Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comprehensive DNA methylation analysis of neuronal and non-neuronal nuclei in the human brain

ABSTRACT: We performed comprehensive DNA methylation analysis in neuronal and non-neuronal nuclei obtained from the human prefrontal cortex. This revealed that neuronal and non-neuronal nuclei manifest qualitatively and quantitatively distinctive DNA methylation patterns.

ORGANISM(S): Homo sapiens

PROVIDER: GSE15014 | GEO | 2011/02/21

SECONDARY ACCESSION(S): PRJNA114731

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability [ATAC-Seq]

Project description:We analyzed differential methylation (via WGBS) between four distinct human brain regions (NAcc-nucleus accumbens, BA9-dorsolateral prefrontal cortex, BA24-anterior cingulate cortex, and HC-hippocampus) in both sorted nuclei and intact tissues. We isolated neuronal and non-neuronal (glial) nuclei from the same six individuals for each tissue via FACS using the neuronal marker, NeuN. Additionally, we performed WGBS from non-sorted tissues from these same brain regions in a total of 12 individuals (BA9 n = 9; BA24 n = 5; HC n = 6; NAcc n = 7). To complement our DNA methylation analyses, we measured gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) in neuronal and non-neuronal nuclei from the nucleus accumbens and dorsolateral prefrontal cortex from six more individuals. We then performed an integrative analysis to understand how the epigenome contributes to brain region-specific function.

2018-12-17 | GSE96614 | GEO

Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability [RNA-Seq]

2018-12-17 | GSE96613 | GEO

Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability [Bisulfite-Seq]

2018-12-17 | GSE96612 | GEO

Developmental Regulation and Individual Differences of Neuronal Epigenomes in the Prefrontal Cortex

Project description:We report global distribution of trimethylated Histone H3 Lysine 4 (H3K4me3) in human prefrontal cortex neurons at different ages Neuronal nuclei from human prefrontal cortex were isolated by FACS. Regions marked by H3K4me3 were identified by chromatin immunoprecipiation followed by deep sequencing.

2010-04-20 | E-GEOD-21172 | biostudies-arrayexpress

Brain neuronal cell nuclei with exceptionally high levels of hydroxymethylcytosine

Project description:We recently reported that a significant subpopulation of adult mouse brain cellular nuclei (NeuN-High) have highly decondensed chromatin characteristic of multipotent cells types (Yu et al., DNEU, 2015). Herein we show that NeuN-High nuclei also have significantly higher levels of 5´-hydroxymethylcytosine (5hmC), a rate limiting intermediate in the turnover of modified cytosine. TET-assisted bisulfite sequencing demonstrated that 5hmC levels in NeuN-High nuclei spiked rapidly from 20% to nearly 40% of CG dinucleotides at the start of gene regions for various classes of the most highly transcribed neuron-specific genes, but were variably distributed among different functional gene categories and in well-defined gene regions. NeuN-Low neuronal and non-nueronal neuronal nuclei had significantly lower levels of 5hmC for all classes of expressed genes. In summary, these data support the view that an elevated turnover rate for chromatin modifications may potentiate the cellular memory of the most active subclasses of neurons.

2022-07-07 | GSE72432 | GEO

Deciphering H3K4me3 Broad Domains Associated With Gene Regulatory Networks and Conserved Epigenomic Landscapes in the Human Brain [ChIP-Seq]

Project description:Trimethylated histone H3-lysine 4 is primarily distributed in the form of sharp peaks, extending in neuronal chromatin on average only across 500-1500 base pairs mostly in close proximity to annotated transcription start sites. To explore whether H3K4me3 peaks could also extend across much broader domains, we undertook a detailed analysis of broadest domain cell-type specific H3K4me3 peaks in ChIP-seq datasets from sorted neuronal and non-neuronal nuclei in human, non-human primate and mouse prefrontal cortex (PFC), and blood for comparison. In this GEO submission, we list six newly generated ChIP-seq data sets. FACS sorted Neuronal (NeuN+) nuclei and non-neuronal (NeuN-) nuclei collected from prefrontal cortex (PFC) and processed by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq). In addition we collected nucleated blood cells from 3 control subjects. These are additional subjects unrelated to brain cohort.

