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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Transplanting Tobacco Seedlings in the Greenhouse Resource Report Resource Website |
Lynn Doran | Ag SynBio Lab UIUC | Realizing Increased Photosynthetic Efficiency (RIPE) | 2 | 2021 | Lynn Doran 2021. Transplanting Tobacco Seedlings in the Greenhouse. protocols.io https:// | 2021-04-15 09:14:27 | |||||
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Human Trajectory Sampling at the City-Day Scale Resource Report Resource Website |
John Palmer | DOI:10.17504/protocols.io.njgdcjw | A protocol for sampling people for purposes of understanding patterns of mobility and activity-space segregation at the scale of city-days. | Universitat Pompeu Fabra | http://activityspaceproject.com/ | 1 | 2018 | John Palmer 2018. Human Trajectory Sampling at the City-Day Scale. protocols.io https://dx.doi.org/10.17504/protocols.io.njgdcjw | 2021-04-15 09:14:30 | |||
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Protocolo de avaliação clínica audiológica para crianças com microcefalia Resource Report Resource Website |
Klinger Vagner Teixeira Da Costa, Luis Pedro Coelho | DOI:10.17504/protocols.io.5czg2x6 | Trata-se de uma ficha de anamneses direcionada para avaliação audiológica em crianças com a síndrome congênita do vírus da Zica. | Universidade Federal de Alagoas, Universidade Federal de Alagoas | 1 | 2019 | Klinger Vagner Teixeira Da Costa, Luis Pedro Coelho 2019. Protocolo de avaliação clínica audiológica para crianças com microcefalia. protocols.io https://dx.doi.org/10.17504/protocols.io.5czg2x6 | 2021-04-15 09:14:25 | ||||
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR ORF1ab 2020 Resource Report Resource Website |
Judy Northill, Ian Mackay | DOI:10.17504/protocols.io.bgtmjwk6 | Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community | A real-time RT-PCR to specifically detect SARS-CoV-2 betacoronavirus also called nCoV-2019 or Wuhan seafood market pneumonia virus. Based on sequence MN908947 made available by Professor Yong-Zhen Zhang, Fudan University, Shanghai, China. The target region is within the ORF1ab sequence.NotesAssay is fully optimised (as of 24Jan2020).This test has identified a clinical positive cases of coronavirus disease (COVID-19) | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 1 | 2020 | Judy Northill, Ian Mackay 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR ORF1ab 2020. protocols.io https://dx.doi.org/10.17504/protocols.io.bgtmjwk6 | 2021-04-15 09:14:24 | |||
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Dephosphorylation using AnP (M0289) Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.cdns5d | New England Biolabs (NEB) | This is the protocol for dephosphorylation of 5'-ends of DNA using AnP (Antarctic Phosphatase - M0289). | New England Biolabs | https://www.neb.com/protocols/1/01/01/vector-dephosphorylation-protocol | 1 | 2014 | New England Biolabs 2014. Dephosphorylation using AnP (M0289). protocols.io https://dx.doi.org/10.17504/protocols.io.cdns5d | 2021-04-15 09:14:24 | ||
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Isolation of Artemia nauplii for DNA extraction Resource Report Resource Website |
Dave Lunt | DOI:10.17504/protocols.io.ifbcbin | EvoHull | Nauplii, ie newly hatched Artmemia (3-5 days), are processed to concentrate and separate from the eggs, before a DNA extraction | EvoHull Group, University of Hull, UK | 1 | 2017 | Dave Lunt 2017. Isolation of Artemia nauplii for DNA extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.ifbcbin | 2021-04-15 09:14:27 | |||
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Teacher Sense of Efficacy Scale Short Form Resource Report Resource Website |
Kevin Crouse | DOI:10.17504/protocols.io.2j2gcqe | Teachers’ Sense of Efficacy is the beliefs in their capability to make a difference in student learning, to be able to get through even to students who are difficult or unmotivatedd. The Teacher Sense of Efficacy Scale asks teachers to assess their capability concerning instructional strategies, student engagement, and classroom management.This protocol taken from Megan Tschannen-Moran's classic work on Teacher Self-Efficacy. | Rutgers University | http://wmpeople.wm.edu/asset/index/mxtsch/tsesshort | 1 | 2020 | Kevin Crouse 2020. Teacher Sense of Efficacy Scale Short Form. protocols.io https://dx.doi.org/10.17504/protocols.io.2j2gcqe | 2021-04-15 09:14:24 | |||
