Ontology highlight
ABSTRACT:
PROVIDER: PRJEB75981 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Seminole.Steers.May.2024.vcf.csi | Other | |||
| Seminole.Steers.May.2024.vcf.gz | Vcf |
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Project description:Background: Plasma microRNAs (miRNAs), which exist in exosomal (EX) and non-exosomal free circulating (FC) fractions, can be utilized as blood biomarkers. To identify early indicators of carcass traits, we performed comprehensive analysis of plasma miRNAs separately on EX and FC fractions in Japanese Black cattle at 20, 25, and 30 months of age. Results: We found a total of 1,071 miRNAs including 39 novel miRNA candidates, in which 345 and 358 miRNAs exhibited in measurable amounts in EX and FC fractions, respectively. Profiles of these miRNAs were similar at 20 and 25 months, but collectively different from those at 30 months. We identified 86 and 80 differentially existed miRNAs (DE-miRNAs) between 25 and 30 months in EX and FC fractions, respectively. Among the DE-miRNAs, we revealed significant correlations of bta-miR-150 (EX and FC), -30b-5p (EX), -423-3p (EX), and -222 (FC) with several carcass traits including marbling score. Interestingly, target genes of these DE-miRNAs were functionally enriched in KEGG pathways such as PI3-Akt and MAPK signaling pathways, suggesting their functional relevance to carcass quality and quantity traits. Conclusions: We clarified changes in plasma EX and FC miRNA profiles during the fattening period and identified several miRNAs having correlations with carcass traits. These results could support the utility of plasma miRNAs as potential early indicators of carcass traits in Japanese Black cattle.
2026-02-16 | GSE319307 | GEO
Project description:It has been proved that intramuscular fat (IMF) or marbling in beef improves palatability. Recently, consumers have considered not only the degree of marbling but also the size and distribution of marbling flecks for their health and appetizing looking of beef. Computer image analysis (CIA) systems have been developed to assess various characteristics of marbling particles (MPs) such as the number, size, and distribution (fineness or coarseness) objectively. Some CIA indexes about MPs indicating how MPs are distributed evenly had significant positive relationship with price which represents consumers’ interest. RNA-seq research about formation of fine MPs in the longissimus thoracis (LT) muscle tissue of cattle have not yet been tried in transcriptome level. This study was conducted to reveal the DEGs between groups which have high or low number of fine MPs in the Longissimus thoracis muscle of Korean beef cattle and to understand molecular events associated with marbling fineness.
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Project description:Vitamin A (VA) restriction for beef cattle improves meat marbling. However, its molecular mechanisms are not completely elucidated. We performed microarray analysis to clarify effect of VA restriction on longissimus thoracis muscle gene expressions in Japanese Black steers.
2017-10-03 | GSE94886 | GEO
Project description:Beef marbling is caused by intramuscular deposition, and it is an economically important trait in the beef industry. Vitamin A (VA) is an important feed supplement for cattle, but it can hinder marbling if provided in excess. In cattle, VA forms various derivatives such as all-trans retinoic acid (ATRA) and 9-cis retinoic acid (9cRA). Therefore, we investigated the genes involved in bovine intramuscular adipogenesis after VA treatment with ATRA and 9cRA. Differential gene expression levels were validated by microarray analysis in a clonal bovine intramuscular preadipocyte (BIP) cell line derived from the intramuscular adipose tissue of Japanese Black cattle. BIP cells were harvested six days after adipogenic stimulation with either 1 μM ATRA, 1 μM 9cRA, or nonretinoic acids control. The ATRA- and 9cRA-treated cells exhibited reduced transcription of genes involved in the circulatory system and muscle development compared with the no retinoic acid (RA) treatment. In addition, the ATRA- and 9cRA-treated cells exhibited increased transcription of genes involved in the immune system, protein kinase B signaling, and responses to various stimuli. These results demonstrate the lower expression of muscle development in ATRA- and 9cRA-treated BIP cells during adipogenesis.
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Project description:The performances of label-based SWATH-MS, SRM and PRM to accurately quantify ten candidate biomarkers of beef meat tenderness or marbling, in a cohort of 64 bovine muscle tissues expected to cover a wide biological range of these traits, were evaluated. Limits of quantification, dynamic range and quantification performances were assessed. Moreover, protein amounts for all proteins detected in SWATH-MS were estimated in a label-free manner.
