GEO DataSets

(Submitter supplied) Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation. In lower vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. more...

Organism:

Xenopus tropicalis; Homo sapiens; Mus musculus; Anolis carolinensis; Danio rerio; Gallus gallus; Ornithorhynchus anatinus

Type:

Methylation profiling by high throughput sequencing

10 related Platforms

24 Samples

Download data: BED

(Submitter supplied) DNA methylation is an epigenetic modification of the vertebrate genome that contributes to transcriptional repression, imprinting, and X-chromosome inactivation. While the majority of the genome is blanketed in DNA methylation, regions known as CpG islands (CGIs) remain remarkably refractory to this modification. CpG islands are associated with roughly two thirds of gene promoters, are evolutionarily conserved, and play central roles in gene regulation, yet how they are protected from DNA methylation remains enigmatic. more...

Organism:

Mus musculus; Danio rerio

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL13112 GPL20828

17 Samples

Download data: BED

(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:

Mus musculus; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9052 GPL9185

32 Samples

Download data: BEDGRAPH

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL6887 GPL9185

28 Samples

Download data: BEDGRAPH

(Submitter supplied) Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites. In both species, about 50% of all CGIs are remote from annotated promoters, but nevertheless often have promoter-like features. To document the role of CGI methylation in cell differentiation, we analysed DNA methylation at a comprehensive CGI set in cells of the mouse hematopoietic lineage. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL9185

10 Samples

Download data: BEDGRAPH

(Submitter supplied) Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites. In both species, about 50% of all CGIs are remote from annotated promoters, but nevertheless often have promoter-like features. To document the role of CGI methylation in cell differentiation, we analysed DNA methylation at a comprehensive CGI set in cells of the mouse hematopoietic lineage. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

18 Samples

Download data: TXT

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

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13112 GPL19415 GPL18573

8 Samples

Download data: BW

(Submitter supplied) The human genome contains approximately 27,700 CpG islands (CGIs). Most are associated with promoters and their DNA is nearly always unmethylated. By contrast, CGIs lying within the bodies of genes usually become methylated during differentiation and development. CGIs also normally become methylated at X-inactivated and imprinted genes and abnormally methylated in genome rearrangements and in malignancy. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: BW

(Submitter supplied) The human genome contains approximately 27,700 CpG islands (CGIs). Most are associated with promoters and their DNA is nearly always unmethylated. By contrast, CGIs lying within the bodies of genes usually become methylated during differentiation and development. CGIs also normally become methylated at X-inactivated and imprinted genes and abnormally methylated in genome rearrangements and in malignancy. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19415

2 Samples

Download data: BW

(Submitter supplied) The human genome contains approximately 27,700 CpG islands (CGIs). Most are associated with promoters and their DNA is nearly always unmethylated. By contrast, CGIs lying within the bodies of genes usually become methylated during differentiation and development. CGIs also normally become methylated at X-inactivated and imprinted genes and abnormally methylated in genome rearrangements and in malignancy. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: BW

(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 performed microarray experiments on gastric tissue samples to identify the differential expression patterns between tumor and normal condition.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL2895

52 Samples

Download data: TXT

(Submitter supplied) To profile the Daphnia species methylome and to achieve a better understanding of the level of variations in the methylome of Daphnia species, we performed whole genome bisulfite sequencing (WGBSeq) of adult Daphnia magna Bham2 strain and Daphnia pulex Eloise Butler strain (EB45 and EB31 strains). We also analysed the correlation between gene expression and methylation in the two species, using data generated in this study and RNA-seq data from Orsini, et al. more...

Organism:

Daphnia pulex; Daphnia magna

Type:

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

Platforms:

GPL24022 GPL24021 GPL23821

41 Samples

Download data: TXT, VCF

(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) 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

(Submitter supplied) Instructive mechanisms are present for induction of DNA methylation, as shown by methylation of specific CpG islands (CGIs) by specific inducers and in specific cancers. However, instructive factors involved are poorly understood, except for involvement of low transcription and trimethylation of histone H3 lysine 27 (H3K27me3). Here, we used methylated DNA immunoprecipitation (MeDIP) combined with a CGI oligonucleotide microarray analysis, and identified 5510 and 521 genes with promoter CGIs resistant and susceptible, respectively, to DNA methylation in prostate cancer cell lines. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL570 GPL4126

21 Samples

Download data: CEL, TXT

(Submitter supplied) Epigenetic modifications and nucleosome positioning play an important role in modulating gene expression. However, how the patterns of epigenetic modifications and nucleosome positioning are established around promoters is not well understood. Here, we have addressed these questions in a series of genome-wide experiments coupled to a novel bioinformatic analysis approach. Our data reveal a clear correlation between CpG density, promoter activity and accumulation of active or repressive histone marks. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL21103

15 Samples

Download data: BW, WIG, XLSX

(Submitter supplied) Investigate the genome-wide DNA methylation and gene expression changes during human embryonic stem cell differentiation.

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL14617 GPL4133

16 Samples

Download data: 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) 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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