GEO DataSets

(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) Foot-and-mouth disease (FMD) is a vesicular disease of cloven-hoofed animals with devastating economic implications. The current FMD vaccine, routinely used in enzootic countries, requires at least 7 days to induce protection. However, FMD vaccination is typically not recommended for use in non-enzootic areas, underscoring the need to develop new fast-acting therapies for FMD control during outbreaks. more...

Organism:

Bos taurus

Type:

Expression profiling by RT-PCR

Platform:

GPL34326

112 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

(Submitter supplied) A high incidence of pregnancy failures occurs in cattle during the second week of pregnancy as blastocysts transition into an elongated conceptus. This work explored whether interleukin-6 (IL6) supplementation during in vitro embryo production would improve subsequent conceptus development. Bovine embryos were treated with 0 or 100 ng/mL recombinant bovine IL6 beginning on day 5 post-fertilization. At day 7.5 post-fertilization, blastocysts were transferred into estrus synchronized beef cows (n=5 recipients/treatment, 10 embryos/recipient). Seven days after transfer (day 14.5), cows were euthanized to harvest reproductive tracts and collect conceptuses. Individual conceptus lengths and stages were recorded before processing for RNA-sequencing. Increases in conceptus recovery, length, and the proportion of tubular and filamentous conceptuses were detected in conceptuses derived from IL6-treated embryos. The IL6 treatment generated 591 differentially expressed genes (DEG) in conceptuses (n=9-10/treatment). Gene ontology enrichment analyses revealed changes in transcriptional regulation, DNA-binding, and antiviral actions. Only a few DEG were associated with extraembryonic development, but several DEG were associated with embryonic regulation of transcription, mesoderm and ectoderm development, organogenesis, limb formation, and somatogenesis. To conclude, this work provides evidence that IL6 treatment before embryo transfer promotes pre-implantation conceptus development and gene expression in ways that resemble the generation of a robust conceptus containing favorable abilities to survive this critical period of pregnancy.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

20 Samples

Download data: TXT

(Submitter supplied) Satellite cells are myogenic precursor cells in adult skeletal muscle and play a crucial role in skeletal muscle repair, remodeling, and maintenance. Like myoblasts, satellite cells have the ability to proliferate, differentiate, and fuse to form multinucleated myofibers. In this study we aimed to identify the enhancers and the transcription factors binding to these enhancers that control gene expression in proliferating and differentiating bovine satellite cells. more...

Organism:

Bos taurus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26012

16 Samples

Download data: BW

(Submitter supplied) Supporting healthy pregnancy outcomes requires a comprehensive understanding of the cellular hierarchy and underlying molecular mechanisms during peri-implantation development. Here, we presented a single-cell transcriptome-wide view of the bovine peri-implantation embryo development at day 12, 14, 16 and 18, when most of the pregnancy failure occurs. We defined the development and dynamic progression of cellular composition and gene expression of embryonic disc, hypoblast, and trophoblast lineages during bovine peri-implantation development. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

8 Samples

Download data: MTX, TSV

(Submitter supplied) Cumulus cells provide an interesting biological material to perform analyses to understand the molecular clues determining oocyte competence. The objective of this study was to analyze the transcriptional differences between cumulus cells from oocytes exhibiting different developmental potentials following individual in vitro embryo production by RNA‐seq. Cumulus cells were allocated into three groups according to the developmental potential of the oocyte following fertilization: (1) oocytes developing to blastocysts (Bl+), (2) oocytes cleaving but arresting development before the blastocyst stage (Bl-), and (3) oocytes not cleaving (Cl-).

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23295

14 Samples

Download data: TSV

(Submitter supplied) The embryonic loss during early stage of gestation is one of the major causes of infertility for domestic ruminants, causing huge economic losses to pasture. Maternal recognition of pregnancy and implantation are the crucial process for determining the successful establishment and development of pregnancy in cattle. The research on molecular mechanisms of pregnancy recognition will facilitate illustrating the complex process of pregnancy establishment and help to improve pregnancy outcomes. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

9 Samples

Download data: TXT

(Submitter supplied) We measued IgG autoantibodies associated with Connective Tissue Diseases (CTDs) and Anti-Cytokine Antibodies (ACA) in SLE and healthy controls who received the BNT162b2 vaccine.

