GEO DataSets

(Submitter supplied) Heat stress is a major factor that negatively affects animal welfare and production systems. Livestock should adapt to tropical and subtropical areas and to meet this, composite breeds have been developed. This work aimed to evaluate gene expression profiles in the skin of Brangus cattle under heat stress using a case-control design, and to correlate this with skin histological characteristics. Two groups of bulls were set using rectal temperature as a criterion to define stress conditions: stressed (N=5) and non-stressed (N=5) groups. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

10 Samples

Download data: TXT

(Submitter supplied) Exploring the effect of m6A methylation modification on the progression of bovine pituitary tissue before and after the onset of puberty

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26012

12 Samples

Download data: BW

(Submitter supplied) Cattle farming faces challenges linked to intensive exploitation and climate change, requiring the reinforcement of animal resilience in response to these dynamic environments. Currently, genetic selection is used to enhance resilience by identifying animals resistant to specific diseases; however, certain diseases, such as mastitis, pose difficulties in genetic prediction. This study introduced the utilization of enzymatic methyl sequencing (EM-seq) of the blood genomic DNA from twelve dairy cows to identify DNA methylation biomarkers, with the aim of predicting resilience and susceptibility to mastitis. more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26012

12 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to measure the effect of contrasting breed and dietary source on the skeletal muscle miRNA profile of beef cattle divergent for feed efficiency (RFI). Charolais (n=90) and Holstein-Fresian (N=77) steers) were offered two consecutive diets; namely a zero-grazed grass diet followed by a high concentrate diet. Dietary intakes were recorded for all steers throughout each dietary phase and residual feed intake values dertermined for each steer. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19172

64 Samples

Download data: TXT

(Submitter supplied) This study investigates gene expression in round and sirloin muscle tissues from neonatal calves using RNA-seq.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

16 Samples

Download data: TXT

(Submitter supplied) Embryo mortality (EM) contributes to infertility, but its exact mechanism is poorly understood. It was hypothesized that bovine EM pregnancies have impaired conceptus-derived interferon-tau (IFNT) release and action and are associated with altered transcriptome responses. The objective was to discover transcriptome response in EM tissues (endometrium [ENDO], corpus luteum [CL] and peripheral blood mononuclear cells [PBMC]) in lactating Holstein-Friesian cows. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15749

129 Samples

Download data: XLSX

(Submitter supplied) MicroRNAs (miRNA) are important regulators of oocyte maturation, playing a key role in modulating gene expression both in a temporal- and spatial-specific manner. These small non-coding RNAs are involved in important processes during oocyte maturation, acting as messengers between the oocyte and its surrounding cumulus cells. Despite its significance, the bidirectional communication mechanism is still unknown. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23055

39 Samples

Download data: FA, TSV

(Submitter supplied) This objective of this study was to identify gene expression and biological mechanisms related to trace mineral metabolism, central to inflammatory mediation and disease development, through the evaluation of the whole blood transcriptome in post‐weaned cattle receiving different mineral treatments. Here, 56 high‐risk cross-bred beef cattle (~250 kg) were assigned to receive ad libitum access to supplements containing 1 of 3 treatments over a 60-day period: 1) sulfate sources of Cu, Co, Mn, and Zn in feed (INR; custom blend; n= 40); 2) organic complexed source of Cu, Mn, Co, and Zn in feed (AAC; Availa4; n = 40); or 3) organic complexed source of Cu, Mn, Co, and Zn in feed and administration of a drench product [ProFusion] upon arrival (COMBO; n = 40). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

129 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to examine changes in the transcriptional profile of the anterior pituitary gland of heifer calves offered varying planes of nutrition during the early life period. From approximately 3 weeks of age (19 ± 5 days of age) Angus X Holstein-Friesian heifer calves were offered either a high (HP, n=13) or moderate (MP, n=15) plane of nutrition to achieve target growth rates of 1.2 kg/d and 0.5 kg/d, respectively. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

28 Samples

Download data: TXT

(Submitter supplied) Pyruvate, the end-product of glycolysis in aerobic conditions, is converted into acetyl-CoA inside the mitochondria of oocytes as a master fuel input for the tricarboxylic acid (TCA) cycle. The citrate generated in the TCA cycle can be directed to the cytoplasm and converted back to acetyl-CoA, being driven to lipid synthesis or, alternatively, being used as the substrate for histones acetylation. This work aimed to verify the impact of pyruvate metabolism on the dynamics of lysine 9 histone 3 acetylation (H3K9ac) and RNA transcription in bovine oocytes during in vitro maturation (IVM). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

