About: Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: detection of viral proteins and host's biological processes altered by the infection

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About: Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: detection of viral proteins and host's biological processes altered by the infection Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: detection of viral proteins and host's biological processes altered by the infection
Creator	Moratorio, Gonzalo Moreno, Pilar Duran, Rosario Leyva, Alejandro Lima, Analía Portela, Magdalena Portela, María Rivera, Bernardina
Source	Elsevier; Medline; PMC
abstract	Since January 2020, the world is facing the COVID-19 pandemic caused by SARS-CoV-2. In a big effort to cope with this outbreak, two Uruguayan institutions, Institut Pasteur de Montevideo and Universidad de la República, have developed and implemented a diagnosis pipeline based on qRT-PCR using entirely local resources. In this context, we performed comparative quantitative proteomic analysis from oro- and naso-pharyngeal swabs used for diagnosis. Tryptic peptides obtained from five positive and five negative samples were analysed by nano-LC-MS/MS using a Q-Exactive Plus mass spectrometer. Data analysis was performed using PatternLab for Proteomics software. From all SARS-CoV-2 positive swabs we were able to detect peptides of the SARS-CoV-2 nucleoprotein that encapsulates and protect the RNA genome. Additionally, we detected an average of 1100 human proteins from each sample. The most abundant proteins exclusively detected in positive swabs were “Guanylate-binding protein 1”, “Tapasin” and “HLA class II histocompatibility antigen DR beta chain”. The biological processes overrepresented in infected host cells were “SRP-dependent cotranslational protein targeting to membrane”, “nuclear-transcribed mRNA catabolic process, nonsense-mediated decay”, “viral transcription” and “translational initiation”. Data is available via ProteomeXchange with identifier PXD020394. We expect that this data can contribute to the future development of mass spectrometry based approaches for COVID-19 diagnosis. Also, we share this preliminary proteomic characterization concerning the host response to infection for its reuse in basic investigation.
has issue date	2020-08-05(xsd:dateTime)
bibo:doi	10.1016/j.dib.2020.106121
bibo:pmid	32835036
has license	no-cc
sha1sum (hex)	6db0b1feda5f5f60dbfe4d6381a2855455a7b728
schema:url	https://doi.org/10.1016/j.dib.2020.106121
resource representing a document's title	Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: detection of viral proteins and host's biological processes altered by the infection
has PubMed Central identifier	PMC7405904
has PubMed identifier	32835036
schema:publication	Data Brief
resource representing a document's body	covid:6db0b1feda5f5f60dbfe4d6381a2855455a7b728#body_text
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