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| Name | Authors | DOI | Group |
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MojoSort™ Mouse Neutrophil Isolation Kit Column Protocol Resource Report Resource Website |
Sam Li | 10.17504/protocols.io.7bjhikn | BioLegend | BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple protocol consists of following the MojoSort™ protocol to label the cells with pre-diluted MojoSort™ reagents and using the columns as indicated by the manufacturer.Note: Due to the properties of our beads, it may be possible to use far fewer beads and less antibody cocktail that with other commercial suppliers. We recommend a titration to find the best dilution factor. However, as a general rule, dilutions ranging from 1:2 to 1:10 for the antibody cocktail can be used. Dilutions ranging from 1:5 to 1:20 for the Streptavidin Nanobeads can be used. Please contact BioLegend Technical Service ([email protected]) if further assistance is needed. | BioLegend | https://www.biolegend.com/protocols/mojosort-mouse-neutrophil-isolation-kit-column-protocol/4770/ | 1 | 2019 | Sam Li 2019. MojoSort™ Mouse Neutrophil Isolation Kit Column Protocol. protocols.io dx.doi.org/10.17504/protocols.io.7bjhikn | 2021-03-29 03:10:30 | ||
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Adoption and evaluation of the Doha agreement classification system of groin pain in athletes (part 2): a worldwide survey Resource Report Resource Website |
Willem Heijboer, Adam Weir, Eamonn Delahunt, Per Hölmich, Anthony G. Schache, Johannes L. Tol, Robert-Jan de Vos, Zarko Vuckovic, Andreas Serner | 10.17504/protocols.io.bgkfjutn | Sports Groin Pain Centre, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar, Sports Groin Pain Centre, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar; Department of Orthopaedics and Sports Medicine, Erasmus University Medical Centre, Rotterdam, The Netherlands, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland; Institute for Sport and Health, University College Dublin, Dublin, Ireland, Department of Orthopedic Surgery, Sports Orthopedic Research Center—Copenhagen (SORC-C), Arthroscopic Center, Copenhagen University Hospital, Amager-Hvidovre, Denmark, La Trobe Sport and Exercise Medicine Research Centre, La Trobe University, Melbourne, Australia, Aspetar, Orthopaedic and Sports Medicine Hospital, Doha, Qatar; Department of Orthopaedic Surgery, Amsterdam UMC, University of Amsterdam, Amsterdam Movement Sciences, Amsterdam, The Netherlands; Academic Center for Evidence based Sports Medicine (ACES), Amsterdam UMC, Amsterdam, The Netherlands; Amsterdam Collaboration for Health and Safety in Sports (ACHSS), AMC/VUmc IOC Research Center, Amsterdam, The Netherlands, Department of Orthopaedics and Sports Medicine, Erasmus University Medical Centre, Rotterdam, The Netherlands, Sports Groin Pain Centre, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar, Sports Groin Pain Centre, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar | 1 | 2020 | Willem Heijboer, Adam Weir, Eamonn Delahunt, Per Hölmich, Anthony G. Schache, Johannes L. Tol, Robert-Jan de Vos, Zarko Vuckovic, Andreas Serner 2020. Adoption and evaluation of the Doha agreement classification system of groin pain in athletes (part 2): a worldwide survey. protocols.io dx.doi.org/10.17504/protocols.io.bgkfjutn | 2021-03-29 03:10:29 | |||||
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Mothur Amplicon Analysis Resource Report Resource Website |
James Thornton | 10.17504/protocols.io.feibjce | ECOGEO | Hurwitz Lab | 1 | 2016 | James Thornton 2016. Mothur Amplicon Analysis. protocols.io dx.doi.org/10.17504/protocols.io.feibjce | 2021-03-29 03:10:30 | ||||
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Immunohistochemical classification of sensory and autonomic neurons projecting to the lower urinary tract in rats [keast-001] Resource Report Resource Website |
