Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Messenger RNA Biomarkers of Bovine Respiratory Syncytial Virus Infection in whole blood of dairy calves

ABSTRACT: Messenger RNA Biomarkers of Bovine Respiratory Syncytial Virus Infection in whole blood of dairy calves

PROVIDER: PRJNA641081 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12066976_1.fastq.gz	Fastqsanger.gz
	SRR12066976_2.fastq.gz	Fastqsanger.gz
	SRR12066977_1.fastq.gz	Fastqsanger.gz
	SRR12066977_2.fastq.gz	Fastqsanger.gz
	SRR12066978_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Messenger RNA Biomarkers of Bovine Respiratory Syncytial Virus Infection in whole blood of dairy calves

Project description:Bovine Respiratory Syncytial Virus (BRSV) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Infection with BRSV induces global gene expression changes in respiratory tissues. If these changes are observed in tissues which are accessible in live animals, such as whole blood, they may be used as biomarkers of the disease. Therefore, the objective of the current study was to elucidate the whole blood transcriptomic response to an experimental challenge with BRSV, in dairy calves. Holstein-Friesian calves were either inoculated with virus (103.5 TCID50/ml x 15 ml) (n=12) or mock challenged with sterile phosphate buffered saline (n=6). Clinical signs were scored daily and whole blood was collected in Tempus RNA tubes immediately prior to euthanasia, at day 7 post-challenge. RNA was extracted from blood and sequenced (150 bp paired-end). Sequence reads were aligned to the UMD3.1 bovine reference genome and differential gene expression analysis was performed using EdgeR. An MDS plot displayed an obvious separation between BRSV challenged and control calves based on whole blood gene expression changes, despite an observed mild clinical manifestation of the disease. There were 281 differentially expressed (DE) genes (p < 0.05, FDR < 0.1, fold change > 2) between the BRSV challenged and control calves. The top enriched KEGG pathways and gene ontology terms were associated with viral infection and included “Influenza A”, “defense response to virus”, “regulation of viral life cycle” and “innate immune response”. Highly DE genes involved in these pathways are may be beneficial for the diagnosis of subclinical BRD from blood samples.

2021-05-05 | GSE152959 | GEO

Elucidation of the open chromatin regions in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus, using ATAC-Seq

Project description:Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). The objective of this study was to elucidate the chromatin regions which were differentially open in the bronchial lymph nodes (BLN) of dairy calves experimentally challenged with BRSV, relative to unchallenged control calves. Holstein-Friesian calves were either challenged with BRSV inoculum (n=12) or mock challenged with PBS (n=6). Calves were euthanised on day 7 post-challenge. ATAC-Seq libraries were prepared from fresh BLN tissues and sequenced (75 bp paired-end). Sequence reads were aligned to the UMD3.1 reference genome and peak calling (q < 0.01) was performed with MACS2, employing the BAMPE model. Using Diffbind, 9,144 and 5,096 differentially accessible peaks were identified between BRSV challenged and control calves (P < 0.05, FDR < 0.05) using DeSeq2 and EdgeR, respectively. There were 169 and 110 genes previously found to be differentially expressed using RNA-Seq located within or up to 2kb upstream of the differentially accessible peaks identified by the DeSeq 2 and EdgeR analyses, respectively. There were 237 differentially accessible peaks positioned within 40 previously identified susceptibility loci for BRD. These open chromatin regions are likely involved in the gene transcriptional and regulatory response to infection by BRSV.

2021-01-13 | GSE148056 | GEO

Blood immune transcriptome analysis of artificially fed dairy calves and naturally suckled beef calves from birth to 7 days of age

Project description:The aim of the overall study was to investigate the development of immune competence in artificially reared dairy calves and in two breeds of naturally suckled beef calves over the first 168h of life. Dairy calves were fed 5% total body weight of colostrum, with beef calves monitored to ensure natural ingestion of colostrum. Blood samples were taken from all calves at 24h 48h 72h and 168h, and analysed for alterations to immunes genes.

