GEO DataSets

(Submitter supplied) To gain insights into the function of DNA methylation at cis-regulatory regions and its impact on gene expression, we measured methylation, RNA polymerase II and histone modifications at 24.000 promoters in primary human soma and germline cells. Keywords: DNA methylation, MeDIP

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array

Platform:

GPL3497

11 Samples

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(Submitter supplied) Understanding cell-type-specific epigenetic codes on a global level is a major challenge after the sequencing of the human genome has been completed. Here we applied methyl-CpG immunoprecipitation (MCIp) to obtain comparative methylation profiles of coding and noncoding genes in three human tissues, testis, brain, and monocytes. Forty-four mainly testis-specific promoters were independently validated using bisulfite sequencing or single-gene MCIp, confirming the results obtained by the MCIp microarray approach. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL4090 GPL4089

8 Samples

Download data: TIFF, TXT

(Submitter supplied) The goal of the experiment – genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters Keywords: DNA methylation, Methylated CpG island amplification coupled with promoter arrays, normal tissue

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

4 related Platforms

4 Samples

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(Submitter supplied) Eukaryotic gene regulatory information is contained within the DNA sequences of cis-regulatory elements and the epigenetic features of the chromatin surrounding these elements. Recent investigations in yeast, fly, and mammalian systems have made significant contributions toward our understanding of the relationship between gene activation and chromatin architecture at transcriptional promoters, but much work remains to improve our knowledge of this relationship at human promoters and other transcriptional regulatory elements, such as enhancers. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4558 GPL4559 GPL1454

64 Samples

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(Submitter supplied) Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. more...

Organism:

Oryza sativa; Tribolium castaneum; Nematostella vectensis; Volvox carteri; Coprinopsis cinerea; Bombyx mori; Ciona intestinalis; Tetraodon nigroviridis; Chlorella variabilis; Physcomitrium patens; Phycomyces blakesleeanus; Drosophila melanogaster; Apis mellifera; Laccaria bicolor; Uncinocarpus reesii; Selaginella moellendorffii; Postia placenta

Type:

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

17 related Platforms

33 Samples

Download data: GFF, TXT

(Submitter supplied) This experiment series sought to detect genome-wide methylation in sporadic amyotrophic lateral sclerosis brains and compare it to normal control brains. Methylation across the whole genome was measured in brain DNA of 10 SALS patients and 10 neurologically-normal controls. Methylated DNA was immunoprecipitated and interrogated by Affymetrix GeneChip Human Tiling 2.0R Array Sets. Methylation calls were compared between SALS patients and controls at each methylated site. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

7 related Platforms

148 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) We profiled CpG methylation for human T cells and compared this pattern with public T cell nucleosome (H2A.Z) and polymerase II profiles (SRA000234). Focusing on DNA regions surrounding the start codon and stop codon, instead of the transcription start and end sites, we discovered a very intriguing pattern, namely methylation and nucleosomal peaks at those regions, more prominent than peaks near transcript boundaries. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9052

1 Sample

Download data: BED

(Submitter supplied) We report a new method for genome-wide methylation profiling that is able to probe methylation status in both single-copy DNA and interspersed repeats. This method, MethylMAPS, uses methylation-sensitive and -dependent enzymes to fractionate the genome according to methylation state. Methylated and unmethylated fragments are then sequenced with Next-Gen sequencing to map methylated and unmethylated CpG sites in the genome. more...

Organism:

Mus musculus; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL10010 GPL9520

8 Samples

Download data: BED, TXT

(Submitter supplied) We used HCT116 colorectal cancer cells with and without mutations in DNA methyltransferases (resulting in a 95% reduction in global DNA methylation levels) to study the relationship between DNA methylation, histone modifications, and gene expression. (The double knockout cell line is called DKO1)

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

11 Samples

Download data: BED, BW, GFF

(Submitter supplied) Using a methylated-DNA enrichment technique (MIRA) in combination with whole genome tiling arrays, we have characterized by MIRA-chip the entire B cell ‘methylome’ of an individual human at 100 base pair resolution.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

38 related Platforms

38 Samples

Download data: TXT

(Submitter supplied) Chromosomal methylation profiles of normal and transformed cell lines Keywords: parallel sample

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL2047 GPL2043

4 Samples

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(Submitter supplied) We compare the methylation status of CpG island clones by MeDIP in SW48 colon cancer cells relative to normal colon mucosa and WI38 primary fibroblasts. Keywords: ordered

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL2040

7 Samples

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

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

12 Samples

Download data: BED, FPKM_TRACKING

(Submitter supplied) DNA methylation is a dynamic epigenetic modification that plays a key role in various cellular processes. Proteins that bind to DNA depending on its methylation status are thought to play an important role in DNA methylation-mediated gene expression. Using a variety of genomics and proteomics approaches, we identified ZBTB2 as a novel reader of unmethylated DNA. ZBTB2, which forms a complex with ZBTB25 and ZNF639, preferentially binds at CpG island promoters in mouse embryonic stem cells, from where it regulates genes that are involved in the exit from pluripotency. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: DIFF, FPKM_TRACKING

(Submitter supplied) DNA methylation is a dynamic epigenetic modification that plays a key role in various cellular processes. Proteins that bind to DNA depending on its methylation status are thought to play an important role in DNA methylation-mediated gene expression. Using a variety of genomics and proteomics approaches, we identified ZBTB2 as a novel reader of unmethylated DNA. ZBTB2, which forms a complex with ZBTB25 and ZNF639, preferentially binds at CpG island promoters in mouse embryonic stem cells, from where it regulates genes that are involved in the exit from pluripotency. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: BED

(Submitter supplied) By depleting CGGBP1 in normal human fibroblasts 1064Sk using lentiviral shmiR (non-targeting or targeting CGGBP1) and by performing genome-wide sequencing (on bisulfite converted genomic DNA from both samples) we show that both gain and loss of cytosine methylation occurs upon CGGBP1 depletion. This gain and loss of methylation is clustered, spatially overlapping at major functional genomic regions and transcends all three cytosine sequence contexts. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9052

2 Samples

Download data: BED, TXT

(Submitter supplied) Publication title: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions throughout the genome. Performing Methyl-seq on human embryonic stem cells (hESCs), their derivatives and human tissues allowed us to identify several trends during hESC and in vivo liver differentiation. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9052

17 Samples

Download data: TXT

(Submitter supplied) Publication title: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions throughout the genome. Performing Methyl-seq on human embryonic stem cells (hESCs), their derivatives and human tissues allowed us to identify several trends during hESC and in vivo liver differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5060

15 Samples

Download data: TXT

(Submitter supplied) Publication title: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions throughout the genome. Performing Methyl-seq on human embryonic stem cells (hESCs), their derivatives and human tissues allowed us to identify several trends during hESC and in vivo liver differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by high throughput sequencing

Platforms:

GPL5060 GPL9052

32 Samples

Download data: TXT

(Submitter supplied) DNA methylation in sperm is among the most important factors shaping evolution of the mammalian genome. By directly altering germline mutation rates, the DNA methylation system has shaped the CpG landscape of mammalian genomes, resulting in the CpG island phenomenon. Yet little is known about how this system itself has co-evolved with its substrate during mammalian evolution. We analyzed full-genome single-CpG DNA methylation profiles in sperm from human, chimp, gorilla, rhesus, mouse, rat and dog. more...

Organism:

Gorilla gorilla; Rattus norvegicus; Canis lupus familiaris

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL18694 GPL16540 GPL21650

12 Samples

Download data: TXT