Organism:

Triticum aestivum; Capra hircus; Homo sapiens; Sus scrofa; Escherichia coli; Spodoptera frugiperda; Bos taurus

Type:

Protein profiling by protein array

Platform:

GPL34257

102 Samples

Download data: TXT, XLSX

(Submitter supplied) In order to investigate the transcriptomic responses of bovine mammary epithelial cells to various essential amino acid administrations

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

72 Samples

Download data: TXT

(Submitter supplied) Mycobacterium bovis causes bovine tuberculosis (bTB), an infectious disease of cattle that poses a zoonotic threat to humans. Research has shown that bTB susceptibility is a heritable trait, and that the peripheral blood (PB) transcriptome is perturbed during bTB disease. Hitherto, no study has integrated PB transcriptomic, genomic and GWAS data to study bTB disease, and little is known about the genomic architecture underpinning the PB transcriptional response to M. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

123 Samples

Download data: BED, TXT

(Submitter supplied) While dietary phosphorus (P) deprivation extending from the dry period into early lactation impairs health and productivity of cows, restricting dietary P supply during the dry period not only appears to be innocuous but rather effectively mitigates hypocalcemia during the first wk of lactation. To investigate possible negative metabolic effects of P deprivation during the dry period, the present study tested the hypothesis that restarted dietary P supply during the dry period alters the liver transcriptome of dairy cows during the periparturient period. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL16500

20 Samples

Download data: CEL, XLSX

(Submitter supplied) Lineage specification and X chromosome dosage compensation are two crucial biological processes that occur during preimplantation embryonic development. While these processes have been studied extensively in mice and humans, they are less understood in other species. This study aims to provide fundamental insights into bovine preimplantation development using single-cell RNA-sequencing. The study analyzes the transcriptomes of 286 individual cells and reveals that bovine trophectoderm/inner cell mass transcriptomes diverge at the early blastocyst stage, after cavitation but before blastocyst expansion. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

8 Samples

Download data: TXT

(Submitter supplied) Purpose: Screening the sperm sncRNAs that are responsible for dairy cattle fertility is of great interest, however, exploring the fertility-associated sncRNAs in sperm and linking them with the epigenetic inheritance in bovine has not been performed yet. Here in this study, we hypothesized that some sncRNAs in bovine sperm have a great potential to be linked with direct and immediate bull fertility data and could later influence the embryo and possibly impacting the daughter fertility. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26012

10 Samples

Download data: XLSX

(Submitter supplied) To describe the gene expression profile of brain and muscle across ruminants, we performed gene expression analysis of brain and muscle using RNA-seq data for three ruminants.

Organism:

Bos taurus; Capra hircus; Ovis aries

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23810 GPL25639 GPL24230

18 Samples

Download data: TXT

(Submitter supplied) This study is the first to report a genome-wide comparative DNA methylation map in three ruminants using WGBS technology.

Organism:

Ovis aries; Bos taurus; Capra hircus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL24230 GPL23810 GPL25639

24 Samples

Download data: TXT

(Submitter supplied) Cattle-yak is the hybrid offspring of yak and cattle. It has obvious heterosis in production performance, but the male sterility of cattle-yak has always been the focus of attention. Studies have shown that non-coding RNA is involved in the regulation of spermatogenesis. We comprehensively compared the testicular transcription profiles of cattle, yak and cattle-yak. More DEGs, DECs and DEMs were found in the intersection of the two comparison groups of cattle and cattle-yak, yak and cattle-yak, with 4,968, 360 and 59, respectively. more...

Organism:

Bos taurus; Bos grunniens x Bos taurus; Bos grunniens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL32499 GPL22950 GPL19172

18 Samples

Download data: XLSX

(Submitter supplied) This study aims to investigate the potential implication of epigenetic mechanisms in the transmission of maternal metabolic information to the embryo, in order to better understand how maternal metabolic stress influences fertility. To do this, we exposed the oocytes of 54 cows to different environments during maturation (24 hours). The treatments include normal glucose concentration (5.5 mM), low glucose concentration (2.75 mM) and low glucose concentration with supplementation of BHB (1.8 mM). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

9 Samples

Download data: CSV, XLSX

(Submitter supplied) Epigenetic markers, such as DNA methylation, in sperm plays crucial roles in spermatogenesis and fertilization, and a portion of methylation escape the early embryonic genome-wide DNA demethylation and affect later growth and development of offspring. DNA methylation is influenced by various exogenous factors such as nutrition, temperature, toxicants, and stress. The effects of this cold exposure on the methylation dynamics of bovine sperm remain unexamined. more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26012

6 Samples

Download data: COV