Bos taurus
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ABSTRACT:
PROVIDER: PRJNA327098 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We assessed the transcriptomic adaptation of the calf rumen epithelium to changes in ruminal pH caused by feeding calf starter with and without forage during weaning transition. The calves were divided into a gorage provision group (HAY group, n = 3) and forage non-provision group (CON group, n = 4) 3 weeks after weaning.
2016-06-29 | E-GEOD-83813 | biostudies-arrayexpress
Project description:We assessed the transcriptomic adaptation of the calf rumen epithelium to changes in ruminal pH caused by feeding calf starter with and without forage during weaning transition.
2016-06-29 | GSE83813 | GEO
Project description:The objectives of the study were to use RNA-Seq to examine the effect of (i) breed and (ii) gradual weaning, on the whole blood mRNA transcriptome of artificially reared Holstein-Friesian and Jersey calves. The calves were gradually weaned over 14 days (day (d) -13 to d 0) and mRNA transcription was examined one day before gradual weaning was initiated (d -14), one day after weaning (d 1) and 8 days after weaning (d 8). RNA-seq analysis was carried out on RNA extracted from whole blood. Gradual weaning had no effect on gene expression (P>0.05).There were 550 differentially expressed genes at a false discovery rate of 10% and with a â¥1.5-fold change, between Holstein-Friesian and Jersey calves on d -14, 490 on d 1, and 411 on d 8. GOseq/KEGG pathway analysis showed that the cytokine-cytokine receptor interaction pathway and the neuroactive ligand-receptor interaction pathway were over-represented between breeds on all days (P<0.01; Qâ¤0.1). These results demonstrate that the gradual weaning practiced here does not compromise the welfare of artificially-reared dairy calves, evidenced by the lack of expression changes in any genes in response to gradual weaning. These data also suggest differences in cell signalling and immune responses between breeds. Eight Holstein-Friesian and eight Jersey bull calves were group housed indoors and individually fed milk replacer and concentrate using an automatic feeder. Calves were gradually weaned by reducing milk-replacer from 6 litres to 0 litres over 14 days (d) (d -13 to d 0). Calves were blood sampled on d -14, 1, and 8, relative to weaning (d 0). RNA-seq analysis was carried out on RNA extracted from whole blood.
2016-08-19 | E-GEOD-76841 | biostudies-arrayexpress
Project description:We investigated the effects of wood kraft pulp (WP) supplementation on ruminal pH, fermentation, and epithelial transcriptomic dynamics in Holstein cattle during the high-grain diet challenge.
2019-03-19 | GSE128461 | GEO
Project description:The objectives of the study were to use RNA-Seq to examine the effect of (i) breed and (ii) gradual weaning, on the whole blood mRNA transcriptome of artificially reared Holstein-Friesian and Jersey calves. The calves were gradually weaned over 14 days (day (d) -13 to d 0) and mRNA transcription was examined one day before gradual weaning was initiated (d -14), one day after weaning (d 1) and 8 days after weaning (d 8). RNA-seq analysis was carried out on RNA extracted from whole blood. Gradual weaning had no effect on gene expression (P>0.05).There were 550 differentially expressed genes at a false discovery rate of 10% and with a ≥1.5-fold change, between Holstein-Friesian and Jersey calves on d -14, 490 on d 1, and 411 on d 8. GOseq/KEGG pathway analysis showed that the cytokine-cytokine receptor interaction pathway and the neuroactive ligand-receptor interaction pathway were over-represented between breeds on all days (P<0.01; Q≤0.1). These results demonstrate that the gradual weaning practiced here does not compromise the welfare of artificially-reared dairy calves, evidenced by the lack of expression changes in any genes in response to gradual weaning. These data also suggest differences in cell signalling and immune responses between breeds.
2016-08-19 | GSE76841 | GEO
Project description:Comprehensive analyses of tissues at single-cell level will benefit our understanding of genetic bases for complex traits. Here we present an initial effort of single-cell transcriptomic analyses of cattle ruminal epithelial cells during the rumen development. We obtained 5064 and 1372 cells from Holstein ruminal epithelial cells before and after weaning, respectively. We reported 6 cell types across their temporal and spatial distributions, which were partially correlated with rumen epithelium layer’s structures and functions. We also reported a distinct sets of cell markers for these cell types, for example, CRA1, HMMR, MKI67, and EZH2 for the dividing epithelial cells and the TGFB pathway and the keratin gene family for keratinized epithelial cells. Our proposed a cell lineage model may contribute to the understanding of cattle rumen epithelial proliferation and development.
