GEO DataSets

(Submitter supplied) To better study the bovine circRNA, we assessed the outcomes of circRNA identification using six enrichment approaches. RNA-sequencing analysis revealed that different approaches led to varied the ratio of uniquely mapped reads, false positive rate of identifying circRNAs, and the number of circRNAs per million clean reads. Besides, 507 of 4,051 identified bovine high confident circRNAs had shared splicing sites with human circRNAs.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL23295 GPL26012

28 Samples

Download data: XLSX

(Submitter supplied) Greater progesterone (P4) concentrations during the follicular growth have been associated with greater quality of embryos produced by superovulated cows and heifers. However, it is yet to be determined the mechanisms by which oocyte exposure to greater P4 concentrations improves early embryo quality. The objective of this study was to evaluate the impact of different P4 concentrations during superovulation on the transcriptome profile of early bovine embryos. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

6 Samples

Download data: CSV

(Submitter supplied) High fertility and low fertility bulls were screened from the a 6000 bull database and then identify the sperm-derived DMR and DMC that assoiated with bull ferrtility via whole genome methtlation sequencing

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24230

12 Samples

Download data: CSV, XLSX

(Submitter supplied) Hanwoo cattle are a Korean breed renowned for their cultural significance and high-quality beef, characterized by low cholesterol and high unsaturated fat ratio. Growth is divided into a growing phase focused on development and a fattening phase for marbling. Proper feed management, considering genetic and environmental factors, is vital for maximizing growth potential. The rumen plays a crucial role in digestion and gene expression regulation, with rumen fermentation being central to nutrient absorption and cattle health. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

61 Samples

Download data: TXT

(Submitter supplied) Adipose tissue plays essential roles in adapting to harsh environmental conditions in Mongolian cattle. To dig out the cellular and molecular mechanism of adipose tissue taking part in the tolerance of rough feeding, cold temperature and disease of Mongolian cattle, here, we applied single-nucleus RNA-seq to map the landscape of cell types and profiles of transcriptome of adipose tissues at different anatomical depots at single-nucleus resolution. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

5 Samples

Download data: ZIP

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

Organism:

Bos taurus

Type:

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

Platform:

GPL26012

48 Samples

Download data: BEDGRAPH, BW, NARROWPEAK, TXT

(Submitter supplied) While DNA methylation in other tissues can be approximated through model species, the dynamic distribution and regulatory significance of DNA methylation in the rumen, a unique organ in ruminant, remain largely unknown. Here, we employed whole-genome bisulfite sequencing (WGBS), transcriptomics, and histone modification data to compare fetal and adult stages of bovine rumen with other tissues, including pluripotent stem cells (PSCs) approximating pre-implantation embryos. more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26012

16 Samples

Download data: TXT

(Submitter supplied) While DNA methylation in other tissues can be approximated through model species, the dynamic distribution and regulatory significance of DNA methylation in the rumen, a unique organ in ruminant, remain largely unknown. Here, we employed whole-genome bisulfite sequencing (WGBS), transcriptomics, and histone modification data to compare fetal and adult stages of bovine rumen with other tissues, including pluripotent stem cells (PSCs) approximating pre-implantation embryos. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

6 Samples

Download data: TSV

(Submitter supplied) While DNA methylation in other tissues can be approximated through model species, the dynamic distribution and regulatory significance of DNA methylation in the rumen, a unique organ in ruminant, remain largely unknown. Here, we employed whole-genome bisulfite sequencing (WGBS), transcriptomics, and histone modification data to compare fetal and adult stages of bovine rumen with other tissues, including pluripotent stem cells (PSCs) approximating pre-implantation embryos. more...

Organism:

Bos taurus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26012

4 Samples

Download data: BEDGRAPH

(Submitter supplied) While DNA methylation in other tissues can be approximated through model species, the dynamic distribution and regulatory significance of DNA methylation in the rumen, a unique organ in ruminant, remain largely unknown. Here, we employed whole-genome bisulfite sequencing (WGBS), transcriptomics, and histone modification data to compare fetal and adult stages of bovine rumen with other tissues, including pluripotent stem cells (PSCs) approximating pre-implantation embryos. more...

