GEO DataSets

(Submitter supplied) Pregnant C3H mice were given tap water (control group) and tap water containing 85 ppm sodium arsenite from gestational day 8 to 18 (arsenic group), respectively. The DNA methylomes of sperm of F1 mice were investigated by RRBS method. The results showed that gestational arsenic exposure increased hypomethylated cytosines in active retrotransposon subfamilies. The present study has indicated environmental impacts on sperm DNA methylome establishment.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21273

10 Samples

Download data: XLSX

(Submitter supplied) Pregnant C3H mice were given tap water (control group) and tap water containing 85 ppm sodium arsenite from gestational day 8 to 18 (arsenic group), respectively. The DNA methylomes of sperm of F1 mice were investigated by RRBS method. The results showed that gestational arsenic exposure increased hypomethylated cytosines in the F1 sperm genome. The present study has indicated environmental impacts on sperm DNA methylome establishment.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

10 Samples

Download data: XLSX

(Submitter supplied) Background: C3H mice have been frequently used in cancer studies as animal models of spontaneous liver tumors and chemically induced hepatocellular carcinoma (HCC). Epigenetic modifications, including DNA methylation, are among pivotal control mechanisms of gene expression leading to carcinogenesis. Although information on somatic mutations in liver tumors of C3H mice is available, epigenetic aspects are yet to be clarified. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: XLSX

(Submitter supplied) Background: DNA methylation (DNAme) erasure and reacquisition occurs during prenatal male germ cell development; some further remodelling takes place after birth during spermatogenesis. Environmental insults during germline epigenetic reprogramming may affect DNAme, presenting a potential mechanism for transmission of environmental exposures across multiple generations. Objectives: We investigated how germ cell DNAme is impacted by lifetime exposures to diets containing either low or high, clinically relevant, levels of the methyl donor folic acid and whether resulting DNAme alterations were inherited in germ cells of male offspring of subsequent generations. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

77 Samples

Download data: TXT

(Submitter supplied) IAP is one of the most transpositinally active retrotransposons in the mouse. Its transcription starts from the 5' long terminal repeat (LTR), and the expression level varied between cell types. This variation is thought to arise from differences in the epigenetic states, such as DNA methylation, of some copies of the 5' LTR between the cells. However, due to the high copy number and high sequence similarity, it was difficult to comprehensively and individually analyze epigenetic state of the IAP LTRs. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18480

2 Samples

Download data: TXT

(Submitter supplied) Sperm cells are characterized by a unique epigenome, and an incorrect establishment of DNA methylation patterns during the differentiation of male germ cells into spermatozoa has been associated with male infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine sperm is still scarce. The purpose of this study is to compare the methylomes of sperm and somatic cell types in cattle using the MeDIP-chip technology (methylated DNA immunoprecipitation followed by microarray hybridation).

Organism:

Bos taurus

Type:

Methylation profiling by array

Platform:

GPL20918

22 Samples

Download data: PAIR, TXT

(Submitter supplied) Sperm cells are characterized by a unique epigenome, and an incorrect establishment of DNA methylation patterns during the differentiation of male germ cells into spermatozoa has been associated with male infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine sperm is still scarce. The purpose of this study is to compare the methylomes of sperm and somatic cell types in cattle using the RRBS technology.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19172

6 Samples

Download data: TXT

(Submitter supplied) Previous observations have demonstrated that the agricultural fungicide vinclozolin and the pesticide DDT (dichlorodiphenyltrichloroethane) induce transgenerational sperm epimutations involving DNA methylation. These two environmental toxicants were used to investigate the impacts of parent-of-origin outcross on the epigenetic transgenerational inheritance of disease. Male and female rats were collected from a paternal outcross (POC) or a maternal outcross (MOC) F4 generation control and exposure lineages for pathology and epigenetic analysis. more...