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Project description:To identify transcriptional markers for beef traits related to meat tenderness and moisture, we measured the transcriptome of the Longissimus dorsi skeletal muscle in 10 Korean native cattle (KNC). We analyzed the correlation between the beef transcriptome and measurements of four different beef traits, shear force (SF), water holding capacity (WHC), cooking loss (CL), and loin eye area (LEA). We obtained non-overlapping and unique panels of genes showing strong correlations (|r| > 0.8) with SF, WHC, CL, and LEA, respectively. Functional studies of these genes indicated that SF was mainly related to energy metabolism, and LEA to rRNA processing. Interestingly, our data suggested that WHC is influenced by protein metabolism. Overall, the skeletal muscle transcriptome pointed to the importance of energy and protein metabolism in determining meat quality after the aging process. The panels of transcripts for beef traits may be useful for predicting meat tenderness and moisture. Experiment Overall Design: Gene expression profiles were correlated with beef traits measured at the same cattle.
2008-11-01 | E-GEOD-9256 | biostudies-arrayexpress
Project description:The goal was to identify beef marbling related genes. Comparisons of skeletal muscle of well-marbled beef (HER, H-F) vs. lean beef (LIM). H-F vs. LIM -Dye-swap experiment
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Project description:The goal was to identify beef marbling related genes
2014-02-28 | GSE46411 | GEO
Project description:Beef quality is the first deciding factor for consumers to consider before purchasing. The aim of this study was to evaluate the effects of suspension and aging time on beef quality. We compared the differences in pH, drip loss, cooking loss, color, shear force, myofibril fragmentation index (MFI) and electron microscope of three muscle tissues between Achilles tendon (AT) and neck-arm restraint (NR) suspensions during seven aging periods (day 0, 1, 2, 3, 7, 14 and 21) after slaughter using the carcasses of six Xinjiang brown cattle. We found that NR suspension could significantly increase water loss rate and MFI, as well as reduce shear force compared to AT suspension. The muscle fiber structure with NR suspension was more severely damaged. The proteomics of longissimus dorsi were checked for the post-mortem day 1, 7 and 14. We detected 50, 26, and 29 differential expressed proteins (DEPs) between NR and AT suspension at post-mortem day 1, 7 and 14, respectively. These proteins were involved in metabolic and muscle structure associated pathways, and contributed to a comprehensive understanding of suspension-dependent meat quality regulation by proteins in beef cattle. To conclude, NR suspension can accelerate the aging time of beef carcasses, which will reduce the cost of carcass suspension and bring more benefits in beef industry.
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Project description:Intramuscular fat (IM; marbling) deposition is the deciding factor of beef quality grade in the U.S. Defining molecular mechanisms regulating adipogenesis in distinct anatomical areas in beef cattle is key to the development of strategies for marbling enhancement while limiting accumulation of excess subcutaneous adipose tissue (SAT; backfat). Our objective was to define the IM and SAT transcriptional heterogeneity at the whole tissue and single-cell levels in beef cattle. Longissimus dorsi muscle (9-11th rib) samples were collected from two harvested finished beef steers to dissect matched IM and adjacent SAT. Nuclei were isolated by dounce homogenization, then sequenced via bulk RNA sequencing (RNAseq) and single-nuclei RNA sequencing (snRNAseq) with 10x Genomics in an Illumina NovaSeq 6000. Analysis was conducted via Cell Ranger pipeline and Seurat in R Studio. By the expression of signature marker genes, snRNAseq analysis identified mature adipocytes (AD; ADIPOQ, LEP), adipose stromal and progenitor cells (ASPC; PDGFRA), endothelial cells (EC; VWF, PECAM1), smooth muscle cells (SMC; NOTCH3, MYL9) and immune cells (IMC; CD163, MRC1). We detected six cell clusters in SAT and nine in IM. Across IM and SAT, AD was the most abundant cell type, followed by ASPC, SMC, and IMC. In SAT, AD made up 50% of the cellular population, followed by ASPC (31%), EC (14%), IMC (1%), and SMC (4%). In IM depot, AD made up 23% of the cellular population, followed by ASPC with 19% of the population, EC with 28%, IMC with 7% and SMC with 12%. The abundance of ASPC and AD was lower in IM vs. SAT, while IMC was increased, suggesting a potential involvement of immune cells on IM deposition. Accordingly, both bulk RNAseq and snRNAseq analyses identified activated pathways of inflammation and metabolic function in IM. These results demonstrate distinct transcriptional cellular heterogeneity between SAT and IM depots in beef cattle, which may underly the mechanisms by which fat deposits in each depot. The identification of depot-specific cell populations in IM and SAT via snRNAseq analysis has the potential to reveal target genes for the modulation of fat deposition in beef cattle.
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