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The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates (bulk RNA-Seq)

ABSTRACT: The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates (bulk RNA-Seq)

PROVIDER: PRJNA673890 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12967108_1.fastq.gz	Fastqsanger.gz
	SRR12967108_2.fastq.gz	Fastqsanger.gz
	SRR12967109_1.fastq.gz	Fastqsanger.gz
	SRR12967109_2.fastq.gz	Fastqsanger.gz
	SRR12967110_1.fastq.gz	Fastqsanger.gz

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The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates (scRNA-Seq)

Project description:Colonies of induced pluripotent stem cells (iPSCs) reveal aspects of self-organization even under culture conditions that maintain pluripotent state. To investigate the dynamics of this process under spatial confinement we used either PDMS pillars or micro-contact printing of vitronectin. OCT4, E-cadherin, and NANOG were progressively upregulated within about 70 µm from the outer rim of iPSC colonies. Single-cell RNA-sequencing demonstrated that OCT4high subsets have pronounced up-regulation of the TGF-β pathway, particularly of NODAL and its inhibitor LEFTY, at the rim of the colonies. Furthermore, calcium-dependent cell-cell interaction seemed to be relevant for the self-organization. After 5 to 7 days, the iPSC colonies detached spontaneously from micro-contact printed substrates to form 3D aggregates. This new method allowed generation of embryoid bodies (EBs) of controlled size, without any enzymatic or mechanical treatment. Within the early 3D aggregates, the radial organization and differential gene expression continued in analogy to the changes observed during self-organization of flat iPSC colonies. Our results provide further insight into the gradual self-organization within iPSC colonies and at their transition into EBs.

2022-08-26 | GSE184603 | GEO

The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates (bulk RNA-Seq)

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The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates

Project description:The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates

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The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates (scRNA-Seq)

Project description:The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates (scRNA-Seq)

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The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates

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

2022-08-26 | GSE184604 | GEO

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ITS within aggregates in black soil

Project description:ITS within aggregates in black soil Raw sequence reads

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Cyanobacterial Aggregates

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Nanotopography guides morphology and spatial patterning of induced pluripotent stem cell colonies

Project description:The role of topographic cues in controlling commitment of induced pluripotent stem cells (iPSCs) is largely unknown. Here we demonstrate that groove-ridge nanostructures induce the elongation of iPSC colonies, guide the orientation of apical actin fibers and direct the polarity of cell division. Elongation of iPSC colonies impacts also on the intrinsic molecular patterning which seems to be orchestrated starting from the rim of the colonies. We followed the hypothesis that nanotopography directly modulates the transcriptional program of iPSC, further to guiding the overall spatial organization of the colonies. Single iPSC were seeded on flat (PI flat) and nanostructured polyimide (PI 650) and gene expression profiles were analyzed after three days. No significant differences were observed when cells were kept under culture conditions that sustained pluripotency. Then, we analyzed gene expression changes upon two weeks of multi-lineage differentiation. Many genes revealed significant expression changes in the course of differentiation and this was more pronounced on PI flat as compared to PI 650. Comparison of iPSC that were either differentiated on flat or nanostructured biomaterials revealed differential expression of several genes. Noteworthy, among significantly regulated genes, the biggest fold change on PI 650 versus PI flat after differentiation was observed in ANKRD1, which is one of the best readouts of YAP/TAZ activity. Our study suggests that nanotopography impacts on orientation and organization of iPSC colonies and highlight a possible interaction between mechanosensors and mechanotransducers.

2017-09-18 | GSE84848 | GEO

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