RNA-seq analysis of uterine flushing fluids of three donor and recipient Xianan cows 7 days after fertilization
Ontology highlight
ABSTRACT:
ORGANISM(S): Bos taurus
PROVIDER: GSE216746 | GEO | 2022/11/01
REPOSITORIES: GEO
Similar Datasets
Project description:We report the breed-dependent differences in the innate immune response of dermal fibroblasts following exposure to lipopolysaccharide (LPS). Skin biopsies were collected from Angus (a beef breed) and Holstein (a dairy breed) animals and isolated fibroblasts were exposed to LPS to investigate differences in gene expression between these two cattle breeds.
2016-05-23 | GSE72070 | GEO
Project description:MicroRNAs (miRNAs) are small noncoding RNAs that participate in regulation of gene expression. Their role during mammary gland development is still largely unknown. In the present study, we performed a microarray analysis to identify miRNAs associated with high mammogenic potential of bovine mammary gland. We identified 54 miRNAs differing significantly between mammary tissue of dairy (Holstein-Friesian, HF) and beef (Limousine, LM) post-pubertal heifers. Fifty two miRNAs had higher expression in the mammary tissue of LM heifers. Enrichment analyses for targeted genes revealed that the major differences between miRNA expression in the mammary gland of HF vs. LM were associated with regulation of signalling pathways crucial for mammary gland development, such as: TGF-beta, insulin, WNT and inflammatory pathways. Moreover, a number of genes potentially targeted by differentially expressed miRNAs was associated with mammary stem cells’ activity. These data indicate that in dairy cattle high developmental potential of the mammary gland, leading to high milk productivity, not only depends on central neuro-endocrine regulation but also on specific miRNA expression pattern. miRNA profiling of Holstein Freisian (dairy breed) and Limousne heifers (beef breed) mammay glands. Two-condition experiment, LM (test) vs. HF (reference). Total RNA was isolated from quarters of 4 LM and 4 HFmammary glands.
2014-09-15 | E-GEOD-61227 | biostudies-arrayexpress
Project description:The selection of cattle with high feed efficiency is of paramount importance with regard to reducing feed costs in the beef industry. Developing predictive biological markers specifically for improved feed efficiency is an attractive alternative to direct measurement on large numbers of animals.Evidence is provided that, effects of RFI on gene expression in muscle of beef cattle are not consistent across breed type or dietary phase. These novel observations challenge the practicality of selecting and breeding for low RFI animals across different diets and stages of development. Perhaps, future research should be directed at utilising different diets to harness the full genetic potential of animal based on breed or stage of maturity. Further to this, evidence is provided from our own work and that of others that less efficient HF steers consuming zero grazed grass are under increased stress as demonstrated by an upregulation of immune function in these animals.
2023-06-07 | GSE113135 | GEO
Project description:RNA-seq analysis of uterine flushing fluids of three donor and recipient Xianan cows 7 days after fertilization
| PRJNA895091 | ENA
Project description:Arouquesa breed is an autochthonous Portuguese breed produced under a traditional mountain system. It is known for its Arouquesa PDO beef, a high-quality product with valued organoleptic characteristics. There is a need to improve production systems without affecting beef quality. The aim of this work is to compare the proteomics profile from the Longissimus thoracis muscle from Arouquesa animals produced under different systems. Sixty weaners were produced under the following systems: traditional (TF) and traditional with starter feed supplementation (TF+S1) with weaning and slaughtering at 8 months, the S1+S2 (weaning at 5 months and grower supplement until slaughter) and two rearing periods with finishing supplementation (TF+S3 and S3). Upon slaughter, samples of L. thoracis were taken and analyzed using a shotgun proteomics workflow. Several putative biomarkers of beef quality for the Arouquesa breed were identified: VIM, FSCN1, SERPINH1, ALDH1A1, NDUFB5, ANXA1, PDK4, CEMIP2, NDUFB9, PDLIM1, OXCT1, MYH4. These proteins were involved in actin binding, skeletal muscle development and in the mitochondrial respiratory chain and they can influence mostly meat tenderness and color. Our results demonstrate the link between production practices and putative meat quality signatures, that have potential to improve traceability of certified products.
2024-08-08 | PXD048338 | Pride
Project description:miRNA profiling of bovine satellite cells (BSC) differentiated into myotubes (6th day of in vitro differentiation). BSC isolated from m. semitendinosus of beef (Hereford & Limousine) and dairy (Holstein-Friesian) cattle. Goal was to determine differences in miRNA expresion during in vitro myogenesis in beef vs dairy cattle used as a control.
2018-01-27 | GSE73778 | GEO
Project description:Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 mega bases or ~1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions such as immunity, lactation, reproduction and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research. The custom aCGH chips that interrogated the whole genome CNVs were build for 90 cattles from diverse breeds, with Hereford L1 Dominette 01449 as refference sample.
2010-03-02 | E-GEOD-19866 | biostudies-arrayexpress
Project description:Elevated ambient temperature during the summer season is a main cause of stress in dairy and beef cows, leading to impaired reproductive function and fertility. Follicular fluid extracellular vesicles (FF-EVs) play an important role in intrafollicular cellular communication by in part mediating the deleterious effects of heat stress (HS). Here we aimed to investigate the changes in FF-EV miRNA cargoes in beef cows in response to HS during the summer (SUM) compared to the winter (WIN) season using high throughput sequencing of FF-EV-coupled miRNAs.
2023-05-23 | GSE221198 | GEO
Project description: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. At the end of each dietary phase the most efficient (Low-RFI; n=8) and least efficient (High-RFI; n=8) steers were selected across each breed for longissmus dorsi biopsy collection. RNA was isolated from all muscle tissue samples and subsequently used for small RNA sequencing. Ten miRNA were differentially expressed between the steers divergent for RFI across each diet and breed contrast. Biological pathway analyssi revealed enrichment of pathways related to both metabolic and growth processes.
2024-09-13 | GSE269311 | GEO
Project description:Wandong cattle are an autochthonous Chinese breed used extensively for beef production. The breed tolerates extreme weather conditions and raw feed and are resistant to tick-borne diseases. However, the genetic basis of testis development and sperm production as well as breeding management is not well established in local cattle. In this study, we performed total RNA-Seq and comprehensively analyzed the circ-RNA expression profiling of the testes samples of six bulls at 3 years and 3 months of developmental age. In total, 17 013 circ-RNAs were identified, of which 681 circRNAs (P-adjust < 0.05) were differentially expressed (DE). Among these DE circ-RNAs, 579 were upregulated and 103 were downregulated in calf and bull testes. The Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the identified target genes were classified into three broad functional categories, including biological process, cellular component, and molecular function, and were enriched in the lysine degradation, cell cycle, and cell adhesion molecule pathways.
2021-09-05 | GSE183347 | GEO