GEO DataSets

(Submitter supplied) We report the existence of both methylcytosine and hydroxymethylcytosine in the genomic DNA of the ciliate Oxytricha trifallax during its genome rearrangement process. These modifications are dynamically added, de novo, to sequences targeted for elimination and are not present after the rearrangement process (in vegetative cells). We performed methyl-DNA immunoprecipitation-sequencing (meDIP-seq) with antibodies against methylcytosine and hydroxymethylcytosine.

Organism:

Oxytricha trifallax

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15459

6 Samples

Download data: TXT

(Submitter supplied) Here we report that soon after mating of Oxytricha trifallax, abundant 27nt small RNAs are produced that are not present prior to mating. We performed next generation sequencing of these 27nt RNAs from various times after mating. Using sequence comparisons between macronuclear and micronuclear versions of genes, we found that this 27nt RNA class derives from the parental macronucleus, not the developing macronucleus. more...

Organism:

Oxytricha trifallax

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15459

11 Samples

Download data: TXT

(Submitter supplied) As part of sexual reproduction, the stichotrichous ciliate Oxytricha trifallax orchestrates a remarkable transformation of one of the newly formed germline micronuclear genomes, in which hundreds of thousands of gene pieces are stitched together, excised from chromosomes, and amplified dozens of times, to yield a functional somatic macronuclear genome composed of ~16,000 distinct DNA molecules that typically encode a single gene. more...

Organism:

Oxytricha trifallax

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15459

14 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Honey bee non-CG DNA hydroxymethylation is enriched in the introns, which supplements previous findings that honey bee CG DNA methylation is enriched in exons.

Organism:

Apis mellifera; Apis mellifera scutellata

Type:

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

Platforms:

GPL17742 GPL9909

8 Samples

Download data: BED, TXT, VCF

(Submitter supplied) To study the biogenesis of long non-coding RNAs transcribed during genome rearrangements in Oxytricha development, genome-wide localization pattern of Rpb1 (RNA Pol-II largest subunit) was studied from Oxytricha cells undergoing conjugation.

Organism:

Oxytricha trifallax

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18396

2 Samples

Download data: TXT

(Submitter supplied) DNA hydroxymethylation (5hmC) represents a new layer of epigenetic regulation in addition to DNA methylation (5mC). The genome-wide patterns of 5hmC distribution in many tissues and cells have recently been revealed by hydroxymethylated DNA immunoprecipitation (hMeDIP) followed by high throughput sequencing or tiling arrays. However, the DNA hydroxymethylome data generated by the conventional hMeDIP-seq method can not be used for direct quantitative comparison across different samples. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

16 Samples

Download data: WIG

(Submitter supplied) 5-methylcytosine (5-mC) can be oxidized to 5-hydroxymethylcytosine (5-hmC). Genome-wide profiling of 5-hmC thus far indicated 5-hmC may not only be an intermediate form of DNA demethylation but could also constitute an epigenetic mark per se. We describe a cost-effective and selective method to detect both the hydroxymethylation and methylation status of cytosines in more than 1.8 million MspI sites in the human genome. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: WIG

(Submitter supplied) 5-methylcytosine (5-mC) can be oxidized to 5-hydroxymethylcytosine (5-hmC). Genome-wide profiling of 5-hmC thus far indicated 5-hmC may not only be an intermediate form of DNA demethylation but could also constitute an epigenetic mark per se. We describe a cost-effective and selective method to detect both the hydroxymethylation and methylation status of cytosines in more than 1.8 million MspI sites in the human genome. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: TXT

(Submitter supplied) 5-methylcytosine (5-mC) can be oxidized to 5-hydroxymethylcytosine (5-hmC). Genome-wide profiling of 5-hmC thus far indicated 5-hmC may not only be an intermediate form of DNA demethylation but could also constitute an epigenetic mark per se. We describe a cost-effective and selective method to detect both the hydroxymethylation and methylation status of cytosines in more than 1.8 million MspI sites in the human genome. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: TXT

(Submitter supplied) In Oxytricha, the somatic genome is responsible for vegetative growth, while the germline contributes DNA to the next sexual generation. Somatic nuclear development eliminates all transposons and other so-called "junk DNA", which constitute ~95% of the germline. We demonstrate that Piwi-interacting small RNAs (piRNAs) from the maternal nucleus can specify genomic regions for retention in this process. more...