9 Samples

Download data: TXT

(Submitter supplied) The bovine conceptus elongates near Day 16 of development and releases interferon-tau (IFNT), disrupting the endometrial luteolytic mechanism to sustain luteal P4 and pregnancy. Conceptus factors other than IFNT modify local endometrial activities in support of pregnancy; however, the microenvironment is largely uncharacterized. We utilized a bovine conceptus-endometrial culture system to elucidate the microenvironment in the form of RNA and protein. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

45 Samples

Download data: XLSX

(Submitter supplied) Next-Generation Sequencing (NGS) catalyzed breakthroughs across various scientific domains. Illumina's sequencing by synthesis method has long been essential for NGS but emerging technologies like Element Biosciences' sequencing by avidity (AVITI) represent a novel approach. It has been reported that AVITI offers improved signal-to-noise ratios and cost reductions. However, the method relies on rolling circle amplification which can be impacted by polymer size, raising questions about its efficacy sequencing small RNAs (sRNAs) libraries including microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and others that are crucial regulators of gene expression and involved in various biological processes. more...

Organism:

Homo sapiens; Bison bison; Bos taurus

Type:

Other; Non-coding RNA profiling by high throughput sequencing

5 related Platforms

28 Samples

Download data: BEDGRAPH, GTF, TXT

(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) This study explores how yaks, an ideal animal model for studying plateau adaptability, adapt to high-altitude environments. The lung is a representative organ of the yak’s adaptation to high-altitude environments. The F1 hybrids of yak and cattle, known as dzho, also exhibit adaptability to plateau conditions. This study constructed a single-cell transcriptome atlas of the lungs in yak, dzho and cattle, containing 51 subtypes. more...

Organism:

Bos grunniens; Bos taurus; Bos grunniens x Bos taurus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32644 GPL30409 GPL26012

9 Samples

Download data: MTX, TSV

(Submitter supplied) Alcelaphine gammaherpesvirus 1 (AlHV-1) is a member of the Gammaherpesvirinae subfamily and establishes asymptomatic latent infection in its natural host species, the wildebeest. Cross-species transmission to various ruminant species including cattle can occur, resulting in the induction of malignant catarrhal fever (MCF), a deadly peripheral T cell lymphoproliferative disease. Here, we experimentally infected calves to confirm that AlHV-1 latency-associated gene expression is essential for persistent infection of CD8+ T cells and MCF development. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26012

4 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Alcelaphine gammaherpesvirus 1 (AlHV-1) is a member of the Gammaherpesvirinae subfamily and establishes asymptomatic latent infection in its natural host species, the wildebeest. Cross-species transmission to various ruminant species including cattle can occur, resulting in the induction of malignant catarrhal fever (MCF), a deadly peripheral T cell lymphoproliferative disease. Here, we experimentally infected calves to confirm that AlHV-1 latency-associated gene expression is essential for persistent infection of CD8+ T cells and MCF development. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

14 Samples

Download data: TXT

(Submitter supplied) Alcelaphine gammaherpesvirus 1 (AlHV-1) is a member of the Gammaherpesvirinae subfamily and establishes asymptomatic latent infection in its natural host species, the wildebeest. Cross-species transmission to various ruminant species including cattle can occur, resulting in the induction of malignant catarrhal fever (MCF), a deadly peripheral T cell lymphoproliferative disease. Here, we experimentally infected calves to confirm that AlHV-1 latency-associated gene expression is essential for persistent infection of CD8+ T cells and MCF development. more...

Organism:

Bos taurus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26012

13 Samples

Download data: BIGWIG

(Submitter supplied) Mammalian follicle development is characterised by extensive changes in morphology, endocrine responsiveness, and function, providing the optimum environment for oocyte growth, development, and resumption of meiosis. In cattle, the first signs of transcription activation in the oocyte are observed in the secondary follicle, later than during mouse and human oogenesis. While many studies have generated extensive datasets characterising gene expression in bovine oocytes, they are mostly limited to the analysis of fully grown and matured oocytes. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

179 Samples

Download data: TXT

(Submitter supplied) The objective of this research was to identify a set of genes whose transcript abundance is predictive of a cow’s ability to become pregnant following artificial insemination (AI). Endometrial epithelial cells from the uterine body were collected for RNA sequencing using the cytobrush method from 193 first-service Holstein cows at estrus prior to AI (day 0). A group of 253 first-service cows not used for cytobrush collection were controls. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

193 Samples

Download data: TXT

(Submitter supplied) DNA polymerase β (DNA polymerase beta, POLB) belongs to a member of the DNA polymerase X family, mainly involved in various biological metabolic processes such as eukaryotic DNA replication, DNA damage repair, gene recombination and cell cycle regulation. In this study, the muscle development-related gene POLB was screened by selection signature and RNA-seq analysis, and then validated for the proliferation and apoptosis of bovine primary myocytes. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

5 Samples

Download data: TXT