GEO DataSets

(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

Platforms:

GPL23055 GPL26012

31 Samples

Download data: BIGWIG, CSV, MTX, TSV, 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:

Expression profiling by high throughput sequencing

Platform:

GPL23055

14 Samples

Download data: TXT

(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) Intracellular pathogens develop elaborate mechanisms to survive within the hostile environments of host cells. Theileria parasites infect bovine leukocytes and cause devastating diseases in cattle in developing countries. Theileria spp. have evolved sophisticated strategies to hijack host leukocytes, inducing proliferative and invasive phenotypes characteristic of cell transformation. Intracellular Theileria parasites secrete proteins into the host cell and recruit host proteins to induce oncogenic signaling for parasite survival. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

12 Samples

Download data: TSV, ZIP

(Submitter supplied) In this study we compared the transcriptome of bovine macrophages infected with two Mycobacterium bovis strains of variable virulence, co-cultured with autologous lymphocytes. We used the highly virulent M. bovis strain called Mb04-303 and the attenuated Mb534 strain. We first observed that only the infection of bovine macrophages with the virulent strain, Mb04-303, induced in peripheral bovine mononuclear cells a powerful innate immune response capable of controlling the intracellular mycobacterial replication.By RNAseq analysis we found that infections with Mb04-303 downregulated the KEAP1-NFE2L2 pathway that encodes a transcriptional factor involved in antioxidant genes and inflammasome activation and upregulated the type 1 interferon signalling pathway, compared to the infections with the attenuated Mb534 strain. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

6 Samples

Download data: CSV

(Submitter supplied) To investigate the influence of the feed additive (milk replacer) on biological processes occuring in cow mammary parenchyma, mammary fat pad and liver via miRNA-mediated regulation. To this end, we performed microRNA expression profiling using next-generation sequencing.

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23055

48 Samples

Download data: CSV

(Submitter supplied) Hear shock (HS) treatment protocols were designed to examine the short- or long-term effects of exposure to mild HS conditions on transcriptome of MSCs.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

13 Samples

Download data: TXT

(Submitter supplied) The miRNA profiles were measured using small-RNA sequencing in beef heifers sampled at weaning that was retrospectively classified as fertile or subfertile following the breeding protocol. To accomplish this, the miRNA profiles were generated from the blood samples (10 mL) collected from crossbred heifers (Angus-Simmental) at the time of weaning (~238 days after birth). Peripheral white blood cells (PWBC) were extracted from the blood samples and stored at -80°C until further processing. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23055

14 Samples

Download data: CSV, TXT

(Submitter supplied) This study is the first to investigate the transcriptomic changes occurring in severe udder cleft dermatitis lesions (UCD) in Holstein-Friesian cows. An examination of the gene expression levels in natural UCD lesions and healthy udder skin through RNA Seq-Technology provided a deeper insight into the inflammatory pathways associated with this disease. A clear distinction between the gene expression patterns of UCD lesions and healthy skin was shown in the principal component analysis. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

15 Samples

Download data: XLSX

(Submitter supplied) Comparison of goat and cow milk-derived extracellular vesicle miRNomes (microRNA expression profiles) determined usiing RNA-sequencing (NGS).

Organism:

Bos taurus; Capra hircus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL23055 GPL21299

9 Samples

Download data: XLSX

(Submitter supplied) Profiles of H3K4me3, H3K27ac, H3K27me3 and H3K9me3 in bovine GV oocytes and preimplantation embryos, and the characterization of chromatin accessibility in bovine blastocyst, inner cell mass and trophectoderm.

