GEO DataSets

(Submitter supplied) Background: As couples struggle with infertility and livestock producers wish to rapidly improve genetic merit in their herd, assisted reproductive technologies (ART) have become increasingly popular in human medicine as well as the livestock industry. Utilizing ART can cause an increased risk of congenital overgrowth syndromes, such as Large Offspring Syndrome (LOS) in ruminants. A dysregulation of transcripts has been observed in bovine fetuses with LOS, which is suggested to be a cause of the phenotype. more...

Organism:

Bos indicus x Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32674

17 Samples

Download data: TXT

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

Organism:

Bos indicus x Bos taurus; Bos indicus

Type:

Other; Genome variation profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL31971 GPL31972 GPL31970

50 Samples

Download data: BEDGRAPH, VCF

(Submitter supplied) Large offspring syndrome (LOS) and Beckwith-Wiedemann syndrome are a similar epigenetic congenital overgrowth conditions in ruminants and humans, respectively. We have reported global loss-of-imprinting, methylome epimutations, and global misregulation of genes in LOS. However, less than 4% of gene misregulation can be explained with short range (<20Kb) alterations in DNA methylation. Therefore, we hypothesized that methylome epimutations in LOS affect chromosome architecture which results in misregulation of genes located at distances >20Kb in cis and also in trans (other chromosomes). more...

Organism:

Bos indicus x Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL31972

8 Samples

Download data: BEDGRAPH

(Submitter supplied) Large offspring syndrome (LOS) and Beckwith-Wiedemann syndrome are a similar epigenetic congenital overgrowth conditions in ruminants and humans, respectively. We have reported global loss-of-imprinting, methylome epimutations, and global misregulation of genes in LOS. However, less than 4% of gene misregulation can be explained with short range (<20Kb) alterations in DNA methylation. Therefore, we hypothesized that methylome epimutations in LOS affect chromosome architecture which results in misregulation of genes located at distances >20Kb in cis and also in trans (other chromosomes). more...

Organism:

Bos indicus x Bos taurus

Type:

Other

Platform:

GPL31970

41 Samples

Download data: BEDGRAPH

(Submitter supplied) Identify specific genetic regulatory and signaling mechanisms that result in occurrence of “dark cutting meat” from beef carcasses in order to develop novel strategies for reducing incidence

Organism:

Bos indicus x Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25325

78 Samples

Download data: CSV

(Submitter supplied) The use of assisted reproductive technologies (ART) can induce a congenital overgrowth condition in humans and ruminants, namely Beckwith-Wiedemann syndrome (BWS) and large offspring syndrome (LOS), respectively. Shared phenotypes and epigenotypes have been found between BWS and LOS. We have observed global misregulation of transcripts in bovine foetuses with LOS. microRNAs (miRNAs) are important post-transcriptional gene expression regulators. more...

Organism:

Bos indicus x Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25325

45 Samples

Download data: TXT

(Submitter supplied) Assisted reproductive therapies (ART) have become increasingly common worldwide and up to ~6% of children currently born in developed countries were conceived employing these technologies. Numerous retrospective studies have suggested that ART-conceived children are more likely to develop the overgrowth syndrome Beckwith-Wiedemann (BWS). In bovine, the use of ART can induce a similar overgrown condition, which is referred to as large offspring syndrome (LOS). more...

Organism:

Bos indicus x Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL22943 GPL22942

8 Samples

Download data: BW

(Submitter supplied) Genomic imprinting is an epigenetic mechanism that leads to parental-allele-specific gene expression. Approximately 150 imprinted genes have been identified in humans and mice but less than 30 genes have been described as imprinted in cattle. For the purpose of de novo identification of imprinted genes in bovine, we determined global monoallelic gene expression in brain, skeletal muscle, liver, kidney and placenta of day ~105 Bos taurus indicus X Bos taurus taurus F1 conceptuses using RNA sequencing. more...

Organism:

Bos indicus; Bos indicus x Bos taurus

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing

Platforms:

GPL21383 GPL20723

5 Samples

Download data: VCF, XLSX

(Submitter supplied) Bovine tropical theileriosis is a major haemoprotozoan disease associated with high rates of morbidity and mortality particularly in exotic and crossbred cattle. It is one of the major constraints for of the livestock development programmes in India and southern Asia. Indigenous cattle (Bos indicus) are less affected by this disease than exotic and crossbred cattle. Genetic basis of resistance to tropical theileriosis in indigenous cattle is not well studied. more...

Organism:

Bos indicus; Bos indicus x Bos taurus; Bos taurus

Type:

Expression profiling by array

Platform:

GPL11648

8 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of bovine skeletal muscle comparing expression differences of a population of beef cattle selected for divergent response (shear force residuals) to post-mortem treatment (electrical stimulation)

Organism:

Bos taurus; Bos indicus x Bos taurus

Type:

Expression profiling by array

Platform:

GPL11649

47 Samples

Download data: TXT

(Submitter supplied) Embryos generated with the use of assisted reproductive technologies (ART) can develop overgrowth syndromes. In ruminants, the condition is referred to as large offspring syndrome (LOS) and exhibits variable phenotypic abnormalities including overgrowth, enlarged tongue, and abdominal wall defects. These characteristics recapitulate those observed in the human loss-of-imprinting (LOI) overgrowth syndrome Beckwith-Wiedemann (BWS). more...

Organism:

Bos indicus x Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21383

32 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of bovine skeletal muscle comparing metabolically efficient steers to metabolically inefficient steers to ascertain what expression differences can be found in muscle tissue that might help explain differences in this economically significant phenotype.

Organism:

Bos taurus; Bos indicus x Bos taurus

Type:

Expression profiling by array

Platform:

GPL9712

16 Samples

Download data: TXT