Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tethered Oligonucleotide-Primed sequencing (TOP-seq): a high resolution economical approach for DNA epigenome profiling

ABSTRACT: We describe the development and thorough validation of a new approach for epigenome analysis (named TOP-seq) that is based on a novel concept – combination of selective covalent tagging and targeted genomic sequencing of the genome. The technique reports the modification status of each genomic CpG site by priming the DNA polymerase action from a tethered oligonucleotide probe that is selectively attached to the unmodified CpG sites.

ORGANISM(S): Homo sapiens

PROVIDER: GSE91023 | GEO | 2017/01/16

SECONDARY ACCESSION(S): PRJNA356692

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

DNA unmethylome profiling by covalent capture of CpG sites

Project description:Here we present an approach for the mapping of unmethylated DNA. Our technique is based on DNA methyltransferase-directed transfer of activated groups (mTAG) and covalent biotin tagging of unmodified CpG sites followed by affinity enrichment and interogation on tiling microarrays or next generation sequencing. mTAG labeled genomic DNA of one sample

2013-08-27 | E-GEOD-48994 | biostudies-arrayexpress

DNA unmethylome profiling by covalent capture of CpG sites (microarray)

2013-08-27 | E-GEOD-49044 | biostudies-arrayexpress

DNA unmethylome profiling by covalent capture of CpG sites (microarray)

2013-08-27 | GSE49044 | GEO

DNA unmethylome profiling by covalent capture of CpG sites

2013-08-27 | GSE48994 | GEO

Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling.

Project description: Not available

| S-EPMC5291818 | biostudies-literature

DNA unmethylome profiling via covalent capture of CpG sites

Project description:Cytosine 5-modification is a widespread epigenetic mark in eukaryote genomes including humans, but its large scale populational studies are hampered by substantial limitations of the existing analytical techniques. We have developed a new approach for mapping of the unmodified fraction of the genome, i.e. DNA unmethylome, which is based on covalent tagging of unmodified CpG sites with biotin. Sequence-specific tagging of DNA was achieved by using an engineered version of the SssI cytosine-5 methyltransferase and a synthetic analog of the S-adenosylmethionine cofactor carrying a transferable 6-aminohex-2-ynyl group. Analysis of the streptavidin-enriched human unmethylome on tiling DNA microarrays showed that the new approach (named mTAG-chip) offers nanogram sensitivity, a substantially higher precision in the low and medium CpG density regions and added versatility as compared with the existing epigenome profiling techniques.

2012-03-08 | GSE36305 | GEO

Unified analysis of DNA methylation, hydroxymethylation and chromatin accessibility through targeted DNA labeling [TOP-Seq]

Project description:Epigenetic regulation depends on complex interactions between different epigenetic factors, such as DNA methylation and chromatin accessibility. As the gene activation potential cannot be predicted by looking at chromatin accessibility or DNA modification alone, methods capable of relating multiple factors are highly desirable. Existing methods for combined chromatin accessibility and DNA modification analysis rely on bisulfite sequencing, which has a number of well known drawbacks. We developed a novel cost-efficient method for simultaneous profiling of DNA methylation and hydroxymethylation within open chromatin loci. Our approach is based on chemo-enzymatic covalent tagging of unmodified (uCG) and hydroxymethylated (5hmC) CG sites along with GC sites in native chromatin, which are then mapped by tag-selective sequencing. Validation of the technology on model DNA systems and mammalian cells demonstrated a great applicability of this method for epigenomic studies. We employed the technology for tracking chromatin dynamics combined with changes of two different cytosine states, unmodified and hydroxymethylated, during differentiation of embryonic stem cells (ESC) which revealed extensive chromatin dynamics and DNA modification changes across gene bodies of development-associated genes at early transition from ESC. Strong DNA demethylation in the ESC-to-neuron differentiation pathway proceeds independently from cell transcriptional programs and highlights the value of separate 5hmC and 5mC analysis in understanding cell fate decisions.

2023-12-01 | GSE231928 | GEO

DNA unmethylome profiling via covalent capture of CpG sites

2012-03-08 | E-GEOD-36305 | biostudies-arrayexpress

Transcription profiling of yeast strains in which Hsk1-Dfp1 has been tethered near a replication origin

Project description:Transcription profiling of strains in which Hsk1-Dfp1 has been tethered near a replication origin.

2008-09-25 | E-MEXP-1811 | biostudies-arrayexpress

Large-scale tethered function assays identify factors that regulate mRNA stability and translation (eCLIP)

Project description:Enhanced UV crosslinking and immunoprecipitation (eCLIP) identifies thousands of endogenous mRNA targets for these prioritized RBPs that respond to protein level changes reminiscent of their effects in tethered functional assay.

2020-08-18 | GSE117290 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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