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Zobell Broth Resource Report Resource Website |
Sarah Hessen-Schmidt | DOI:10.17504/protocols.io.e7wbhpe | University of Southern California | 1 | 2016 | Sarah Hessen-Schmidt 2016. Zobell Broth. protocols.io https://dx.doi.org/10.17504/protocols.io.e7wbhpe | 2021-04-15 09:14:23 | |||||
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Overviews on adverse events in pharmacological interventions Resource Report Resource Website |
Elena Dorando, Thilo Sachse, Tim Mathes, Simone Heß, Petra Thürmann, Sven Schmiedl, Salmaan Kanji, Carole Lunny, Pierre Thabet, Dawid Pieper | DOI:10.17504/protocols.io.bfgqjjvw | Please find detailed information on our protocol in the attached PDF file. | Institute for Research in Operative Medicine, Witten/Herdecke University, Germany, Institute for Research in Operative Medicine, Witten/Herdecke University, Germany, Institute for Research in Operative Medicine, Witten/Herdecke University, Germany, Institute for Research in Operative Medicine, Witten/Herdecke University, Germany, Philipp Klee-Institute of Clinical Pharmacology, Helios University Hospital Wuppertal, Witten/Herdecke University, Germany, Philipp Klee-Institute of Clinical Pharmacology, Helios University Hospital Wuppertal, Witten/Herdecke University, Germany, The Ottawa Hospital and Ottawa Hospital Research Institute, Ottawa, Ontario, Canada, Cochrane Hypertension Group and the Therapeutics Initiative, Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, Canada, Hôpital Montfort, Ottawa, Ontario, Canada, Institute for Research in Operative Medicine, Witten/Herdecke University, Germany | 1 | 2020 | Elena Dorando, Thilo Sachse, Tim Mathes, Simone Heß, Petra Thürmann, Sven Schmiedl, Salmaan Kanji, Carole Lunny, Pierre Thabet, Dawid Pieper 2020. Overviews on adverse events in pharmacological interventions. protocols.io https://dx.doi.org/10.17504/protocols.io.bfgqjjvw | 2021-04-15 09:14:25 | ||||
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SPARC Pig2 acute wired ColoMOCA implantation Resource Report Resource Website |
Brett Hanzlicek, Dennis Bourbeau, Margot Damaser | DOI:10.17504/protocols.io.bfxgjpjw | SPARC | In this study, we will be using Yorkshire Pigs, 50-70kg. The purpose of this study is to develop a tool to measure bowel fullness and activity. This system will eventually be able to provide continuous, wireless, battery−powered data and ultimately be translated for use in research and clinicalapplications of bowel function. We will measure porcine bowel compliance, pressures, and dimensions in acute live animal studies. | Advanced Platform Technology Center, Louis Stokes VA Hospital, Cleveland, Ohio, MetroHealth Medical Center, Cleveland, Ohio, Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio | 1 | 2021 | Brett Hanzlicek, Dennis Bourbeau, Margot Damaser 2021. SPARC Pig2 acute wired ColoMOCA implantation. protocols.io https://dx.doi.org/10.17504/protocols.io.bfxgjpjw | 2021-04-15 09:14:30 | |||
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Mobile Device Quantification of Lateral Flow Tests: Modular illumination and sensor chamber (US patent US20160131592A1) Resource Report Resource Website |
Don Cooper | DOI:10.17504/protocols.io.bmmwk47e | Neuroganics Diagnostics LLC | 1 | 2020 | Don Cooper 2020. Mobile Device Quantification of Lateral Flow Tests: Modular illumination and sensor chamber (US patent US20160131592A1). protocols.io https://dx.doi.org/10.17504/protocols.io.bmmwk47e | 2021-04-15 09:14:29 | |||||
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Cantilever functionalisation for AFM single molecule force spectroscopy Resource Report Resource Website |
