Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomic wastewater-based surveillance of influenza A virus using tiling amplicon sequencing

ABSTRACT: Establishing protocol for sequencing HA, NA and M segments Influenza A (H1N1 & H3N2) from wastewater.

PROVIDER: PRJEB85534 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR14861900.fastq.gz	Fastqsanger.gz
	ERR14860801.fastq.gz	Fastqsanger.gz
	ERR14861901.fastq.gz	Fastqsanger.gz
	ERR14860802.fastq.gz	Fastqsanger.gz
	ERR14861902.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 59

Similar Datasets

Seasonal influenza A virus lineages exhibit divergent abilities to antagonize interferon induction and signaling

Project description:The circulation of seasonal influenza A viruses (IAVs) in humans relies on effective evasion and subversion of the host immune response. While the evolution of seasonal H1N1 and H3N2 viruses to avoid humoral immunity is well characterized, relatively little is known about the evolution of innate immune antagonism phenotypes in these viruses. Numerous studies have established that only a small subset of infected cells are responsible for initiating the type I and type III interferon (IFN) response during IAV infection, emphasizing the importance of single cell studies to accurately characterize the IFN response during infection. We developed a flow cytometry-based method to examine transcriptional changes in IFN and interferon stimulated gene (ISG) expression at the single cell level. We observed that NS segments derived from seasonal H3N2 viruses are more efficient at antagonizing IFN signaling but less effective at suppressing IFN induction, compared to the pdm2009 H1N1 lineage. We compared a collection of NS segments spanning the natural history of the current seasonal IAV lineages, and demonstrate long periods of stability in IFN antagonism potential, punctuated by occasional phenotypic shifts. Altogether, our data reveal significant differences in how seasonal and pandemic H1N1 and H3N2 viruses antagonize the human IFN response at the single cell level.

2024-07-12 | GSE272070 | GEO

Identification of H3N2 specific antibodies cross-reacting with H7 strains

Project description:Binding profile of H3N2 hemagglutinin (HA) reactive antibodies for various H3N2 and H7 HA proteins

2014-11-14 | GSE63249 | GEO

Viral determinants in H5N1 influenza A virus enable productive infection of HeLa cells

Project description:Influenza A virus (IAV) is a human respiratory pathogen that causes yearly global epidemics, and sporadic pandemics due to human adaptation of pathogenic strains. Efficient replication of IAV in different species is, in part, dictated by its ability to exploit the genetic environment of the host cell. To investigate IAV tropism in human cells, we evaluated the replication of IAV strains in a diverse subset of epithelial cell lines. HeLa cells were refractory to growth of human H1N1 and H3N2, and low pathogenic avian influenza (LPAIs) viruses. Interestingly, a human isolate of the highly pathogenic avian influenza (HPAI) virus H5N1 successfully propagated in HeLa cells to levels comparable to a human lung cell line. Heterokaryon cells generated by fusion of HeLa and permissive cells supported H1N1 growth, suggesting the absence of a host factor(s) required for replication of H1N1, but not H5N1, in HeLa cells. The absence of this factor(s) was mapped to reduced nuclear import, replication, and translation, and deficient viral budding. Using reassortant H1N1:H5N1 viruses, we found that the combined introduction of nucleoprotein (NP) and hemagglutinin (HA) from H5N1 was necessary and sufficient to enable H1N1 growth. Overall, this study suggests the absence of one or more cellular factors in HeLa cells that results in abortive replication of H1N1, H3N2, and LPAI viruses, but can be circumvented upon introduction of H5N1 NP and HA. Further understanding of the molecular basis of this restriction will provide important insights into virus-host interactions that underlie IAV pathogenesis and tropism.

2019-11-21 | GSE140759 | GEO

Role of IFITM3 during primary influenza infection and reinfection

Project description:WT or IFITM3-KO mice were infected with PR8 H1N1 influenza virus and reinfected with X31 H3N2 influenza virus

2021-11-22 | GSE183890 | GEO

Host microRNA molecular signatures associated with human H1N1 and H3N2 influenza A viruses

Project description:In this study, we performed a miRNA global profiling in human lung epithelial cells (A549) infected by two different subtypes of human influenza A viruses (H1N1 and H3N2).

