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U Mass - Hemoglobin A1c Resource Report Resource Website |
Jason Kim | DOI:10.17504/protocols.io.xy3fpyn | Mouse Metabolic Phenotyping Centers | Summary:This experiment provides the quantification of multiple cytokines and chemokines using multiplexed-Luminex technology based on beads containing specific antibodies. Serum cytokine levels reflect chronic or acute inflammation, and circulating cytokines and chemokines are altered in obesity. Cytokines Panel I include IL-1α, IL-1β, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, KC (IL-8 homologue), IL-9, IL-10 (interleukin-10), IL-12 (p40), IL-12 (p70), IL-13, IL-15, IL-17A, TNFα (tumor necrosis factor alpha), IFNγ (interferon gamma), IP-10 (interferon gamma-induced protein 10; CXCL-10), Eotaxin (CCL-11), G-CSF (granulocyte colony stimulating factor), GM-CSF (granulocyte macrophage colony stimulating factor), LIF (leukemia inhibitory factor), LIX (LPSinduced CXC chemokine), MCP-1 (monocyte chemotactic protein-1; CCL-2), M-CSF (macrophage colony stimulating factor), MIG (monokine induced by gamma interferon; CXCL9), MIP-1α (macrophage inflammatory protein alpha; CCL-3), MIP-1β (macrophage inflammatory protein beta; CCL-4), and MIP-2/RANTES (macrophage inflammatory protein 2alpha; CXCL-2). A service can be requested for all or any combination of listed cytokines/chemokines for customized multiplexed Luminex assay. | University of Massachusetts | https://mmpc.org/shared/document.aspx?id=160&docType=Protocol | 1 | 2019 | Jason Kim 2019. U Mass - Hemoglobin A1c. protocols.io https://dx.doi.org/10.17504/protocols.io.xy3fpyn | 2021-04-15 09:15:45 | ||
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Study Population (Part 4 of Phase 3 study of Vaccine Candidate for COVID-19) Resource Report Resource Website |
Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores | DOI:10.17504/protocols.io.bj5xkq7n | Coronavirus Method Development Community | This is Part 4 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. | Center for Vaccine Innovation and Access, PATH (Washington D.C. and Seattle, Washington), Center for Vaccine Innovation and Access, PATH (Washington D.C. and Seattle, Washington), Center for Vaccine Innovation and Access, PATH (Washington D.C. and Seattle, Washington), Center for Vaccine Innovation and Access, PATH (Washington D.C. and Seattle, Washington) | 1 | 2020 | Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores 2020. Study Population (Part 4 of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj5xkq7n | 2021-04-15 09:15:45 | |||
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Dissolved silica colorimetric assay using a plate reader (96-well plate) Resource Report Resource Website |
Jian Gong | DOI:10.17504/protocols.io.bd7ni9me | Bosak Lab | This protocol describes the adaption of a silica colorimetric assay originally described in Strickland and Parsons, 1972 (p65-70), modified for use on a multi-mode plate reader spectrophotometer (BioTek, Synergy 2, Winooski, VT, USA), using standard 96-well plates for rapid measurements of 1 mL, diluted water samples. This assay measures the concentration of molybdate-reactive silica (monomeric and short polymers of silicic acid) in solution.Samples for this assay should be filtered (0.2 µm syringe filter) and placed in 2 mL microcentrifuge tubes. Avoid sample freezing. Store samples in the dark whenever possible. | Massachusetts Institute of Technology | 1 | 2020 | Jian Gong 2020. Dissolved silica colorimetric assay using a plate reader (96-well plate). protocols.io https://dx.doi.org/10.17504/protocols.io.bd7ni9me | 2021-04-15 09:15:49 | |||
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Trace Metal Solution for ESAW Media Resource Report Resource Website |
Ashley Humphrey | DOI:10.17504/protocols.io.gdabs2e | Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | Trace metals solution to be used in ESAW Media for Marine Phytoplankton | University of Tennessee, Knoxville | 1 | 2016 | Ashley Humphrey 2016. Trace Metal Solution for ESAW Media. protocols.io https://dx.doi.org/10.17504/protocols.io.gdabs2e | 2021-04-15 09:15:45 | |||
