GEO DataSets

(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) 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 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) 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 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) 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) 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:

GPL16791 GPL11154

12 Samples

Download data: TXT

(Submitter supplied) Comprehensive analyses of tissues at single-cell level will benefit our understanding of genetic bases for complex traits. Here we present an initial effort of single-cell transcriptomic analyses of cattle ruminal epithelial cells during the rumen development. We obtained 5064 and 1372 cells from Holstein ruminal epithelial cells before and after weaning, respectively. We reported 6 cell types across their temporal and spatial distributions, which were partially correlated with rumen epithelium layer’s structures and functions. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23295

2 Samples

Download data: MTX, TSV

(Submitter supplied) Comprehensive analyses of tissues at the single-cell level will benefit our understanding of genetic bases for complex traits. We performed single-cell RNA sequencing (scRNA-seq) analyses of peripheral blood mononuclear cells (PBMCs) from Holstein cattle, investigating their cell types and responses to lipopolysaccharide (LPS) treatment in vitro. The responses to LPS treatment include innate immunity activation of monocytes, macrophages, and dendritic cells, as well as B cell proliferation. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

4 Samples

Download data: MTX, TSV

(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 objectives of the study were to use RNA-Seq to examine the effect of (i) breed and (ii) gradual weaning, on the whole blood mRNA transcriptome of artificially reared Holstein-Friesian and Jersey calves. The calves were gradually weaned over 14 days (day (d) -13 to d 0) and mRNA transcription was examined one day before gradual weaning was initiated (d -14), one day after weaning (d 1) and 8 days after weaning (d 8). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

48 Samples

Download data: TXT

(Submitter supplied) Resistance traits of parasitic infestation and diseases in bovine breeds display various unknown differences in the immune response indicating to be related to the host`s genomic background. We studied the differential gene expression of monocyte-derived macrophages (MDMs) stimulated or unstimulated with LPS in vitro, from two bovine breeds by RNA sequence methodology. MDMs were grown in supplemented RPMI medium for 11 days. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

16 Samples

Download data: TXT

(Submitter supplied) In this study, we use mRNA-Seq to characterize and compare the leukocyte transcriptomes of Holstein, Jersey, and Cholistani with respect to variations in sequence, expression, and splicing.

Organism:

Bos taurus; Bos indicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17401 GPL15750

3 Samples

Download data: TXT

(Submitter supplied) B-cell precursor acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer. Although the genetic origin of the disease remains unclear, epigenetic modifications including DNA methylation are suggested to contribute significantly to leukemogenesis. We assessed the DNA methylation status of 402,842 CpG-sites across the genome (Illumina 450k array) in tumor and remission samples of 46 pre-B ALL patients, thus generating the most comprehensive single CpG-site resolution pre-B ALL methylomes so far. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

92 Samples

Download data: TXT

(Submitter supplied) We reported the bovine liver gene expression database of Polish-HF, Polish-Red and Hereford cattle breeds.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24980

18 Samples

Download data: ZIP

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by array

Platforms:

GPL11154 GPL13534

43 Samples

Download data: IDAT

(Submitter supplied) Differentiating pluripotent cells from fibroblast progenitors is a potentially transformative tool in personalized medicine. We previously identified relatively greater success culturing dura-derived fibroblasts than scalp-derived fibroblasts from postmortem tissue. We hypothesized that these differences in culture success were related to epigenetic differences between the cultured fibroblasts by sampling location, and therefore generated genome-wide DNA methylation and transcriptome data on 11 intrinsically matched pairs of dural and scalp fibroblasts from donors across the lifespan (infant to 85 years). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

21 Samples

Download data: CSV, IDAT