Organism:

Rattus norvegicus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18694

36 Samples

Download data: CSV

(Submitter supplied) Genome wide DNA methylation profiling of arsenic exposure and non-exposure population and patients with skin leisons. The Illumina Infinium HumanMethylation450 BeadChip (HM450K) was used to obtain DNA methylation profiles across approximately 450,000 CpGs in genomic DNA extracted from blood buffy coat samples. Samples included 66 arsenic exposure individuals, 35 non-exposure individuals and 18 arsenical skin lesion patients.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

119 Samples

Download data: IDAT

(Submitter supplied) During germ cell and preimplantation development, mammalian cells undergo nearly complete reprogramming of DNA methylation patterns. We profiled the methylomes of human and chimp sperm as a basis for comparison to methylation patterns of ES cells. While the majority of promoters escape methylation in both ES cells and sperm, the corresponding hypomethylated regions show substantial structural differences. more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9378 GPL9115

4 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) 5-methylcytosine is a major epigenetic modification sometimes called "the fifth nucleotide". However, our knowledge of how offspring inherit the DNA methylome from parents is limited. We generated nine single-base resolution DNA methylomes including zebrafish gametes and early embryos. The oocyte methylome is significantly hypo-methylated compared to sperm. Strikingly, the paternal DNA methylation pattern is maintained throughout early embryogenesis. more...

Organism:

Danio rerio

Type:

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

Platform:

GPL14875

19 Samples

Download data: TXT, WIG

(Submitter supplied) Microarray experiment to identify changes in gene expression in 18.5 day post coitum Tex19.1-/- mouse placenta. Tex19.1 is expressed in trophectoderm-derived cells in the placenta. Tex19.1-/- placentas are small and have defects in junctional zone and labyrinth layers of the placenta, Tex19.1-/- embryos exhibit intra-uterine growth retardation. Data provides insight into the changes in gene expression and cell composition in Tex19.1-/- placentas.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

12 Samples

Download data: TXT

(Submitter supplied) The pre and postnatal environment can affect both an individual’s risk of adult onset metabolic disease and that of subsequent generations. Although animal models and epidemiological data implicate epigenetic inheritance, little is known of the mechanisms involved. In a robust intergenerational model of developmental programming we demonstrate that the nutritional environment experienced in utero by F1 generation embryos alters the DNA methylome of the F1 adult male germ line in a locus-specific manner, without affecting overall methylation levels. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL11002 GPL13112

4 Samples

Download data: BW

(Submitter supplied) Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperms through comparison with three bovine somatic tissues (mammary grand, brain and blood). Large differences between cattle sperms and somatic tissues were observed in the methylation patterns.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24230

10 Samples

Download data: BED

(Submitter supplied) DNA methylation patterns were analyzed in blood samples from humans unexposed or exposed to arsenic Using a state-of-the-art technique to map the methylomes of our study subjects, we identified a large interactome of hypermethylated genes that are enriched for their involvement in arsenic-associated diseases, such as cancer, heart disease, and diabetes. Notably, we have uncovered an arsenic-induced “suppressorome” - a complex of 17 known and putative tumor suppressors silenced in human cancers. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL5082

16 Samples

Download data: CEL, TXT

(Submitter supplied) Study question: Do short-term and long-term exposures to low dose folic acid supplementation alter DNA methylation in sperm? Summary answer: No alterations in sperm DNA methylation patterns were found following the administration of low dose folic acid supplements of 400 μg/day for 90 days (short-term exposure) or when pre-fortification of food with folic acid and post-fortification sperm samples (long-term exposure) were compared. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

46 Samples

Download data: TXT

(Submitter supplied) Background: Previously, we showed that gestational arsenite (As) exposure of F0 females increases hepatic tumors in the F2 males in C3H mice. However, the mechanisms have not yet been clarified. Methods: We detected genome wide site-specific DNA methylation by using reduced representative bisulfite sequence (RRBS) method. We used the data uploaded here and those with GSE Series accession number GSE111420 (CCN and CCTt) to detect differential methyrated cytosines between control groups and arsenite groups. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: XLSX

(Submitter supplied) We have employed microarray analysis to detect gene expression changes that were affected in the F2 mice of arsenite group.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

12 Samples

Download data: TXT

(Submitter supplied) To analyse Cd74 and Tmem54 function as tumor associated genes, we carried out overexpression analysis of Cd74 or Tmem54 using Hepa1c1c7 and investigated downstream genes expression by microarray.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21810

3 Samples

Download data: TXT

(Submitter supplied) We have employed microarray analysis to detect tumor-related genes of liver tissues in C3H mice

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

6 Samples

Download data: TXT