2018-10-29 | GSE114432 | GEO

dairy calves feces

Project description:dairy calves feces Raw sequence reads

| PRJNA549568 | ENA

Whole blood transcriptomic analysis in BoHV-1 experimentally challenged dairy calves and comparison to a Bovine Respiratory Syncytial Virus (BRSV) challenge

Project description:Bovine Herpesvirus 1 (BoHV-1) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Therefore, the objective of the current study was to elucidate the whole blood mRNA transcriptomic response to an experimental challenge with BoHV-1, in dairy calves. Holstein-Friesian calves were either challenged by intranasal atomisation with BoHV1 virus (6.3 x 10^7/mL x 1.35mL) (n=12) or mock challenged with sterile phosphate buffered saline (n=6). Clinical signs were scored daily until euthanasia at day 6 post-challenge. Total RNA was extracted and sequenced from whole blood (100 bp paired-end). Sequence reads were aligned to the ARS-UCD1.2 bovine reference genome and differential gene expression analysis was performed using EdgeR. An MDS plot displayed an obvious separation between BoHV-1 challenged and control calves based on the gene expression changes in whole blood. There were 488 differentially expressed (DE) genes (p < 0.05, FDR < 0.1, fold change > 2) between the BoHV-1 challenged and control calves.

2022-08-19 | GSE199108 | GEO

Transcriptomic analysis of adipose and muscle of dairy calves supplemented with 5-hydroxytryptophan

Project description:Serotonin is a monoamine that regulates processes such as energy balance and immune function. Manipulating this pathway in growing dairy calves could promote growth and development by modulating functions and signaling pathways within key organs. In this study, we characterized the adipose and muscle transcriptome of pre-weaned calves with increased serotonin bioavailability through the elucidation of differentially expressed genes.

2020-06-05 | GSE151781 | GEO

dairy calves

Project description:Acidification of colostrum affects the fecal microbiota of pre-weaned dairy calves

| PRJNA843323 | ENA

Messenger RNA biomarkers of Bovine Respiratory Syncytial Virus infection in the whole blood of dairy calves.

Project description:Bovine Respiratory Syncytial Virus (BRSV) is a primary viral cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Infection with BRSV induces global gene expression changes in respiratory tissues. If these changes are observed in tissues which are more accessible in live animals, such as whole blood, they may be used as biomarkers for diagnosis of the disease. Therefore, the objective of the current study was to elucidate the whole blood transcriptomic response of dairy calves to an experimental challenge with BRSV. Calves (Holstein-Friesian) were either administered BRSV inoculate (103.5 TCID50/ml × 15 ml) (n = 12) or sterile phosphate buffered saline (n = 6). Clinical signs were scored daily and whole blood was collected in Tempus RNA tubes immediately prior to euthanasia, at day 7 post-challenge. RNA was extracted from blood and sequenced (150 bp paired-end). The sequence reads were aligned to the bovine reference genome (UMD3.1) and EdgeR was subsequently employed for differential gene expression analysis. Multidimensional scaling showed that samples from BRSV challenged and control calves segregated based on whole blood gene expression changes, despite the BRSV challenged calves only displaying mild clinical symptoms of the disease. There were 281 differentially expressed (DE) genes (p < 0.05, FDR < 0.1, fold change > 2) between the BRSV challenged and control calves. The top enriched KEGG pathways and gene ontology terms were associated with viral infection and included "Influenza A", "defense response to virus", "regulation of viral life cycle" and "innate immune response". Highly DE genes involved in these pathways may be beneficial for the diagnosis of subclinical BRD from blood samples.

| S-EPMC8087838 | biostudies-literature

Elucidation of the host transcriptomic response to bovine respiratory syncytial virus

Project description:Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in calves over one month of age. In a controlled challenge study in artificially-reared dairy calves, the influence of the host response to bovine respiratory syncytial virus (BRSV) was examined. Holstein-Friesian calves were either inoculated with BRSV (10^5/ml × 15 ml/animal) (n=12) or mock challenged with phosphate buffer saline (10ml/animal) (n=6). Calves were euthanised on day 7 post-challenge. Bronchial lymph nodes were collected; RNA was extracted and sequenced (75bp paired-end). Sequenced reads were adapter trimmed, quality assessed (FastQC) and aligned to the bovine genome (UMD 3.1) using STAR. Differential gene expression analysis was performed using EdgeR, and pathway and gene ontology analyses were carried out using g:Profiler, IPA and DAVID. There was a clear separation between BRSV challenged and control calves based on log2 fold gene expression changes, despite an observed mild clinical manifestation of the disease. There were 934 differentially expressed genes (DEG) (p < 0.05, FDR < 0.1, fold change > 2) between the BRSV challenged and control calves. Over-represented gene ontology terms, pathways and molecular functions, among the DEG, were associated with immune responses and defense responses to a virus.

2019-10-29 | GSE131452 | GEO

Fecal microbiota in dairy calves with diarrhea

Project description:Fecal microbiota in dairy calves with diarrhea

| PRJNA407697 | ENA