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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (5hmC) [5hmC-Seal]

ABSTRACT: An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (5hmC) [5hmC-Seal]

PROVIDER: PRJNA670168 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12850251_1.fastq.gz	Fastqsanger.gz
	SRR12850251_2.fastq.gz	Fastqsanger.gz
	SRR12850252_1.fastq.gz	Fastqsanger.gz
	SRR12850252_2.fastq.gz	Fastqsanger.gz
	SRR12850253_1.fastq.gz	Fastqsanger.gz

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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (5hmC) [5hmC-Seal]

Project description:We report the 5hmC in human hippocampus subject to normal aging and Alzheimer's disease.

2020-10-21 | GSE159671 | GEO

Intestinal stem cell differentiation is associated with dynamic changes in the chromatin landscape [5hmc-seal-seq]

Project description:The global localization of 5-hydroxymethylcytosine (5hmc) were measured by 5hmc-seal-seq in four populations of intestinal epithelium defined by their levels of a GFP reporter transgene that is driven by the regulatory elements of the Sox9 gene.

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RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development [5hmC-Seal]

Project description:RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development [5hmC-Seal]

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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

Project description:An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

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A highly sensitive and robust method for genome-wide 5hmC profiling of rare cell populations

Project description:Investigations of 5-hydroxymethylcytosine (5hmC) in biologically and clinically samples and models with low cell numbers have been hampered by the low sensitivity and reproducibility using current 5hmC mapping approaches. Here, we develop a selective 5hmC chemical labeling approach using tagmentation-based library preparation in order to profile nanogram levels of 5hmC isolated from ~1,000 cells (nano-hmC-Seal). Using this technology, we profiled the dynamics of 5hmC across different stages of mouse hematopoietic differentiation. Additionally, applying nano-hmC-Seal to the hematopoietic multipotent progenitor cells in an acute myeloid leukemia (AML) mouse model, we identified leukemia-specific, differentially hydroxymethylated regions that harbor previously reported and as-yet-unidentified functionally relevant factors. The change of 5hmC patterns in AML strongly correlates with the altered gene expression on a global scale. Together, our new approach offers a highly sensitive and robust method to study and detect DNA methylation dynamics from in vivo model and clinical samples. Selective 5hmC chemical labeling approach using tagmentation-based library preparation in order to profile nanogram levels of 5hmC isolated from ~1,000 cells

2016-09-01 | E-GEOD-77967 | biostudies-arrayexpress

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

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

2020-07-07 | GSE153875 | GEO

Jump-seq: Capture and amplify 5hmC Sites Whole Genome-Wide

Project description:We developed an efficient and precise method, which we name as Jump-seq, to capture and amplify 5hmC signal whole genome-wide, bridge the gap between base resolution (TAB-seq) and economic cost (hmC-seal).

2019-03-07 | GSE127906 | GEO

A highly sensitive and robust method for genome-wide 5hmC profiling of rare cell populations

2016-09-01 | GSE77967 | GEO

Sequencing analysis for 5hmC pull-down DNA

Project description:The gene body regions of cardiomyocyte-specific genes in cardiomyocytes are hypomethylated. We confirmed that the DNA methylation in gene body regions were demethylated during development. We speculated that the demethylation of gene body regions in cardiomyocyte-specific genes might be associated with active demethylation by Tet oxidation.To explore 5hmC distribution in cells and tissues, we performed 5hmC-specific chemical labeling-mediated pull-down DNA sequencing (hMe-Seal)(Song 2011 Nat genet, PMID:21151123). We found that the 5hmC in gene body regions are associated with demethylation, but not exclusively, and also with transcriptional activity. We concluded that gene body DNA hypomethylation in cardiomyocyte specific genes were mediated by oxidative demethylation.

2016-09-22 | GSE87165 | GEO

Metabolic changes during human adipocyte differentiation promote stable DNA hydroxymethylation and binding of acetylated NEIL1 to adipogenic enhancers [hMe-Seal]

Project description:In the present study, we applied two whole-genome sequencing techniques (WGBS/oxBS and hMe-Seal) to detect 5hmC (and 5mC) changes during the differentiation of the human SGBS preadipocyte cell line to mature adipocytes. As technical and biological validation we performed BS and oxBS followed by 450k array analysis. RNA-seq data was performed in parallel to study transcriptional changes associated with differential hydroxymethylation. In human white adipose tissue (WAT) hydroxymethylation (hME-Seal) was characterized in comparison with histone modifications and acNEIL1 binding (ACT-seq).

2024-02-01 | GSE161110 | GEO

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