Ontology highlight
ABSTRACT:
PROVIDER: PRJNA478608 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7457531.fastq.gz | Fastqsanger.gz | |||
| SRR7457531_1.fastq.gz | Fastqsanger.gz | |||
| SRR7457531_2.fastq.gz | Fastqsanger.gz | |||
| SRR7457532.fastq.gz | Fastqsanger.gz | |||
| SRR7457532_1.fastq.gz | Fastqsanger.gz |
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Project description:The rumen plays an essential role in ruminant digestion, absorption, metabolism, and health. The rumen undergoes substantial changes in size and function from birth to adulthood. The molecular mechanisms underlying these changes are not fully understood. This study was aimed to identify the transcription factors and signaling pathways mediating these changes in cattle. We used 6 neonatal bull calves and 6 adult steers, all Angus-crossbred, in this study. We found that the ratios of the emptied rumen, reticulum, omasum, and abomasum to total body weight in adult steers were 4.8 (P < 0.01), 3.1 (P < 0.01), 6.0 (P < 0.01), and 0.8 (P = 0.9) times those in neonatal calves, respectively. Histological examinations showed a 7.4-, 2.0-, 3.0-, 2.9-, and 4.6-fold increase (P < 0.01 for all) in the length of the rumen papillae and the thickness of the rumen epithelium, tunica mucosa and submucosa, tunica muscularis, and tunica serosa, respectively, from neonatal calves to adult steers. Papilla density was lower in adult steers than in neonatal calves (P < 0.05). The size of the rumen epithelial cells was not different between neonatal calves and adult steers (P = 0.57). RNA sequencing identified 2,906 genes differentially expressed (adjusted P < 0.05 and |log2fold change| ≥ 1) in the rumen between neonatal calves and adult steers, of which 1,586 were downregulated and 1,320 upregulated in adult steers. Bioinformatic analyses indicated organ development and morphogenesis, neuronal differentiation, blood vessel development, Ras signaling, and Wnt signaling were among the functional terms enriched in genes downregulated in adult steers, while fatty acid metabolism, ketogenesis, immune responses, PPAR signaling, and Rap1 signaling were among those enriched in genes upregulated in adult steers. Bioinformatic analyses also indicated that SRF, IRF4, SPI1, ETS1, and PURA were the major transcription factors mediating gene upregulation and that TCF4, MESP1, TCF3, ID4, and SNAI2 were the major transcription factors mediating gene downregulation in the rumen from neonatal calves to adult steers. Taken together, these results suggest that the rumen grows by increasing the number, not by the size, of individual cells from birth to adulthood, that the absorptive, metabolic, immune, and motility functions of the rumen are attained or enhanced during the postnatal life, and that the changes in rumen size and function from birth to adulthood are mediated by many transcription factors including SRF and TCF4 and many signaling pathways including the PPAR and Wnt signaling pathways.
2025-02-05 | GSE280816 | 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: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:RNA sequencing (RNA-Seq) was performed on rumen papillae from 16 steers with variation in gain and feed intake.
2015-07-22 | GSE71153 | 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:In order to test the development of gastrointestinal tract (GIT) in pre-weaned cavles, the GIT tissues were collected from day 0, day 7, day 21 and day 42 calves. RNA-seq was used to measure the transcriptome profiles. The RNA-seq analysis revealed the fast development of small intestine and rumen tissue during the first week after birth.
2016-05-01 | GSE74329 | 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.
2009-08-28 | GSE17849 | GEO
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: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