Ontology highlight
ABSTRACT:
PROVIDER: PRJNA627439 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11594890.fastq.gz | Fastqsanger.gz | |||
| SRR11594891.fastq.gz | Fastqsanger.gz | |||
| SRR11594892.fastq.gz | Fastqsanger.gz | |||
| SRR11594893.fastq.gz | Fastqsanger.gz | |||
| SRR11594894.fastq.gz | Fastqsanger.gz |
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Project description:Cattle are often fed high concentrate diets to increase energy intake and improve overall animal performance. Such diets also cause changes in fermentation patterns and epithelial function. However, the molecular mechanisms involved in regulating epithelial function for cattle fed high concentrate diets have not been elucidated. In this study, we aimed to gain a broad overview of the involved molecular mechanisms by detecting differentially expressed genes (DEG) in rumen tissue from dairy cows fed a low concentrate (LC; 8%) compared to a high concentrate (HC; 64%) diet using a bovine-specific microarray platform containing 16,846 unique gene loci and 5,943 ESTs from the bovine genome. Feeding the HC diet increased the total volatile fatty acid concentration and markedly reduced ruminal pH, suggesting that the dietary treatments used did induce changes in ruminal fermentation. In response to changes in the ruminal environment, a total of 5,200 elements were detected as DEG in ruminal tissue with >1.5-fold expression change (P < 0.05) for cows fed HC relative to LC. Of the 5,200 DEG, 2,233 and 2,967 were up- and down-regulated, respectively. The GENECODIS analysis elucidated that relationships among the DEG represented 19 annotations characterized with GO molecular function and KEGG pathways with 26 DEG identified in multiple annotations such as calcium signaling and gap junction pathways. Among those DEG that were identified numerous times, catalytic subunit of cAMP-dependent protein kinase (PRKACB) was down-regulated in ruminal tissue from cows fed HC, suggesting that this gene may have important roles including regulation of cell proliferation and differentiation, and intracellular pH regulation. Two-condition experiment, High concentrate vs. Low concentrate diets. Biological replicates: 5 high concentrate fed, 5 low concentrate, independently grown and harvested. Two replicates per array.
2010-10-02 | E-GEOD-19802 | biostudies-arrayexpress
Project description:Cattle are often fed high concentrate diets to increase energy intake and improve overall animal performance. Such diets also cause changes in fermentation patterns and epithelial function. However, the molecular mechanisms involved in regulating epithelial function for cattle fed high concentrate diets have not been elucidated. In this study, we aimed to gain a broad overview of the involved molecular mechanisms by detecting differentially expressed genes (DEG) in rumen tissue from dairy cows fed a low concentrate (LC; 8%) compared to a high concentrate (HC; 64%) diet using a bovine-specific microarray platform containing 16,846 unique gene loci and 5,943 ESTs from the bovine genome. Feeding the HC diet increased the total volatile fatty acid concentration and markedly reduced ruminal pH, suggesting that the dietary treatments used did induce changes in ruminal fermentation. In response to changes in the ruminal environment, a total of 5,200 elements were detected as DEG in ruminal tissue with >1.5-fold expression change (P < 0.05) for cows fed HC relative to LC. Of the 5,200 DEG, 2,233 and 2,967 were up- and down-regulated, respectively. The GENECODIS analysis elucidated that relationships among the DEG represented 19 annotations characterized with GO molecular function and KEGG pathways with 26 DEG identified in multiple annotations such as calcium signaling and gap junction pathways. Among those DEG that were identified numerous times, catalytic subunit of cAMP-dependent protein kinase (PRKACB) was down-regulated in ruminal tissue from cows fed HC, suggesting that this gene may have important roles including regulation of cell proliferation and differentiation, and intracellular pH regulation.
