GEO DataSets

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

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18384

8 Samples

Download data: TXT

(Submitter supplied) The DNA methylation pattern in spermatozoa of bulls at different age was investigated. Spermatozoa collected from 4 different bulls at 12 and 16 month each. Genome-wide DNA methylation analysis was performed by micro array using EDMA platform.

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18384

4 Samples

Download data: TXT

(Submitter supplied) The DNA methylation pattern in spermatozoa of bulls at different age was investigated. Spermatozoa collected from 4 different bulls at 10 and 16 month each. Genome-wide DNA methylation analysis was performed by micro array using EDMA platform.

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18384

4 Samples

Download data: TXT

(Submitter supplied) Sperm carries information to the presumptive embryo upon fertilization in terms of epigenetic codes and transcripts along with the haploid genome. The epigenetic code includes DNA methylation and histone modifications. During spermatogenesis, the DNA of sperm undergoes overall methylation changes and this could have some role to play in fertilizing ability of the sperm. Many of the studies have shown that the altered methylation can cause sub fertility. more...

Organism:

Bubalus bubalis

Type:

Methylation profiling by array

Platform:

GPL17086

6 Samples

Download data: TXT

(Submitter supplied) In this study, we generated whole genome bisulfite sequencing data of 19 samples for 13 tissues in Holstein cattle. We analyzed the variations of DNA methylation among tissues. In this study, we generated whole genome bisulfite sequencing data of 6 samples for 5 tissues in Hereford cattle. We analyzed the variations of DNA methylation among tissues.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24230

25 Samples

Download data: TXT

(Submitter supplied) In this study, we generated whole genome sequencing data from two Holstein cows using Lung tissue.

Organism:

Bos taurus

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL27907

2 Samples

Download data: VCF

(Submitter supplied) DNA from expanded bovine blastocysts and bovine sperm were extracted then subjected to methylation-sensitive enzymatic digestion and LM-PCR enrichment before being hybridized onto a microarray.

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18700

4 Samples

Download data: TXT

(Submitter supplied) Epigenetics (DNA methylation) profiling of sperm from Monozygotic (MZ) twin bull brothers comparing with each other

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18700

8 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by array; Methylation profiling by high throughput sequencing

Platforms:

GPL20301 GPL13534

65 Samples

Download data: IDAT, TXT

(Submitter supplied) Background: Combination chemotherapy has contributed to increased survival from Hodgkin disease (HD) and testicular cancer (TC). However, questions concerning the quality of spermatozoa after treatment have arisen. While studies have shown evidence of DNA damage and aneuploidy in spermatozoa years following anticancer treatment, the sperm epigenome has received little attention. Our objectives here were to determine the impact of HD and TC, as well as their treatments, on sperm DNA methylation. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: TXT

(Submitter supplied) Background: Combination chemotherapy has contributed to increased survival from Hodgkin disease (HD) and testicular cancer (TC). However, questions concerning the quality of spermatozoa after treatment have arisen. While studies have shown evidence of DNA damage and aneuploidy in spermatozoa years following anticancer treatment, the sperm epigenome has received little attention. Our objectives here were to determine the impact of HD and TC, as well as their treatments, on sperm DNA methylation. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

57 Samples

Download data: CSV, IDAT

(Submitter supplied) Dietary folate is a major source of methyl groups required for DNA methylation, an epigenetic modification that is actively maintained and remodelled during spermatogenesis. While high dose folic acid supplementation (up to ten times the daily recommended dose) has been shown to improve sperm parameters in infertile men, the effects of supplementation on the sperm epigenome are unknown. To assess the impact of six months of high dose folic acid supplementation on the sperm epigenome, we studied 30 men with idiopathic infertility. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

56 Samples

Download data: TXT

(Submitter supplied) Data about the entire sperm DNA methylome are limited to two sperm donors whereas studies dealing with a greater number of subjects focused only on a few genes or were based on low resolution arrays. This implies that information about what we can consider as a normal sperm DNA methylome and whether it is stable among different normozoospermic individuals is still missing. The definition of the DNA methylation profile of normozoospermic men, the entity of inter-individual variability and the epigenetic characterization of quality-fractioned sperm subpopulations in the same subject (intra-individual variability) are relevant for a better understanding of pathological conditions. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

28 Samples

Download data: TXT

(Submitter supplied) Sperm carries information to the presumptive embryo upon fertilization in terms of epigenetic codes and transcripts along with the haploid genome. The epigenetic code includes DNA methylation and Histone modifications. During spermatogenesis the chromatin of sperm undergoes wide level of modifications and histone proteins are replaced by Protamine proteins. But some modified Histone forms still remain and they carry epigenetic codes essential for fertility and embryo development. more...

Organism:

Bos taurus; Bubalus bubalis

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL17505

12 Samples

Download data: TXT

(Submitter supplied) Using whole-genome bisulfite sequencing (WGBS), we profiled 18 DNA methylomes of cattle sperms that were collected from 18 representative age-matched Holstein bulls with high reliable phenotypes on many complex traits, including sire-conception rate (SCR), gestation length (GL), sire calving ease (SCE), cow conception rate (CCR) and body depth (BDE). Through comparison with human sperm methylome, we observed that genomic regions with differetial DNA methylation levels were enriched for GWAS signals and had important evolutionary impact. more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24230

18 Samples

Download data: BED

(Submitter supplied) Preconception environmental conditions have been demonstrated to shape sperm epigenetics and subsequently offspring health and development. Our previous findings in humans showed that urinary anti-androgenic phthalate metabolites in males were associated with altered sperm methylation and blastocyst-stage embryo development. To corroborate this, we examined the effect of preconception exposure to di(2-ethylhexyl) phthalate (DEHP) on genome-wide DNA methylation and gene expression profiles in mice. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL19057

42 Samples

Download data: TXT

(Submitter supplied) Epidemiological studies in humans suggest that acquired paternal traits, such as obesity, are associated with a higher risk of fathering small for gestational age offspring. Studies in non-human mammals suggest that such associations could be mediated by DNA methylation changes in spermatozoa that influence offspring development in utero. Human obesity is associated with differential DNA methylation in peripheral blood. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

180 Samples

Download data: TXT