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Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells

ABSTRACT: Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells

PROVIDER: PRJNA1021169 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26183120_1.fastq.gz	Fastqsanger.gz
	SRR26183120_2.fastq.gz	Fastqsanger.gz
	SRR26183121_1.fastq.gz	Fastqsanger.gz
	SRR26183121_2.fastq.gz	Fastqsanger.gz
	SRR26183122_1.fastq.gz	Fastqsanger.gz

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Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells [ATAC-seq]

Project description:Chromatin accessibility is key epigenomic regulatory mechanisms of transcription. Herein, to profile open chromatin maps and transcriptional feature associated with odontogenic tropism of dental pulp stem cells (DPSCs), we conducted integrative analysis of epigenomic alteration and transcriptome changes during odontogenic differentiation of DPSCs. DPSCs were long-term cultured in odontogenic induction medium to evaluate differentiation abilities. ATAC-seq and RNA-seq samples were collected before and after the 9-day culture. One of the day 9 specific-super-enhancer was constructed in ALPL (Alkaline Phosphatase, Biomineralization Associated) intragenic region in which all the day 9-specific open chromatin peaks were included and BMP-mediated Smad binding element are specifically accumulated. These results suggest that the specific local chromatin regions were selectively opened and, particularly, super-enhancers were constructed, which was able to guide differentiative transcriptional factors such as Smad1/4 to their target gene loci in differentiating DPSCs; hence, epigenetic modifications such as histone deacetylase (HDACs) inhibitor application have therapeutic potential for DPSCs-induced dentin/pulp regeneration.

2023-09-29 | GSE244058 | GEO

Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells [RNA-seq]

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Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells [RNA-seq]

Project description:Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells [RNA-seq]

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Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells [ATAC-seq]

Project description:Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells [ATAC-seq]

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Effects of endogenous GDF11 on the odontogenic differentiation of dental pulp stem cells

Project description:Knockdown of endogenous GDF11 downregulated the odontogenic differentiation of human dental pulp stem cells (hDPSCs). We performed RNA-seq analysis on hDPSCs transfected with GDF11 small interfering RNA (siRNA) and control siRNA after 7 days of odontogenic induction, in order to investigate the underlying mechanisms of endogenous GDF11 regulating odontogenic differentiation in hDPSC.

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Effects of glucose on gene expression of human dental pulp cells under odontogenic differentiation

Project description:Human dental pulp cells have the ability to differentiate into odontoblast cells under various stimuli. The objective of our study is to investigate the efffects of glucose on gene expression of human dental pulp cells that under go odontogenic differentiation. Expression microarray were performed to identify the genes that were affected by short-term and long-term exposure to high glucose levels.

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Characterization of odontogenic differentiation from human dental pulp stem cells using TMT-based proteomic analysis

Project description:The repair of dental pulp injury relies on the odontogenic differentiation of dental pulp stem cells (DPSCs). To better understand the odontogenic differentiation of DPSCs and identify proteins involved in this process, tandem mass tags (TMTs) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) were applied to compare the proteome profiles of induced and control DPSCs. The proteins expressed during osteogenic differentiation of human DPSCs were profiled using the TMT method combined with LC-MS/MS analysis. The identified proteins were subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Then a protein-protein interaction (PPI) network was constructed. Two selected proteins were confirmed by western blot (WB) analysis. A total of 223 proteins that were differentially expressed were identified. Among them, 152 proteins were significantly upregulated and 71 were downregulated in the odontogenic differentiation group compared with the control group. On the basis of biological processes in GO, the identified proteins were mainly involved in cellular processes, metabolic processes, and biological regulation, which connected with the signaling pathways highlighted by KEGG pathway analysis. PPI networks showed that most of the differentially expressed proteins were implicated in physical or functional interaction. The protein expression levels of FBN1 and TGF-β2 validated by WB were consistent with the TMT analysis. This is the first proteomic analysis of human DPSC odontogenesis using a TMT method. We identified many new differentially expressed proteins that are potential targets for pulp-dentin complex regeneration and repair.

2021-09-09 | PXD021279 | Pride

Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells

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

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Effect of Ginsenoside Rb1 on inflammatory reaction and odontogenic differentiation of human dental pulp cell

Project description:Ginsenoside Rb1 (G-Rb1) has been reported to diminish inflammation associated with diseases. We investigated the effect of G-Rb1 on the inflammatory reactions and the odontogenic differentiation of human dental pulp cells (hDPCs). G-Rb1 affected the levels of TNF-α, IL-6, and IL-8, as these showed reduced levels with exposure to lipopolysaccharide (LPS). Additionally, less mRNA and protein expressions of vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1) were shown. G-Rb1 suppressed the LPS-induced increase of cell adhesion molecules and inflammatory cytokines, while also inhibiting PI3K/Akt, phosphorylation of NF-κB transcription factors, ERK and JNK of MAPK signaling in hDPCs.

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Project description:Using the HumanMethylation450 Beadchip, whole genomes of human dental pulp stem cells (DPSCs), periodontal ligament stem cells (PDLSCs), and dental follicle progenitor cells (DFPCs) were compared.The DNA methylation profiles were obtained across approximately 485,512 CpGs in human odontogenic stem cells samples. Samples included DPSCs, DFPCs and PDLSCs from each 4 (12 in total) human individuals.

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