Rumen microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1251683 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Investigation of whole genome gene expression level changes in rumen epithelium of dairy cattle at different stages of rumen development and on different diets.
2009-11-01 | GSE18382 | GEO
Project description:RNA-Seq is ubiquitous, but depending on the study, sub-optimal sample handling may be required, resulting in repeated freeze-thaw cycles. However, little is known about how each cycle impacts downstream analyses, due to a lack of study and known limitations in common RNA quality metrics, e.g., RIN, at quantifying RNA degradation following repeated freeze-thaws. Here we quantify the impact of repeated freeze-thaw on the reliability of downstream RNA-Seq analysis. To do so, we developed a method to estimate the relative noise between technical replicates independently of RIN. Using this approach we inferred the effect of both RIN and the number of freeze-thaw cycles on sample noise. We find that RIN is unable to fully account for the change in sample noise due to freeze-thaw cycles. Additionally, freeze-thaw is detrimental to sample quality and differential expression (DE) reproducibility, approaching zero after three cycles for poly(A)-enriched samples, wherein the inherent 3’ bias in read coverage is more exacerbated by freeze-thaw cycles, while ribosome-depleted samples are less affected by freeze-thaws. The use of poly(A)-enrichment for RNA sequencing is pervasive in library preparation of frozen tissue, and thus, it is important during experimental design and data analysis to consider the impact of repeated freeze-thaw cycles on reproducibility.
2020-05-09 | GSE150097 | GEO
Project description:Four mature, non-lactating dairy cattle were transitioned from a high forage diet (HF; 0% grain) to a high grain diet (HG; 65% grain) that was fed for three weeks. Rumen papillae biopsies were performed during the HF baseline (week 0) and after the first (week 1) and third week (week 3) of the grain challenge to create a transcript profile for the the short and long-term adaption of the rumen epithelium during ruminal acidosis. Comparison between three weekly means (n=4 for each week, 12 arrays in total)
2009-08-28 | E-GEOD-17849 | biostudies-arrayexpress
Project description:Four mature, non-lactating dairy cattle were transitioned from a high forage diet (HF; 0% grain) to a high grain diet (HG; 65% grain) that was fed for three weeks. Rumen papillae biopsies were performed during the HF baseline (week 0) and after the first (week 1) and third week (week 3) of the grain challenge to create a transcript profile for the the short and long-term adaption of the rumen epithelium during ruminal acidosis.
2009-08-28 | GSE17849 | GEO
Project description:We performed single-cell RNA-sequencing on the rumen epithelium of dairy cows to construct an epithelial single-cell map of the rumen.
2021-10-21 | GSE175652 | GEO
Project description:As the unique organ, rumen plays vital roles in providing products for humans, however, the underlying cell composition and interactions with epithelium-attached microbes remain largely unknown. Herein, we performed an integrated analysis in single-cell transcriptome, epithelial microbiome, and metabolome of rumen tissues to explore the differences of microbiota-host crosstalk between newborn and adult cattle models. We found that fewer epithelial cell subtypes and more abundant immune cells (e.g., Th17 cells) in the rumen tissue of adult cattle. Metabolism-related functions and oxidation-reduction process were significantly upregulated in the adult rumen epithelial cell subtypes. The epithelial Desulfovibrio was significantly enriched in the adult cattle. To further clarify the role of Desulfovibrio in host’s oxidation-reduction process, we performed metabolomics analysis of rumen tissues and found that Desulfovibrio showed a high co-occurrence probability with the pyridoxal in the adult cattle compared with newborn ones. The adult rumen epithelial cell subtypes also showed stronger ability of pyridoxal binding. These indicates that Desulfovibrio and pyridoxal likely play important roles in maintaining redox balance in adult rumen. The integrated analysis provides novel insights into the understanding of rumen function and facilitate the future precision improvement of rumen function and milk/meat production in cattle.
