GEO DataSets

(Submitter supplied) Nicolaides-Baraitser syndrome (NCBRS) is a neurodevelopmental disorder caused by pathogenic sequence variants in SMARCA2 which encodes the catalytic component of the chromatin remodeling BAF (SWI/SNF) complex. We identified an NCBRS-SMARCA2 DNA methylation (DNAm) signature of 429 differentially methylated CpG sites in blood cells of individuals with NCBRS (n=8) compared to neurotypical controls (n=23) using the Illumina MethylationEPIC array. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

44 Samples

Download data: IDAT, TXT

(Submitter supplied) Coffin-Siris and Nicolaides-Baraitser syndromes (CSS and NCBRS) are Mendelian disorders caused by mutations in subunits of the BAF chromatin remodeling complex. We report overlapping peripheral blood DNA methylation epi-signatures in individuals with various subtypes of CSS (ARID1B, SMARCB1, and SMARCA4) and NCBRS (SMARCA2). We demonstrate that the degree of similarity in the epi-signatures of some CSS subtypes and NCBRS can be greater than that within CSS, indicating a link in the functional basis of the two syndromes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL21145

29 Samples

Download data: IDAT, TXT

(Submitter supplied) Autism spectrum disorder (ASD) is a common and etiologically heterogeneous neurodevelopmental disorder. Although many genetic causes have been identified (>200 ASD-risk genes), no single gene mutation accounts for >1% of all ASD cases. A role for epigenetic mechanisms in ASD etiology is supported by the fact that many ASD-risk genes function as epigenetic regulators and evidence that epigenetic dysregulation can interrupt normal brain development. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

134 Samples

Download data: IDAT

(Submitter supplied) Disease-specific DNA methylation patterns (DNAm signatures) have been established for an increasing number of genetic disorders and represent a valuable tool for classification of genetic variants of uncertain significance (VUS). Sample size and batch effects are critical issues for establishing DNAm signatures, but their impact on the sensitivity and specificity of an already established DNAm signature as a predictive tool of variant pathogenicity has not previously been tested. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

62 Samples

Download data: IDAT, TXT

(Submitter supplied) Background: DNA methylation is influenced by both environmental and genetic factors and is increasingly thought to affect variation in complex traits and diseases. Yet, the extent of ancestry-related differences in DNA methylation, its genetic determinants, and their respective causal impact on immune gene regulation remain elusive. Results: We report extensive population differences in DNA methylation between 156 individuals of African and Europeandescent —detected in primary monocytes that were used as a model of a major innate immunity cell type. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL23976

156 Samples

Download data: CSV

(Submitter supplied) The vertebrate-specific transcription factor RE-1 silencing transcription factor or neuron-restrictive silencer factor (REST/NRSF) was first described as a negative regulator restricting expression of neuronal genes to neurons in a variety of genetic contexts. However, REST/NRSF has a more general role in the regulation of gene expression that involves chromatin remodelling via a SWI/SNF complex. We identified a 677 gene repertoire of potential REST/NRSF-dependent genes taking advantage of Rest/Nrsf gene silencing in a mouse cell line. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2872

6 Samples

Download data: GPR

(Submitter supplied) The molecular mechanisms that lead to the cognitive defects characteristic of Down syndrome (DS), the most frequent cause of mental retardation, have remained elusive. Here we use a transgenic DS mouse model to show that DYRK1A gene dosage imbalance deregulates chromosomal clusters of genes located near neuron-restrictive silencer factor (REST/NRSF) binding sites. We found that DYRK1A binds the SWI/SNF-complex known to interact with REST/NRSF. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2872

5 Samples

Download data: GPR

(Submitter supplied) The methylation status of a cohort of choroid plexus tumors was examined and unsupervised hierarchical clustering was used to identify molecular distinct clusters of samples.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

36 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array

Platforms:

GPL15793 GPL6801 GPL5175

115 Samples

Download data: CEL, TXT

(Submitter supplied) Genome wide DNA methylation profiling of whole blood at birth (Guthrie blood spots) and adulthood of individuals conceived by assisted reproductive technology (ART) and matched non-ART controls. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in guthrie cards and whole adult blood.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

440 Samples

Download data: CSV, IDAT

(Submitter supplied) SMARCA2 and SMARCA4 are two mutually exclusive ATPase subunits of SWI/SNF complex. SMARCA4 deficient lung cancer population selectively depend on SMARCA2 for cancer growth phenotype. Rescue experiments with ectopic expression of wild-type, bromodomain mutant and ATPase dead SMARCA2 and SMARCA4 highlight that ATPase domain is the drug target. In this study, we performed genome-wide microarray and differential gene expression profiling on isogenic lung cancer lines expressing cDNA rescue constructs for wild-type, bromodomain mutant and ATPase dead SMARCA2 and SMARCA4

