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Authors: Lola Traverson, Isadora Mathevet, Amanda Paes, Karla Paz, Andrea Andrade, Katarina Ost, Kate Zinszer, Valery Ridde
Proper citation: Lola Traverson, Isadora Mathevet, Amanda Paes, Karla Paz, Andrea Andrade, Katarina Ost, Kate Zinszer, Valery Ridde 2020. Lessons learned from the resilience of public health systems, hospitals and their personnel to the COVID-19 pandemic: a scoping review protocol.. protocols.io dx.doi.org/10.17504/protocols.io.bikwkcxe Copy
Authors: Monto Kuroda, Shinya Kuroda
Group: Optical Clearing of Tissue
Summary: Internal tissues of multicellular organisms cannot directly be seen because they contain pigments. For this reason, whole-body clearing methods have been developed and applied to mammals such as mice. Insects such as beetles, however, cannot be cleared by the mammalian method because of pigments such as melanin in their exoskeletons. In this study, we tried to develop a whole-body clearing method for large beetles. We first bleached the exoskeleton using a hydrogen peroxide treatment, and applied the the advanced Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis (CUBIC) reagents to make the internal tissues transparent. The combined method of hydrogen peroxide and the advanced CUBIC allowed us to successfully perform whole-body clearing of the large beetles.
Proper citation: Monto Kuroda, Shinya Kuroda 2020. Whole-body clearing of beetles by successive treatment of hydrogen peroxide and CUBIC reagents. protocols.io dx.doi.org/10.17504/protocols.io.ba33igqn Copy
Authors: Xiaoyu Zhi, Yabing Li, Yingchun Han, Lu Feng
Proper citation: Xiaoyu Zhi, Yabing Li, Yingchun Han, Lu Feng 2017. Root Growth and Spatial Distribution Characteristics for Seedlings raised in Substrate and Transplanted Cotton. protocols.io dx.doi.org/10.17504/protocols.io.js4cngw Copy
Authors: Sam Li
Group: BioLegend
Proper citation: Sam Li 2019. Sandwich ELISA Protocol. protocols.io dx.doi.org/10.17504/protocols.io.98xh9xn Copy
Authors: Alan J. Cone
Group: Ju Lab
Summary: Method to create a long-term stable store of organisms. Especially useful if you want to store already transformed versions of organisms to aid in future experiments.
Proper citation: Alan J. Cone 2015. Glycerol Stock. protocols.io dx.doi.org/10.17504/protocols.io.dbe2jd Copy
Authors: Maya Brewer, Jamie Allen, Elizabeth Neumann, Agnes Fogo, Raymond Harris, Danielle Gutierrez, Mark De Caestecker, Jeff Spraggins
Group: VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: Scope:Obtain kidney tissue and metadata about tissue location within the whole kidney for storage and analysis.Expected Outcome:A portion of kidney tissue and a series of images that provide information about the original location of the smaller tissue.
Proper citation: Maya Brewer, Jamie Allen, Elizabeth Neumann, Agnes Fogo, Raymond Harris, Danielle Gutierrez, Mark De Caestecker, Jeff Spraggins 2019. Collection and Post-Surgical Excision of Human Kidney Tissue through the Cooperative Human Tissue Network. protocols.io dx.doi.org/10.17504/protocols.io.7gehjte Copy
Authors: Juan Jesus Torres-Gordillo
Summary: The purpose of this questionnaire is to know the impact of the implementation of the ECO method in the University. It is part of an innovation project, entitled ECO in Higher Education. Teaching inspired by the environment, funded by the University of Seville's 3rd Teaching Plan. It is intended for teachers who have been part of the innovation project. The data collected will be analysed to be used in the final report, as well as in some conference communications or journal articles.The questionnaire consists of 29 questions, divided into three blocks: 12 initial questions on demographic data, 9 closed-ended questions with four options and 8 open-ended questions. For open-ended questions, we ask that you answer in detail and as explicitly as possible.Each teacher is requested to complete one questionnaire per course in which they have implemented the ECO method. Similarly, if there have been two teachers in a shared course, each must fulfill, from their experience, a separate questionnaire.Thank you very much for your collaboration.Prof. Juan-Jesús Torres-GordilloUniversity of Seville (Spain)
Proper citation: Juan Jesus Torres-Gordillo 2020. QUESTIONNAIRE ABOUT ECO METHOD IMPLEMENTATION IN THE UNIVERSITY. protocols.io dx.doi.org/10.17504/protocols.io.bhp5j5q6 Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Proper citation: New England Biolabs 2015. PNGase F Mixture 1. protocols.io dx.doi.org/10.17504/protocols.io.cqgvtv Copy
Authors: Rosa Leon
Group: Leon Zayas Lab
Summary: This protocol series will guide students through the experience of analyzing metagenomic data.