2021-10-01 | GSE166473 | GEO
Project description:This study aimed to investigate the effect of postbiotic from dead cell Lactobacillus ingluviei CR37 on growth performance, antioxidant capacity, and liver transcriptional response of calves. Fourteen Holstein bull calves were assigned to 2 treatment groups: CON (n = 7) or DCLI (n = 7, fed 1 g/d of dead cell Lactobacillus ingluviei CR37 strain, containing 108 CFU/g). Calves received milk replacer (MR) at 1.75% of BW (based on air-dry weight) and the amount was adjusted weekly according to body weight, while fresh and clean water was provided ad libitum. All calves had free access to starter starting on day 33. On day 82, the MR solution was reduced to 50% of the previous week's allocation, and calves were completely weaned by day 89. Liver samples were collected after slaughter on day 90. Transcriptome analysis identified 33 DEGs, including 16 upregulated DEGs such as Endothelial lipase (LIPG), Peroxisomal Acyl-CoA oxidase 1 (ACOX1), Solute carrier family 27 member 6 (SLC27A6), and 17 downregulated DEGs such as Family with sequence similarity 107 member A (FAM107A), 4-Hydroxy-2-oxoglutarate aldolase 1 (HOGA1), Farnesyl diphosphate synthase (FDPS). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 11 significant pathways, including the PPAR signaling pathway and Pentose phosphate pathway. Taken together, postbiotic supplementation demonstrated potential benefits in improving lipid metabolism and mitigating oxidative stress in weaning calves.
2025-04-03 | GSE293736 | GEO
Project description:To evaluate how commercially available vaccines and marketing strategy affect the host transcriptome of commercial beef cattle overtime, we sequenced the whole blood RNA of 73 commercial beef bull calves enrolled in a split plot study. Calves were randomized to one of four groups, having received a commercially available vaccine during the cow-calf phase or not, and placed in a commercial salebarn system after weaning (auction) or directly shipped to backgrounding (direct). Samples were acquired from six time points: T1 (modified live viral (MLV) vaccination; age: ~107 d.), T2 (seven days post-vaccination; age: ~114 d.), T3 (revaccination; age: ~183 d.), T4 (abrupt weaning; age: ~230 d.), T5 (arrival to backgrounding after marketing decision; age: ~233 d.), and T6 (45 days post-arrival to backgrounding; age: ~278 d.). Further evaluation was made based on whether calves were clinically diagnosed with bovine respiratory disease (BRD) after weaning.
2025-11-07 | GSE248477 | GEO
Project description:An abrupt transition from high forage to high fermentable diet may induce digestive disorders in the rumen. To date, the host mechanisms regulate the adaption to such dietary transition are largely unknown. To understand the molecular mechanisms involved in such phenomena, RNA-sequencing was performed to identify the changes in the transcriptomes of ruminal epithelia during a rapid high grain transition from 3% to 92% grain. In total, the expression of 11,044, 11,322 and 11,282 genes was detected in ruminal epithelia of beef heifers (n=15) fed 3%, 75% and 92% barley grain diet, respectively. When diet was changed from 75% to 92% grain, a significant difference was observed in the mean ruminal pH change among the individuals with five heifers decreased (DG; pH from 6.30 ± 0.09 to 5.87 ± 0.15, P < 0.01) and five other ones increased (UG; pH from 5.84 ± 0.42 to 6.35 ± 0.37, P < 0.05). In the ruminal epithelia of DG animals, the expression of genes involved in ketogenesis (HMGCL, P < 0.1) and lipid synthesis (SREBF2, P < 0.1; FABP4, P < 0.05) was increased, the abundance of genes involved in short chain fatty acid transporters (SMCT1, P < 0.1) and monocarboxylate transporters (MCT4, P < 0.1) was decreased. The function of “Concentration of lipid” was activated after 75% to 92% grain diet transition. Comparing to DG animals, the expression of ketogenesis (ACAT2, P < 0.05; HMGCS P < 0.1) and cholesterol synthesis related genes (HMGC and FDPs, P < 0.1) was deceased, while the expression of proton and cholesterol efflux related genes NHE3 and ABCA1 were increased (P < 0.05), and the function of “Storage of lipid” was inhibited in the ruminal epithelial of UG heifers. In addition, the function of differentially expressed (DE) genes in DG were involved in “T cell receptor signaling” and “complement and coagulation cascades” pathways, while the functions “metabolism of xenobiotics by cytochrome P450” and “p53 signaling pathway” were enriched for DE genes in UG animals. Furthermore, the single nucleotide polymorphisms (SNP) discovery by RNA-seq was performed, and SNP (g.46834311A > G) in FABP4 identified between two groups of animals (P < 0.1). The expression of genes involved in regulating lipid transport and fatty acid metabolism varied between DG and UG heifers during rapid 75% to 92% grain transition. The identified genes and SNP could be potential markers and may account for the varied ruminal pH responses between DG and UG heifers, which can be potentially applied in breeding and selecting beef cattle with more tolerance in dietary transition stress.
2018-02-13 | GSE89874 | GEO
Project description:The study examined changes in the transcriptional profile of skeletal muscle tissue in heifer calves offered varying planes of nutrition during the early life period. From approximately 3 weeks of age Angus X Holstein-Friesian heifer calves were offered either a high or moderate plane of nutrition to achieve target growth rates of 1.2 kg/d and 0.5 kg/d, respectively. After 18 weeks of differential feeding all calves were euthanized and skeletal muscle tissue samples collexted from each calf. RNA was extracted and subsequently subjected to RNAseq analysis. 482 genes were significantly differentially expressed between calves on the High plane of nutrition and those on the Moderate plane of nutrition. Biological pathway analysis revealed an enrichement from these genes for processes and pathways related to energy production and cellular growth and proliferation.
2025-07-09 | GSE266506 | GEO