Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA [MeDIP-seq]

PROVIDER: PRJNA369510 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5221900.fastq.gz	Fastqsanger.gz
	SRR5221901.fastq.gz	Fastqsanger.gz
	SRR5221902.fastq.gz	Fastqsanger.gz
	SRR5221903.fastq.gz	Fastqsanger.gz
	SRR5221899.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 5

Similar Datasets

Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA

Project description:Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA

| PRJNA369511 | ENA

Homo sapiens

Project description:Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA [BiSulfite-seq]

| PRJNA369396 | ENA

Homo sapiens

Project description:Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA [HumanMethylation450]

| PRJNA369383 | ENA

Genome-wide DNA methylation analysis in SSCs, iGSCs, and FGSCs

Project description:We use MeDIP-seq to report the most comprehensive survey to date of genome-wide DNA methylation in germline stem cells

2021-10-06 | GSE134727 | GEO

Semiconductor-based sequencing of genome-wide DNA methylation states

Project description:Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is a widely used approach to study DNA methylation genome-wide. Here, we present a novel MeDIP-Seq protocol compatible with the Ion Torrent semiconductor-based sequencing platform that is scalable and accurately identifies sites of differential DNA methylation. Additionally, we demonstrate that the high-throughput data derived from MeDIP-Seq on the Ion Torrent platform provides adequate coverage of CpG cytosines, the methylation states of which we validated at single-base resolution on the Infinium HumanMethylation450K Beadchip array. We applied this integrative approach to further investigate the role of DNA methylation in alternative splicing and to profile 5-mC and 5-hmC variants of DNA methylation in normal human brain tissue that we observed localize over distinct genomic regions. These applications of MeDIP-Seq on the Ion Torrent platform have broad utility and add to the current methodologies for profiling genome-wide DNA methylation states in normal and disease conditions. MeDIP-Seq on Ion Torrent Platform in HCT116 and Human Brain

2015-06-10 | E-GEOD-61968 | biostudies-arrayexpress

Semiconductor-based sequencing of genome-wide DNA methylation states

2015-06-10 | GSE61968 | GEO

Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax.

2012-09-26 | GSE41060 | GEO

Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax.

Project description:We report the existence of both methylcytosine and hydroxymethylcytosine in the genomic DNA of the ciliate Oxytricha trifallax during its genome rearrangement process. These modifications are dynamically added, de novo, to sequences targeted for elimination and are not present after the rearrangement process (in vegetative cells). We performed methyl-DNA immunoprecipitation-sequencing (meDIP-seq) with antibodies against methylcytosine and hydroxymethylcytosine. We performed methyl-DNA immunoprecipitation-sequencing (meDIP-seq) with antibodies against methylcytosine and hydroxymethylcytosine, and used an IgG control for nonspecific immunoprecpitation. Immunoprecipitation was performed on both vegetative (negative control) and 46h cells (with methylation). The data were normalized to RPKM, then the number of vegetative reads was subtracted from the number of 46h reads, giving excess reads at 46h, which we denote as the methylation/hydroxymethylation "signal". Those data are reported in the tab-deliminated data files included with this dataset.

2012-09-26 | E-GEOD-41060 | biostudies-arrayexpress

Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array

Project description:Methylated DNA enrichment is a key step in a microarray based genome-wide methylation profiling study, and even for future high-throughput sequencing based methylome analysis. In order to evaluate the sensitivity and accuracy of methylated DNA enrichment, we investigated and optimized a number of important parameters to improve the performance of several enrichment assays, including differential methylation hybridization (DMH), microarray-based methylation assessment of single samples (MMASS), and methylated DNA immunoprecipitation (MeDIP). With advantages and disadvantages unique to each approach, we found that assays based on methylation-sensitive enzyme digestion and those based on immunoprecipitation detected different methylated DNA fragments, indicating that they are complementary in their relative ability to detect methylation differences. Our study provides the first comprehensive evaluation for widely used methodologies for methylated DNA enrichment, and could be helpful for developing a cost effective approach for DNA methylation profiling.

2010-01-22 | GSE19974 | GEO

DNA hydroxymethylation profiles reveal possible role of highly methylated TLR signaling on Fasciola gigantica excretory/secretory products (FgESPs) modulation of buffalo DCs [hMeDIP-seq]

Project description:Purpose: To investigate whether FgESP affects the hydroxylmethylation level of DCs Methods: we have profiled the DNA hydroxymethylome by using hydroxymethylated DNA immunoprecipitation sequencing (h)MeDIP-Seq in the current study Results: DNA hydroxymethylation profiles revealed significant changes in the 5-hydroxymethylcytosine (5hmC) levels in 360 genes when DCs were treated with FgESPs. These differentially expressed genes were highly enriched in pathways associated with immune function. Conclusion: For the first time, our study provides a genome-wide mapping of DNA hydroxylmethylation for DCs that interacted with FgESPs.

2019-09-25 | GSE125735 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data