Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenetic optical mapping of 5-hydroxymethylcytosine in nanochannel arrays

ABSTRACT: We present a long-read, single-molecule mapping technology that generates hybrid genetic/epigenetic profiles of native chromosomal DNA. The genome-wide distribution of 5-hmC in human peripheral blood cells correlates well with 5-hmC DNA immunoprecipitation (hMeDIP) sequencing. However, the long single-molecule read-length of 100 kbp-1 Mbp produces 5-hmC profiles across variable genomic regions that failed to show up in the sequencing data. In addition, optical 5-hmC mapping shows a strong correlation between the 5-hmC density in gene bodies and the corresponding level of gene expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE115454 | GEO | 2018/06/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Epigenetic optical mapping of 5-hydroxymethylcytosine in nanochannel arrays

Project description:Epigenetic optical mapping of 5-hydroxymethylcytosine in nanochannel arrays

| PRJNA475101 | ENA

5-Hydroxymethylcytosine profiling of aging hippocampi

Project description:We profiled 5-hydroxymethylcytosine patterns in hippocampi using hydroxymethylated DNA immunoprecipitation followed by Illumina deep sequencing (hMeDIP-Seq). We profiled the hippocampi of 4 young (3 month old) and 4 aged (18 month old) C57BL/6 mice. Additionally, we profiled the 5-hmC patterns of hippocampi that were stereotactically injected with lentiviral constructs that overexpressed Tet2 or luciferase.

2018-02-25 | GSE102473 | GEO

Optical mapping data for 16 cattle

Project description:Bionano optical mapping data for 16 cattle

| PRJEB52551 | ENA

5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer [seq]

Project description:The discovery of cytosine hydroxymethylation (5-hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behavior in colon cancer. 5-hmC is globally reduced in proliferating cells such as colon tumors and the gut crypt progenitors, from which tumors can arise. Here, we show that colorectal tumors and cancer cells express Ten-Eleven Translocation (TET) transcripts at levels similar to normal tissues. Genome-wide analyses show that promoters marked by 5-hmC in normal tissue, and those identified as TET2 targets in colorectal cancer cells, are resistant to methylation gain in cancer. In vitro studies of TET2 in cancer cells confirm that these promoters are resistant to methylation gain independently of sustained TET2 expression. We also find that a considerable number of the methylation gain-resistant promoters marked by 5-hmC in normal colon overlap with those that are marked with poised bivalent histone modifications in embryonic stem cells. Together our results indicate that promoters that acquire 5-hmC upon normal colon differentiation are innately resistant to neoplastic hypermethylation by mechanisms that do not require high levels of 5-hmC in tumors. Our study highlights the potential of cytosine modifications as biomarkers of cancerous cell proliferation. 5 normal colon samples and 4 matching tumor samples were profiled for 5-hydroxymethylcytosine content genomewide using hmeDIP-seq. The colorectal cancer cell line HCT116 was profiled for binding of TET2 genomewide by chromatin immunoprecipitation sequencing (ChIP-seq).

2015-02-03 | E-GEOD-47590 | biostudies-arrayexpress

Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma

Project description:DNA methylation at the 5-position of cytosine (5-mC) is a key epigenetic mark critical for varius biological and pathological processes. 5-mC can be converted to 5-hydroxymethylcytosine (5-hmC) by the Ten-Eleven Translocation (TET) family of DNA hydroxylases. Here we report that "loss of 5-hmC" is an epigenetic hallmark of melanoma with diagonostic and prognostic implications. Genome-wide mapping of 5-hmC in nevi and melanomas for the first time revealed loss of 5-hmC landscape in the melanoma epigenome. Downregulation of Isocitrate Dehydrogenase 2 (IDH2) and TET family enzymes proved to be one of the mechanisms underlying the loss of 5-hmC during melanoma development, and rebuilding the 5-hmC landscape in the melanoma epigenome by reintroducing active TET2 or IDH2 suppressed melanoma growth and increased tumor-free survival. Thus, our study establishes that "loss of 5-hmC" is a new epigenetic hallmark of melanoma and links IDH and TET family enzymes-mediated 5-hmC putative tumor suppressor pathway to the suppression of melanoma progression.

2012-09-18 | GSE38231 | GEO

9f28ba52-b3d6-4dbe-8d3a-6985af609115 - samples

Project description:Bionano DLS optical mapping data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a molecule depth of ~153ÃƒÂ—. Optical mapping was performed at the Weatherall Institute of Molecular Medicine using the Bionano Saphyr platform.

| EGAD00001007049 | EGA

Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma

2012-09-18 | E-GEOD-38231 | biostudies-arrayexpress

Tet1 and hydroxymethylcytosine in transcription and DNA methylation fidelity (ChIP/DIP-Seq data)

Project description:We analyzed the genome-wide binding of Tet1 in control (shScr) and Tet1 knockdown (shTet1) mouse ES cells using two different Tet1 antibodies (Tet1-C and Tet1-N). Furthermore, we generated genome-wide mapping of hydroxymethyl cytosine (hmC) and methyl cytosine (mC). We find that hmC, in contrast to mC, is also found at transcription start sites (TSSs), and that there is a significant overlap between Tet1 binding and hmC positive regions. Surprisingly, our results also suggest, that Tet1 has a role in transcriptional repression. We showed that Tet1 associates with Sin3A co-repressor complex, and by performing ChIP-sequencing of Sin3A, we find co-localisation of Tet1 and Sin3a throughout the genome Examination of Tet1 and Sin3A binding as well as hmC and mC localization in mouse ES cells

2011-04-13 | E-GEOD-24841 | biostudies-arrayexpress

Tet1 and hydroxymethylcytosine in transcription and DNA methylation fidelity (ChIP/DIP-Seq data)

2011-04-13 | GSE24841 | GEO