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

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

PROVIDER: PRJNA1021175 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26183071_1.fastq.gz	Fastqsanger.gz
	SRR26183071_2.fastq.gz	Fastqsanger.gz
	SRR26183072_1.fastq.gz	Fastqsanger.gz
	SRR26183072_2.fastq.gz	Fastqsanger.gz
	SRR26183073_1.fastq.gz	Fastqsanger.gz

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Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells [RNA-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 | GSE244057 | GEO

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

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

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

| PRJNA1021169 | ENA

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]

| PRJNA1021174 | ENA

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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Effect of hsa_circ_0001599 on gene expression during odontogenic differentiation of human dental pulp stem cells

Project description:Dental pulp regeneration is significantly aided by human dental pulp stem cells (hDPSCs). An increasing number of studies have demonstrated that circular RNAs (circRNAs) are crucial in the multidirectional differentiation of many mesenchymal stem cells, but their specific functions and mechanisms remain unknown. This work aimed at elucidating the molecular mechanism by which hsa_circ_0001599 works in hDPSCs during odontogenic differentiation. The expression of hsa_circ_0001599 in hDPSCs and dental pulp tissue was determined by using quantitative real-time PCR (qRT‒PCR). The role of hsa_circ_0001599 in the odontogenic differentiation of hDPSCs and its mechanism were studied using a variety of in vivo and in vitro assessments. The odontogenic differentiation of hDPSCs was facilitated by the overexpression of hsa_circ_0001599, which activated the PI3K/AKT signalling pathway in vitro. In vivo, hsa_circ_0001599 can promote the formation of new dentin-like structures. Mechanistically, hsa_circ_0001599 enhanced ITGA2 expression by sponging miR-889-3p. Furthermore, hsa_circ_0001599 interacts with the methylation reader hnRNPA2B1, promoting hnRNPA2B1 translocation from the nucleus to the cytoplasm and increasing ITGA2 mRNA stability. This research revealed the important role of hsa_circ_0001599 in odontogenic differentiation. Thus, hDPSCs engineered with hsa_circ_0001599 have the potential to be effective therapeutic targets for dental pulp repair and regeneration

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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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Proteomics of odontogenic differentiated human dental pulp cells

Project description:human dental pulp cells was odontogenic induced to evaluate the changed protein files

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Effect of GATA4 overexpression on gene expression during odontogenic differentiation of human dental pulp stem cells

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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

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