2016-07-21 | E-GEOD-72929 | biostudies-arrayexpress

Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites [methylation array]

Project description:We applied Illumina Human Methylation450K array to perform a genomic-scale single-site resolution DNA methylation analysis in neuronal and nonneuronal (primarily glial) nuclei separated from the orbitofrontal cortex of postmortem human brain. The findings were validated using enhanced reduced representation bisulfite sequencing. We identified thousands of sites differentially methylated (DM) between neuronal and nonneuronal cells. The DM sites were depleted within CpG island–containing promoters but enriched in predicted enhancers. Classification of the DM sites into those undermethylated in neurons (neuronal type) and those undermethylated in nonneuronal cells (glial type), combined with findings of others that methylation within control elements typically negatively correlates with gene expression, yielded large sets of predicted neuron-specific and non– neuron-specific genes. These sets of predicted genes were in excellent agreement with the available direct measurements of gene expression in human and mouse. We also found a distinct set of DNA methylation patterns that were unique for neuronal cells. In particular, neuronal-type differential methylation was overrepresented in CpG island shores, enriched within gene bodies but not in intergenic regions, and preferentially harbored binding motifs for a distinct set of transcription factors, including neuron-specific activity-dependent factors. Finally, non-CpG methylation was substantially more prevalent in neurons than in nonneuronal cells. Genomic DNA was isolated from FACS-sorted human brain neuronal and nonneuronal nuclei. DNA was bisulfite converted and hybridised to the Illumina Infinium 450K Human Methylation Beadchip array. Six subjects in two technical replicate expriments were analyzed.

2013-09-13 | E-GEOD-50798 | biostudies-arrayexpress

Neuronal Methylome in Multiple Sclerosis

Project description:DNA methylation profiling of NeuN+sorted neuronal nuclei from post-mortem brain tissue of Multiple Sclerosis (MS) patients (n=10) (MS) and non-neurological controls (n=7) (non-MS). Genomic DNA was subjected to conventional BS-treatment as well as oxidative BS (oxBS)-conversion using TrueMethylTM 96 kit of CEGXTM (Cambridge Epigenetix Limited) to allow for subsequent detection of hydroxymethylation (5hmC = BS - oxBS).

2019-06-21 | GSE119532 | GEO

Microglial remodeling of the extracellular matrix promotes synapse plasticity [Neuronal nuclei]

Project description:Microglial remodeling of the extracellular matrix promotes synapse plasticity [Neuronal nuclei]

| PRJNA633364 | ENA

Profiling the transcriptome of excitatory neuronal nuclei during pilocarpine-induced seizure

Project description:The initial seizure-induced events in neuronal nuclei can lead to long-term changes in gene expression and cellular responses that likely contribute toward epileptogenesis. Using a transgenic mouse model to specifically isolate excitatory neuronal nuclei, we profiled the seizure-induced nuclear transcriptome by RNA-seq, as well as proteome via tandem mass tag mass spectrometry (available at ProteomeXchange via PRIDE; Accession ID: PXD030637). In the transcriptome, we observed robust induction of genes involved in multiple processes, including MAPK signalling, and downregulation of zinc finger genes harbouring Krüppel-associated box (KRAB) domains, which were strongly enriched for binding sites of the Thap11/Ronin transcriptional repressor. Additionally, we characterised gene expression in introns, which provided further insights into seizure-driven transcriptional regulation and dynamics, including repression of transcription mediated by zinc finger transcription factors. Our results provide a detailed snapshot of nuclear events induced by seizure activity and demonstrate a robust method for cell-type-specific nuclear profiling that can be applied to other cell types and models.

2023-03-31 | GSE205454 | 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