GEO DataSets

(Submitter supplied) A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation, particularly within the context of human tissues. We describe a set of integrated experiments designed to investigate the effects of common genetic variability on DNA methylation, mRNA expression and microRNA (miRNA) expression in four distinct human brain regions. We show that brain tissues may be readily distinguished based on methylation status or expression profile. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array; Methylation profiling by array

Platforms:

GPL8490 GPL6104 GPL8178

1658 Samples

Download data: TXT

(Submitter supplied) In this study, we investigated the interaction between CpG methylation and genetic polymorphisms by taking the advantage of the family structure in 22 nuclear pedigrees. We have identified CpG sites that exhibit heritable methylation patterns, among which the majority are SNPs ditrectly disrupting CpG dinucleotides. We also identified 27.2% of the heritable non-SNP CpGs were associated with cis-regulatory SNPs. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

96 Samples

Download data: TXT

(Submitter supplied) Background DNA methylation has long been known to play an essential role in the epigenetic regulation of gene expression and other cellular functions, and has been in some cases linked to genetic variation. While its presence near the transcription start site of a gene has been associated with reduced expression, the variation in methylation levels across individuals, its environmental or genetic causes, and its association with gene expression remain poorly understood. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; SNP genotyping by SNP array; Genome variation profiling by SNP array; Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing

4 related Platforms

304 Samples

Download data: IDAT, TXT

(Submitter supplied) Background: DNA methylation has long been known to play an essential role in the epigenetic regulation of gene expression and other cellular functions, and has been in some cases linked to genetic variation. While its presence near the transcription start site of a gene has been associated with reduced expression, the variation in methylation levels across individuals, its environmental or genetic causes, and its association with gene expression remain poorly understood. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

64 Samples

Download data: TXT

(Submitter supplied) Background DNA methylation has long been known to play an essential role in the epigenetic regulation of gene expression and other cellular functions, and has been in some cases linked to genetic variation. While its presence near the transcription start site of a gene has been associated with reduced expression, the variation in methylation levels across individuals, its environmental or genetic causes, and its association with gene expression remain poorly understood. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL6984

174 Samples

Download data: TXT

(Submitter supplied) Background DNA methylation has long been known to play an essential role in the epigenetic regulation of gene expression and other cellular functions, and has been in some cases linked to genetic variation. While its presence near the transcription start site of a gene has been associated with reduced expression, the variation in methylation levels across individuals, its environmental or genetic causes, and its association with gene expression remain poorly understood. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

62 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL21145 GPL13534

1812 Samples

Download data: IDAT

(Submitter supplied) African-American individuals of the GENOA study

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

1394 Samples

Download data: IDAT, TXT

(Submitter supplied) African-American individuals of the GENOA study

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

418 Samples

Download data: IDAT, TXT

(Submitter supplied) We measured the methylation status at 27,578 CpG sites using the Human Methylation27 DNA array in 77 HapMap Yoruba lymphoblastoid cell lines.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

160 Samples

Download data: IDAT, TXT

(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) Genome wide DNA methylation profiling of normal lung tissue samples. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in nor mal lung tissue samples. Samples included 244 normal lung tissue samples from lung cancer patients.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

244 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by array; SNP genotyping by SNP array

4 related Platforms

105 Samples

Download data

(Submitter supplied) 48 ǂKhomani San living in the South African Kalahari were genotyped using the Illumina OmniExpress, OmniExpress Plus, and HumanHap550 arrays

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platforms:

GPL18900 GPL6982 GPL20333

48 Samples

Download data: BIM, DATA, FAM, MAP, PED

(Submitter supplied) Genome-wide DNA methylation profiling was conducted in two batches for 56 ǂKhomani San living in the South African Kalahari using the Illumina 450k array on saliva-derived DNA

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

57 Samples

Download data: CSV

(Submitter supplied) Elucidating cytosine modification difference between human populations can enhance our understanding of ethnic specificity in complex traits such as disease predisposition and drug response. In this study, cytosine modification levels in 133 HapMap lymphoblastoid cell lines (LCLs) derived from individuals of European or African ancestry were profiled using the Illumina HumanMethylation450 BeadChip. Approximately 13% of the analyzed CpG sites showed differential modification between the two populations at false discovery rate (FDR) of 1%. CpG sites with greater modification levels in European descents were enriched in the proximal regulatory regions, while those greater in African descents were biased toward gene bodies. More than half of the detected population-specific cytosine modifications could be explained by genetic variation. A substantial proportion of local modification quantitative trait loci (mQTL) exhibited population-specific effects, suggesting that genetic epistasis and/or genotype × environment interaction could be common. Distinct inter-individual correlations were observed between gene expression and cytosine modifications in both proximal promoters and gene bodies, demonstrating a regulatory role of inter-individual variation in cytosine modification. Furthermore, a number of SNPs (single nucleotide polymorphisms) previously identified for complex traits with known racial disparities could be annotated as mQTLs for population-specific CpGs. Our findings revealed abundant population-specific cytosine modifications and the underlying genetic basis, as well as the relatively independent contribution of genetic and epigenetic variations to population differences in gene expression.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

133 Samples

Download data: TXT

(Submitter supplied) DNA methylation in CpG context is fundamental to the epigenetic regulation of gene expression in high eukaryotes. Disorganization of methylation status is implicated in many diseases, cellular differentiation, imprinting, and other biological processes. Techniques that enrich for biologically relevant CpG-rich genomic regions are desired since, depending on the size of an oragnism's methylome, the depth of sequencing required to cover all CpGs can be prohibitively expensive. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16791

7 Samples

Download data: TXT