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The effect of different concentrations of ruminal VFAs on the circadian rhythm of gene expression in ovine ruminal epithelial cells using RNA-seq

ABSTRACT: The effect of different concentrations of ruminal VFAs on the circadian rhythm of gene expression in ovine ruminal epithelial cells using RNA-seq

PROVIDER: PRJNA1210569 | ENA |

REPOSITORIES: ENA

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The effect of different concentrations of ruminal VFAs on the circadian rhythm of gene expression in ovine ruminal epithelial cells using RNA-seq

Project description:This experiment aimed to investigate the effect of different concentrations of ruminal VFAs on the circadian rhythm of gene expression in ORECs of Grain-diet and Hay-diet groups. The ORECs treated with Grain-VFAs and Hay-VFAs were collected at six different timepoints (T0, T4, T8, T12, T16, and T20) for the circadian rhythm analysis using RNA sequencing.

2025-01-14 | GSE286932 | GEO

Study the role of different concentrations of VFAs on chromatin accessibility in ovine ruminal epithelial cells at am and pm using ATAC-seq

Project description:This experiment employed ATAC-seq (Assay for Transposase Accessible Chromatin with sequencing) to explore the mechanism of how different concentrations of VFAs regulate ruminal epithelial chromatin accessibility under the Grain-diet and Hay-diet patterns in both am and pm. Cells from Grain-am, Grain-pm, Hay-am, and Hay-pm treatment groups were havest for ATAC-seq experiments, n=3 pooled biological replicates per library.

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Study the role of different concentrations of VFAs on histone modifications in ovine ruminal epithelial cells at am and pm using CUT&Tag-seq

Project description:This experiment employed CUT&Tag-seq (Cleavage Under Targets and Tagmentation with sequencing) to explore the mechanism of how different concentrations of VFAs regulate ruminal epithelial histone modifications under the Grain-diet and Hay-diet patterns in both am and pm. Cells from Grain-am, Grain-pm, Hay-am, and Hay-pm treatment groups were havest for CUT&Tag-seq experiments, n=3 pooled biological replicates per library. The primary histones used for CUT&Tag were Acetyl-Histone H3 (Lys27) Rabbit mAb (H3K27ac, 8173S, CST), Acetyl-Histone H3 (Lys9) (C5B11) Rabbit mAb (H3K9ac, 9649S, CST), and Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb (H3K4me3, 9751S, CST).

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Gene expression profiles in ruminal tissue from cows fed high or low concentrate diets

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.

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