Janet Keast, Peregrine Osborne | 10.17504/protocols.io.w3gfgjw | SPARC | This collection describes the procedures required to label, visualise, characterise and quantify neurons that innervate the lower urinary tract tissues of adult male and female Sprague-Dawley rats. This collection includes protocols for:STAGE 1: Surgery to micro-inject fluorescent retrograde tracer dyes into one or more sites within the lower urinary tractSTAGE 2: Intracardiac perfusion with fixative to preserve neural tissues of interestSTAGE 3: Fluorescence immunohistochemistry of ganglion cryosections. | University of Melbourne, University of Melbourne | 1 | 2019 | Janet Keast, Peregrine Osborne 2019. Immunohistochemical classification of sensory and autonomic neurons projecting to the lower urinary tract in rats [keast-001]. protocols.io dx.doi.org/10.17504/protocols.io.w3gfgjw | 2021-03-29 03:10:28 | |||
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Anti-BrdU Staining Protocols Using DNAse with Surface and Fluorescent Proteins Resource Report Resource Website |
Sam Li | 10.17504/protocols.io.bac9iaz6 | BioLegend | BioLegend | https://www.biolegend.com/protocols/anti-brdu-staining-using-dnase-with-surface-and-fluorescent-proteins/4241/ | 3 | 2019 | Sam Li 2019. Anti-BrdU Staining Protocols Using DNAse with Surface and Fluorescent Proteins. protocols.io dx.doi.org/10.17504/protocols.io.bac9iaz6 | 2021-03-29 03:10:29 | |||
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Transformation Resource Report Resource Website |
宏亮 董 | 10.17504/protocols.io.7idhka6 | 2019 iGEM NEFU_China | Northeast Forest University | 1 | 2019 | 宏亮 董 2019. Transformation. protocols.io dx.doi.org/10.17504/protocols.io.7idhka6 | 2021-03-29 03:10:29 | ||||
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Enzymatic Assay of Protease Using Azocasein as Substrate Resource Report Resource Website |
Neilier Junior | 10.17504/protocols.io.bhqnj5ve | Universidade Federal de Viçosa | 2 | 2020 | Neilier Junior 2020. Enzymatic Assay of Protease Using Azocasein as Substrate. protocols.io dx.doi.org/10.17504/protocols.io.bhqnj5ve | 2021-03-29 03:10:28 | |||||
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The role of multiprotein bridging factor 1 (MBF1c) in Funariaceae species under salt stress Resource Report Resource Website |
Maria Victória Magalhães de Vargas, Guilherme Afonso Kessler de Andrade, Sara Navarrete Bohi Goulart, Bruna Mota Bernardes, Filipe Victoria | 10.17504/protocols.io.be3sjgne | Bryophytes are one of the most successful plants in nature and can tolerate several environmental stresses, such as saline stress. MBF1 is a transcription factor that may be involved in reprogramming transcription, which in turn may confer tolerance to stress conditions. The objective of this study was to quantify PaMBF1c under saline stress in three species of moss:Funaria hygrometrica,Physcomitrium acutifolium, andPhyscomitrella patens. All moss species underwent 12 h and 24 h treatment with salt at different concentrations, followed by qRT-PCR experiments.In F. hygrometrica, the MBF1c gene was up-regulated when subjected to 12 h salt treatment at a medium concentration, and may be an important factor for the tolerance of plants to NaCl concentrations. InP. acutifolium,24 h NaCl treatment at of 400, 600, and 800 mM resulted in a gradual up-regulation of MBF1c expression, reflective of the increasing NaCl concentration. InPhyscomitrella,the expression profile of MBF1c showed a down-regulation when treated with 200, 400, and 800 mM NaCl, suggesting that MBF1c may not interfere with the saline stress response in this plant.The diversity of these expression profiles demonstrate that the MBF1c response is not universal neither among plants nor between species of the same family, as shown in the mosses studied. | Núcleo de Estudos da Vegetação Antártica (NEVA), Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, Brazil; [email protected], Núcleo de Estudos da Vegetação Antártica (NEVA), Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, Brazil; [email protected], Núcleo de Estudos da Vegetação Antártica (NEVA), Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, Brazil; [email protected], Núcleo de Estudos da Vegetação Antártica (NEVA), Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, Brazil; [email protected], Núcleo de Estudos da Vegetação Antártica (NEVA), Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, Brazil; [email protected] | 1 | 2020 | Maria Victória Magalhães de Vargas, Guilherme Afonso Kessler de Andrade, Sara Navarrete Bohi Goulart, Bruna Mota Bernardes, Filipe Victoria 2020. The role of multiprotein bridging factor 1 (MBF1c) in Funariaceae species under salt stress. protocols.io dx.doi.org/10.17504/protocols.io.be3sjgne | 2021-03-29 03:10:30 | ||||
