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Items: 1 to 20 of 28806

1.

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

(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:
Homo sapiens; Bos taurus; Elephas maximus indicus; Equus asinus; Mammuthus primigenius
Type:
Other; Third-party reanalysis
10 related Platforms
126 Samples
Download data: BED, BEDGRAPH, BEDPE, FASTA, HIC, SW, TXT, XLSX
Series
Accession:
GSE268050
ID:
200268050
2.

Endotoxin stimulates lipolysis in bovine adipocytes

(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
Series
Accession:
GSE267141
ID:
200267141
3.

The role of interleukin-10 receptor alpha (IL10Rα) in Mycobacterium avium subsp. paratuberculosis infection of a mammary epithelial cell line

(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
Series
Accession:
GSE247921
ID:
200247921
4.

Transcriptome of endometrium and blood leukocytes in response to conceptus proteins in dairy cattle

(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
Series
Accession:
GSE241886
ID:
200241886
5.

Transcriptome of blood leukocytes in response to conceptus proteins in dairy cattle [PBLs]

(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
Series
Accession:
GSE241885
ID:
200241885
6.

Transcriptome of endometrium in response to conceptus proteins in dairy cattle [ENDO]

(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
Series
Accession:
GSE241884
ID:
200241884
7.

TEAD4 role in trophectoderm commitment and development is not conserved in non-rodent mammals

(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
Series
Accession:
GSE266304
ID:
200266304
8.

Exploring the mechanisms of high-altitude adaptation in yak based on single-cell transcriptome atlas.

(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 taurus; Bos grunniens x Bos taurus; Bos grunniens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL32644 GPL30409 GPL26012
9 Samples
Download data: MTX, TSV
Series
Accession:
GSE266061
ID:
200266061
9.

Deep sequencing after alcelaphine gammaherpesvirus 1 infection reveals the nature of CD8+ T cell expansion and identify an essential viral protein for fatal bovine malignant catarrhal fever [scRNA-seq]

(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
Series
Accession:
GSE253762
ID:
200253762
10.

Deep sequencing after alcelaphine gammaherpesvirus 1 infection reveals the nature of CD8+ T cell expansion and identify an essential viral protein for fatal bovine malignant catarrhal fever

(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
Series
Accession:
GSE253729
ID:
200253729
11.

Deep sequencing after alcelaphine gammaherpesvirus 1 infection reveals the nature of CD8+ T cell expansion and identify an essential viral protein for fatal bovine malignant catarrhal fever [RNA-seq]

(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
Series
Accession:
GSE253728
ID:
200253728
12.

Deep sequencing after alcelaphine gammaherpesvirus 1 infection reveals the nature of CD8+ T cell expansion and identify an essential viral protein for fatal bovine malignant catarrhal fever [ATAC-seq]

(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
Series
Accession:
GSE253727
ID:
200253727
13.

Comparative transcriptional analysis identifies genes associated with the attenuation of Theileria parva infected cells after long-term in vitro culture

(Submitter supplied) Administration of attenuated autologous Theileria parva infected cells can be used as an alternative to the infection-and-treatment method for inducing immunological protection against East Coast Fever. The mechanism of attenuation however has not been described. Using RNA sequencing, the transcriptomes of both host and parasite in uninfected (control), pathogenic (day 7 post-infection) and attenuated (day 69 post-infection) T. more...
Organism:
Theileria parva; Bos taurus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL32030 GPL33841
16 Samples
Download data: CSV
Series
Accession:
GSE245180
ID:
200245180
14.

Genome-wide methylation profile of mitochondrial DNA across bovine preimplantation development

(Submitter supplied) This study characterized variations in the methylation profile of mitochondrial DNA (mtDNA) during initial bovine embryo development and correlated the presence of methylation with mtDNA transcription. Bovine oocytes were obtained from abattoir ovaries and submitted to in vitro culture procedures. Oocytes and embryos were collected at various stages (immature oocyte, IM; mature oocyte, MII; zygote, ZY; 4-cells, 4C; 16-cells, 16C and blastocysts, BL). more...
Organism:
Bos taurus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL26012
18 Samples
Download data: TXT
Series
Accession:
GSE230476
ID:
200230476
15.

Single-cell profiling reveals transcriptome dynamics during bovine oocyte growth

(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
Series
Accession:
GSE249434
ID:
200249434
16.

Machine learning analysis to identify endometrial transcriptomic biomarkers predictive of pregnancy success following artificial insemination in dairy cows

(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
Series
Accession:
GSE248266
ID:
200248266
17.

PEGboIFN-lambda as a FMD preexposure prophylactic and vaccine adjuvant in cattle—ISG and adaptive immunity gene expression

(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
Series
Accession:
GSE262192
ID:
200262192
18.

POLB regulates proliferation and apoptosis of bovine primary myocytes

(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
Series
Accession:
GSE262289
ID:
200262289
19.

Interleukin-6 supplementation improves bovine conceptus elongation and transcriptomic indicators of developmental competence

(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
Series
Accession:
GSE261707
ID:
200261707
20.

Chromatin profiling reveals many transcriptional regulators of proliferation and differentiation of bovine satellite cells

(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
Series
Accession:
GSE253395
ID:
200253395
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