assess the effects of quantitative SOX9 dosage changes on chromatin accessibility in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of differing concentrations of the degrader molecule dTAGV-1 results in different SOX9 concentrations, as measured by flow cytometry. We then profiled chromatin accessibility in each of these SOX9 concentrations

2022-07-04 | GSE205900 | GEO

Effect of SOX9 depletion on transcription mRNA in hESC-derived cranial neural crest cells [SLAM-seq]

Project description:To assess the effects of SOX9 depletion on transcription in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of the degrader molecule dTAGV-1 results in SOX9 depletion. We then profiled transcription by metabolic labeling of RNA (SLAM-Seq) in undepleted CNCCs or CNCCs in which SOX9 was depleted for 3h or 24h

2022-07-04 | GSE205903 | GEO

Effect of SOX9 depletion on active chromatin marks in hESC-derived cranial neural crest cells [ChIP-seq]

Project description:To assess the effects of SOX9 depletion on active chromatin marks in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of the degrader molecule dTAGV-1 results in SOX9 depletion. We then profiled the active chromatin mark H3K27ac by ChIP-Seq in undepleted CNCCs or CNCCs in which SOX9 was depleted for 3h or 24h. We also titrated SOX9 to four distinct levels with dTAGV-1 and assessed SOX9 binding by V5 ChIP-seq, as well as TWIST1 and TFAP2A binding by ChIP-seq.

2022-07-04 | GSE205901 | GEO

Effect of SOX9 dosage changes on gene expression in hESC-derived cranial neural crest cells [RNA-seq]

Project description:Effect of SOX9 dosage changes on gene expression in hESC-derived cranial neural crest cells [RNA-seq]

| PRJNA848205 | ENA

Effect of SOX9 depletion on transcription mRNA in hESC-derived cranial neural crest cells [SLAM-seq]

Project description:Effect of SOX9 depletion on transcription mRNA in hESC-derived cranial neural crest cells [SLAM-seq]

| PRJNA848204 | ENA

Effect of SOX9 depletion on active chromatin marks in hESC-derived cranial neural crest cells [ChIP-seq]

Project description:Effect of SOX9 depletion on active chromatin marks in hESC-derived cranial neural crest cells [ChIP-seq]

| PRJNA848206 | ENA

Human ESC differentiation into cranial neural crest cells in the presence of PhenDC3

Project description:Human ESC differentiation into cranial neural crest cells in the presence of PhenDC4. Human embryonic stem cells (hESC) were differentiated into cranial neural crest cells in presence of the G-quadruplex stabilising ligand PhenDC3 or DMSO control. The case when no PhenDC3 or DMSO have been included in the differentiation protocol represent an additional control experiment.

2021-11-10 | GSE166246 | GEO

Post-transcriptional regulation in cranial neural crest cells expands developmental potential [I]

Project description:Developmental potential is progressively restricted after germ layer specification during gastrulation. However, cranial neural crest cells challenge this paradigm, as they develop from anterior ectoderm yet give rise to both mesodermal derivatives of the craniofacial skeleton and ectodermal derivatives of the peripheral nervous system. How cranial neural crest cells differentiate into multiple lineages is poorly understood. Here, we demonstrate that cranial neural crest cells possess a transient state of increased chromatin accessibility; and that the earliest premigratory neural crest are biased towards either a neuronal or ectomesenchymal fate, with each lineage expressing distinct factors from the pluripotent state. We profile the spatiotemporal emergence of each neural crest population and demonstrate that the ectomesenchymal lineage forms prior to the neuronal progenitors. Expression of the pluripotency microRNA family miR-302 is maintained in cranial neural crest cells and genetic deletion leads to precocious specification of the ectomesenchymal lineage. We find that miR-302 directly targets Sox9 to slow the timing of ectomesenchyme induction and regulates multiple genes involved in chromatin condensation to maintain accessibility for neuronal differentiation. Loss of mir-302 results in reduced chromatin accessibility in the neuronal progenitor lineage of neural crest and a reduction in peripheral neuron differentiation. Our findings reveal a post-transcriptional mechanism governed by miRNAs from pluripotency as an important mechanism to expand developmental potential of cranial neural crest.

2022-10-25 | GSE215977 | GEO

Post-transcriptional regulation in cranial neural crest cells expands developmental potential [II]

2022-10-25 | GSE216136 | GEO

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