GEO DataSets

(Submitter supplied) Enhancing climate resilience and sustainable production for animals in harsh environments are important goals for the livestock industry given the predicted impacts of climate change. Rapid adaptation to extreme climatic conditions has already been imposed on livestock species, including those exported after Columbus’ arrival in the Americas. We compared the methylomes of two Creole cattle breeds living in tropical environments with their putative Spanish ancestors to understand the epigenetic mechanisms underlying rapid adaptation of a domestic species to a new and more physiologically challenging environment. more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19172

6 Samples

Download data: TXT

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

Organism:

Bos taurus

Type:

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

Platform:

GPL15749

18 Samples

Download data: TXT

(Submitter supplied) As a key epigenetic modification, DNA methylation is essential for normal development by regulating processes like gene expression, genomic imprinting, and suppression of repetitive elements. However, DNA methylation in the cattle genome is not well understood. Here we presented the first single-base-resolution maps of DNA methylation in 10 diversely somatic tissues harvested from the sequenced Hereford cow L1 Dominette 01449 and her relatives using reduced representation bisulphite sequencing (RRBS). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15749

8 Samples

Download data: TXT

(Submitter supplied) As a key epigenetic modification, DNA methylation is essential for normal development by regulating processes like gene expression, genomic imprinting, and suppression of repetitive elements. However, DNA methylation in the cattle genome is not well understood. Here we presented the first single-base-resolution maps of DNA methylation in 10 diversely somatic tissues harvested from the sequenced Hereford cow L1 Dominette 01449 and her relatives using reduced representation bisulphite sequencing (RRBS). more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15749

10 Samples

Download data: TXT

(Submitter supplied) Background: Differences in DNA methylation are known to contribute to the development of immune-related disorders in humans but relatively little is known about how methylation regulates immune function in cattle. Utilizing whole-transcriptome analyses of bovine dermal fibroblasts, we have previously identified an age and breed-dependent up-regulation of genes within the toll-like receptor 4 (TLR4) pathway that correlates with enhanced fibroblast production of IL-8 in response to lipopolysaccharide (LPS). more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15749

12 Samples

Download data: BIGBED, CSV, TXT

(Submitter supplied) Genome wide DNA methylation profiling of normal and adjacent OSCC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 4,50,000 CpGs in tissue samples. Total 21 samples were taken including 10 paired and 1 unpaired tissues. 6 were HPV Positive and 5 were HPV negative.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

21 Samples

Download data: IDAT

(Submitter supplied) Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these 'relatively young' genes was critical for the origin and radiation of eukaryotes.

Organism:

Magallana gigas

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13986

2 Samples

Download data: TXT

(Submitter supplied) Deep sequencing of samples from different development stages, different adult organs and different stress treatments of Pacific oyster Crassostrea gigas

Organism:

Magallana gigas

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13986

112 Samples

Download data: BEDGRAPH

(Submitter supplied) Heat stress has a detrimental impact on cattle health, welfare and productivity by affecting gene expression, metabolism and immune response, but little is known on the epigenetic mechanisms mediating the effect of temperatureat the cellular and organism level. In this study, we investigated genome-wide DNA methylation in blood samples collected from 5 bulls of the heat stress resilient Nellore breed and 5 bulls of the Angus that are more heat stress susceptible, exposed to the sun and high temperature-high humidity during the summer season of the Brazilian South-East region. more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19646

20 Samples

Download data: COV

(Submitter supplied) We performed a comparative genome-wide methylation analysis of longissimus dorsi muscles between the Japanese Black (Wagyu) and Chinese Red Steppes cattle, which exhibit significant differences in meat quality traits. This will allow us to better understand the correlation between DNA methylation variants and meat quality traits.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19172

6 Samples

Download data: BW

(Submitter supplied) Using 1 melanocyte and 6 melanoma cell line (3 pair of primary and metastatic), we generated base-resolution DNA methylation maps to document DNA methylation drivers of melanoma metastasis.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16791

7 Samples

Download data: TXT

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

Organism:

Bos taurus

Type:

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

Platform:

GPL19150

32 Samples

Download data: TXT

(Submitter supplied) We report the results of MIRA-Seq based high-throughput profiling of the bovine dermal fibroblast methylome from two different breeds of cattle (n=4/breed) to determine the breed-dependent differences in methylation.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19150

8 Samples

Download data: TXT

(Submitter supplied) We report the breed-dependent differences in the innate immune response of dermal fibroblasts following exposure to lipopolysaccharide (LPS). Skin biopsies were collected from Angus (a beef breed) and Holstein (a dairy breed) animals and isolated fibroblasts were exposed to LPS to investigate differences in gene expression between these two cattle breeds.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19150

24 Samples

Download data: TXT

(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) 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

(Submitter supplied) To analysis Mst1r and slpi function as a tumor associated gene, we carried out overexpression analysis of Mst1r or Slpi to Hepa1c1c7 and investigated downstream genes expression by microarray.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21163

3 Samples

Download data: TXT

(Submitter supplied) DNA methylation is a widely conserved epigenetic modification that is established and maintained by the cooperative activity of DNA methyltransferases. While the complement of DNA methyltransferase genes can vary substantially between animal species, whole-genome methylation analyses have suggested that major features of animal methylomes are widely conserved. We have now used genome-scale bisulfite sequencing to analyze the methylome of the desert locust, Schistocerca gregaria, which represents an economically important pest with a high degree of phenotypic plasticity. more...

Organism:

Schistocerca gregaria

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16114

2 Samples

Download data: BEDGRAPH

(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

Platforms:

GPL10999 GPL11154

111 Samples

Download data: BED