2022-11-17 | GSE183285 | GEO
Project description:In dairy cows, administration of high dosages of niacin (NA) was found to cause anti-lipolytic effects, which are mediated by the NA receptor hydroxyl-carboxylic acid receptor 2 (HCAR2) in white adipose tissue (WAT), and thereby to an altered hepatic lipid metabolism. However, almost no attention has been paid to possible direct effects of NA in cattle liver, despite showing that HCAR2 is expressed also in the liver of cattle and is even more abundant than in WAT. Due to this, we hypothesized that feeding of rumen-protected NA to dairy cows influences critical metabolic and/or signaling pathways in the liver through inducing changes in the hepatic transcriptome. In order to identify these pathways, we applied genome-wide transcript profiling in liver biopsies obtained at 1 wk postpartum (p.p.) from dairy cows of a recent study (Zeitz et al., 2018) which were fed a total mixed ration without (control group) or with rumen-protected NA from 21 d before calving until 3 wk p.p. Hepatic transcript profiling revealed that a total of 487 transcripts were differentially expressed [filter criteria fold change (FC) > 1.2 or FC < -1.2 and P < 0.05] in the liver at 1 wk p.p. between cows fed NA and control cows. Substantially more transcripts were down-regulated (n = 338), while only 149 transcripts were up-regulated by NA in the liver of cows. Gene set enrichment analysis (GSEA) for the up-regulated transcripts revealed that the most enriched gene ontology (GO) biological process terms were exclusively related to immune processes, such as leukocyte differentiation, immune system process, leukocyte differentiation, activation of immune response and acute inflammatory response. In line with this, the plasma concentration of the acute phase protein haptoglobin tended to be increased in dairy cows fed rumen-protected NA compared to control cows (P < 0.1). GSEA of the down-regulated transcripts showed that the most enriched biological process terms were related to metabolic processes, such as cellular metabolic process, small molecule metabolic process, lipid catabolic process, organic cyclic compound metabolic process, small molecule biosynthetic process and cellular lipid catabolic process. In conclusion, hepatic transcriptome analysis shows that rumen-protected NA induces genes which are involved mainly in immune processes including acute phase response and stress response in dairy cows at wk 1 p.p. These findings indicate that supplementation of rumen-protected NA to dairy cows in the periparturient period may induce or amplify the systemic inflammation-like condition which is typically observed in the liver of high-yielding dairy cows in the p.p. period.
2018-06-21 | GSE116058 | GEO
Project description:This study investigates the impact of cryopreservation and freezing media on RNA quality and gene expression profiles of peripheral blood mononuclear cells (PBMC). No significant difference in cell viability or RNA quality was observed between freshly isolated and cryopreserved cells, even after two freeze-thaw cycles. Transcriptome analysis revealed no significant differences in alignment rates or read counts across various conditions. Differential gene expression analysis identified changes between fresh and thawed samples, with a consistent downward trend of mRNA abundance in the frozen samples, but minimal changes were observed between the first and second freeze-thaw cycles. Gene set enrichment analysis showed only minor significant differences, and stress-related gene sets were not upregulated. Freezing medium appears to be the safer option compared to freezing in trizol. These results confirm that cryopreservation and thawing processes do not compromise RNA integrity or sequencing reliability in PBMC, supporting the use of cryopreserved samples for gene expression studies.
2025-06-19 | GSE299980 | GEO
Project description:Saccharomyces cerevisiae is exposed to freeze-thaw stress in commercial processes including frozen dough baking. The cell viability and fermentation activity after freeze-thaw were dramatically decreased due to freeze-thaw injury. Because freeze-thaw injury involves complex phenomena, the mechanisms of it are not fully understood. We attempted to analyze the mechanisms of freeze-thaw injury by indirect gene expression analysis during post-thaw incubation after freeze-thaw treatment using DNA microarray profiling. The results showed that a high frequency of the genes involved in the homeostasis of metal ions were up-regulated depending on the freezing period. The phenotype of the deletion mutants of the up-regulated genes extracted by indirect gene expression analysis was assessed. The deletion strains of the MAC1 and CTR1 genes involved in copper ion homeostasis exhibited freeze-thaw sensitivity, suggesting that copper ion homeostasis is required for freeze-thaw tolerance. Supplementation with copper ions during post-thaw incubation increased intracellular superoxide dismutase activity. Inverse correlated with intracellular superoxide dismutase activity, intracellular levels of reactive oxygen species were decreased. Moreover, cell viability increased by supplementation with copper ions under specific assessment conditions. This study suggested that insufficiency of copper ion homeostasis may be one of the causes of freeze-thaw injury.
2009-08-31 | GSE15461 | GEO