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Authors: Johannes Wolfram Debler
Summary: This is a slightly modified version of Thermo Fisher's gateway LR protocol which uses less enzyme and is therefore more economical.

Proper citation: 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 Copy   

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Authors: Maci Heal, Susan Tappan
Group: SPARC
Summary: Convert binary mask tracings from Nikon's NIS Elements software into MBF XML format.

Proper citation: 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 Copy   

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Authors: G-Biosciences
Group: G-Biosciences
Summary: 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.

Proper citation: G-Biosciences 2016. MegaLong™ Protocols Collection for Isolation of >100kb Genomic DNA. protocols.io https://dx.doi.org/10.17504/protocols.io.e7kbhkw Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.

Proper citation: Allen Institute for Brain Science 2020. Mouse Cardiac Perfusion Fixation and Brain Collection. protocols.io https://dx.doi.org/10.17504/protocols.io.beudjes6 Copy   

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Authors: Marijn Ceelen
Group: iGEM Wageningen 2019
Summary: This is a protocol to make yeast competent cells, which can be then stored at 4 ºC for up to a week.

Proper citation: Marijn Ceelen 2019. Yeast competent cells. protocols.io https://dx.doi.org/10.17504/protocols.io.7jphkmn Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.

Proper citation: Allen Institute for Brain Science 2020. DAB Solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.bgndjva6 Copy   

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Authors: James Angstman
Group: The Center for Genome Editing and Recording
Summary: 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.

Proper citation: James Angstman 2019. BiomekFXp Robot Minipreps (RoboPreps). protocols.io https://dx.doi.org/10.17504/protocols.io.3zqgp5w Copy   

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Authors: Ruby Lab
Summary: Hybridized Chain Reaction Fluroescent In Situ Hybridization for squid tissue and colonized V. fischeri.

Proper citation: Ruby Lab 2015. Hybridized Chain Reaction Fluorescent in situ Hybridization (HCR-FISH). protocols.io https://dx.doi.org/10.17504/protocols.io.dsg6bv Copy   

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Authors: Ed Emmott
Group: Emmott Lab

Proper citation: Ed Emmott 2020. Preparing Annotated Spectra from MaxQuant Output in xiSpec. protocols.io https:// Copy   

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Authors: Chin Yee Tan

Proper citation: Chin Yee Tan 2019. RNA isolation for tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.zvqf65w Copy   

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Authors: John Stack, Gary Cline
Group: Mouse Metabolic Phenotyping Centers
Summary: 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.

Proper citation: John Stack, Gary Cline 2019. Yale - Creatine Kinase Activity. protocols.io https://dx.doi.org/10.17504/protocols.io.y3sfyne Copy   

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Authors: Qutaiba Saleh, Edward Hensel, Risa Robinson
Group: Respiratory Technologies Lab
Summary: 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.

Proper citation: 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 Copy   

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Authors: Roey Angel, Eva Petrova
Group: SoWa RI Anaerobic and Molecular Microbiology (public)
Summary: 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.

Proper citation: Roey Angel, Eva Petrova 2021. cDNA synthesis using SuperScript™ IV. protocols.io https://dx.doi.org/10.17504/protocols.io.brqum5ww Copy   

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Authors: Mengchen Shi

Proper citation: Mengchen Shi 2017. Isolation of cell fractionation. protocols.io https://dx.doi.org/10.17504/protocols.io.kcfcstn Copy   

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Authors: Rachele Cesaroni
Group: Protist Research to Optimize Tools in Genetics (PROT-G)

Proper citation: Rachele Cesaroni 2017. Quick staining procedure of nuclei in Euplotes crassus using DAPI. protocols.io https://dx.doi.org/10.17504/protocols.io.g3tbynn Copy   

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Authors: Simon Blanchoud
Group: Blanchoud lab, UNIFR

Proper citation: Simon Blanchoud 2021. Haematoxylin-Eosin stain for cryosections. protocols.io https://dx.doi.org/10.17504/protocols.io.bru8m6zw Copy   

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Authors: Gabriel Magalhães Nunes Guimarães, Helga Bezerra Gomes da Silva
Summary: 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.

Proper citation: 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 Copy   

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Authors: Eva Feldman
Group: Diabetic Complications Consortium
Summary: 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:

Proper citation: Eva Feldman 2019. Biochemical Measures of Neuropathy - GSSG (Non-Enzymatic). protocols.io https://dx.doi.org/10.17504/protocols.io.3qpgmvn Copy   

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Authors: 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
Group: Coronavirus Method Development Community, Reclone.org (The Reagent Collaboration Network)

Proper citation: 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:// Copy   

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Authors: Dr. Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.

Proper citation: Dr. Steven Wilhelm 2017. M12 Tangential Flow Filtration . protocols.io https://dx.doi.org/10.17504/protocols.io.icscawe Copy   

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