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Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [RNA-Seq]

ABSTRACT: Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [RNA-Seq]

PROVIDER: PRJNA479996 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7478630.fastq.gz	Fastqsanger.gz
	SRR7478631.fastq.gz	Fastqsanger.gz
	SRR7478626.fastq.gz	Fastqsanger.gz
	SRR7478627.fastq.gz	Fastqsanger.gz
	SRR7478628.fastq.gz	Fastqsanger.gz

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Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions

Project description:Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions

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Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [4C]

Project description:Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [4C]

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Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [ChIP-Seq]

Project description:Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [ChIP-Seq]

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Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [4C]

Project description:we report that regional expression of the Hoxc genes is regulated by antagonistic switch between repression and activation epigenetic modification. In freshly isolated dermal cells from P50 telogen Wt/Wt ear skin, no enrichment of H3K27ac was detected at Hoxc cluster, consistent with their lack of expression; in contrast, robust peaks of this marker are observed in 3’ region of the Hoxc cluster in dorsal skin dermal cells. Secondly we looked at H3K27 trimethylation (H3K27me3), a marker for polycomb-dependent gene repression, which antagonizes H3K27ac. Concomitantly, we found that H3K27me3 spread across the entire Hoxc cluster in adult ear skin dermal cells but was restricted to the 5’ region of the Hoxc cluster in adult dorsal skin dermal cells . In adult dorsal skin dermal cells, we found three occupied CTCF binding sites inside Hoxc cluster. The rostral CTCF binding site marks the discontinuity point of H3K27me3 modification at the intergenic region between Hoxc11 and Hoxc10 in dorsal skin dermal cells. This indicates the CTCF binding event within Hoxc cluster might forge a topological barrier that can insulate activation region from repression region and therefore lead to the region specific expression of the Hoxc cluster genes.To directly test whether there is ectopic interaction between Hoxc cluster and the active domain in proximal-TAD, we used circularized chromosome conformation capture (4C) with Hoxc4 as bait. In Wt/Koa ear skin dermal cells, there are clear ectopic interactions of Hoxc4 with the remaining active regulatory landscape in proximal-TAD; on the other hand, all of the interactions of Hoxc4 remained inside the distal-TAD with repressive domain in Wt/Wt ear skin.

2018-07-09 | GSE116720 | GEO

Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [RNA-Seq]

2018-07-09 | GSE116722 | GEO

Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [ChIP-Seq]

2018-07-09 | GSE116721 | GEO

Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions

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

2018-07-07 | GSE116723 | GEO

Altered dermal architecture in PKCα-/- skin

Project description:Global gene expression analysis in PKCα-/- mouse skin reveals structural changes in the dermis and defective wound granulation tissue. The skin's mechanical integrity is maintained by an organised and robust dermal extracellular matrix (ECM). Resistance to mechanical disruption hinges primarily on homeostasis of the dermal collagen fibril architecture which is regulated, at least in part, by members of the small leucine-rich proteoglycan (SLRP) family. This array study presents data linking protein kinase C alpha (PKCα) to the regulated expression of multiple ECM components including SLRPs.

2016-01-20 | E-MTAB-3836 | biostudies-arrayexpress

A map of nucleosome positions in yeast at base-pair resolution

Project description:The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function, yet existing methods for mapping nucleosomes do not provide the necessary single base pair accuracy to determine these positions. Here we develop and apply a new approach for direct mapping of nucleosome centers based on chemical modification of engineered histones. The resulting map locates nucleosome center positions genome-wide in unprecedented detail and accuracy. It reveals novel aspects of the in vivo nucleosome organization that are linked to transcription factor binding, RNA polymerase pausing, and the higher order structure of the chromatin fiber itself.

2012-05-17 | GSE36063 | GEO

Epigenome analysis of human epidermal and dermal samples with aging and sun exposure

Project description:Genome wide DNA methylation profiling of epidermal and dermal samples obtained from sun-exposed and sun-protected body sites from younger (<35 years old) and older (>60 years old) individuals. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in dermal and epidermal samples. Samples included 10 younger sun protected dermal samples, 10 younger sun exposed dermal samples, 10 older sun protected dermal samples, 10 older sun exposed dermal samples, 9 younger sun protected epidermal samples, 9 younger sun exposed epidermal samples, 10 older sun protected epidermal sample, 10 older sun exposed epidermal samples.

2015-03-23 | GSE51954 | GEO

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