Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25552201_1.fastq.gz | Fastqsanger.gz | |||
| SRR25552201_2.fastq.gz | Fastqsanger.gz | |||
| SRR25552202_1.fastq.gz | Fastqsanger.gz | |||
| SRR25552202_2.fastq.gz | Fastqsanger.gz | |||
| SRR25552203_1.fastq.gz | Fastqsanger.gz |
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Project description:A healthy rumen is crucial for normal growth and improved production performance of ruminant animals. Rumen microbes participate in and regulate rumen epithelial function, and the diverse metabolites produced by rumen microbes are important participants in rumen microbe-host interactions. SCFAs, as metabolites of rumen microbes, have been widely studied, and propionate and butyrate have been proven to promote rumen epithelial cell proliferation. Succinate, as an intermediate metabolite in the citric acid cycle, is a final product in the metabolism of certain rumen microbes, and is also an intermediate product in the microbial synthesis pathway of propionate. However, its effect on rumen microbes and rumen epithelial function has not been studied. It is unclear whether succinate can stimulate rumen epithelial development. Therefore, in this experiment, Chinese Tan sheep were used as experimental animals to conduct a comprehensive analysis of the rumen microbiota community structure and rumen epithelial transcriptome, to explore the role of adding succinate to the diet in the interaction between the rumen microbiota and host.
2023-06-12 | GSE233696 | GEO
Project description:RNA sequencing (RNA-Seq) was performed on rumen papillae from 16 steers with variation in gain and feed intake. Sixteen rumen papillae samples were sequenced by Cofactor Genomics (St.Louis, MO).
2015-07-22 | E-GEOD-71153 | biostudies-arrayexpress
Project description:In this study, we studied the fibrolytic potential of the rumen microbiota in the rumen of 6 lambs separated from their dams from 12h of age and artificially fed with milk replacer (MR) and starter feed from d8, in absence (3 lambs) or presence (3 lambs) of a combination of the live yeast Saccharomyces cerevisiae CNCM I-1077 and selected yeast metabolites. The fibrolytic potential of the rumen microbiota of the lambs at 56 days of age was analyzed with a DNA microarray (FibroChip) targeting genes coding for 8 glycoside hydrolase (GH) families.
2019-10-01 | GSE122256 | GEO
Project description:AIMS: To explore and validate the utility of rumen endoscopy for collection of rumen papillae for gene expression measurement. METHODS: Four adult Coopworth ewes were fasted for either 4 or 24 hours. Animals were sedated, placed in a dorsally recumbent position at 45 degrees with the head upright, and an endoscope inserted via a tube inserted into the mouth. Biopsies of rumen papillae were taken from the ventral surface of the rumen atrium under visual guidance. Two biopsies were collected from one of the animals that had been fasted for 4 hours, and three from one of the animals that had been fasted for 24 hours. Video of the rumen atrium and reticulum was also collected. The animals recovered uneventfully. Biopsies were subsequently used for extraction and sequencing of mRNA. RESULTS: The ventral surface of the rumen atrium was accessible after 4 hours off pasture, but a larger region was accessible after 24 hours of fasting. Sedation allowed access for endoscope use for around 5 to 10 minutes after which increased saliva flow was noted. Rumen papillae biopsies were easily collected, with samples from a variety of sites collected in the ∼10 minute time window. High quality RNA was obtained for stranded mRNA sequencing. Of the resulting reads, 69–70% mapped uniquely to version 3.1 of the ovine genome, and 48–49% to a known gene. The rumen mRNA profiles were consistent with a previously reported study. CONCLUSIONS: This method for obtaining rumenal tissue was found to be rapid and resulted in no apparent short or long term effects on the animal. High quality RNA was successfully extracted and amplified from the rumen papillae biopsies, indicating that this technique could be used for future gene expression studies. The use of rumen endoscopy could be extended to collection of a variety of rumen and reticulum anatomical measurements and deposition and retrieval of small sensors from the rumen. Rumen endoscopy offers an attractive and cost effective approach to repeated rumen biopsies compared with serial slaughter or use of cannulated animals.
