GEO DataSets

(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) 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) 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) 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) In this study, we generated whole genome bisulfite sequencing data of 2 samples for Bones in Holstein cattle. We analyzed the variations of DNA methylation among tissues compared to other tissues we generated before.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19172

2 Samples

Download data: TXT

(Submitter supplied) Aberrant DNA methylation profiles have been associated with male infertility and some semen parameters. However, few studies systematically surveyed DNA methylation profiles associated with sperm motility in normozoospermia and asthenozoospermia. In this study, based on promoter targeted bisulfite sequencing technology, we provided a quantitative description on global DNA methylation profiles. The average global methylation values were 24.7% and the inter-individual variance was about 14.4%, while the intra-individual variance was about 3.9%. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

30 Samples

Download data: TXT

(Submitter supplied) To describe the gene expression profile of brain and muscle across ruminants, we performed gene expression analysis of brain and muscle using RNA-seq data for three ruminants.

Organism:

Bos taurus; Capra hircus; Ovis aries

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24230 GPL23810 GPL25639

18 Samples

Download data: TXT

(Submitter supplied) This study is the first to report a genome-wide comparative DNA methylation map in three ruminants using WGBS technology.

Organism:

Ovis aries; Bos taurus; Capra hircus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL25639 GPL24230 GPL23810

24 Samples

Download data: TXT

(Submitter supplied) To investigate the evolutionary changes of regulatory elements in ruminants, we then performed regulatory elements profiling analysis using ChIP-seq datasets (H3K27ac and H3K4me3) of liver from three ruminants.

Organism:

Bos taurus; Capra hircus; Ovis aries

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19778 GPL19149 GPL19172

26 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) This study is the first to report a genome-wide comparative DNA methylation map of liver in three ruminants using WGBS technology.

Organism:

Bos taurus; Capra hircus; Ovis aries

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL23810 GPL24230 GPL25639

9 Samples

Download data: TXT

(Submitter supplied) To investigate the evolutionary changes of gene expression in ruminants, we performed gene expression profiling analysis using RNA-seq data of liver from three ruminants.

Organism:

Capra hircus; Ovis aries; Bos taurus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23810 GPL24230 GPL25639

9 Samples

Download data: TXT

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

Organism:

Gallus gallus; Sus scrofa; Bos taurus

Type:

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

9 related Platforms

334 Samples

Download data: BED, TXT

(Submitter supplied) Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. more...

Organism:

Bos taurus; Sus scrofa; Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23499 GPL23295 GPL22475

48 Samples

Download data: BED

(Submitter supplied) Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. more...

Organism:

Sus scrofa; Bos taurus; Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL22475 GPL23499 GPL23295

48 Samples

Download data: BED

(Submitter supplied) Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. more...

Organism:

Gallus gallus; Bos taurus; Sus scrofa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23499 GPL22475 GPL23295

48 Samples

Download data: BED

(Submitter supplied) Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. more...

Organism:

Sus scrofa; Bos taurus; Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL22475 GPL23499 GPL23295

48 Samples

Download data: BED

(Submitter supplied) Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19005

15 Samples

Download data: BED

(Submitter supplied) Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. more...

Organism:

Sus scrofa; Bos taurus; Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23295 GPL23499 GPL22475

48 Samples

Download data: BED