Ontology highlight
ABSTRACT:
PROVIDER: PRJNA982518 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24891400_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR24891389_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR24891390_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR24891391_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR24891392_subreads.fastq.gz | Fastqsanger.gz |
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Project description:ruminal contents in yak calves Targeted loci environmental
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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.
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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.
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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.
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Project description:Deep sequencing of mRNA from 6 organs of yak (Bos grunniens) Analysis of ploy(A)+ RNA of brain,heart,liver,lung,spleen, and stomach of yak (Bos grunniens)
2012-05-18 | E-GEOD-33300 | biostudies-arrayexpress
Project description:Cattle-yak is the hybrid offspring of yak and cattle. It has obvious heterosis in production performance, but the male sterility of cattle-yak has always been the focus of attention. Studies have shown that non-coding RNA is involved in the regulation of spermatogenesis. We comprehensively compared the testicular transcription profiles of cattle, yak and cattle-yak. More DEGs, DECs and DEMs were found in the intersection of the two comparison groups of cattle and cattle-yak, yak and cattle-yak, with 4,968, 360 and 59, respectively. The DEGs of cattle-yak, cattle and yak were mainly enriched in biological processes such as spermatogenesis, male gamete generation and sexual reproduction. At the same time, GO and KEGG analysis suggested that DECs host genes and DEMs source genes were also involved in the regulation of spermatogenesis. The construction of potential ceRNA networks found that some differentially expressed ncRNAs may be involved in the regulation of genes related to testicular spermatogenesis, including miR-423-5p, miR-449b, miR-34b/c, miR-15b, etc., as well as unreported miR-6123, miR-1306 and some miRNA and circRNA interaction pairs. This study provides a reference for further study on the mechanism of male sterility in cattle-yak.
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Project description:Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle. Ruminal wall samples from two randomly chosen animals per group were obtained, totaling four samples. The animals were born, raised and maintained at the Wye Angus farm. This herd, which has been closed for almost 75 years and yielded genetically similar progenies, constitutes an excellent resource to perform transcriptomic analysis. The genetic resemblance among individuals permits us to better control the cause of variation between experimental clusters and individuals. The randomly chosen pairs of animals were part of larger sets of steers that received a particular treatment. All animals received the same diet until weaning. The grain group received conventional diet consisting of corn silage, shelled corn, soy bean and trace minerals. The grass fed steers consumed normally grazed alfalfa; during wintertime, bailage was utilized. The alfalfa has been harvested from land without any fertilizers, pesticides or other chemicals. The steers ate no animal, agricultural or industrial byproducts and never receive any type of grain. Then, the calves were randomly assigned to one diet and exclusively received that regimen until termination. Grain–fed animals reached the market weight around the age of 14 month-old, however, grass-fed steers required approximately 200 additional days to achieve the same weight. Immediately after termination at the Old Line Custom Meat Company (Baltimore, MD) a small piece of ruminal wall was excised, cleaned and preserved at -80°C for posterior processing.
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