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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Gateway LR recombination of entry clones in pDONR/zeo into destination plasmid (5 µl assay) Resource Report Resource Website |
Johannes Wolfram Debler | DOI:10.17504/protocols.io.g5sby6e | This is a slightly modified version of Thermo Fisher's gateway LR protocol which uses less enzyme and is therefore more economical. | Curtin University | https://www.thermofisher.com/order/catalog/product/11791020 | 1 | 2017 | Johannes Wolfram Debler 2017. Gateway LR recombination of entry clones in pDONR/zeo into destination plasmid (5 µl assay). protocols.io https://dx.doi.org/10.17504/protocols.io.g5sby6e | 2021-04-15 09:15:41 | |||
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SPARC Segmentation Conversion: Binary mask tracings to MBF XML Resource Report Resource Website |
Maci Heal, Susan Tappan | DOI:10.17504/protocols.io.bchjit4n | SPARC | Convert binary mask tracings from Nikon's NIS Elements software into MBF XML format. | MBF Bioscience, MAP-CORE, MBF Bioscience, MAP-CORE | 1 | 2020 | Maci Heal, Susan Tappan 2020. SPARC Segmentation Conversion: Binary mask tracings to MBF XML. protocols.io https://dx.doi.org/10.17504/protocols.io.bchjit4n | 2021-04-15 09:15:49 | |||
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MegaLong™ Protocols Collection for Isolation of >100kb Genomic DNA Resource Report Resource Website |
G-Biosciences | DOI:10.17504/protocols.io.e7kbhkw | G-Biosciences | This is a collection of G-Biosciences MegaLong™ protocols for the isolation of >100kb Genomic DNA .MegaLong™ isolates high molecular weight (>100kb) genomic DNA from a variety of samples, including animal tissues, cultured cells, whole blood, bacterial and yeast. Please refer to the appropriate protocol below, depending on your application. | https://www.gbiosciences.com/image/pdfs/protocol/786-146_protocol.pdf | 1 | 2016 | G-Biosciences 2016. MegaLong™ Protocols Collection for Isolation of >100kb Genomic DNA. protocols.io https://dx.doi.org/10.17504/protocols.io.e7kbhkw | 2021-04-15 09:15:57 | |||
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Mouse Cardiac Perfusion Fixation and Brain Collection Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.beudjes6 | BICCN, Allen Institute for Brain Science | This protocol describes the procedures for intracardiac perfusion fixation of postnatal mice, including anesthesia, exsanguination, fixation, brain removal and post-fixation storage. Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 3 | 2020 | Allen Institute for Brain Science 2020. Mouse Cardiac Perfusion Fixation and Brain Collection. protocols.io https://dx.doi.org/10.17504/protocols.io.beudjes6 | 2021-04-15 09:15:49 | |||
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Yeast competent cells Resource Report Resource Website |
Marijn Ceelen | DOI:10.17504/protocols.io.7jphkmn | iGEM Wageningen 2019 | This is a protocol to make yeast competent cells, which can be then stored at 4 ºC for up to a week. | Wageningen University | 1 | 2019 | Marijn Ceelen 2019. Yeast competent cells. protocols.io https://dx.doi.org/10.17504/protocols.io.7jphkmn | 2021-04-15 09:15:49 | |||
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DAB Solutions Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bgndjva6 | BICCN, Allen Institute for Brain Science | 3, 3´ Diaminobenzidine (DAB) is a commonly used chromogen for histological staining. In the presence of peroxidase enzyme, DAB produces a brown precipitate that is insoluble in alcohol and xylene. Peroxidase catalyzes hydrogen peroxide oxidation of substrate DAB. This SOP provides instructions to prepare four different formulations of DAB. DAB for Immunohistochemical staining (IHC), DAB for Acetylcholinesterase (AChE) Staining, Nickel Enchanced DAB for Biocytin staining, and DAB for Biocytin staining.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 6 | 2020 | Allen Institute for Brain Science 2020. DAB Solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.bgndjva6 | 2021-04-15 09:15:48 | |||
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BiomekFXp Robot Minipreps (RoboPreps) Resource Report Resource Website |
James Angstman | DOI:10.17504/protocols.io.3zqgp5w | The Center for Genome Editing and Recording | RoboPreps are great for high-throughput cloning and subcloning, especially if you’re going to be doing Maxipreps afterward anyway. RoboPreps must be done in 96 well format as of now, though future generations may one day break through this technological barrier. | Harvard University | 1 | 2019 | James Angstman 2019. BiomekFXp Robot Minipreps (RoboPreps). protocols.io https://dx.doi.org/10.17504/protocols.io.3zqgp5w | 2021-04-15 09:15:56 | |||