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AccuBlue®Broad Range RNA Quantitation Resource Report Resource Website |
Ajit N Shah | DOI:10.17504/protocols.io.87bhzin | Self | https://biotium.com/wp-content/uploads/2018/06/PI-31073.pdf | 2 | 2019 | Ajit N Shah 2019. AccuBlue®Broad Range RNA Quantitation. protocols.io https://dx.doi.org/10.17504/protocols.io.87bhzin | 2021-04-15 09:15:48 | ||||
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Fluorescence In Situ Hybridization (FISH - RNAscope) in mouse brain sections Resource Report Resource Website |
Yu Lin Tan, Oriol Pavón Arocas, Lucille Duquenoy, Tiago Branco | DOI:10.17504/protocols.io.bq2imyce | Here we describe a protocol to perform fluorescence in situ hybridization (FISH) in thin sections from frozen murine brain tissue. The protocol can be divided in several days or can be completed in two successive days: one day for extracting and slicing the brain and a second one for the FISH. | Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, Howland Street, London, W1T 4JG, UK, Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, Howland Street, London, W1T 4JG, UK, Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, Howland Street, London, W1T 4JG, UK, Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, Howland Street, London, W1T 4JG, UK | 1 | 2021 | Yu Lin Tan, Oriol Pavón Arocas, Lucille Duquenoy, Tiago Branco 2021. Fluorescence In Situ Hybridization (FISH - RNAscope) in mouse brain sections. protocols.io https://dx.doi.org/10.17504/protocols.io.bq2imyce | 2021-04-15 09:15:49 | ||||
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Electroporation of Caecitellus sp. with FITC-dextran Resource Report Resource Website |
Nick Irwin, Elisabeth Hehenberger, Patrick Keeling | DOI:10.17504/protocols.io.35kgq4w | Protist Research to Optimize Tools in Genetics (PROT-G) | Caecitellus sp. is a small phagotroph belonging to the biocosoecid order of the stramenopiles. Caecitellus is found across global oceans but it's role in marine ecosystems, as with many heterotrophic flagellates, is unclear. We isolated a strain of Caecitellus (small subunit rRNA gene was 99.53% identical to Caecitellus parvulus and Caecitellus paraparvulus) from a contaminated culture of Oxyrrhis marina and assessed its amenability to transformation. Fluorescein isothiocyanate conjugated to dextran was successfully introduced into Caecitellus sp. using a high voltage exponential decay pulse (1000 V, 10 µF, ∞ Ω) from a BioRad GenePulser Xcell (cuvette width 0.2 cm). Cell viability was confirmed by observing motility and fluorescence 24 h after electroporation (Figure 1). Lower voltage pulses did not result in FITC uptake. Estimates of transformation effifiency were difficult to obtain due to the small size of the cells.Unfortunately, the isolated strain of Caecitellus perished in an incubator malfunction. However, these results may be transferable to Caecitellus parvulus, a model for heterotrophic flagellates. | University of British Columbia, University of British Columbia, University of British Columbia | 1 | 2019 | Nick Irwin, Elisabeth Hehenberger, Patrick Keeling 2019. Electroporation of Caecitellus sp. with FITC-dextran. protocols.io https://dx.doi.org/10.17504/protocols.io.35kgq4w | 2021-04-15 09:15:48 | |||
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The production of monocyte-derived dendritic cells from human iPSCs Resource Report Resource Website |
Lucas Armitage, Mark Wallet | DOI:10.17504/protocols.io.ng8dbzw | This protocol is a modification of a previously published method by Wilgenburg et al (PLoS One, 2013) to obtain monocytes and Dendritic cells (DCs) from induced Pluripotent Stem Cells (iPSCs) lines. | University of Florida, University of Florida | 1 | 2018 | Lucas Armitage, Mark Wallet 2018. The production of monocyte-derived dendritic cells from human iPSCs. protocols.io https://dx.doi.org/10.17504/protocols.io.ng8dbzw | 2021-04-15 09:15:45 | ||||
