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Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition

ABSTRACT: Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition

PROVIDER: PRJNA736091 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14762238.fastq.gz	Fastqsanger.gz
	SRR14762239.fastq.gz	Fastqsanger.gz
	SRR14762240.fastq.gz	Fastqsanger.gz
	SRR14762241.fastq.gz	Fastqsanger.gz
	SRR14762242.fastq.gz	Fastqsanger.gz

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Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (RNA-Seq)

Project description:Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (RNA-Seq)

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Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (MethylCap-seq)

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Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (Spatial RNA-Seq)

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Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (single cell RNA-Seq)

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Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (MethylCap-seq)

Project description:Unbiased whole-genome methylome was studied in the wound-edge (WE) tissue of chronic wound patients. Methylation status of proximal promoter (1Kb) was calculated using MethylCap-Seq and PrEMeR-CG data analyses. A total of 4689 differentially methylated regions (DMRs) were identified in chronic WE compared to unwounded (UW) human skin. Hypermethylation was more frequently observed (3661 DMRs) in the chronic WE compared to hypomethylation (1028 DMRs). Twenty-six hypermethylated DMRs were involved in epithelial to mesenchymal transition (EMT). Bisulfite sequencing validated hypermethylation of a predicted specific upstream regulator TP53. Whole genome RNA sequencing analysis was performed to qualify findings from methylome analysis. Hierarchical clustering analyses identified a large set of genes, the expression of which were significantly downregulated in chronic WE compared to UW skin. Analysis of the downregulated genes identified the TP53 signaling pathway, including P63, P73, FOXO3, SIRT1 and HDAC1, as being significantly silenced. Direct comparison of hypermethylation and downregulated gene expression identified four genes, ADAM17, NOTCH, TWIST1 and SMURF1, that were common to both data sets and functionally represented the EMT pathway. Single cell RNA sequencing studies identified that these effects on gene expression were limited to the keratinocyte cell compartment.

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Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (RNA-Seq)

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Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (Spatial RNA-Seq)

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Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (single cell RNA-Seq)

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Gene Expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice

Project description:Gene Expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice Affymetrix GeneChipÂ® Mouse Genome 430 array was used to study the gene expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice Gene Expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice

2016-07-21 | E-GEOD-73229 | biostudies-arrayexpress

Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition

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

2022-05-04 | GSE176417 | GEO