Organism:

Bos taurus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23055

81 Samples

Download data: BED

(Submitter supplied) While prior work has established that articular cartilage arises from Prg4-expressing perichondrial cells, it is not clear how this process is specifically restricted to the perichondrium of synovial joints. We document that the transcription factor Creb5 is necessary to initiate the expression of signaling molecules that both direct the formation of synovial joints and guide perichondrial tissue to form articular cartilage instead of bone. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

16 Samples

Download data: CSV

(Submitter supplied) Bovine herpesvirus 1 (BoHV-1), an important pathogen of cattle, establishes lifelong latency in sensory neurons within trigeminal ganglia (TG) after acute infection. The BoHV-1 latency-reactivation cycle, like other -herpesvirinae subfamily members, is essential for viral persistence and transmission. Notably, cells within pharyngeal tonsil (PT) also support a quiescent or latent BoHV-1 infection. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

12 Samples

Download data: DIFF, FPKM_TRACKING, TXT

(Submitter supplied) The severity of negative energy balance (NEB) in high-producing dairy cows has a high incidence among health diseases. The periparturient period is crucial for the health status and reproductive performance of dairy cows. During this period, dairy cows experience a transition from a pregnant, non-lactating state to a non-pregnant, lactating state. At the beginning of lactation, the energy needs for milk production are higher than the available energy consumed from feed intake, resulting in a negative energy balance (NEB)]. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

15 Samples

Download data: TXT

(Submitter supplied) Purpose: Perform RNA-seq study on infectious bovine endometrial tissues to reveal important genes and biological pathways regulating uterine physiology following uterine infections Methods:RNA sequencings were done using Illumina platform. Single-end reads in the FASTQ format were explored using FastQC, low-quality reads were trimmed from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found, reads having a mean quality score less than 30 and length below 30 nucleotides were filtered out. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

9 Samples

Download data: XLSX

(Submitter supplied) Purpose: Perform RNA-seq study on short bovine endometrial tissues to reveal important genes and biological pathways related to uterine development and physiology Methods:RNA sequencings were done using Illumina platform. Single-end reads in the FASTQ format were explored using FastQC, low-quality reads were trimmed from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found, reads having a mean quality score less than 30 and length below 30 nucleotides were filtered out. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

9 Samples

Download data: XLSX

(Submitter supplied) Purpose: Perform RNA-seq study on bovine endometrial tissues during the peri-implantation period (Day16-17 of gestation) to reveal important genes and biological pathways required for conceptus growth and development Methods:RNA sequencing was done using Illumina NextSeq500. Single-end reads in the FASTQ format were explored using FastQC, low-quality reads were trimmed from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was not found, reads having a mean quality score less than 30 and length below 30 nucleotides were filtered out. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

12 Samples

Download data: XLSX

(Submitter supplied) Maternal undernutrition during pregnancy followed by ad libitum access to nutrients during postnatal life induces postnatal metabolic disruptions in multiple species. As skeletal muscle is a major metabolic organ, RNAseq was performed on the longissimus dorsi muscles of slaughter-weight adult females that had been exposed to nutrient-restriction in utero.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

14 Samples

Download data: CSV, XLSX

(Submitter supplied) The aim of this study was to examine the effect of sire fertility status on conceptus-induced changes in the endometrial transcriptome. Holstein Friesian bulls (3 High fertility, HF, 3 Low fertility, LF) were selected from the Irish national population of AI bulls (minimum of 500 inseminations/bull) based on adjusted fertility scores (HF: +4.37% and LF: -12.7%; mean = 0%). To generate elongated conceptuses, Day 7 blastocysts produced in vitro using sperm from these six bulls were transferred in groups of 5-10 to synchronized heifers (n=7 heifers per bull; total 42 heifers). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23055

32 Samples

Download data: CSV

(Submitter supplied) PIWIs are crucial guardians of genome integrity, particularly in germ cells. While mammalian PIWIs have been primarily studied in mouse and rat, a homologue for the human PIWIL3 geneis absent in the Muridae family, and hence the unique function of PIWIL3 in germ cells cannot be effectively modeled by mouse knockouts. Herein, we investigated the expression,distribution and interaction of PIWIL3 in bovine oocytes. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23055

4 Samples

Download data: TXT