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Screening Sequencing Datasets for Marker Genes in CLC Genomics Resource Report Resource Website |
Steven Wilhelm | DOI:10.17504/protocols.io.g5vby66 | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | The University of Tennessee, Knoxville | 1 | 2017 | Steven Wilhelm 2017. Screening Sequencing Datasets for Marker Genes in CLC Genomics. protocols.io https://dx.doi.org/10.17504/protocols.io.g5vby66 | 2021-04-15 09:15:45 | ||||
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Copy of ELISA for quantification of IL-30 in human serum. Resource Report Resource Website |
Angel Justiz-Vaillant | DOI:10.17504/protocols.io.bj33kqqn | Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. They play essential roles in the activation and differentiation of immune cells, as well as proliferation, maturation, migration, and adhesion. They also have pro-inflammatory and anti-inflammatory properties. The primary function of interleukins is, therefore, to modulate growth, differentiation, and activation during inflammatory and immune responses. Interleukins consist of a large group of proteins that can elicit many reactions in cells and tissues by binding to high-affinity receptors in cell surfaces. IL-31 is produced mainly by Th2 cells and dendritic cells. It is a proinflammatory cytokine and a chemotactic factor that direct polymorphonuclear cells, monocytes, and T cells to inflammatory lesions. IL-31 induces chemokines production and synthesis of IL-6, IL-16, and IL-32. [1]Reference1. Justiz Vaillant AA, Qurie A. Interleukin. In:StatPearls. Treasure Island (FL): StatPearls Publishing; June 12, 2019. | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. Copy of ELISA for quantification of IL-30 in human serum.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj33kqqn | 2021-04-15 09:15:46 | ||||
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Fluorescence aggregation imaging Resource Report Resource Website |
Serena Ding | DOI:10.17504/protocols.io.vx9e7r6 | Behavioural Genomics | For imaging aggregation behaviour of 40 young adult C. elegans on agar using the Twinnie TwinCam system. Worms are synchronised by bleaching and refeeding for 72 hours, and then 40 young adult hermaphrodites are transferred by glass pipette onto a 35 mm regular NGM plate for imaging for 1 hour at 9 fps. | Imperial College London | https://www.biorxiv.org/content/early/2018/11/01/398370 | 1 | 2018 | Serena Ding 2018. Fluorescence aggregation imaging. protocols.io https://dx.doi.org/10.17504/protocols.io.vx9e7r6 | 2021-04-15 09:15:46 | ||
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ClearLab Flu+COVID19 Antigen Assay IFU Resource Report Resource Website |
petercb3 | DOI:10.17504/protocols.io.bj8fkrtn | Coronavirus Method Development Community | Indication: Qualitative detection of the nucleocapsid protein antigen from SARS-CoV-2 in nasopharyngeal aspirate specimens directly or after the aspirate have been added to viral transport media from individuals who are suspected of COVID-19 by their healthcare provider. Emergency use of this test is limited to authorized laboratories and other authorized testing locations. | Chris Baker MD (Aardvark Medical, Inc), Roger Kang (Princeton BioMediTech) | http://www.clearmynose.com | 1 | 2020 | petercb3 2020. ClearLab Flu+COVID19 Antigen Assay IFU. protocols.io https://dx.doi.org/10.17504/protocols.io.bj8fkrtn | 2021-04-15 09:15:48 | ||
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Viability Estimation of Islets for Distribution Using Inclusion and Exclusion Fluorescent Dyes (FDA/PI) Resource Report Resource Website |