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Hybridized Chain Reaction Fluorescent in situ Hybridization (HCR-FISH) Resource Report Resource Website |
Ruby Lab | DOI:10.17504/protocols.io.dsg6bv | Hybridized Chain Reaction Fluroescent In Situ Hybridization for squid tissue and colonized V. fischeri. | University of Hawaii | 1 | 2015 | Ruby Lab 2015. Hybridized Chain Reaction Fluorescent in situ Hybridization (HCR-FISH). protocols.io https://dx.doi.org/10.17504/protocols.io.dsg6bv | 2021-04-15 09:15:48 | ||||
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Preparing Annotated Spectra from MaxQuant Output in xiSpec Resource Report Resource Website |
Ed Emmott | Emmott Lab | University of Liverpool | http://emmottlab.org | 1 | 2020 | Ed Emmott 2020. Preparing Annotated Spectra from MaxQuant Output in xiSpec. protocols.io https:// | 2021-04-15 09:15:56 | ||||
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RNA isolation for tissue Resource Report Resource Website |
Chin Yee Tan | DOI:10.17504/protocols.io.zvqf65w | Duke University | 3 | 2019 | Chin Yee Tan 2019. RNA isolation for tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.zvqf65w | 2021-04-15 09:15:48 | |||||
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Yale - Creatine Kinase Activity Resource Report Resource Website |
John Stack, Gary Cline | DOI:10.17504/protocols.io.y3sfyne | Mouse Metabolic Phenotyping Centers | Procedure used to determine the creatine kinase activity in blood , serum, and plasma. Creatine kinase activity is measured by the enzymatically coupled reactions of creatine kinase, hexokinase, and glucose-6-P dehydrogenase. The rate of NADPH formation is monitored by the change in absorbance at 340 nm. | Yale University, Yale University | https://mmpc.org/shared/document.aspx?id=219&docType=Protocol | 1 | 2019 | John Stack, Gary Cline 2019. Yale - Creatine Kinase Activity. protocols.io https://dx.doi.org/10.17504/protocols.io.y3sfyne | 2021-04-15 09:15:44 | ||
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Coil Resistance Testing Apparatus for VUSE ALTO Resource Report Resource Website |
Qutaiba Saleh, Edward Hensel, Risa Robinson | DOI:10.17504/protocols.io.bibnkame | Respiratory Technologies Lab | Measuring coil resistance of Electronic Nicotine Delivery Systems (ENDS) accurately is critical in any research studying the characteristics of electronic cigarettes and their effects on the performance of these devices. It has been shown in several papers that changing coil resistance has the potential to change the Hazardous and Potentially Hazardous Constituents (HPHC) of emissions and consequently health effects on users. This protocol describes how to build a test apparatus for coil resistance measurement for ENDS. This apparatus mimics the geometrical and electrical characteristics of the ENDS and thus provides accurate measurements of the effective coil resistance. The steps shown in this protocol are illustrated for creating a VUSE ALTO test apparatus, but the general idea can be applied to other devices. | MDPI and ACS Style Saleh, Q.M.; Hensel, E.C.; Robinson, R.J. Method for Quantifying Variation in the Resistance of Electronic Cigarette Coils. Int. J. Environ. Res. Public Health 2020, 17, 7779. | Respiratory Technologies Lab, Rochester Institute of Technology, Respiratory Technologies Lab, Rochester Institute of Technology, Respiratory Technologies Lab, Rochester Institute of Technology | 1 | 2020 | Qutaiba Saleh, Edward Hensel, Risa Robinson 2020. Coil Resistance Testing Apparatus for VUSE ALTO. protocols.io https://dx.doi.org/10.17504/protocols.io.bibnkame | 2021-04-15 09:15:44 | ||
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cDNA synthesis using SuperScript™ IV Resource Report Resource Website |
Roey Angel, Eva Petrova | DOI:10.17504/protocols.io.brqum5ww | SoWa RI Anaerobic and Molecular Microbiology (public) | The following protocol is intended as a downstream application for our Purification of RNA from a DNA/RNA Extract protocol. This protocol describes how to synthesise a first-strand non-specific complementary DNA (cDNA) from a purified RNA extract using SuperScript IV Reverse Transcriptase. The second strand synthesis is usually not required for most downstream applications. This protocol is a simplified and condensed version of the full protocol provided by the manufacturer. | Soil and Water Research Infrastructure, Soil and Water Research Infrastructure | 2 | 2021 | Roey Angel, Eva Petrova 2021. cDNA synthesis using SuperScript™ IV. protocols.io https://dx.doi.org/10.17504/protocols.io.brqum5ww | 2021-04-15 09:15:44 | |||
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Isolation of cell fractionation Resource Report Resource Website |
