Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comprehensive analysis of plasma exosomal and non-exosomal microRNA profiles identifies potential early indicators of carcass traits in Japanese Black cattle

ABSTRACT: 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.

ORGANISM(S): Bos taurus

PROVIDER: GSE319307 | GEO | 2026/02/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	GSE319307_CPM_normalized_counts_ALL_samples.csv.gz	Csv
	GSE319307_raw_counts_All_samples.txt.gz	Txt

Items per page:

1 - 3 of 3

Similar Datasets

Time trajectory analysis reveals age-modulated small RNA cargo of circulating extracellular vesicles

Project description:Previous work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mouse plasma fractions at five time points across the lifespan from 2-18 months: (1) sncRNAs that are free-circulating (fc-RNA) and (2) sncRNAs bound outside or inside EVs (EV-RNA). Different sncRNA classes exhibit unique ageing patterns that vary between the fcRNA and EV-RNA fractions. While tRNAs showed the highest correlation with ageing in both fractions, rRNAs exhibited inverse correlation trajectories between the EV- and fc-fractions. For miRNAs, the EV-RNA fraction was exceptionally strongly associated with ageing, especially the miR-29 family in adipose tissues. Sequencing of sncRNAs and coding genes in fat tissue of an independent cohort of aged mice up to 27 months highlighted the pivotal role of miR-29a-3p and miR-29b-3p in ageing-related gene regulation that we validated in a third cohort by RT-qPCR.

2023-03-10 | GSE222857 | GEO

Difference in circulating microRNAs between grazing and grain-fed Japanese Black cattle

Project description:We aimed to elucidate the effects of feeding condition (indoor grain-feeding vs. grazing on pasture) on c-miRNAs in Japanese Black (JB) cattle (Wagyu). The cattle at 18 months old were divided into pasture feeding and conventional indoor grain feeding for 5 months. Microarray analysis of c-miRNAs from the plasma extracellular vesicles led to the detection of a total of 202 bovine miRNAs in the plasma, including 15 miRNAs that differed between the feeding conditions.

2017-02-09 | GSE81946 | GEO

Changes in exosomal circulating microRNAs in grazing cattle

Project description:To investigate the potential effect of grazing movement on miRNA circulation in cattle, here we profiled miRNA expression in centrifugally prepared exosomes from the plasma of both grazing and housed Japanese Shorthorn cattle. Microarray analysis of the c-miRNAs resulted in detection of a total of 231 bovine exosomal miRNAs in the plasma, with a constant expression level of let-7g across the duration and cattle groups. Expression of muscle-specific miRNAs such as miR-1, miR-133a, miR-206, miR-208a/b, and miR-499 were undetectable, suggesting the mildness of grazing movement as exercise. Changes in miRNA expression in plasma exosome of cattle was measured at during 0, 1, 2 and 4 months of grazing or housing. Plasma exosome samples prepared from three cattle for each treatment were collected and mixed within the treatment at each time for microarray analysis .

2016-07-03 | E-GEOD-69717 | biostudies-arrayexpress

Plasma exosomes miRNAs high-throughput sequencing in patients after STEMI 3-6 months

Project description:ST-segment elevated myocardial infarction (STEMI) is one of the most severe forms of cardiovascular heart diseases. In the present study, we aim to describe differential expressed plasma exosome-miRNAs in patients with post-STEMI 3-6 months. Methods: Consecutive patients with ages from 40 to 80 years and 25 males among them 3-6 months after STEMI (n=11) were compared to sex-matched healthy control (n=10). The mean age of the patient was 64.71±10.40 years and 89.2% were male. Compared to the healthy control group, the plasma exosome-miRNAs were assessed by using microarray assay (IIIumnia Hiseq 2500). Profile of plasma exosome-miRNAs related to heart diseases was established both in the patient and control groups. The specificity of the lowest expressed exosome-miRNAs for all subjects was evaluated by using a quantitative real-time polymerase chain (qPCR). plasma exosomes miRNAs were obtained from STEMI patients after 3-6 months and healthy subjects

2022-06-29 | GSE185729 | GEO

Total exRNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects

Project description:<p>There are currently few datasets describing baseline expression levels for total cell-free circulating RNA from healthy control subjects. Total extracellular RNA was isolated from plasma, urine, and saliva samples from healthy controls. We sequenced small RNAs from 183 plasma samples, 204 urine samples and 46 saliva samples from 55 college athletes ages 18-25 years. Many of the participants provided more than one sample, weeks or months apart, allowing us to assess variability in an individual's exRNA expression levels over time. Several individuals provided all three biofluid types at one time, producing data on individual expression levels across several biofluid types. Here we provide a systematic analysis of small exRNAs present in each biofluid, as well as an analysis of exogenous RNAs. We find that a large number of RNA fragments in plasma (63%) and urine (54%) have sequences that are assigned to YRNA and tRNA fragments respectively. Surprisingly, while many miRNAs can be detected, there are few miRNAs that are consistently detected in all samples from a single biofluid.</p>

| phs001258 | dbGaP

Liver gene expression patterns in pigs as indicators of serum plasma levels and meat quality atributes

