Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

AMR target-enriched metagenomic and 16S sequence reads from beef feedlot cattle fecal samples

ABSTRACT: AMR target-enriched metagenomic and 16S sequence reads from beef feedlot cattle fecal and pen-floor samples

PROVIDER: PRJNA755709 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23460500_1.fastq.gz	Fastqsanger.gz
	SRR23460500_2.fastq.gz	Fastqsanger.gz
	SRR23460600_1.fastq.gz	Fastqsanger.gz
	SRR23460600_2.fastq.gz	Fastqsanger.gz
	SRR23460700_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 820

Similar Datasets

Hepatic transcriptome profiling in beef cattle: effects of rumen-protected niacin supplementation

Project description:The objective of our study was to assess the effect of rumen-protected niacin supplementation on the overall transcriptomics profile of liver tissue on growing Angus × Simmental steers and heifers. Consequently, the vasodilatory, detoxifying, and immune suppressor effects of niacin were evaluated in hepatocytes. After a 30-day supplementation period with rumen-protected niacin on normal weaned beef calves, we observed a significant list of benefits at the liver transcriptome level. Several metabolic pathways revealed positive effects of administration of rumen-protected niacin; for example, a decrease in lipolysis, apoptosis, inflammatory responses, atherosclerosis, oxidative stress, fibrosis, and vasodilation-related pathways. Therefore, results from this study could potentially promote supplementation of rumen-protected niacin on beef cattle backgrounding operations or new arrivals to a feedlot, especially during the acclimation period when the health status of growing beef cattle is usually compromised.

2025-06-19 | GSE206468 | GEO

Longitudinal blood transcriptomic analysis to identify molecular regulatory patterns of Bovine Respiratory Disease in beef cattle

Project description:We profiled blood transcriptomics of 24 beef steers at three important stages (Entry: on arrival at the feedlot; Pulled: when sickness is identified; and Close-out: recovered, healthy cattle at shipping to slaughter) to reveal the key biological functions and regulatory factors of BRD and identify gene markers of BRD for early diagnosis and potentially use in selection.

2020-12-31 | GSE150706 | GEO

Applying multi-omics data to study the genetic background of bovine respiratory disease infection in feedlot crossbred cattle

Project description:Bovine respiratory disease (BRD) is the most common and costly infectious disease affecting the well-being and productivity of beef cattle in North America. BRD is a complex disease whose development is dependent on environmental factors and host genetics. Due to the polymicrobial nature of BRD, our understanding of the genetic and molecular mechanisms underlying the disease is still limited. This knowledge would augment the development of better genetic/genomic selection strategies and more accurate diagnostic tools to reduce BRD prevalence. Therefore, this study utilized multi-omics data (genomics, transcriptomics, and metabolomics) analyses to study the associations between genome, transcriptome, metabolome, and BRD phenotype of feedlot crossbred cattle. The findings may be useful for the development of genomic selection strategies for BRD susceptibility, and for the development of new diagnostic and therapeutic tools.

2023-01-11 | GSE217317 | GEO

Beef cattle multi-tissue transcriptome

Project description:The transcriptome of 189 samples across four tissues from 48 beef steers with varied feed efficiency were generated using Illumina HiSeq4000

2021-05-05 | GSE116775 | GEO

High altitude disease in yearling beef cattle

Project description:This study examined tolerance to hypoxia-induced pulmonary hypertension in yearling beef cattle raised at high elevation (7120 ft/2170m).