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

32 Samples

Download data: CEL

(Submitter supplied) Acute chorioamnionitis (aCA) is a commonly reported histologic lesion in at least 40% of spontaneous preterm deliveries. It is typically characterized by an infiltration of maternal neutrophils into the chorioamniotic membranes and is also associated with other placental inflammatory lesions such as acute intervillositis and acute villitis. DNA methylation (DNam) is an easily measurable epigenetic mark, which is more stable than mRNA. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

79 Samples

Download data: CSV, IDAT

(Submitter supplied) Background: The widespread use of accessible peripheral tissues for epigenetic analyses has prompted increasing interest in the study of tissue-specific DNA methylation (DNAm) variation in human populations. To date, characterizations of inter-individual DNAm variability and DNAm concordance across tissues have been largely performed in adult tissues and therefore are limited in their relevance to DNAm profiles from pediatric samples. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

215 Samples

Download data: IDAT

(Submitter supplied) Background: Patients with paediatric-onset systemic lupus erythematosus (SLE) often present with more severe clinical courses than adult-onset patients. Although genome-wide DNA methylation (DNAm) profiling has been performed in adult-onset SLE patients, parallel data on paediatric-onset SLE are not available. Therefore, we undertook a genome-wide DNAm study in paediatric-onset SLE patients across multiple blood cell lineages. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

145 Samples

Download data: IDAT, TXT

(Submitter supplied) Genome-wide DNA methylation was measured using the Illumina 450K array in T cells, monocytes, granulocytes and nucleated red blood cells (nRBCs) isolated from cord blood of term and extreme preterm (<31 weeks gestational age) individuals. 36 samples in total: 5 each of T cells, monocytes, granulocytes and nRBCs from term births; and 5 T cells, 4 monocytes, 4 nRBCs and 3 granulocytes from preterm births.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

36 Samples

Download data: IDAT

(Submitter supplied) Epigenetic dysregulation has emerged as mechanism in the etiology of neurodevelopmental disorders. Two such disorders, CHARGE and Kabuki syndromes, result from loss of function mutations in chromodomain helicase DNA-binding protein 7 (CHD7LOF) and lysine (K) methyltransferase 2D (KMT2DLOF), respectively. We expected that epigenetically driven developmental pathways regulated by CHD7 and KMT2D would overlap and that DNA methylation (DNAm) alterations downstream of the mutations in these genes would identify common target genes, elucidating a mechanistic link between these conditions, as well as specific target genes for each. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

235 Samples

Download data: IDAT

(Submitter supplied) Neonatal molecular biomarkers of neurobehavioral responses (measures of brain-behavior relationships), when combined with neurobehavioral performance measures, could lead to better predictions of long-term developmental outcomes. To this end, we examined whether variability in epigenomic measures from buccal cells were associated with neurobehavioral profiles in a cohort of infants born less than 30 weeks postmenstrual age (PMA) and participating in the Neonatal Neurobehavior and Outcomes in Very Preterm Infants (NOVI) Study (N=536). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

542 Samples

Download data: IDAT, TXT

(Submitter supplied) Recently, it has been proposed that local DNA methylation profiles might be dictated by cis-regulatory DNA sequences that mainly operate via DNA-binding factors. Combining blood genome-wide DNA methylation profiles (Illumina Infinium MethylationEPIC BeadChiP), whole genome sequencing-derived single nucleotide variants (SNVs) along with predicted transcription factor binding site (TFBS), we were able to observe that rare regulatory variants, i.e, SNVs that disrupt TFBSs, are associated with DNA methylation at both local and, to a lesser extent, broader locations. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

267 Samples

Download data: IDAT, TXT

(Submitter supplied) DNA methylation profiling of airway epithelial cells (AECs) and peripheral blood mononuclear cells (PBMCs) from normal, atopic and asthmatic subjects. The Illumina GoldenGate Methylation Cancer Panel I was used to obtain DNA methylation profiles across approximately 1505 CpGs in AECs and PBMCs. Samples included 7 healthy, 9 atopic, 4 atopic asthmatic and 5 non-atopic asthmatic subjects. Please note that only some of the samples are matched (i.e. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

41 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of psoriatic (PP), paired uninvolved psoriatic (PN) and normal skin tissues (NN). The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 485,000 CpGs in 135 PP, 41PN and 62 NN tissues which were obtained from those who underwent skin biospsies. We not only revealed a genome-wide methylation level pattern for psoriasis, but also identified a strong association between the skin-specific DNAm of 9 DMS and psoriasis.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

219 Samples

Download data: TXT