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Adult mouse kidney dissociation (on ice) Resource Report Resource Website |
Andrew Potter | 10.17504/protocols.io.rnmd5c6 | Human Cell Atlas Method Development Community | Protocol for adult (8-10 week) mouse kidney dissociation performed on ice to reduce artifact gene expression. The first layer, consisting of collagenase digestion, breaks down the tissue and releases some cells and glomeruli and tubules. The second layer consists of bacillus licheniformis digestion for 15 min. augmented with a thermomixer at 1400 RPM and passaging with a 27 gauge needle. The second layer is meant to thoroughly break up remaining tubules and glomeruli, releasing cells such as podocytes. The final yield is 250K cells from 18 mg tissue with 98% viability, approximately 14,000 cells/mg tissue. Approximately 1% of released cells are podocytes (visualized using kidneys from MAFB-GFP+ mice using a hemocytometer). | Cincinnati Children's Hospital Medical Center | 6 | 2018 | Andrew Potter 2018. Adult mouse kidney dissociation (on ice). protocols.io dx.doi.org/10.17504/protocols.io.rnmd5c6 | 2021-03-29 03:10:28 | |||
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Starting a MinION sequencing run using MinKNOW Resource Report Resource Website |
Josh Quick | 10.17504/protocols.io.7q6hmze | Diaz-Munoz Lab, Coronavirus Method Development Community, Szentagothai Research Centre Virology | Fernández-Rodríguez A, Casas I, Culebras E, Morilla E, Cohen MC, Alberola J, COVID-19 and post-mortem microbiological studies. Spanish Journal of Legal Medicine doi: 10.1016/j.remle.2020.05.007 | University of Birmingham | https://doi.org/10.1016/j.remle.2020.05.007 | 1 | 2019 | Josh Quick 2019. Starting a MinION sequencing run using MinKNOW. protocols.io dx.doi.org/10.17504/protocols.io.7q6hmze | 2021-03-29 03:10:28 | ||
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Transcriptomics During One-Step Growth Curves for Cellulophaga Phages Resource Report Resource Website |
Matthew Sullivan | 10.17504/protocols.io.dem3c5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Transcriptomics During One-Step Growth Curves for Cellulophaga Phages. protocols.io dx.doi.org/10.17504/protocols.io.dem3c5 | 2021-03-29 03:10:30 | ||||
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622.2 URMC HTC Rapid Clearing of Thick Human Lung Tissue Sections Resource Report Resource Website |
Cory Poole, Gloria Pryhuber | 10.17504/protocols.io.7d7hi9n | Optical Clearing of Tissue | Purpose and Scope of the Procedure: Provide a relatively rapid clearing of lung tissue sections up to 1 millimeter thick for immunofluorescence staining and imaging with confocal or multiphoton microscopy.Current protocol is limited to tissue sections that are free from severe hemorrhage/thrombosis, containing mostly parenchyma, vessels, and smaller bronchioles. Times and solution volumes may need to be altered slightly if one wishes to clear sections containing a lot of cartilage and/or blood.Scientific Principles: One of the major challenges in conventional brightfield, epifluorescence, and even confocal microscopy is the limitation in imaging depth. This is primarily due to the scattering and absorption of light within the sample of both the excitation light and the emission light leading to a drastic reduction in the image brightness and contrast when deeper than a 100µm. Clearing offers a way around this by both reducing the components that negatively impact the light and by matching the refractive index of the mounting medium to that of the components which make up the tissue, leading to an almost transparent appearance.This protocol is a slight modification of a Clear Unobstructed Brain/Body Imaging Cocktail (CUBIC) protocol described by Kubota et al. developed originally to allow the analysis of cancer metastasis within the bodies of entire mice. By taking advantage of the fact lung tissue has plenty of open spaces and a very large surface area we can reduce the time in each of the solutions to allow complete clearing of the tissue sections to within just a few days.References:·Light Microscopy Methods and Protocols (2017). p. 74·Kubota et al., (2017). Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution.Cell Reports 20, 236–250 | University of Rochester, University of Rochester Medical Center | 1 | 2020 | Cory Poole, Gloria Pryhuber 2020. 622.2 URMC HTC Rapid Clearing of Thick Human Lung Tissue Sections. protocols.io dx.doi.org/10.17504/protocols.io.7d7hi9n | 2021-03-29 03:10:30 | |||
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RNA isolation and cDNA synthesis from the marine ichthyosporean Sphaeroforma arctica Resource Report Resource Website |
Sebastian Najle | 10.17504/protocols.io.wqdfds6 | Multicellgenomelab | This protocol describes the steps for isolation of total RNA for cDNA synthesis in the marine Ichthyosporean Sphaeroforma arctica. In general, Ichthysoporeans are characterized by having a thick cell wall, of uncknown composition, that is particularly hard to brake, making cell lysis difficult. Here we have introduce a simple modification on the conventional RNA extraction protocol using TRIzol reagent, by including two cycles of freezing-tawing of the cells-TRIzol suspension, in order to facilitate cell lysis. This modification improved significantly the RNA isolation yield. Total RNA is further treated with DNAse I enzyme and purified by precipitation to minimize genomic DNA contamination. Highly pure total RNA is then used to synthetize cDNA for downstream applications. .justify:after { content: ""; display:inline-block; width: 100%; } .justify:after { content: ""; display:inline-block; width: 100%; } | Ocaña-Pallarès E, Najle SR, Scazzocchio C, Ruiz-Trillo I (2019) Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway. PLoS Genet 15(2): e1007986. doi: 10.1371/journal.pgen.1007986 | Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra) | https://doi.org/10.1371/journal.pgen.1007986 | 1 | 2019 | Sebastian Najle 2019. RNA isolation and cDNA synthesis from the marine ichthyosporean Sphaeroforma arctica. protocols.io dx.doi.org/10.17504/protocols.io.wqdfds6 | 2021-03-29 03:10:30 | |
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Western Blot Detection using Licor NIR Fluorescence - CHEM 584 Resource Report Resource Website |
Ken Christensen | 10.17504/protocols.io.bj9ckr2w | Brigham Young University | 1 | 2020 | Ken Christensen 2020. Western Blot Detection using Licor NIR Fluorescence - CHEM 584 . protocols.io dx.doi.org/10.17504/protocols.io.bj9ckr2w | 2021-03-29 03:10:31 | |||||
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Introduction to Prokaryotic gene prediction (CDS and rRNA) Resource Report Resource Website |
Frank Aylward | 10.17504/protocols.io.pigdkbw | Virginia Tech | 1 | 2018 | Frank Aylward 2018. Introduction to Prokaryotic gene prediction (CDS and rRNA). protocols.io dx.doi.org/10.17504/protocols.io.pigdkbw | 2021-03-29 03:10:31 | |||||
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Parabodo caudatus post-electroporation cell viability quantification using exponential decay electroporation Resource Report Resource Website |