Proper citation: Rosa Leon 2018. BIOL 354W - Research Methods in Advance Microbiology. protocols.io dx.doi.org/10.17504/protocols.io.m3dc8i6 Copy
Authors: Denville Scientific
Group: Denville Scientific, Inc.
Summary: Denville LE Agarose is an all purpose agarose for routine nucleic acid electrophoresis of fragments between 500bp-23,000 bp.Denville LE Agarose has no detectable DNase or RNase activity.Please refer to the appropriate protocol below, depending on whether you are using a hot plate or a microwave.
Proper citation: Denville Scientific 2016. Protocols for Agarose Preparation Using Denville LE Agarose. protocols.io dx.doi.org/10.17504/protocols.io.gskbwcw Copy
Authors: Martin Thomas Jahn
Group: hostmicrobeprotocols
Summary: Protocoll to create a fixed suspension of sponge associated prokaryotes (SAP) from sponge tissue.This can serve as the basis for Fluorescence in situ hybridisation and/or cell sorting.This protocol was tested for different sponge species but might also be adapted to other organisms (let others know)The protocol was modified from :Fieseler L, Horn M, Wagner M, Hentschel U. (2006) Discovery of the novel candidate phylum "Potibactetia" in marine sponges (vol 70, pg 3724, 2004). Applied and Environmental Microbiology;72(8):5677-.PMID:15184179 DOI:10.1128/AEM.70.6.3724-3732.2004
Proper citation: Martin Thomas Jahn 2019. Isolate prokaryotes from sponge tissue (SAP). protocols.io dx.doi.org/10.17504/protocols.io.u8vezw6 Copy
Authors: Brian Aevermann, Richard Scheuermann
Group: Human Cell Atlas Method Development Community
Summary: NS-Forest is an alogrithm that determines the minimum set of genes that are necessary and sufficient to define a cell type cluster derived from single cell RNAseq expression data. Development and stable releases can be found at : https://github.com/JCVenterInstitute/NSForest
Proper citation: Brian Aevermann, Richard Scheuermann 2018. NS-Forest version 2. protocols.io dx.doi.org/10.17504/protocols.io.un7evhn Copy
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 dx.doi.org/10.17504/protocols.io.y3sfyne Copy
Authors: Talita Gagliardi
Summary: Total RNA extraction using TRizol reagent.Attention: for nasopharyngeal aspirates, we use regular TRizol reagent in this assay, but for blood samples it is better to use a special one as "TRizol LS".
Proper citation: Talita Gagliardi 2019. Adapted protocol to extract total RNA using TRIzol® (Invitrogen, Thermo). protocols.io dx.doi.org/10.17504/protocols.io.w8vfhw6 Copy
Authors: Antoine ZILLER
Proper citation: Antoine ZILLER 2016. Digestion BclI. protocols.io dx.doi.org/10.17504/protocols.io.ecvbaw6 Copy
Authors: Aleksandra Kozyczkowska
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Multicellgenomelab, Emerging Organisms for Biology
Proper citation: Aleksandra Kozyczkowska 2018. Transient tranfection of unicellular relative of animals, Creolimax fragrantissima, using Lonza Nucleofector. protocols.io dx.doi.org/10.17504/protocols.io.r65d9g6 Copy
Authors: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
Group: Coronavirus Method Development Community
Summary: 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.
Proper citation: 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 dx.doi.org/10.17504/protocols.io.bj5xkq7n Copy
Authors: Xin Liu
Group: GigaScience Press, BGI
Summary: From here, You can learn about the detail methods of genome assembly and gene annotation of the Betta splendens genome.
Proper citation: Xin Liu 2018. An analytical pipeline of assembly and annotation of the Betta splendens genome.. protocols.io dx.doi.org/10.17504/protocols.io.qq9dvz6 Copy
Authors: Ashley Humphrey
Group: Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Trace metals solution to be used in ESAW Media for Marine Phytoplankton
Proper citation: Ashley Humphrey 2016. Trace Metal Solution for ESAW Media. protocols.io dx.doi.org/10.17504/protocols.io.gdabs2e Copy
Authors: James Thornton
Group: Hurwitz Lab, MetaFunc Course
Summary: This protocol provides the procedure to generate gene calls on your contigs using Prodigal.
Proper citation: James Thornton 2016. MG_HW6: Gene Calls with Prodigal. protocols.io dx.doi.org/10.17504/protocols.io.f4ubqww Copy
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