Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Porcine Nasal Consortium (PNC8)

PROVIDER: PRJNA1175893 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR31074840_1.fastq.gz	Fastqsanger.gz
	SRR31074841_1.fastq.gz	Fastqsanger.gz
	SRR31074842_1.fastq.gz	Fastqsanger.gz
	SRR31074843_1.fastq.gz	Fastqsanger.gz
	SRR31074843_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 15

Similar Datasets

pig metagenome

Project description:Porcine nasal microbiota Metagenome

| PRJNA239714 | ENA

Multi-angled transcriptome analyses reveal chameleon-like behavior of macrophages in the porcine respiratory tract

Project description:Macrophages have a pivotal role during viral infections in pigs. By expressing cell surface receptors, macrophages become viral targets and reservoirs. In the case of upper respiratory tract infections, many viruses target the peripheral nasal mucosa. Recent in vivo and in vitro (primary nasal cell cultures) porcine reproductive and respiratory syndrome virus (PRRSV) studies demonstrated that several macrophage subsets exist in the porcine nasal mucosa, and that virus strains with different virulence showed altered tropism for these different macrophage populations. To further investigate these macrophage subsets, total RNA sequencing was performed in parallel on two subsets from the nasal mucosa and lung macrophages. Macrophages were isolated by either fluorescent activated cell sorting (FACS; cf. bulk RNAseq) or laser capture microdissection (LCM; cf. LCM RNAseq) in combination with immunofluorescence staining against two macrophage markers, CD163 and Sialoadhesin (Sn). With both RNAseq methods, nasal macrophages showed a different transcriptomic profile compared to lung macrophages. Differentially expressed genes were identified in the two subsets of nasal macrophages. Gene set enrichment analysis on the three macrophage populations showed that GO terms and KEGG pathways on LCM RNAseq data were more specific to the spatial location of macrophage subsets than bulk RNAseq data. Cell type signature analysis revealed that nasal CD163+Sn- cells resemble squamous epithelial cells (LCM RNAseq) or antigen presenting cells (bulk RNAseq) while nasal CD163+Sn+ cells are more like fibroblasts/stromal cells (LCM RNAseq) or vascular endothelial cell (bulk RNAseq). Our results confirmed that not only macrophages in different tissues but also macrophages in different areas within the same tissue have different transcriptional programs, suggesting their differential roles in their interaction with pathogens and corresponding immune responses.

2023-09-29 | E-MTAB-12120 | biostudies-arrayexpress

Transcriptome analysis of a novel alveolar porcine epithelial cells line infected with different live attenuated Influenza Viruses

Project description:The project aim at studying transcriptional changes by BRB-seq of porcine alveolar epithelial cells line infected with wild type influenza virus compared to live attenuated influenza viruses. In addition, primary porcine nasal epithelial cells was also added to be able to compare how the alveolare epithelial cells line compare to primary cells. Finally, additional positive control including procine alveolar epithelial cells stimulated with Poly I:C or infected with IFN inducing Sendei virus was added.

2023-08-31 | E-MTAB-13128 | biostudies-arrayexpress

Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium

Project description:Staphylococcus aureus is a common human and animal opportunistic pathogen. In humans nasal carriage of S. aureus is a risk factor for various infections. Methicillin-resistant S. aureus ST398 is highly prevalent in pigs in Europe and North America. The mechanism of successful pig colonization by MRSA ST398 is poorly understood. Previously, we developed a nasal colonization model of porcine nasal mucosa explants to identify molecular traits involved in nasal MRSA colonization of pigs. Here, we report the analysis of the transcriptome of MRSA ST398 strain S0462 during colonization on the explant epithelium. Major regulated genes were encoding metabolic processes and regulation of these genes represents metabolic adaptation to nasal mucosa explants. Colonization was not accompanied by significant changes in transcripts of main virulence associated genes or known human colonization factors. Here, we document regulation of two genes which have potential influence on S. aureus colonization; cysteine extracellular proteinase (scpA) and von Willebrand factor-binding protein (vwbp, located on SaPIbov5). Colonization with isogenic-deletion strains (Î?vwbp and Î?scpA) did not alter the nasal S. aureus colonization compared to wild type. Our results suggest that nasal colonization with MRSA ST398 is a complex event that is accompanied with changes in bacterial gene expression regulation and metabolic adaptation. Number of the samples: 5 (timepoint 0 min, 30 min, 60 min, 90 min and 180 min) in 4 replicates. 4 control samples

2015-12-31 | E-GEOD-47910 | biostudies-arrayexpress

Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium

Project description:Staphylococcus aureus is a common human and animal opportunistic pathogen. In humans nasal carriage of S. aureus is a risk factor for various infections. Methicillin-resistant S. aureus ST398 is highly prevalent in pigs in Europe and North America. The mechanism of successful pig colonization by MRSA ST398 is poorly understood. Previously, we developed a nasal colonization model of porcine nasal mucosa explants to identify molecular traits involved in nasal MRSA colonization of pigs. Here, we report the analysis of the transcriptome of MRSA ST398 strain S0462 during colonization on the explant epithelium. Major regulated genes were encoding metabolic processes and regulation of these genes represents metabolic adaptation to nasal mucosa explants. Colonization was not accompanied by significant changes in transcripts of main virulence associated genes or known human colonization factors. Here, we document regulation of two genes which have potential influence on S. aureus colonization; cysteine extracellular proteinase (scpA) and von Willebrand factor-binding protein (vwbp, located on SaPIbov5). Colonization with isogenic-deletion strains (Δvwbp and ΔscpA) did not alter the nasal S. aureus colonization compared to wild type. Our results suggest that nasal colonization with MRSA ST398 is a complex event that is accompanied with changes in bacterial gene expression regulation and metabolic adaptation.

2015-12-31 | GSE47910 | GEO

Staphylococcus cohnii strain:M21 | isolate:Porcine nasal swab

Project description:Staphylococcus cohnii strain:M21 | isolate:Porcine nasal swab Genome sequencing

| PRJNA1230604 | ENA

Staphylococcus cohnii strain:M28 | isolate:Porcine nasal swab

Project description:Staphylococcus cohnii strain:M28 | isolate:Porcine nasal swab Genome sequencing

| PRJNA1230605 | ENA

Staphylococcus cohnii strain:M29 | isolate:Porcine nasal swab

Project description:Staphylococcus cohnii strain:M29 | isolate:Porcine nasal swab Genome sequencing

| PRJNA1230607 | ENA

Staphylococcus cohnii strain:M29 | isolate:Porcine nasal swab

Project description:Staphylococcus cohnii strain:M29 | isolate:Porcine nasal swab Genome sequencing