GEO DataSets

(Submitter supplied) Open chromatin is implicated in regulatory processes, and thus variation in chromatin structure may contribute to variation in gene expression and other molecular phenotypes. In this work, we performed a targeted deep sequencing to identify somatic mutations and genetic polymorphisms underlying accessible chromatin in the genomes of 72 monozygotic twins.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

72 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL10558 GPL11154

144 Samples

Download data: BED

(Submitter supplied) Open chromatin is implicated in regulatory processes, and thus variation in chromatin structure may contribute to variation in gene expression and other molecular phenotypes. In this work, we performed a targeted deep sequencing to identify somatic mutations and genetic polymorphisms underlying accessible chromatin in the genomes of 72 monozygotic twins.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

72 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of Rett syndrome monozygotic twins. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles in primary skin fibroblast cells from Rett syndrome monozygotic twins.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

2 Samples

Download data: TXT

(Submitter supplied) In this study, we used Illumina Infinium HumanMethylation450 Beadchips to compare DNA methylation profiles in blood from 10 pairs of MZ twins and 8 individuals recruited at 0, 3, 6, and 9 months.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

60 Samples

Download data: TXT

(Submitter supplied) Two families with monozygotic twins discordant for schizophrenia

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL17148

8 Samples

Download data: GFF, PAIR

(Submitter supplied) Comparison between groups of monozygotic (MZ) and dizygotic (DZ) twins enables an estimation of the relative contribution of genetic, shared and non-shared environmental factors to phenotypic variability. Using DNA methylation profiling of ~20,000 CpG sites as a phenotype, we have examined discordance levels in multiple tissues in neonatal twins. MZ twins exhibit a wide range of within-pair differences at birth, but show discordance levels generally lower than DZ pairs. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

123 Samples

Download data: TXT

(Submitter supplied) Epigenetic profiling of birth-weight discordant twins using Illumina's 450K Human DNA methylation BeadChip

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

312 Samples

Download data: CSV, IDAT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ~300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing

Platforms:

GPL13534 GPL11154

74 Samples

Download data: TXT

(Submitter supplied) DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ~300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

64 Samples

Download data: TXT

(Submitter supplied) DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ~300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

10 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 genome tiling array

Platforms:

GPL6244 GPL5082

68 Samples

Download data: BED, CEL

(Submitter supplied) Human intelligence demonstrates one of the highest heritabilities among human quantitative traits. Phenotypically discordant monozygotic twins provide a way to identify loci reponsible for the phenotypical differences. We performed comprehensive DNA methylation analysis in monozygotic twins manifesting differences in IQ scores. Genes with significantly different methylation status are considered as candidates related to human intelligence.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL5082

34 Samples

Download data: BED, CEL

(Submitter supplied) Human intelligence demonstrates one of the highest heritabilities among human quantitative traits. Phenotypically discordant monozygotic twins provide a way to identify loci responsible for normal-range intelligence. We conducted array-based genome-wide gene expression analysis aiming to identify genes displaying significant difference among monozygotic twin pairs manifesting between-co-twins IQ differences.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

34 Samples

Download data: CEL

(Submitter supplied) Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enhancers, insulators, silencers, replication origins, and recombination hotspots. For a quantitative getic analysis of chromatin regulation, we generated open chromatin maps of 100 yeast samples including the parental strains (BY and RM, and two replicates for each) and their descendants by using the FAIRE-seq technique

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

96 Samples

Download data: BED

(Submitter supplied) Human tumors are comprised of heterogeneous cell populations that display diverse molecular and phenotypic features. To examine the extent to which epigenetic differences contribute to intratumoral cellular heterogeneity, we have developed a high-throughput method, termed MAPit-patch. The method uses multiplexed amplification of targeted sequences from sub-microgram input quantities of genomic DNA followed by next generation bisulfite sequencing. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL14603

4 Samples

Download data: FA, TSV, TXT

(Submitter supplied) To compare the expression profile of differentiated mouse bone marrow macrophages (BMM) in response to IL-4, we have employed whole genome microarray expression profiling. For this purpose, bone marrow cells were isolated from 8 to 12 weeks old C57BL6/J and Balb/cAnNCrl mice and cultured in the presence of the macrophage colony-stimulating factor (M-CSF). After seven days of culture, IL-4 was added for 4 and 18 hours. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

12 Samples

Download data: TXT

(Submitter supplied) DNA-methylation is a vital epigenetic mark that participates in establishing and maintaining chromatin structures and in regulating gene transcription during mammalian development and cellular differentiation. Inter-individual differences in methylation patterns may represent a major source of phenotypic variation, however, the determinants, inheritance, extent, and consequences of such differences are poorly understood. more...

Organism:

Mus musculus

Type:

Methylation profiling by genome tiling array; Genome variation profiling by genome tiling array

Platform:

GPL8085

4 Samples

Download data: TXT

(Submitter supplied) Background: Low birth weight is associated with an increased adult metabolic disease risk. It is widely discussed that poor intrauterine conditions could induce long-lasting epigenetic modifications, leading to systemic changes in regulation of metabolic genes. In a unique cohort of 17 monozygotic (MZ) monochorionic female twins very discordant for birth weight (relative differences ranging from 21.3-35.7%), we examined if adverse prenatal growth conditions experienced by the smaller co-twins lead to systemic long-lasting DNA methylation changes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

34 Samples

Download data

(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