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ABSTRACT: Transcriptome analysis of lamb rumen epithelium

PROVIDER: PRJNA1021964 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26222635_1.fastq.gz	Fastqsanger.gz
	SRR26222635_2.fastq.gz	Fastqsanger.gz
	SRR26222636_1.fastq.gz	Fastqsanger.gz
	SRR26222636_2.fastq.gz	Fastqsanger.gz
	SRR26222637_1.fastq.gz	Fastqsanger.gz

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Project description:Transcriptome of lamb rumen epithelium

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Multi-omic biogeography of the gastrointestinal microbiota of a pre-weaned lamb

Project description:Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to study the pre-weaned lamb proteome and metaproteome in ten different gastrointestinal tracts: rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum.

2017-12-14 | PXD008192 | Pride

Microbiota-host crosstalk mechanism in the newborn and adult rumen at single-cell resolution

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.

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Project description:lamb rumen fluid

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Raw single-cell RNA sequencing data of adult rumen tissues

Project description:We performed single-cell RNA-sequencing on the rumen epithelium of dairy cows to construct an epithelial single-cell map of the rumen.

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Project description:Investigation of whole genome gene expression level changes in rumen epithelium of dairy cattle at different stages of rumen development and on different diets.

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Proteome Changes of Diary Calve Rumen Epithelium from Birth to Postweaning

Project description:Rumen epithelium plays a central role in absorbing, transporting, and metabolizing of short-chain fatty acids. For diary calve, the growth of rumen papillae greatly enhances the rumen surface area to absorb nutrients. However, the molecular mechanism underlying diary calve rumen postnatal development remains rarely understood. Here, we firstly performed a shotgun approach and bioinformatics analyses were used to investigate and compare proteomic profiles of Holstein calve rumen epithelium on day 0, 30, 60 and 90 of age. Then,a total of 4372 proteins were identified, in which we found 852, 342, 164 and 95 differentially expressed proteins (DEPs) between D0 and D30, between D30 and D60, between D60 and D90, respectively. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to provide a comprehensive proteomic landscape of diary calve rumen development at tissue level.To conclude, our data indicated that keratinocyte differentiation, mitochondrion formation, the establishment of urea transport and innate immune system play central roles during rumen epithelium development. BH4 presents an important role in rumen epithelial keratinization. The biological processes of BH4 biosynthesis and molecular function of NADP binding participate in mitochondrial cristae formation. The proposed datasets provide a useful basis for future studies to better comprehend diary calve rumen epithelial development.

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Project description:Hu lamb rumen fluid

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Project description:Metagenome of lamb rumen

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Establishment of a bovine rumen epithelial cell line

Project description:The goal of this study was to characterize a single-cell clone derived from bovine rumen epithelium. Analyses including RNA-seq demonstrated that this clone was derived from a rumen epithelial cell. This clone is named BREC1 in the manuscript.

2021-10-27 | GSE181659 | GEO

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