Integrated Islet Distribution Program | DOI:10.17504/protocols.io.bhdmj246 | Integrated Islet Distribution Program | This Standard Operating Procedure is adapted from the work of the 'National Institutes of Health-Sponsored Clinical Islet Transplantation Consortium Phase 3 Trial: Manufacture of a Complex Cellular Product at Eight Processing Facilities'' following the SOP cited in the document 'Purified Human Pancreatic Islet - Viability Estimation of Islet Using Fluorescent Dyes (FDA/PI): Standard Operating Procedure of the NIH Clinical Islet Transplantation Consortium'This SOP defines the procedure for assessment of viability of human isolated islet preparations, which include endocrine and exocrine tissue, for use in the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) sponsored research in the Integrated Islet Distribution Program (IIDP). This protocol is written to assist the participating islet isolation centers and investigators who are part of this program.Fluorescein Diacetate/ Propidium Iodide (FDA)/(PI) Viability Assay is a rapid fluorometric method to test the integrity of the plasma membrane simultaneously using inclusion and exclusion dyes; the assay differentiates between viable and nonviable cells and is, consequently, used for determination of viability of islet preparations. | Integrated Islet Distribution Program, City of Hope, Duarte, CA | 2 | 2020 | Integrated Islet Distribution Program 2020. Viability Estimation of Islets for Distribution Using Inclusion and Exclusion Fluorescent Dyes (FDA/PI). protocols.io https://dx.doi.org/10.17504/protocols.io.bhdmj246 | 2021-04-15 09:15:56 | |||
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Quanti-iT™ Pico Green dsDNA Assay (Invitrogen P7589) Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c5zy75 | Earth Microbiome Project | Ul-Hasan S, Bowers RM, Figueroa-Montiel A, Licea-Navarro AF, Beman JM, Woyke T, Nobile CJ, Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California. PLoS ONE 14(2). doi: 10.1371/journal.pone.0212355 | Matthew Sullivan Lab, University of Arizona/Ohio State University | https://doi.org/10.1371/journal.pone.0212355 | 1 | 2019 | Matthew Sullivan Lab 2019. Quanti-iT™ Pico Green dsDNA Assay (Invitrogen P7589). protocols.io https://dx.doi.org/10.17504/protocols.io.c5zy75 | 2021-04-15 09:15:46 | ||
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Dispersing Labyrinthulomycete Cell Aggregates by Sonication Resource Report Resource Website |
Mariana Rius, Kashyapa Bandaralage | DOI:10.17504/protocols.io.hg2b3ye | Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab | Sonication procedure implemented to reduce labyrinthulomycete cell aggregation from culture for subsequent growth analyses. | Stony Brook University, Stony Brook University | 1 | 2017 | Mariana Rius, Kashyapa Bandaralage 2017. Dispersing Labyrinthulomycete Cell Aggregates by Sonication. protocols.io https://dx.doi.org/10.17504/protocols.io.hg2b3ye | 2021-04-15 09:15:46 | |||
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Dental Calculus Field-Sampling Protocol (Sabin version) Resource Report Resource Website |
Susanna Sabin, James Fellows Yates | DOI:10.17504/protocols.io.bqecmtaw | WarinnerGroup, MPI-SHH Archaeogenetics | This protocol describes how to sample dental calculus from skeletal remains for biomolecular analysis. This protocol is particularly recommended for sampling calculus from teeth attached to a jaw bone, skull, or skeleton. The primary use-case is for DNA and proteomic analysis. | Max Planck Institute for the Science of Human History, Max Planck Institute for the Science of Human History | http://christinawarinner.com/resources/archaeologists/ | 2 | 2020 | Susanna Sabin, James Fellows Yates 2020. Dental Calculus Field-Sampling Protocol (Sabin version). protocols.io https://dx.doi.org/10.17504/protocols.io.bqecmtaw | 2021-04-15 09:15:46 | ||
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Adult mouse thymus dissociation (on ice) Resource Report Resource Website |
Andrew Potter | DOI:10.17504/protocols.io.q7edzje | Human Cell Atlas Method Development Community | Protocol for thymus dissociation (10-week old CD-1 female). | Cincinnati Children's Hospital Medical Center | 3 | 2018 | Andrew Potter 2018. Adult mouse thymus dissociation (on ice). protocols.io https://dx.doi.org/10.17504/protocols.io.q7edzje | 2021-04-15 09:15:46 | |||
