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Authors: Peter Szabo, Steven Wells, Peter A. Sims, Donna Farber
Group: Human Cell Atlas Method Development Community, Coronavirus Method Development Community
Summary: This protocol describes the isolation of lymphocytes and pan-mononuclear cells from human whole blood for scRNAseq analysis.
Proper citation: Peter Szabo, Steven Wells, Peter A. Sims, Donna Farber 2020. COVID Blood Processing for scRNAseq. protocols.io https://dx.doi.org/10.17504/protocols.io.bjm6kk9e Copy
Authors: Muhammad Faisal, Olin Silander, Nikki Freed
Group: Coronavirus Method Development Community
Proper citation: Muhammad Faisal, Olin Silander, Nikki Freed 2020. Amplicon clean-up using SPRI beads. protocols.io https://dx.doi.org/10.17504/protocols.io.bfwpjpdn Copy
Authors: Anurag Patnaik, Ben Lepene, Robert Barclay
Group: Coronavirus Method Development Community, Nanotrap Applications
Proper citation: Anurag Patnaik, Ben Lepene, Robert Barclay 2020. Pooled sample testing (VTM/UTM) for SARS-CoV-2 using Magnetic Nanotrap® particles for direct RNA extraction.. protocols.io https:// Copy
Authors: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
Group: Coronavirus Method Development Community
Summary: This is Part 3 of "Phase 3 randomized, double-blinded, placebo-controlled trial to evaluate the safety, immunogenicity, and efficacy of Vaccine Candidate against COVID-19 in adults > 18 years of age"This generic Phase 3 protocol was developed by the PATH team with support of the Bill and Melinda Gates Foundation. The aim of the collection is to share recommended best practices in designing and implementing a Phase 3 study of a COVID-19 vaccine candidate. As Phase 3 trials of different Vaccine Candidates proceed around the world, following the same protocols will ensure consistency and comparability of the Phase 3 trial results.Please note that this is an evolving document, to be versioned and updated, based on community feedback and new data.
Proper citation: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores 2020. Study Design (Part 3 of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj5wkq7e Copy
Authors: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
Group: Coronavirus Method Development Community, PATH
Summary: This is Part 7 of "Phase 3 randomized, double-blinded, placebo-controlled trial to evaluate the safety, immunogenicity, and efficacy of Vaccine Candidate against COVID-19 in adults > 18 years of age"This generic Phase 3 protocol was developed by the PATH team with support of the Bill and Melinda Gates Foundation. The aim of the collection is to share recommended best practices in designing and implementing a Phase 3 study of a COVID-19 vaccine candidate. As Phase 3 trials of different Vaccine Candidates proceed around the world, following the same protocols will ensure consistency and comparability of the Phase 3 trial results.Please note that this is an evolving document, to be versioned and updated, based on community feedback and new data.
Proper citation: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores 2020. Safety Assessment and Reporting (Part 7 of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj52kq8e Copy
Authors: David Eccles
Group: Coronavirus Method Development Community
Summary: This is a fast "gunk to graph" protocol for analysing viral RNA from nasopharyngeal swabs. The approach involves swab lysis and inactivation at the point of sampling, uses a cellulose binding / wash protocol to reduce extraction cost, incorporates sample-specific barcodes during first-strand synthesis, nanopore rapid-attachment primers during PCR amplification, and nanopore sequencing with parallel RAMPART analysis for fast assembly and phylogenetics.An alternative protocol using both forward and reverse primers can be found here.
Proper citation: David Eccles 2020. Viral Sequencing, from Gunk to Graph (Two-step, strand-switching). protocols.io https://dx.doi.org/10.17504/protocols.io.bebujanw Copy
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