Organism:

Bos taurus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26012

18 Samples

Download data: BW

(Submitter supplied) While DNA methylation in other tissues can be approximated through model species, the dynamic distribution and regulatory significance of DNA methylation in the rumen, a unique organ in ruminant, remain largely unknown. Here, we employed whole-genome bisulfite sequencing (WGBS), transcriptomics, and histone modification data to compare fetal and adult stages of bovine rumen with other tissues, including pluripotent stem cells (PSCs) approximating pre-implantation embryos. more...

Organism:

Bos taurus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26012

4 Samples

Download data: NARROWPEAK

(Submitter supplied) Milk contains microRNAs (miRNAs) that are protected by extracellular vesicles (EV). Beyond variations among individuals, the nutritional conditions of cattle play a role in shaping these milk miRNA profiles. This study explored milk-derived EV-miRNA variations induced by inulin supplementation and analyzed involved pathways. Fourteen lactating cows with sub-clinical mastitis were equally and randomly divided into an inulin and a control group. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26012

14 Samples

Download data: CSV

(Submitter supplied) The impact of late-term fetal bovine viral diarrhea virus (BVDV) transient infections (TI) on fetal growth and methylome was examined by inoculating pregnant heifers with a noncytopathic (ncp) type 2 BVDV suspended in media or media alone (sham-inoculated controls) on day 175 of gestation to generate TI (n=11) and control heifer calves (n=12). Blood samples were collected at birth. White blood cells (WBC) were separated for DNA extraction. more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26012

10 Samples

Download data: BEDGRAPH, CSV

(Submitter supplied) Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides, and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) which died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding twenty-eight chromosome-length scaffolds. more...

Organism:

Elephas maximus indicus; Homo sapiens; Bos taurus; Equus asinus; Mammuthus primigenius

Type:

Other; Third-party reanalysis

10 related Platforms

128 Samples

Download data: BED, BEDGRAPH, BEDPE, FASTA, HIC, SW, TXT, XLSX

(Submitter supplied) As cows progress from pregnancy to lactation, the adipose tissues (AT) undergo adaptations characterized by the mobilization of free fatty acids (FFA) through lipolysis to address energy deficiencies. Typically, in clinically healthy cows, the intensity of lipolysis decreases during lactation. However, when the release of FFA surpasses tissue requirements, it leads to the accumulation of lipid-derived products, heightening the susceptibility of cows to metabolic and infectious diseases. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

15 Samples

Download data: TXT

(Submitter supplied) Background: Johne’s disease is a chronic wasting disease caused by the bacterium Mycobacterium avium subspecies paratuberculosis (MAP). Johne’s disease is highly contagious and MAP infection in dairy cattle can eventually lead to death. With no available treatment for Johne’s disease, genetic selection and improvements in management practices could help reduce its prevalence. In a previous study, the gene coding interleukin-10 receptor subunit alpha (IL10Rα) was associated with Johne’s disease in dairy cattle. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

16 Samples

Download data: CSV

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

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25962

24 Samples

Download data

(Submitter supplied) This study reproduced in vivo aspects of the temporal signaling of interferon tau (IFNT) and pregnancy associated glycoproteins (PAG) during bovine early pregnancy. The objective of this study was to analyze the short and long-term effects of IFNT, and the effect of PAG on the transcriptome of blood leukocytes.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25962

8 Samples

Download data: XLSX

(Submitter supplied) This study reproduced in vivo aspects of the temporal signaling of interferon tau (IFNT) and pregnancy associated glycoproteins (PAG) during bovine early pregnancy. The objective of this study was to analyze the short and long-term effects of IFNT, and the effect of PAG on the transcriptome of endometrium.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25962

16 Samples

Download data: XLSX

(Submitter supplied) The first lineage differentiation in mammals gives rise to the inner cell mass (ICM) and the trophectoderm (TE). In mice, TEAD4 is a master regulator of TE commitment, as it regulates the expression of other TE-specific genes and its ablation prevents blastocyst formation, but its role in other mammals remains unclear. TEAD4 ablation in bovine embryos did not impede TE differentiation or blastocyst formation, but a transcriptomic analysis was performed to see if there were any transcriptomic anomalies in knockout embryos.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23295

9 Samples

Download data: CSV