GEO DataSets

(Submitter supplied) We report the results of MIRA-Seq-based high-throughput profiling of the bovine fibroblast methylome from three different individuals at two different ages (5 and 16 months of age) to determine the stability of methylation with age.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19150

6 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:

GPL19150

24 Samples

Download data: TXT

(Submitter supplied) We report the responsiveness of bovine dermal fibroblasts to lipopolyssacharide (LPS) within individuals at different ages. Cultures were collected from three different heifers at the ages of approximately 5 and 16 months. Isolated fibroblasts were then exposed to LPS to determine whether there was a differential response within an animal based upon age.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19150

18 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: 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) The innate immune signaling pathway plays a crucial role in the recognition and early response to pathogens associated with disease. Genetic analysis has been unable to completely account for individual variability in the strength of the innate immune response. The aim of this study was to determine the role of the epigenetic markers (DNA methylation or histone acetylation) in controlling bovine gene expression in relation to the response to lipopolysaccharide (LPS). more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL17645

24 Samples

Download data: CEL

(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) Tissue fibrosis is a serious complication of Crohn’s disease (CD) as well as of a variety of other complex, chronic pathologies. Understanding the underlying pathophysiology of tissue fibrosis is crucial for the development of tissue-specific prevention and interventional treatment strategies. To identify molecular states specific to fibrotic disease, we employed deep sequencing to define the genome-wide DNA methylome and the whole transcriptome of purified human intestinal fibrotic fibroblasts (HIFs) isolated from the colon of patients with fibrotic CD. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL16791

12 Samples

Download data: TXT

(Submitter supplied) We developed a new single cell sequencing method to simultaneously sequence methylome and transcriptome for mouse DRG neurons

Organism:

Mus musculus

Type:

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

Platforms:

GPL16417 GPL13112

192 Samples

Download data: TXT

(Submitter supplied) The culture conditions of the early preimplantation embryos affects the DNA methylation landscape of the resulting blastocysts.

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18384

16 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL10558

48 Samples

Download data

(Submitter supplied) DNA methylation has an impact on regulation of gene expression, however the relation between the two is complex. By performing an integrative analysis of the methylome and transcriptome of the four main circulating immune cell-subsets from healthy females, namely B cells, monocytes, CD4 and CD8 T cells, the relation between the two was characterized. In addition, in light of the known sex bias in the prevalence of several immune-mediated diseases, the female datasets were compared with similar public available male datasets. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

24 Samples

Download data: TXT

(Submitter supplied) DNA methylation has an impact on regulation of gene expression, however the relation between the two is complex. By performing an integrative analysis of the methylome and transcriptome of the four main circulating immune cell-subsets from healthy females, namely B cells, monocytes, CD4 and CD8 T cells, the relation between the two was characterized. In addition, in light of the known sex bias in the prevalence of several immune-mediated diseases, the female datasets were compared with similar public available male datasets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

24 Samples

Download data: TXT

(Submitter supplied) We used MethylCap-seq and RRBS to profile methylomes of purified human ovarian granulosa cells. Genomic DNA methylation patterns in ovarian granulosa cells were compared between two groups of women: i) oocyte donors (n=20) who were young (age 26 ± 2.2 years) and had robust response to ovarian stimulation during assisted reproductive technology (ART) (mean number of oocytes retrieved = 25); versus ii) poor responders (n=20) who were older (age 40 ± 2.3 years) and responded poorly to ovarian stimulation during ART (oocytes retrieved ≤4 and peak estradiol level ≤ 1000 pg/ml). more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) We used mRNA-seq to profile transcriptomes of purified human ovarian granulosa cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: TXT

(Submitter supplied) CpG island methylation profiling of human cholangiocarcinoma, ECC and ICC, cases compared to matched normal controls or to pools of corresponding normal controls. Goal was to identify cholangiocarcinoma-specific differentially methylated regions (DMRs).

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL9767

18 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL10558 GPL13534

13 Samples

Download data: IDAT

(Submitter supplied) Dacogen (DAC/ 5-aza-2’deoxycitidine/Aza) is currently used to treat myeloid dysplastic syndrome (MDS) and is in trials for Acute Myeloid Leukaemia (AML) and some solid cancers. As a hypomethylating agent it is thought to act by inhibiting the enzymes which add methyl groups to DNA, chief among them DNMT1. Improved targeting has been hindered by a lack of understanding of the off-target effects following treatment. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

6 Samples

Download data: IDAT