2013-04-03 | GSE42003 | GEO

Influenzavirus serotype association to global whole blood transcriptional changes

Project description:Febrile patients PCR positive for H1N1 swine flu, seasonal H1N1 and seasonal H3N2 in nasal swabs and controls consisting of febrile patients with rhinovirus infection or febrile patients of non-viral etiology (nasal swabs PCR negative for common respiratory viruses and blood PCR negative for dengue and parvovirus B19) were assessed consecutively for global transcriptional changes in whole blood

2014-04-01 | GSE29385 | GEO

feces metagenome

Project description:Amplicon sequencing targeting HA and NA segments of avian influenza from wild bird feces

| PRJDB13596 | ENA

Influenza A virus

Project description:Mapping epistasis on influenza H3N2 NA

| PRJNA790468 | ENA

Early and sustained innate immune response defines pathology and death in nonhuman primates infected by highly pathogenic influenza virus.

Project description:This study revealed important similarities but also critical differences between the H5N1 and 1918-reassortant viruses, highlighting aspects of the host–pathogen interface caused by highly virulent influenza viruses. Animals assigned to 4 experimental groups (n = 8) matched for age, weight, and sex, were inoculated by intratracheal, intranasal, tonsillar, and conjunctival routes with a total of 107 pfu of A/Vietnam/1203/2004 (H5N1) virus, A/Texas/36/91 (H1N1) virus or reassortants of this virus containing either 2 (HA, NA) or 3 (HA, NA, NS) genes from the 1918 virus. Two animals per group were scheduled for sacrifice on days 1, 2, 4, and 7. Two additional animals were used as uninfected control animals and killed on day 7. Oligoarray analyses consisted of comparing array profiles of individual lung samples (with representative pathology and degree of infection) from infected animals to pooled equal masses of mRNA from all lung lobes of 7 reference cynomolgus macaques obtained through the tissue program of the University of Washington National Primate Research Center. There are 2 technical array replicates fro each sample.

2011-11-01 | E-GEOD-33351 | biostudies-arrayexpress

Differential messenger RNA expression in Granulosa Cells from polycystic ovary syndrome with Normoandrogen and Hyperandrogen: Identification of gene sets through bioinformatic Filtering analysis

Project description:PCOS is a widespread disease that primarily caused in-pregnancy in pregnant-age women. Normoandrogen (NA) and Hyperandrogen (HA) PCOS are distinguished under distinct level of testosterone, while markers and expression patterns for both subtypes were not adequately studied. Text-mining analysis stated the correlation for PCOS with granusola cells and thus we performed microarray analysis on granusola cells from HA PCOS, NA PCOS and normal tissue from individuals, and afterwards downloaded RNA-seq and microarray data from NCBI GEO database on granusola cells from PCOS and normal ovary. Applying our newly developed method using Monte Carlo algorithm and text mining method on combined data, we identified several potential markers for HA and NA PCOS. RT-PCR and Western blotting results validated the expression pattern of these markers for HA and NA PCOS as bioinformatical prediction. Further gene ontology (GO) and text-mining analysis discovered that (1) NA PCOS was highly correlated with estrogen-driven tumors including ovarian, breast and endometrial cancer as compared with normal granusola cells. NA PCOS specific genes IL6R and CD274 were bioinformatically predicted and experimentally validated and thus might be the key factor behind the mechanism responsible for the tumor-like pattern for NA PCOS; (2) HA PCOS showed high correlation with keratinization, epidermis development, GTPase activity, glomerular basement membrane development and apoptosis corresponding to the fact HA PCOS patients express characteristic of hirsutism, diabetes and obesity. Meanwhile HA PCOS was sustantially lowerly related with estrogen-driven tumors as compared with normal granusola cells.

2019-09-19 | GSE137684 | 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