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SWCoV1 series; viral detection in Beluga whale liver

ABSTRACT: This series includes 3 microarrays used to detect SWCoV1, a novel group III coronavirus in Delphinapterus leucas (Beluga whale) liver. Keywords: viral detection

ORGANISM(S): Delphinapterus leucas Viruses

PROVIDER: GSE9238 | GEO | 2008/04/15

SECONDARY ACCESSION(S): PRJNA102845

REPOSITORIES: GEO

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SWCoV1 series; viral detection in Beluga whale liver

Project description:This series includes 3 microarrays used to detect SWCoV1, a novel group III coronavirus in Delphinapterus leucas (Beluga whale) liver. The series includes 2 control whale livers and 1 whale liver containing SWCoV1.

2008-04-15 | E-GEOD-9238 | biostudies-arrayexpress

Applying defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs

Project description:Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. The kinetics and efficiency of sgRNAs production during viral replication in different cell types or sgRNA transcription by individual viral strains or variants are yet to be studied to shed light on fundamental mechanisms necessary for viral replication. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study a growing number of next-generation sequencing (NGS) data of SARS-CoV-2. Starting from DI-tector, a bioinformatic tool for the detection of viral defective interfering genomes, here we introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. This new tool allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. As a proof of principle, we analyzed new data sets and successfully detected the nested set of sgRNAs produced with the ranking M>ORF3a>N>ORF6>ORF7a>ORF8>S>E>ORF7b. Our study also compared, for the first time for SARS-CoV-2, the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes.

2021-12-28 | GSE180632 | GEO

Blue Whale and Fin Whale

Project description:Balaenoptera musculus (Blue Whale) and Balaenoptera physalus (Fin Whale) Genome sequencing and assembly

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Viral Detection Microarray Analysis of Unknown Tropical Febrile Illness Cases

Project description:This study aimed to use pan-viral detection microarrays to identify viruses in serum from cases of acute pediatric febrile illness in a tropical setting. Patient clinical data and serum samples were collected between 2005 and 2009 as part of an ongoing pediatric dengue virus study at the Hospital Infantil Manuel de Jesús Rivera in Managua, Nicaragua. This study focused on patients who presented with dengue-like illness but who tested negative for dengue-virus infection. We hypothesized that non-dengue viruses or previously uncharacterized viruses might be causing these illnesses. The Virochip microarray is capable of detecting known viruses and discovering novel viruses. This series includes 153 arrays corresponding to 148 cases and 5 HeLa controls. Keywords: viral detection, tropical febrile illness, dengue virus, Nicaragua, Virochip

2011-12-31 | GSE28142 | GEO

Viral Detection Microarray Analysis of Unknown Tropical Febrile Illness Cases

2011-12-31 | E-GEOD-28142 | biostudies-arrayexpress

Whale Fall Metagenome

Project description:Microbial communities associated with submerged whale carcasses.

| PRJNA81625 | ENA

Whale blow metagenome

Project description:Humpback Whale Blow Metagenome Raw sequence reads

| PRJNA521078 | ENA

Whale blow microbiota

Project description:Using drones to sample whale blow microbiota

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whale fall metagenome

Project description:Microbial communities associated with submerged whale carcasses.

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Transcriptome Analysis of North Atlantic Right Whale Kidney Fibroblast Cell line exposed to cadmium

Project description:An 8X15k oligonucleotide microarray was developed consisting of 2334 E. glacialis probes and 2166 Tursiops truncatus probes and used to measure the transcriptome level effects of right whale kidney fibroblast cells exposed to cadmium. Cells were exposed to three concentrations of cadmium chloride (CdCl2) for three exposure times. Cells exposed to 10-6M CdCl2 for 4 hours and 24 hours showed upregulated genes involved in protection from metal toxicity, oxidative stress, protein renaturation, apoptosis inhibition, and several regulators of cellular processes. Downregulated genes represented a suite of functions including cell proliferation, transcription regulation, actin polymerization, and stress fiber synthesis. The collection of differentially expressed genes in this study support proposed mechanisms of cadmium-induced apoptosis such as mitochondrial membrane potential collapse, reactive oxygen species (ROS) influx, and cell cycle arrest. The results confirm the right whale microarray as a reproducible tool in measuring differentiated gene expression and should be a valuable asset for transcriptome analysis of other baleen whales and potential health assessment protocols.

2009-08-03 | GSE17457 | GEO

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