2010-10-02 | GSE19802 | GEO
Project description:Purpose: Streptomyces albulus is an industrial producer of ε-poly-L-lysine, an antimicrobial cationic homo poly-amino acid used practically as a natural food preservative. Here, we present RNA sequencing data set unveiling differentially expressed transcripts during ε-poly-L-lysine production in the most extensively studied poly-L-Lys producer, S. albulus NBRC14147. Methods: During the poly-L-Lys fermentation, cells grown for 8 hours and 35 hours were harvested as growth phase cells and production phase cells, respectively, and total RNA were extracted individually. A 100-bp paired-end mRNA sequencing was performed for each sample on the Illumina HiSeq 2500 system. Result: Using an optimized data analysis workflow, we were able to map more than 44 million sequence reads per sample to the reference genome (GenBank accession number ASM385166v1). Differential gene expression analysis was performed using the edgeR. The RNA-seq data revealed that a total of 2449 genes were considered to be differentially expressed during poly-L-Lys production using a fold change cutoff of log2 less than -1 and greater than 1 (equivalent to a ±2-fold change). Conclusion: Our data will serve as a primary source for investigating the regulatory mechanism which govern poly-L-Lys production in S. albulus NBRC14147.
2022-01-19 | GSE192684 | GEO
Project description:The effects of anti-lipopolysaccharide (LPS) antibody on ruminal fermentation, LPS activity, and liver transcriptomes were investigated during the subacute ruminal acidosis (SARA) challenge.
2020-05-15 | GSE150553 | GEO
Project description:Emerging data has highlighted the importance of short-chain fatty acids (SCFAs), particularly butyrate, in regulating ruminal homeostasis in vivo isolated epithelial cells. However, little is known about other SCFAs like acetate or propionate, and the interaction between rumen microbes and epithelial immunity are rarely reported. Here, we firstly combined infusion of three SCFAs, to study their different roles in ruminal development, antioxidant capacity, barrier functions, and immunity, as well as cross-talk with ruminal microbiome (16S rRNA sequencing data of rumen digesta) and derived transcriptome (RNA-Seq) and metabolism using an in vivo goat model.
2022-12-26 | GSE221508 | GEO
Project description:Emerging data has highlighted the importance of short-chain fatty acids (SCFAs), particularly butyrate, in regulating ruminal homeostasis in vivo isolated epithelial cells. However, little is known about other SCFAs like acetate or propionate, and the interaction between rumen microbes and epithelial immunity are rarely reported. Here, we firstly combined infusion of three SCFAs, to study their different roles in ruminal development, antioxidant capacity, barrier functions, and immunity, as well as cross-talk with ruminal microbiome (16S rRNA sequencing data of rumen digesta) and derived transcriptome (RNA-Seq) and metabolism using an in vivo goat model.
2022-12-26 | GSE221507 | GEO
Project description:Among multiple interconnected pathways for L-Lysine (L-Lys) catabolism in pseudomonads, Pseudomonas aeruginosa PAO1 employed the decarboxylase and the transaminase pathways. However, up till now several genes involved in the operation and regulation of these pathways were still missing. Transcriptome analyses coupled with promoter activity measurements and mutant growth phenotype analysis lead us to identify several new members of the L-Lys and D-Lys catabolic pathways and their regulatory elements, including argR to trigger lysine decarboxylation into cadaverine, PauR for the γ-glutamylation pathway of polyamine catabolism into 5-aminovalerate, gcdR-gcdHG for glutarate utilization, dpkA, amaR-amaAB and PA2035 for D-Lys catabolism, lysR-lysXE for L-Lys efflux, and lysP for L-Lys uptake.
2015-12-09 | GSE75502 | 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:Emerging data has highlighted the importance of short-chain fatty acids (SCFAs) on ruminal microbiome and derived metabolism profiling, and ruminal epithelial health and nutritional absorption in ruminants. However, little is known about the roles of SCFAs on ileal microbiome profiles. Here, we combined infusion of three SCFAs, to study their different roles in ileal microbiome succession profiling using a in vivo goat model.
2023-08-14 | GSE240818 | GEO
Project description:Purpose: To study the expression and potential significance of tRF and tiRNA in PTC (Papillary thyroid carcinoma) by sequencing tRF and tiRNA in PTC tissues and corresponding paracancer tissues of thyroid cancer patients. Methods: Four pairs of PTC tissues and paracancer tissues were collected. Small RNA sequencing was performed on Illumina NexSeq instrument. Results: If P ≤ 0.05, fold change > 1.5 as the cutoff, there were 27 up-regulated tRFs & tiRNAs and 20 down-regulated tRFs & tiRNAs. Conclusions: Among the differentially expressed tRFs & tiRNAs, tiRNA-1:34-Lys-CTT-2 and tRF-1:30-Gly-CCC-3 may be the potential novel regulatory factors.
2022-02-26 | GSE197438 | GEO