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Paraffin embedding, microtomy and fluorescence in situ hybridization (FISH) of whole adult Drosophila Resource Report Resource Website |
Carolyn Elya, Ciera Martinez | DOI:10.17504/protocols.io.k5ecy3e | Paraffin embedding and sectioning is a classic technique used in a variety of biological disciplines. Though the fruit fly Drosophila melanogaster are one of the most commonly-employed model organisms, the immense Drosophila literature is lacking in current protocols for sectioning whole, adult flies. Here, we adopted a plant histology protocol to embed entire adult flies for thin sectioning and present our protocol for performing FISH on the subsequent sections. In the interest of reproducibility, we have tried to include details that are normally omitted from published protocols. | Elya C, Lok TC, Spencer QE, McCausland H, Martinez CC, Eisen M, Robust manipulation of the behavior of by a fungal pathogen in the laboratory. eLife doi: 10.7554/eLife.34414 | Department of Molecular and Cell Biology, University of California, Berkeley, CA, Department of Molecular and Cell Biology, University of California, Berkeley, CA | https://doi.org/10.7554/eLife.34414 | 1 | 2017 | Carolyn Elya, Ciera Martinez 2017. Paraffin embedding, microtomy and fluorescence in situ hybridization (FISH) of whole adult Drosophila. protocols.io https://dx.doi.org/10.17504/protocols.io.k5ecy3e | 2021-04-15 09:15:46 | ||
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A non-destructive enzymatic method to extract DNA from a single arthropod specimen Resource Report Resource Website |
Daubian Santos, Guilherme Cunha Ribeiro, Aline Diniz Cabral, Márcia Aparecida Sperança | DOI:10.17504/protocols.io.kkqcuvw | Preparation of insect specimens for morphological studies classically employs chaotropic salts which can cause disruption of important structures. Also, extraction of nucleic acids for genetic studies leads to destruction of the specimen. Thus, in this paper is proposed a new technique, based on the use of proteinase K, which allows DNA extraction while keeping intact the entire morphology of insect specimens. The presented technique can contribute to taxonomic and systematic studies on different groups of arthropods. Also, with the global emergency and reemergence of diseases transmitted by arthropod vectors, genetic and morphological investigations performed in an individual-scale would unveil important aspects of environment and host-pathogen interactions. | Santos D, Ribeiro GC, Cabral AD, Sperança MA (2018) A non-destructive enzymatic method to extract DNA from arthropod specimens: Implications for morphological and molecular studies. PLoS ONE 13(2): e0192200. doi: 10.1371/journal.pone.0192200 | Universidade Federal do ABC, Universidade Federal do ABC, Universidade Federal do ABC, Universidade Federal do ABC | https://doi.org/10.1371/journal.pone.0192200 | 1 | 2018 | Daubian Santos, Guilherme Cunha Ribeiro, Aline Diniz Cabral, Márcia Aparecida Sperança 2018. A non-destructive enzymatic method to extract DNA from a single arthropod specimen. protocols.io https://dx.doi.org/10.17504/protocols.io.kkqcuvw | 2021-04-15 09:15:57 | ||
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Wholemount Immunolabeling for GUT Samples Resource Report Resource Website |
Marthe Howard | DOI:10.17504/protocols.io.wr6fd9e | Wholemount Immunolabeling-GutThis protocol is used for immunostaining large blocks of tissue. The application that it was developed for is large pieces of mouse gut tissue. Tissues shold be well washed prior to fixation. | University of Toledo Health Sciences Campus | 1 | 2019 | Marthe Howard 2019. Wholemount Immunolabeling for GUT Samples. protocols.io https://dx.doi.org/10.17504/protocols.io.wr6fd9e | 2021-04-15 09:15:46 |
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