2021-01-23 | GSE164320 | GEO

Beef Cattle

Project description:This study seeks to determine the construction of calves' microbiomes per time point in beef cattle. Raw sequence reads

| PRJNA948924 | ENA

Beef cattle multi-tissue transcriptome

Project description:Beef cattle multi-tissue transcriptome

| PRJNA480220 | ENA

A transcriptome analyses of Longissimus dorsi muscle in Nguni cattle finished on different feedlot diets

Project description:Background: The Nguni is an indigenous Bos taurus Sanga breed which is primarily used in extensive commercial and communal farming systems in South Africa. The Nguni is a small framed early maturing breed not preferred for finishing under feedlot systems, as the large framed later maturing types are favoured for high lean meat yield. In this study we aim to investigate differentially expressed genes in Longissimus dorsi muscle of Nguni cattle fed diets differing in energy levels finished under commercial feedlot conditions. Results: Twenty Nguni and twenty Bonsmara were fed either a low (10.9 MJ ME/kg) or a high (12.00 MJ ME/kg) energy diet for 120 days. At slaughter, muscle samples were taken for RNA extraction and RNA-sequencing. A total of 2214 differentially expressed genes (DEG) were observed between the two breeds regardless of diet. For the low energy diets, 2244 DEG in the Nguni and the Bonsmara were significantly expressed, while a higher number of were differentially expression between the Nguni and Bonsmara on high energy diet (3154 DEG). A difference of 288 DEG were identified between the Nguni fed on the low and high energy diets. Most of the fat deposition genes were upregulated in the Bonsmara (ASIP, OXT, SNAI3, FOX01, PPARGC1A), with lower levels in the Nguni. Conclusion: Clear breed differences were found for the number and level of gene expression, while a larger variation in DEG were observed between the two diets within in the Bonsmara breed.

2018-09-07 | GSE119563 | GEO

Identification of key pathways associated with residual feed intake of beef cattle

Project description:The biological mechanisms associated with the residual feed intake in ruminants have been harnessed immensely via transcriptome analysis of liver and ruminal epithelium, however, this concept has not been fully explored using whole blood. We applied whole blood transcriptome analysis and gene set enrichment analysis to identify key pathways associated with divergent selection for low or high RFI in beef cattle. A group of 56 crossbred beef steers (average BW = 261.3 ± 18.5 kg) were adapted to a high-forage total mixed ration in a confinement dry lot equipped with GrowSafe intake nodes for period of 49 d to determine their residual feed intake (RFI). After RFI determination, weekly whole blood samples were collected three times from beef steers with the lowest RFI (most efficient; low-RFI; n = 8) and highest RFI (least efficient; high-RFI; n = 8). Prior to RNA extraction, whole blood samples collected were composited for each steer. Sequencing was performed on an Illumina NextSeq2000 equipped with a P3 flow. Gene set enrichment analysis (GSEA) was used to analyze differentially expressed gene sets and pathways between the two groups of steers. Results of GSEA revealed pathways associated with metabolism of proteins, cellular responses to external stimuli, stress, and heat stress were differentially inhibited (false discovery rate (FDR) < 0.05) in high-RFI compared to low-RFI beef cattle, while pathways associated with binding and uptake of ligands by scavenger receptors, scavenging of heme from plasma, and erythrocytes release/take up oxygen were differentially enriched (FDR < 0.05) in high-RFI, relative to low-RFI beef cattle. Taken together, our results revealed that beef steers divergently selected for low or high RFI revealed differential expressions of genes related to protein metabolism and stress responsiveness.

2022-04-07 | GSE198068 | GEO

Whole blood transcriptome analysis of feedlot cattle with and without bovine respiratory disease

Project description:In this study we aimed to identify differentially expressed (DE) genes involved in the host immune response to BRD using whole blood and RNA sequencing. Samples were collected from heifers (average arrival weight = 215.0 ± 5.3 kg) with (n = 25) and without (n = 18) BRD at a commercial feedlot in Western Canada. RNAseq analysis showed a distinct whole blood transcriptomic profile between BRD and non-BRD heifers. Further examination of the DE genes revealed that those involved in the host inflammatory response and infectious diseases pathways were enriched in BRD animals, while gene networks associated with metabolism and cell growth and maintenance were downregulated. Overall, the transcriptome profile derived from whole blood provided evidence that a distinct antimicrobial peptide driven host immune response was occurring in the animals with BRD.

2020-11-26 | GSE162156 | 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