GEO DataSets

(Submitter supplied) Micrococcal nuclease (Mnase) treatment and sequencing of mononucleosomal DNA

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

1 Sample

Download data: WIG

(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) Genome wide DNA methylation profiling of normal whole blood samples. The data consist of 100 samples with Illumina HumanMethylation450 BeadChip data.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

100 Samples

Download data: TXT

(Submitter supplied) EpiSELEX-seq method was used to characterize the binding preference of human TF complexes to methylated DNA, including BZIP proteins ATF4 and CEBPb, homeodomain TF heterodimers of HM(Meis1)-Pbx1 together with either HoxA1, HoxA5 or HoxA9 and tumor suppressor protein p53.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

13 Samples

Download data: TXT

(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) DNA methylation stabilizes developmentally programmed gene expression states. Aberrant methylation is associated with disease progression and is a common feature of cancer genomes. Presently, few methods enable quantitative, large-scale, single-base resolution mapping of DNA methylation states in desired regions of a complex mammalian genome. Here, we present an approach that combines array-based hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in genomic regions spanning hundreds of thousands of bases. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL9115

4 Samples

Download data: BED, TXT

(Submitter supplied) Here we used Illumina NGS for high-throughput profiling of the DNA methylome in two human colon cancer derived cell lines, two human normal bone marrow CD34+ controls and in five human Acutre Myeloid Leukeima patient samples. These data can be used to determine the CpG cytosine methylation pattern at base pair resolution in each sample and to determine differentially methylated cytosines and regions between samples

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154

19 Samples

Download data: TXT

(Submitter supplied) Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these 'relatively young' genes was critical for the origin and radiation of eukaryotes.

Organism:

Magallana gigas

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13986

2 Samples

Download data: TXT

(Submitter supplied) Deep sequencing of samples from different development stages, different adult organs and different stress treatments of Pacific oyster Crassostrea gigas

Organism:

Magallana gigas

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13986

112 Samples

Download data: BEDGRAPH

(Submitter supplied) Methylation is a repressive modification of DNA prevalent throughout mammalian genomes yet mostly absent at CG rich stretches referred to as CGI. Here we identify their building principles by parallel genomic targeting of sequence libraries. Iterative insertions generated over 3,000 variants of genome-derived and artificial sequences at the same genomic site. Single molecule profiling of the methylation status of this collection allowed modeling the contribution of CG content and DNA binding factors towards the unmethylated state. more...

Organism:

Mus musculus; Escherichia coli; synthetic construct

Type:

Methylation profiling by high throughput sequencing

5 related Platforms

19 Samples

Download data: 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 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 plays an important role in development and disease. The primary sites of DNA methylation in vertebrates are cytosines in the CpG dinucleotide context, which account for roughly three quarters of the total DNA methylation content in human and mouse cells. While the genomic distribution, inter-individual stability and functional role of CpG methylation are reasonably well understood, little is known about DNA methylation targeting CpA, CpC and CpT dinucleotides. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9115

37 Samples

Download data: BED

(Submitter supplied) Our study supports a role for H3K9 methylation in promoting DNA methylation, it demonstrates for the first time that DNA maintenance methylation in mammalian cells is to large extent independent on H3K9 methylation.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9185

2 Samples

Download data: TXT

(Submitter supplied) We examine genome-wide DNA methylation profiles in 66 pairs of HCC tumor and adjacent non-tumor tissues. After Bonferroni adjustment, a total of 130,512 CpG sites significantly differed in methylation level in tumor compared to non-tumor tissues, with 28,017 CpG sites hypermethylated and 102,495 hypomethylated in tumor tissues. Most (60.1%) significantly hypermethylated CpG sites are located in CpG islands. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

132 Samples

Download data: CSV

(Submitter supplied) We report the application of single molecule-based sequencing technology in combination with CXXC affinity purifcation (CAP-seq), MBD affinity purification (MAP-seq) and chromatin immunoprecipitation (ChIP-seq) to generate reciprocal methylation and chromatin modifcation maps in human and mouse. We find that contrary to sequence based prediction methods that humans and mice possess highly equivalent compliments of CpG islands (CGIs). more...

Organism:

Homo sapiens; Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9185 GPL9052

32 Samples

Download data: BEDGRAPH

(Submitter supplied) Abstract: DNA methylation is an essential epigenetic modification that plays a key role associated with the regulation of gene expression during differentiation but in disease states such as cancer, the DNA methylation landscape is often deregulated. There are now numerous technologies available to interrogate DNA methylation status of CpG sites in a targeted or genome-wide fashion but each method, due to intrinsic biases, potentially interrogates different fractions of the genome. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6801 GPL9115 GPL5082

40 Samples

Download data: CEL, MAP, TXT

(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:

Homo sapiens; Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9520 GPL10010

8 Samples

Download data: BED, TXT

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

Organism:

Nasonia vitripennis

Type:

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

Platforms:

GPL16489 GPL16488

3 Samples

Download data: TXT