2015-09-30 | GSE68791 | GEO
Project description:While DNA methylation in other tissues can be approximated through model species, the dynamic distribution and regulatory significance of DNA methylation in the rumen, a unique organ in ruminant, remain largely unknown. Here, we employed whole-genome bisulfite sequencing (WGBS), transcriptomics, and histone modification data to compare fetal and adult stages of bovine rumen with other tissues, including pluripotent stem cells (PSCs) approximating pre-implantation embryos. We found extensive methylation differences, including CG methylation (mCG) and non-CG methylation (mCH; H represents A, C and T) between the rumen at fetal and adult stages and other tissues and PSCs. These differentially methylated regions (DMRs) are closely associated with other epigenetic regulatory components, such as transcription factors (TFs) and histone modifications. These DMRs can also combine to form large hypo CG-DMRs to regulate a cluster of functionally related genes. We elucidated the reasons for morphological and functional differences between fetal and adult rumen at the epigenetic level and the interactions between epigenetic modifications and gene expression. This study highlights the differences in methylation patterns between the rumen and other tissues during development and the role of DNA methylation in controlling gene expression and establishing tissue-specific functions.
2024-06-01 | GSE264336 | GEO
Project description:While DNA methylation in other tissues can be approximated through model species, the dynamic distribution and regulatory significance of DNA methylation in the rumen, a unique organ in ruminant, remain largely unknown. Here, we employed whole-genome bisulfite sequencing (WGBS), transcriptomics, and histone modification data to compare fetal and adult stages of bovine rumen with other tissues, including pluripotent stem cells (PSCs) approximating pre-implantation embryos. We found extensive methylation differences, including CG methylation (mCG) and non-CG methylation (mCH; H represents A, C and T) between the rumen at fetal and adult stages and other tissues and PSCs. These differentially methylated regions (DMRs) are closely associated with other epigenetic regulatory components, such as transcription factors (TFs) and histone modifications. These DMRs can also combine to form large hypo CG-DMRs to regulate a cluster of functionally related genes. We elucidated the reasons for morphological and functional differences between fetal and adult rumen at the epigenetic level and the interactions between epigenetic modifications and gene expression. This study highlights the differences in methylation patterns between the rumen and other tissues during development and the role of DNA methylation in controlling gene expression and establishing tissue-specific functions.
2024-06-01 | GSE264333 | GEO
Project description:While DNA methylation in other tissues can be approximated through model species, the dynamic distribution and regulatory significance of DNA methylation in the rumen, a unique organ in ruminant, remain largely unknown. Here, we employed whole-genome bisulfite sequencing (WGBS), transcriptomics, and histone modification data to compare fetal and adult stages of bovine rumen with other tissues, including pluripotent stem cells (PSCs) approximating pre-implantation embryos. We found extensive methylation differences, including CG methylation (mCG) and non-CG methylation (mCH; H represents A, C and T) between the rumen at fetal and adult stages and other tissues and PSCs. These differentially methylated regions (DMRs) are closely associated with other epigenetic regulatory components, such as transcription factors (TFs) and histone modifications. These DMRs can also combine to form large hypo CG-DMRs to regulate a cluster of functionally related genes. We elucidated the reasons for morphological and functional differences between fetal and adult rumen at the epigenetic level and the interactions between epigenetic modifications and gene expression. This study highlights the differences in methylation patterns between the rumen and other tissues during development and the role of DNA methylation in controlling gene expression and establishing tissue-specific functions.
2024-06-01 | GSE264339 | 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:A total of 14 samples were used, 12 paired rumen and colon samples, and two rumen only samples. DNA was extracted from each sample, and PCR amplified using universal bacterial primers 27F and 1492R. Trends between anatomical location, age and sex were considered.
2012-11-24 | E-MEXP-3721 | biostudies-arrayexpress