Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Microbiota associated with commercial dry-aged beef in France

PROVIDER: PRJNA1008104 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25726100_1.fastq.gz	Fastqsanger.gz
	SRR25726100_2.fastq.gz	Fastqsanger.gz
	SRR25738600_1.fastq.gz	Fastqsanger.gz
	SRR25738600_2.fastq.gz	Fastqsanger.gz
	SRR25726101_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 218

Similar Datasets

Mucorales

Project description:Dry Aged Beef Mucorales

| PRJDB17581 | ENA

Project description:Microbial community of dry aged beef

| PRJNA1028106 | ENA

Project description:Fungal and bacterial communities dry aged beef (DAB)

| PRJNA858677 | ENA

YDRseries4, Comparison commercial dry active yeast to BY4743

Project description:This series represents the analysis of a commercial dry active yeast (purchased locally). The genetics of this sample is unknown. Keywords = commercial Keywords = dry active yeast Keywords: other

2005-08-01 | GSE1314 | GEO

Influence of metaphylaxis for bovine respiratory disease on host transcriptome responses

Project description:To evaluate how commonly-utilized antimicrobials affect the host transcriptome of commercial beef cattle overtime, we enrolled 105 feedlot beef steers randomly into seven different treatment groups (negative control, tulathromycin, tildipirosin, enrofloxacin, florfenicol, ceftiofur, oxytetracycline) to receive a one-time label dose of a commercial antimicrobial or not (negative control), and collected jugular whole blood into PAXgene RNA blood tubes at six time points: Day 0 (baseline), 3, 7, 14, 21, and 56.

2023-09-26 | GSE225025 | GEO

Tandem mass tag labeling to characterize muscle-specific proteome change in beef during early postmortem

Project description:Bovine longissimus lumborum (LL) and psoas major (PM) muscles biopsy samples were collected from four carcasses (n = 4) at 45 min, 12 h, and 36 h postmortem from a commercial beef processing facility. Proteome profile variation between beef LL and PM during the early postmortem period were evaluated by tandem mass tag labeling containing ten different isobaric compounds.

2020-02-19 | PXD017535 | Pride

Project description:Profiling the skin microbiota composition from the face of healthy women. Exploring the differences between three age groups and between dry skin and not dry.

2023-02-24 | GSE225848 | GEO

Aged gut microbiota contributes to systemical inflammaging after transfer to germ-free mice

Project description:Advanced age is associated with chronic low-grade inflammation, which is usually referred to as inflammaging. Elderly are also known to have an altered gut microbiota composition. However, whether inflammaging is a cause or consequence of an altered gut microbiota composition is not clear. In this study gut microbiota from young or old conventional mice was transferred to young germ-free mice. Four weeks after gut microbiota transfer immune cell populations in spleen, Peyer’s patches, and mesenteric lymph nodes from conventionalized germ-free mice were analyzed by flow cytometry. In addition, whole-genome gene expression in the ileum was analyzed by microarray. Gut microbiota composition of donor and recipient mice was analyzed with 16S rDNA sequencing. Here we show by transferring aged microbiota to young germ-free mice that certain bacterial species within the aged microbiota promote inflammaging. This effect was associated with lower levels of Akkermansia and higher levels of TM7 bacteria and Proteobacteria in the aged microbiota after transfer. The aged microbiota promoted inflammation in the small intestine in the germ-free mice and enhanced leakage of inflammatory bacterial components into the circulation was observed. Moreover, the aged microbiota promoted increased T cell activation in the systemic compartment. In conclusion, these data indicate that the gut microbiota from old mice contributes to inflammaging after transfer to young germ-free mice.

2018-02-14 | GSE104063 | GEO

Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) as an emerging proteomics approach for the discovery of dark-cutting beef biomarkers

Project description:Recent advances in “omics” technologies have opened the possibilities to discover novel biomarkers of meat quality, including the early detection of quality defects such as dark-cutting beef, also known as DFD (dark, firm, and dry) beef characterized by a high ultimate pH. The available studies characterized very few numbers of animals and using mostly gel-based proteomics. The present study uses for the first time a Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) proteomics approach to characterize and comprehensively quantify the post-mortem muscle proteomes of DFD (pH24 ≥ 6.2) compared to CONTROL beef samples (5.4 ≤ pH24 ≤ 5.6) within the largest database of DFD/CONTROL beef samples to date (26 pairs of samples of the young Asturiana de los Valles bulls, n=52). The statistical comparison yielded 35 putative protein biomarkers that significantly differed in their abundances between the DFD and CONTROL samples. Chemometrics methods using both PLS-DA and OPLS-DA applied on the proteome data revealed 31 and 36 proteins with VIP > 2 respectively. The combination of these findings identified 16 common proteins linked with DFD beef, irrespective of the statistical method. These proteins are associated with interconnected biochemical pathways related to energy metabolism (DHRS7B and CYB5R3), binding and signaling (RABGGTA, MIA3, BPIFA2B, CAP2, APOBEC2, UBE2V1, KIR2DL1), muscle contraction, structure and associated proteins (DMD, PFN2), proteolysis, hydrolases, and activity regulation (AGT, C4A, GLB1, CAND2), and calcium homeostasis (ANXA6). These results evidenced the potential of SWATH-MS and chemometrics to accurately identify novel biomarkers for meat quality defects, providing a deeper understanding of the molecular mechanisms underlying dark-cutting beef.

2025-07-31 | PXD059876 | Pride

Bovine host transcriptomics to evaluate how markets and vaccines influence health and disease

Project description:To evaluate how commercially available vaccines and marketing strategy affect the host transcriptome of commercial beef cattle overtime, we sequenced the whole blood RNA of 73 commercial beef bull calves enrolled in a split plot study. Calves were randomized to one of four groups, having received a commercially available vaccine during the cow-calf phase or not, and placed in a commercial salebarn system after weaning (auction) or directly shipped to backgrounding (direct). Samples were acquired from six time points: T1 (modified live viral (MLV) vaccination; age: ~107 d.), T2 (seven days post-vaccination; age: ~114 d.), T3 (revaccination; age: ~183 d.), T4 (abrupt weaning; age: ~230 d.), T5 (arrival to backgrounding after marketing decision; age: ~233 d.), and T6 (45 days post-arrival to backgrounding; age: ~278 d.). Further evaluation was made based on whether calves were clinically diagnosed with bovine respiratory disease (BRD) after weaning.

2025-11-07 | GSE248477 | 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