About: A Streamlined CyTOF Workflow To Facilitate Standardized Multi-Site Immune Profiling of COVID-19 Patients

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	A Streamlined CyTOF Workflow To Facilitate Standardized Multi-Site Immune Profiling of COVID-19 Patients
Creator	Lee, Brian Merad, Miriam Rahman, Adeeb Geanon, Daniel Gnjatic, Sacha Kim-Schulze, Seunghee Leech, John Valle, Diane Handler, Diana Herbinet, Manon Kelly, Geoffrey Upadhyaya, Bhaskar
Source	MedRxiv; Medline
abstract	Mass cytometry (CyTOF) represents one of the most powerful tools in immune phenotyping, allowing high throughput quantification of over 40 single parameters at single-cell resolution. However, wide deployment of CyTOF-based immune phenotyping studies are limited by complex experimental workflows and the need for specialized CyTOF equipment and technical expertise. Furthermore, differences in cell isolation and enrichment protocols, antibody reagent preparation, sample staining and data acquisition protocols can all introduce technical variation that can potentially confound integrative analyses of large data-sets of samples processed across multiple labs. Here, we present a streamlined whole blood CyTOF workflow which addresses many of these sources of experimental variation and facilitates wider adoption of CyTOF immune monitoring across sites with limited technical expertise or sample-processing resources or equipment. Our workflow utilizes commercially available reagents including the Fluidigm MaxPar Direct Immune Profiling Assay (MDIPA), a dry tube 30-marker immunophenotyping panel, and SmartTube Proteomic Stabilizer, which allows for simple and reliable fixation and cryopreservation of whole blood samples. We validate a workflow that allows for streamlined staining of whole blood samples with minimal processing requirements or expertise at the site of sample collection, followed by shipment to a central CyTOF core facility for batched downstream processing and data acquisition. We further demonstrate the application of this workflow to characterize immune responses in a cohort of hospitalized COVID-19 patients, highlighting key disease-associated changes in immune cell frequency and phenotype.
has issue date	2020-06-28(xsd:dateTime)
bibo:doi	10.1101/2020.06.26.20141341
bibo:pmid	32607524
has license	medrxiv
sha1sum (hex)	db5ae41a39dbec683233e424fdd7bc3cfa193c07
schema:url	https://doi.org/10.1101/2020.06.26.20141341
resource representing a document's title	A Streamlined CyTOF Workflow To Facilitate Standardized Multi-Site Immune Profiling of COVID-19 Patients
has PubMed identifier	32607524
schema:publication	medRxiv : the preprint server for health sciences
resource representing a document's body	covid:db5ae41a39dbec683233e424fdd7bc3cfa193c07#body_text
is schema:about of	named entity 'samples' named entity 'antibody' named entity 'Workflow' named entity 'Standardized' named entity 'PROTOCOLS' named entity 'POWERFUL' named entity 'ENRICHMENT' named entity 'LABS' named entity 'RESOLUTION' named entity 'ACROSS' named entity 'PROCESSED' named entity 'WORKFLOWS' named entity 'SPECIALIZED' named entity 'CELL' named entity 'PARAMETERS' named entity 'SAMPLE STAINING' named entity 'staining' named entity 'resolution' named entity 'immune' named entity 'technical' named entity 'limited' named entity 'Profiling' named entity 'high throughput' named entity 'Mass cytometry' named entity 'reagent' named entity 'phenotyping' named entity 'single-cell' named entity 'COVID-19' named entity 'phenotyping' named entity 'eosinophils' named entity 'staining' named entity 'BSA' named entity 'antibody' named entity 'heparin' named entity 'Fluidigm' named entity 'COVID-19' named entity 'medRxiv' named entity 'PHA' named entity 'CD61' named entity 'coagulopathy' named entity 'monocytes' named entity 'staining' named entity 'preprint' named entity 'staining' named entity 'preprint' named entity 'immune cell' named entity 'monocytes' named entity 'epitopes' named entity 'medRxiv' named entity 'antibodies' named entity 'downstream processing' named entity 'immune cell' named entity 'cryovials' named entity 'COVID-19' named entity 'sodium citrate' named entity 'peer review' named entity 'vacutainer' named entity 'IgM' named entity 'multi-center studies' named entity 'preprint' named entity 'CD4+' named entity 'peer review' named entity 'neutrophils' named entity 'staining' named entity 'macrophages' named entity 'preprint' named entity 'preprint' named entity 'chemokine receptor' named entity 'heparin' named entity 'staining' named entity 'antibodies'

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