Project description:In pigs, most of the lipogenic activity takes place in liver and the adipose tissue. Moreover, liver is responsible for the production and release of lipoproteins, which transports lipids from the liver to target tissues such as adipose and muscle. In the context of animal production, the amount and composition of lipoprotein have an implication in the accumulation of fat in adipose deposits but also in muscle in the form or intramuscular fat. These two events have consequences in the quality of the carcasses and meat. We have measured the level of liver gene expression in 104 commercial Duroc pigs belonging to two groups with extreme phenotypes for traits strongly related with lipid deposition and composition. This has allowed us to compare the physiological and metabolic implications of selecting for each of these extreme groups. This information has been complemented with genome-wide genotyping data in order to describe the implication of the liver transcriptome in the production traits which encompass the production and marketing of the products with consumer and industry-relevant added-value characteristics. 104 liver samples form pigs belonging to two groups of animals: HIGH group (n=53) had higher carcass, plasma and muscle fat content; LOW group (n=51) had lower carcass, plasma and muscle fat content

2014-01-01 | E-GEOD-48992 | biostudies-arrayexpress

Analysis of circulating microRNAs during early gestation in Japanese-Black cattle

Project description:We found four circulating miRNAs showing high levels in plasma of pregnant Japanese Black cows. Since these miRNAs are less affected by the measurement system due to hemolysis, it was suggested that they may be used as markers for early pregnancy diagnosis in cattle.

2021-06-26 | GSE178906 | GEO

A Comparative Liver Label-Free Liquid Chromatography-Mass Spectrometry Proteomic Profile Highlights Putative Metabolic Differences Between two Pig Breeds

Project description:Pig breeds have different attitude to traits like growth rate, carcass composition and reproduction parameters as well as other traits. These traits considered as external traits or end phenotypes are the outcome of complex biological processes and interactions. The main goal of pig breeding programs and the basis for crossbreeding is finding a balance between these traits. In pig production, Large White and Duroc breeds are commonly used to optimise respectively fertility and growth ability and differ on several production traits, indeed the first breed as a high fertility characters whereas Duroc is used as terminal sire for her growth performance and good carcass quality traits. In this study, we have used a quantitative label-free LC-MS proteomics approach to characterise and compare the liver proteome of two heavy Italian pig breeds, Italian Duroc and Italian Large White to identify difference due to their different genetic background. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 703094.

2018-09-13 | PXD009771 | Pride

Analysis of the impact of cellular miRNA signatures on the profiles of circulating miRNA biomarkers (variability data)

Project description:Circulating miRNAs are an emerging class of biomarkers correlating their specific expression patterns to disease states. A considerable proportion of hematopoietically-derived miRNAs are present in plasma with the ability to confound the signature of true circulating miRNA species. We use microarray analysis to catalogue a list of 313 haemotopoetic miRNAs and analyze expression profiles of cell-free miRNAs in individual plasma fractions after calibraiting for cellular miRNA signals. Comprehensive global maps of bona fide circulating miRNA species are presented, and inter-individual varibility and gender-specific expession is explored in populations of healthy individuals. Supernatant 1 (S1) fractions from 8 male and 10 female individuals.

2011-06-17 | E-GEOD-27253 | biostudies-arrayexpress

miRNA analysis after three months on GH treatment and contribute to explain the growth response after 12 months.

Project description:Context: There is growing evidence on the role of epigenetic regulation of growth, and miRNAs potentially play a role. Objective: To identify changes in circulating miRNAs following GH treatment in subjects with isolated idiopathic GH deficiency (IIGHD) after the first 3 months on treatment, and verify whether these early changes can predict growth response. Methods: The expression profiles of 384 miRNAs were analyzed in serum in 10 prepubertal patients with IIGHD (5 M,5 F) at two time points before starting GH treatment (t-3, t0), and at 3 months on treatment (t+3). MiRNAs with a fold change (FC) >±1.5 at t+3 were considered as differentially expressed. In silico analysis of target genes and pathways led to a validation step on 8 miRNAs in 25 patients. Clinical and biochemical parameters were collected at baseline, 6 and 12 months. Simple linear regression analysis and multiple stepwise linear regression models were used to explain the growth response. Results: 16 miRNAs were up-regulated and 2 down-regulated at t+3 months. MiR-199a-5p (p=0.020), miR-335-5p (p=0.001), and miR-494-3p (p=0.026) were confirmed to be up-regulated at t+3. Changes were independent of peak GH values at testing, and levels stabilized after 12 months. The predicted growth response at 12 months was considerably improved compared with models using the common clinical and biochemical parameters. Conclusion: miR-199a-5p, miR-335-5p, and miR-494-3p changed after 3 months on GH treatment and likely reflected both the degree of GH deficiency and the sensitivity to treatment. Furthermore, they were of considerable importance to predict growth response.

2022-04-29 | GSE193450 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data