Mengchen Shi | DOI:10.17504/protocols.io.kcfcstn | Shi M, Zhou L, Zhao L, Shang M, He T, Tang Z, Sun H, Ren P, Lin Z, Chen T, Yu J, Xu J, Yu X, Huang Y (2017) Csseverin inhibits apoptosis through mitochondria-mediated pathways triggered by Ca2 + dyshomeostasis in hepatocarcinoma PLC cells. PLoS Negl Trop Dis 11(11): e0006074. doi: 10.1371/journal.pntd.0006074 | Sun Yat-Sen University | https://doi.org/10.1371/journal.pntd.0006074 | 1 | 2017 | Mengchen Shi 2017. Isolation of cell fractionation. protocols.io https://dx.doi.org/10.17504/protocols.io.kcfcstn | 2021-04-15 09:15:48 | |||
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Quick staining procedure of nuclei in Euplotes crassus using DAPI Resource Report Resource Website |
Rachele Cesaroni | DOI:10.17504/protocols.io.g3tbynn | Protist Research to Optimize Tools in Genetics (PROT-G) | 1 | 2017 | Rachele Cesaroni 2017. Quick staining procedure of nuclei in Euplotes crassus using DAPI. protocols.io https://dx.doi.org/10.17504/protocols.io.g3tbynn | 2021-04-15 09:15:44 | |||||
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Haematoxylin-Eosin stain for cryosections Resource Report Resource Website |
Simon Blanchoud | DOI:10.17504/protocols.io.bru8m6zw | Blanchoud lab, UNIFR | University of Fribourg | 1 | 2021 | Simon Blanchoud 2021. Haematoxylin-Eosin stain for cryosections. protocols.io https://dx.doi.org/10.17504/protocols.io.bru8m6zw | 2021-04-15 09:15:55 | ||||
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Analgesia de parto: gabriel.med.br Resource Report Resource Website |
Gabriel Magalhães Nunes Guimarães, Helga Bezerra Gomes da Silva | DOI:10.17504/protocols.io.ri6d4he | Várias descobertas são publicadas mensalmente com potencial de aperfeiçoar a técnica de analgesia de parto.A intenção deste protocolo é registrar sistematicamente as mudanças que adotei. | Universidade de Brasília, Universidade de Brasília | 1 | 2018 | Gabriel Magalhães Nunes Guimarães, Helga Bezerra Gomes da Silva 2018. Analgesia de parto: gabriel.med.br. protocols.io https://dx.doi.org/10.17504/protocols.io.ri6d4he | 2021-04-15 09:15:48 | ||||
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Biochemical Measures of Neuropathy - GSSG (Non-Enzymatic) Resource Report Resource Website |
Eva Feldman | DOI:10.17504/protocols.io.3qpgmvn | Diabetic Complications Consortium | Summary:Oxidative stress is highly correlated with the metabolic changes caused by hyperglycemia. Increased levels of glucose overload mitochondria and result in the production of reactive oxygen species (ROS). In addition, the flow of excess glucose through cellular pathways decreases the cell’s normal ability to detoxify ROS. As a result, the neurons and axons of the peripheral nervous system contain increased levels of ROS and decreased antioxidant capacity. The following assays are used to measure these changes in rodent models of diabetic neuropathy. Diabetic Complication: | University of Michigan - Ann Arbor | https://www.diacomp.org/shared/document.aspx?id=54&docType=Protocol | 1 | 2019 | Eva Feldman 2019. Biochemical Measures of Neuropathy - GSSG (Non-Enzymatic). protocols.io https://dx.doi.org/10.17504/protocols.io.3qpgmvn | 2021-04-15 09:15:56 | ||
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A Simple RNA Preparation Method for SARS-CoV-2 detection by RT-qPCR Resource Report Resource Website |
Aniela Wozniak, Catalina Ibarra-Henriquez, Valentina Sebastian, Grace Armijo, Liliana Lamig, Carolina Miranda, Marcela Lagos, Sandra Solari, Ana María Guzmán, Teresa Quiroga, Susan Hitschfeld, Eleodoro Riveras, Marcela Ferres, Rodrigo A. Gutiérrez, Patricia García, Ariel Cerda | Coronavirus Method Development Community, Reclone.org (The Reagent Collaboration Network) | Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, Laboratorio de Microbiología. Servicio de laboratorios Clínicos. Red de Salud UC-CHRISTUS, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, Laboratorio de Microbiología. Servicio de laboratorios Clínicos. Red de Salud UC-CHRISTUS, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile | https://doi.org/10.1101/2020.05.07.083048 | 1 | 2020 | Aniela Wozniak, Catalina Ibarra-Henriquez, Valentina Sebastian, Grace Armijo, Liliana Lamig, Carolina Miranda, Marcela Lagos, Sandra Solari, Ana María Guzmán, Teresa Quiroga, Susan Hitschfeld, Eleodoro Riveras, Marcela Ferres, Rodrigo A. Gutiérrez, Patricia García, Ariel Cerda 2020. A Simple RNA Preparation Method for SARS-CoV-2 detection by RT-qPCR. protocols.io https:// | 2021-04-15 09:15:47 | ||||
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M12 Tangential Flow Filtration Resource Report Resource Website |
Dr. Steven Wilhelm | DOI:10.17504/protocols.io.icscawe | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol. | 1 | 2017 | Dr. Steven Wilhelm 2017. M12 Tangential Flow Filtration . protocols.io https://dx.doi.org/10.17504/protocols.io.icscawe | 2021-04-15 09:15:47 |
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