Organism:

Oxytricha trifallax

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15927 GPL15459

2 Samples

Download data: FA, TXT

(Submitter supplied) Genome duality in ciliated protozoa offers a unique system to showcase their epigenome as a model of inheritance. In Oxytricha, the somatic genome is responsible for vegetative growth, while the germline contributes DNA to the next sexual generation. Somatic nuclear development eliminates all transposons and other "junk DNA", which constitute ~95% of the germline. We demonstrate that Piwi-interacting small RNAs (piRNAs) from the maternal nucleus can specify genomic regions for retention in this process. more...

Organism:

Sterkiella histriomuscorum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15118

4 Samples

Download data: FA, TXT

(Submitter supplied) The study provides new insights into how 5mC/5hmC vary across different part of brain, and the association and distinct roles of 5mC/5hmC in regulating tissue identity and specification.

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL21273

22 Samples

Download data: BW, FPKM_TRACKING, TXT

(Submitter supplied) Dicer-dependent small non-coding RNAs play important roles in gene regulation in a wide variety of organisms. Endogenous small interfering RNAs (siRNAs) are part of an ancient pathway of transposon control in plants and animals. The ciliate, Oxytricha trifallax, has approximately 16,000 gene-sized chromosomes in its somatic nucleus. Long non-coding RNAs establish high ploidy levels at the onset of sexual development, but the factors that regulate chromosome copy numbers during cell division and growth have been a mystery. more...

Organism:

Oxytricha trifallax

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platform:

GPL18396

14 Samples

Download data: TXT

(Submitter supplied) DNA methylation (5-mC) and hydroxymethylation (5-hmC) are regarded as important epigenetic hallmarks in the carcinogenesis of colorectal cancer by transcriptional regulation. 5hmC is an intermediate during active demethylation and maintains the equilibrium of DNA methylation. Previous studies on DNA methylation don’t differentiate 5-hmC from 5-mC. Here, in order to elucidate the epigenetic mechanisms of carcinogenesis of colorectal cancer, we integrate genome wide levels of 5-mC, 5-hmC and Transcriptional expression. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

36 Samples

Download data: TXT, WIG, XML

(Submitter supplied) We generated WGBS datasets from mESCs treated with the novel drug GSK-3484862 attained from two different commercial sources or the conventional DNMT1 inhitibitor 5-azacytidine. To assess efficacy, datasets were generated from mESCs treated with GSK-3484862 at two concentrations and after treatment for 6 days and 14 days each. Additionally, for comparison purposes, we generated WGBS datasets from Dnmt1/3a/3b deficient mESCs which have very low levels of DNA methylation and WT mESCs treated with DMSO which retain high levels of DNA methylation.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21103

15 Samples

Download data: BEDGRAPH

(Submitter supplied) The newly discovered 5-hydroxymethylcytosine (5hmC) may complicate previous observations of abnormal cytosine methylation statuses used for the identification of new tumor suppressor gene candidates relevant to human hepatocarcinogenesis. The simultaneous detection of 5mC and 5hmC will stimulate the discovery of aberrantly methylated genes with increased accuracy in human hepatocellular carcinoma (HCC). more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

36 Samples

Download data: TXT

(Submitter supplied) This study was carried out to investigate the gene expression profile from arm and hatchlings transcriptome across multiple individual Octopus bimaculoides .

Organism:

Octopus bimaculoides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30957

6 Samples

Download data: TSV

(Submitter supplied) We report an association of DNA hydroxymethylation profiling at single nucleotide resolution with gene expression in the fast muscle of Nile tilapia.

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26254

5 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL9115

14 Samples

Download data: TXT