Fatma Gomma, Paulo A. Garcia, Jennifer Delaney, Peter R. Girguis, Cullen R. Buie, Virginia P. Edgcomb | 10.17504/protocols.io.hmhb436 | Protist Research to Optimize Tools in Genetics (PROT-G) | The process of developing transient transfection protocols in P. caudatus involved initial testing and determination of proper electroporation buffers and parameters (voltage strength, pulse duration and number) to maximize cell viability. Our results suggest that the type of electroporation buffer is critical for maintaining cell viability throughout the experiment and is essential for determining the optimum electric field range. | Woods Hole Oceanographic Institute, MIT, Harvard, Woods Hole Oceanographic Institute, MIT, Harvard, Woods Hole Oceanographic Institute, MIT, Harvard, Woods Hole Oceanographic Institute, MIT, Harvard, Woods Hole Oceanographic Institute, MIT, Harvard, Woods Hole Oceanographic Institute, MIT, Harvard | 3 | 2017 | Fatma Gomma, Paulo A. Garcia, Jennifer Delaney, Peter R. Girguis, Cullen R. Buie, Virginia P. Edgcomb 2017. Parabodo caudatus post-electroporation cell viability quantification using exponential decay electroporation. protocols.io dx.doi.org/10.17504/protocols.io.hmhb436 | 2021-03-29 03:10:31 | |||
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Vandy – Bile Diversion in Mice Resource Report Resource Website |
Vance L. Albaugh | 10.17504/protocols.io.zdcf22w | Mouse Metabolic Phenotyping Centers | This is the protocol for conducting the bile diversion procedure in the mouse. In this procedure the common bile duct is ligated proximal to the confluence of the common bile and the pancreatic ducts and an anastomosis is created at a prespecified point along the gastrointestinal tract to re-establish drainage of the biliary tree. | Vanderbilt University | https://mmpc.org/shared/document.aspx?id=293&docType=Protocol | 1 | 2019 | Vance L. Albaugh 2019. Vandy – Bile Diversion in Mice. protocols.io dx.doi.org/10.17504/protocols.io.zdcf22w | 2021-03-29 03:10:31 | ||
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Single-cell suspensions from primary human esophagus tissue Resource Report Resource Website |
Annette Hayden, Rob Walker, Jack Harrington, Lucy Kimbley, Sara Waise, Chris Hanley, Gareth Thomas, Peter Johnson, Jonathan West, Matthew Rose Zerilli, TIm Underwood | 10.17504/protocols.io.t9ver66 | CZI START Project | A protocol to dissociate fresh esophagus tissue specimens for single-cell transcriptomics. | Cancer Sciences Unit, University of Southampton, Cancer Sciences Unit, University of Southampton, Cancer Sciences Unit, University of Southampton, Cancer Sciences Unit, University of Southampton, Cancer Sciences Unit, University of Southampton, Cancer Sciences Unit, University of Southampton, Cancer Sciences Unit, University of Southampton, Cancer Sciences Unit, University of Southampton, Cancer Sciences Unit, University of Southampton, Cancer Sciences, Faculty of Medicine, University of Southampton, Cancer Sciences Unit, University of Southampton | https://www.southampton.ac.uk/medicine/about/staff/tju.page | 1 | 2021 | Annette Hayden, Rob Walker, Jack Harrington, Lucy Kimbley, Sara Waise, Chris Hanley, Gareth Thomas, Peter Johnson, Jonathan West, Matthew Rose Zerilli, TIm Underwood 2021. Single-cell suspensions from primary human esophagus tissue. protocols.io dx.doi.org/10.17504/protocols.io.t9ver66 | 2021-03-29 03:10:31 | ||
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ND5 sequencing of Oncorhynchus masou masou Resource Report Resource Website |
Yoko Kato-Unoki | 10.17504/protocols.io.bmf7k3rn | Kato-Unoki Y, Umemura K, Tashiro K (2020) Fingerprinting of hatchery haplotypes and acquisition of genetic information by whole-mitogenome sequencing of masu salmon, Oncorhynchus masou masou, in the Kase River system, Japan. PLoS ONE 15(11): e0240823. doi: 10.1371/journal.pone.0240823 | Center for Advanced Instrumental and Educational Supports, Faculty of Agriculture, Kyushu University, Fukuoka, Japan | https://doi.org/10.1371/journal.pone.0240823 | 1 | 2020 | Yoko Kato-Unoki 2020. ND5 sequencing of Oncorhynchus masou masou. protocols.io dx.doi.org/10.17504/protocols.io.bmf7k3rn | 2021-03-29 03:10:31 | |||
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Euplotes transfection using Lipofectamine 3000 (provisional) Resource Report Resource Website |
Angela Piersanti | 10.17504/protocols.io.hhub36w | Protist Research to Optimize Tools in Genetics (PROT-G) | University of Camerino | 2 | 2017 | Angela Piersanti 2017. Euplotes transfection using Lipofectamine 3000 (provisional). protocols.io dx.doi.org/10.17504/protocols.io.hhub36w | 2021-03-29 03:08:45 |
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