Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1072312 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27842822_1.fastq.gz | Fastqsanger.gz | |||
| SRR27842822_2.fastq.gz | Fastqsanger.gz | |||
| SRR27842823_1.fastq.gz | Fastqsanger.gz | |||
| SRR27842823_2.fastq.gz | Fastqsanger.gz | |||
| SRR27842824_1.fastq.gz | Fastqsanger.gz |
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Project description:Hanwoo cattle are a Korean breed renowned for their cultural significance and high-quality beef, characterized by low cholesterol and high unsaturated fat ratio. Growth is divided into a growing phase focused on development and a fattening phase for marbling. Proper feed management, considering genetic and environmental factors, is vital for maximizing growth potential. The rumen plays a crucial role in digestion and gene expression regulation, with rumen fermentation being central to nutrient absorption and cattle health. In this study, we conduct transcriptome analysis of the rumen at eight timepoints. Our goal is to identify genetic factors that influence the growth of Hanwoo steers to enhance our understanding of the rumen’s functions and roles during their growth. In this RNA-sequencing analysis of Hanwoo steer rumen, differential gene expression was examined over eight timepoints, highlighting significant genetic changes, particularly between 12 and 26 months. Weighted gene co-expression network analysis identified and organized as three modules: turquoise, blue, and yellow. The turquoise module, linked to immune response, showed down-regulation in genes at 30 months. The blue module, associated with steroid metabolism, was notably up-regulated at 26 months. The yellow module’s genes showed a consistent increase in expression with growth. These modules and their functional annotations provide a deeper understanding of the biological processes during Hanwoo growth, highlighting the intricate relationship between gene expression and cattle development. The growth stages of Hanwoo steers were explored in our investigation utilizing rumen transcriptome data. The rumen plays critical role in their development, particularly during the growing and fattening phases. Proper feed management, considering the rumen’s function, is essential for optimal growth. Transcriptome analysis helps identify genes associated with growth and provides insights for cattle breeding and management practices. Understanding the complex connection between gene expression and Hanwoo development is essential for maximizing productivity and health.
2024-06-02 | GSE267733 | GEO
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Project description:Creatine pyruvate (CrPyr) is a new multifunctional nutrient that can provide both pyruvate and creatine. It has been shown to relieve the heat stress of beef cattle by improving antioxidant activity and rumen microbial protein synthesis, but the mechanism of CrPyr influencing rumen fermentation remains unclear. This study aimed to use metaproteomics technologies to investigate the bacterial protein function in rumen fluid samples taken from heat-stressed beef cattle treated with or without 60 g/d CrPyr.
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Project description:Rumen fluid from Angus beef cattle Raw sequence reads
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Project description:Selenium (Se) is an essential nutrient for beef cattle health and commercial production. The molecular mechanisms responsible for physiological responses of the animal to dietary Se supplementation, however, have not been evaluated. Furthermore, the potential effect of two chemical forms (organic vs. inorganic) of Se on gene expression by Se-sufficient cattle has not been evaluated. Microarray analysis using the GeneChip Bovine Genome Array (Affymetrix, Inc., Santa Clara, CA) was conducted to determine if dietary Se supplementation in organic vs. inorganic form (OSe vs. ISe) differentially affects the liver gene expression profile in growing beef heifers. Sodium selenite (Prince Se Concentrate; Prince Agri Products, Inc., Quincy, IL) was used as the source of ISe form. Se-enriched yeast (Sel-Plex; Alltech, Inc., Nicholasville, KY) was used as the source of OSe form. Thirty Angus heifers (BW 393 ± 9 kg) were randomly assigned to 3 dietary treatments (n = 10): Control (Ctrl) group received no dietary Se supplementation; ISe treatment group daily received dietary supplementation of Se at 3 mg/animal from ISe source; OSe treatment group daily received dietary supplementation of Se at 3 mg/animal from OSe source. Six animals were randomly selected from each of 3 treatment groups for RNA extraction and microarray analysis.
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Project description:Hong2004 - Genome-scale metabolic network of
Mannheimia succiniciproducens (iSH335)
This model is described in the article:
The genome sequence of the
capnophilic rumen bacterium Mannheimia succiniciproducens.
Hong SH, Kim JS, Lee SY, In YH, Choi
SS, Rih JK, Kim CH, Jeong H, Hur CG, Kim JJ.
Nat. Biotechnol. 2004 Oct; 22(10):
1275-1281
Abstract:
The rumen represents the first section of a ruminant
animal's stomach, where feed is collected and mixed with
microorganisms for initial digestion. The major gas produced in
the rumen is CO(2) (65.5 mol%), yet the metabolic
characteristics of capnophilic (CO(2)-loving) microorganisms
are not well understood. Here we report the 2,314,078 base pair
genome sequence of Mannheimia succiniciproducens MBEL55E, a
recently isolated capnophilic Gram-negative bacterium from
bovine rumen, and analyze its genome contents and metabolic
characteristics. The metabolism of M. succiniciproducens was
found to be well adapted to the oxygen-free rumen by using
fumarate as a major electron acceptor. Genome-scale metabolic
flux analysis indicated that CO(2) is important for the
carboxylation of phosphoenolpyruvate to oxaloacetate, which is
converted to succinic acid by the reductive tricarboxylic acid
cycle and menaquinone systems. This characteristic metabolism
allows highly efficient production of succinic acid, an
important four-carbon industrial chemical.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180025.
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2015-07-30 | MODEL1507180025 | BioModels
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.
2009-11-01 | GSE18382 | GEO
Project description:The development of massively parallel sequencing technologies enables the sequencing of total cDNA to identify unigene expression and to discover novel regions of transcription. Here, we report the first use of RNA-Seq to find the digital gene expression profiles (DGEs) associated with the growth and development of muscle in both Chinese Luxi and Angus beef cattle. More than 9,243,921 clean reads were found in samples of muscle tissue. We found 232 DGEs between Luxi cattle and Angus cattle (FDRM-bM-^IM-$0.001 AND |log2Ratio|M-bM-^IM-%1). Among the DGEs, we determined that 147 genes were down-regulated and 85 genes were up-regulated. GO and Pathway analysis were performed to analyze the biological role of the DGEs and determine their contribution to the differences seen in muscle growth and development between local Chinese Luxi cattle and the introduced Angus cattle. This article suggests that RNA-Seq is a useful tool for predicting differences in gene expression between Luxi and Angus beef cattle; moreover, our result provides unprecedented resolution of mRNAs that are expressed across the two breeds. Three Luxi and three Angus cattle that were eighteen months of age were generated by RNA-Seq
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