GEO DataSets

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

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL9115 GPL11154

9 Samples

Download data: BED, TAR

(Submitter supplied) As genome-scale DNA methylation sequencing technologies have improved it has become apparent that tissue-specific methylation can occur not only at promoters, enhancers, and CpG islands but also over larger genomic regions. In most human tissues, the vast majority of the genome is highly methylated (>70%). However, genomic sequencing of bisulfite-treated DNA (MethylC-seq) has revealed large partially methylated domains (PMDs) in some human cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: FPKM_TRACKING

(Submitter supplied) As genome-scale DNA methylation sequencing technologies have improved it has become apparent that tissue-specific methylation can occur not only at promoters, enhancers, and CpG islands but also over larger genomic regions. In most human tissues, the vast majority of the genome is highly methylated (>70%). However, genomic sequencing of bisulfite-treated DNA (MethylC-seq) has revealed large partially methylated domains (PMDs) in some human cell lines. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL11154 GPL9115

7 Samples

Download data: BED, TAR

(Submitter supplied) DNA methylation is essential for embryonic and neuronal differentiation, but the function of most genomic DNA methylation marks are poorly understood. Generally the human genome is highly methylated (>70%) except for CpG islands and gene promoters. However, it was recently shown that the IMR90 human fetal lung fibroblast cells have large regions of the genome with partially methylated domains (PMDs, <70% average methylation), in contrast to the rest of the genome which is in highly methylated domains (HMDs, >70% average methylation). more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9115

2 Samples

Download data: BED

(Submitter supplied) Epigenetic perturbations in the early embryo could have later effects during development. For a disease such as autism, where a diagnosis is hard before two years of age but earlier intervention is correlated with better outcomes, finding a molecular signature of the disease at birth could have a significant impact of the quality of life. Since placenta also derives from the early embryo, is a readily-available tissue at birth, and has a unique DNA methylation pattern, we tested whether disruptions in placental DNA methylation was predictive of autism. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

51 Samples

Download data: TAR

(Submitter supplied) In this study, we generated whole genome bisulfite sequencing data of 19 samples for 13 tissues in Holstein cattle. We analyzed the variations of DNA methylation among tissues. In this study, we generated whole genome bisulfite sequencing data of 6 samples for 5 tissues in Hereford cattle. We analyzed the variations of DNA methylation among tissues.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24230

25 Samples

Download data: TXT

(Submitter supplied) In this study, we generated whole genome sequencing data from two Holstein cows using Lung tissue.

Organism:

Bos taurus

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL27907

2 Samples

Download data: VCF

(Submitter supplied) Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylation domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. more...

Organism:

Macaca mulatta; Equus caballus; Bos taurus; Mus musculus; Saimiri boliviensis; Homo sapiens; Canis lupus familiaris; Monodelphis domestica

Type:

Methylation profiling by high throughput sequencing

8 related Platforms

20 Samples

Download data: TAR

(Submitter supplied) Here we provided the first single-base resolution DNA methylatome in chicken lungs by whole-genome bisulfite sequencing (MethylC-seq). In addition, two genetically distinct highly inbred chicken lines, Leghorn and Fayoumi, were used to examine how DNA methylation regulates mRNA gene expression between two lines. The methylation profile demonstrated that methylcytosines in the chicken were more likely to occur in CG dinucleotides than in non-CG sites. more...

Organism:

Gallus gallus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9385

2 Samples

Download data: TXT

(Submitter supplied) We sought to compare genome-wide methylation patterns of human placenta with blood neutrophils, a homogenous somatic tissue

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

11 Samples

Download data: TXT

(Submitter supplied) Using neutrophils from a cohort of normal individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

13 Samples

Download data: TXT, XLSX

(Submitter supplied) The placental epigenome plays a vital role in regulating mammalian growth and development. Aberrations in placental DNA methylation are linked to several disease states, including intrauterine growth restriction and preeclampsia. Studying the evolution and development of the placental epigenome is critical to understanding the origin and progression of such diseases. Although high resolution studies have found substantial variation between placental methylomes of different species, the nature of methylome variation has yet to be characterized within any individual species. more...

Organism:

Mus musculus domesticus; Mus spretus; Mus musculus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL17106 GPL22153 GPL17637

35 Samples

Download data: BW

(Submitter supplied) We performed DNA methylome analysis by reduced representation bisulfite sequencing (RRBS) and gene expression analysis by RNA-Seq for both first and third trimester human placenta tissues.The correlation between DNA methylation and gene expression was non-linear and complex, depending on the genomic context (promoter or gene body) and gene expression levels. A wide range of DNA methylation and gene expression changes were observed at different gestational ages. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL10999

20 Samples

Download data: TXT, XLSX

(Submitter supplied) Aberrant DNA methylation is frequently observed in breast cancer. However, the relationship between methylation patterns and the heterogeneity of breast cancer has not been comprehensively characterized. Whole-genome DNA methylation analysis using 450K Illumina BeadArrays was performed on 188 human breast tumors. Unsupervised bootstrap consensus clustering was performed to identify DNA methylation epigenetic subgroups (epitypes). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

188 Samples

Download data: TXT

(Submitter supplied) We performed whole-genome methylation analysis using 450K Illumina BeadArrays on different human cell types. In total 24 experiments were performed. Dermal fibroblasts, three different epidermal melanocytes (dark, medium and light pigmentation), epidermal keratinocytes, mammary fibroblasts, mammary epithelial cells, mammary endothelial cells and mesenchymal stem cells were analyzed in technical duplicates. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

24 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL9115 GPL9851

22 Samples

Download data: GFF, WIG

(Submitter supplied) The aim was to analyze the expression of genes in cytogenetically distinct cases of AML.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL9851

6 Samples

Download data

(Submitter supplied) Methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq) has the potential to identify changes in DNA methylation important in cancer development. In order to understand the role of epigenetic modulation in the development of acute myeloid leukemia (AML) we have applied MeDIP-seq to the DNA of 12 AML patients and 4 normal bone marrows. This analysis revealed leukemia-associated differentially methylated regions that included gene promoters, gene bodies, CpG islands and CpG island shores. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9115

16 Samples

Download data: GFF, TXT, WIG

(Submitter supplied) Genome-wide DNA methylation profiles were obtained from colon adenocarcinoma samples (22), corresponding normal colon tissue (22) and cancer-unrelated normal colon tissue using Illumina HumanMethylation450 BeadChips. Approximately 485000 CpG sites were measured in every sample.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

63 Samples

Download data: TXT

(Submitter supplied) Background: the human placenta facilitates the exchange of nutrients, gas and waste between the fetal and maternal circulations. It also protects the fetus from the maternal immune response. Due to its role at the feto-maternal interface, the placenta is subject to many environmental exposures that can potentially alter its epigenetic profile. Previous studies have reported gene expression differences in placenta over gestation, as well as inter-individual variation in expression of some genes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

42 Samples

Download data: TXT