Stefania Marcotti, Koichiro Maki, Gwendolen C Reilly, Damien Lacroix, Taiji Adachi | DOI:10.17504/protocols.io.ra4d2gw | Four different samples were employed for experiments, designed as follows:HABP/HA: cantilever functionalised with hyaluronic acid binding protein, untreated cell sample;BSA/HA: cantilever functionalised with bovine serum albumin, untreated cell sample;untreated/HA: non-functionalised cantilever, untreated cell sample;HABP/HAase: cantilever functionalised with hyaluronic acid binding protein, cell sample treated with HAaseThe steps of activation are listed in this protocol and were the same for Sample 1 (HABP/HA, functionalisation molecule: hyaluronic acid binding protein), Sample 2 (BSA/HA, functionalisation molecule: bovine serum albumin) and Sample 4 (HABP/HAase, functionalisation molecule: hyaluronic acid binding protein). The cantilevers used to test cells in Sample 3 (untreated/HA) were not treated.Similar protocols were described in:* Maki K et al. Mechano-adaptive sensory mechanism of α-catenin under tension. Sci Rep 2016;6: 24878. doi:10.1038/srep24878* Maki K et al. Real-time TIRF observation of vinculin recruitment to stretched α-catenin by AFM. Sci Rep 2018;8: 1–8. doi:10.1038/s41598-018-20115-8 | Marcotti S, Maki K, Reilly GC, Lacroix D, Adachi T (2018) Hyaluronic acid selective anchoring to the cytoskeleton: An atomic force microscopy study. PLoS ONE 13(10): e0206056. doi: 10.1371/journal.pone.0206056 | University of Sheffield, University of Tokyo, University of Sheffield, University of Sheffield, Kyoto University | https://doi.org/10.1371/journal.pone.0206056 | 1 | 2018 | Stefania Marcotti, Koichiro Maki, Gwendolen C Reilly, Damien Lacroix, Taiji Adachi 2018. Cantilever functionalisation for AFM single molecule force spectroscopy. protocols.io https://dx.doi.org/10.17504/protocols.io.ra4d2gw | 2021-04-15 09:14:30 | ||
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Isolation, culturing, and cryopreservation of Endozoicomonas (Gammaproteobacteria: Oceanospirillales: Endozoicomonadaceae) from reef-building corals Resource Report Resource Website |
Claudia Pogoreutz, Christian Voolstra | DOI:10.17504/protocols.io.t2aeqae | reefgenomics, Aiptasia-Symbiodiniaceae Model System | Endozoicomonas are gram-negative bacteria widely and often abundantly associated with marine invertebrates and fish (Yang et al., 2010; Bayer et al., 2013; Nishijima et al., 2013; Hyun et al., 2014; Katharios et al., 2015; Ding et al., 2016; Neave et al., 2017a; Schreiber et al., 2016; Pogoreutz et al., 2018). Despite their ubiquitous distribution, only few cultured strains are available, as Endozoicomonasare supposedly difficult to isolate and to maintain in pure cultures (Neave et al., 2017b). Here we detail a protocol that allowed us to reproducibly isolate Endozoicomonasfrom stony corals (Acropora humilis) from the Red Sea. This protocol should be useful in isolating abundant Endozoicomonasfrom other corals or marine invertebrates.ReferencesBayer, T., Neave, M.J., Alsheikh-Hussain, A., Aranda, M., Yum, L.K., Mincer, T., et al. (2013) The microbiome of the Red Sea coral Stylophora pistillatais dominated by tissue-associated Endozoicomonasbacteria. Appl. Environ. Microbiol.79: 4759–4762.Ding, J.Y., Shiu, J.H., Chen, W.M., Chiang, Y.R., and Tang, S.L. (2016) Genomic insight into the host-endosymbiont relationship of Endozoicomonas montiporaeCL-33T with its coral host. Front. Microbiol.7: 251.Hyun, D.W., Shin, N.R., Kim, M.S., Oh, S.J., Kim, P.S., Whon, T.W., and Bae, J.W. (2014) Endozoicomonas atrinaesp. nov., isolated from the intestine of a comb pen shell Atrina pectinata. Int. J. Syst. Evol. Microbiol.64: 2312–2318.Katharios, P., Seth-Smith, H.M.B., Fehr, A., Mateos, J.M., Qi, W., Richter, D., et al. (2015) Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: Striking genomic and morphological features of novel Endozoicomonassp. Sci. Rep.5: 1–13.Neave, M.J., Michell, C.T., Apprill, A., and Voolstra, C.R. (2017a) Endozoicomonasgenomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts. Sci. Rep.7: 40579.Neave, M. J., Apprill, A., Ferrier-Pagès, C., & Voolstra, C. R. (2016) Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas. App. Microbiol. Biotech., 100:8315-8324.Neave, M.J., Rachmawati, R., Xun, L., Michell, C.T., Bourne, D.G., Apprill, A., and Voolstra, C.R. (2017b) Differential specificity between closely related corals and abundant Endozoicomonasendosymbionts across global scales. ISMEJ 11: 186-200.Nishijima, M., Adachi, K., Katsuta, A., Shizuri, Y., and Yamasato, K. (2013) Endozoicomonas numazuensissp. nov., a gammaproteobacterium isolated from marine sponges, and emended description of the genus EndozoicomonasKurahashi and Yokota 2007. Int. J. Syst. Evol. Microbiol.63: 709–714.Pogoreutz, C., Rädecker, N., Cárdenas, A., Gärdes, A., Wild, C., and Voolstra, C.R. (2018) Dominance of Endozoicomonasbacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosamicrobiome.Ecol. Evol.8: 2240–2252.Schreiber, L., Kjeldsen, K.U., Funch, P., Jensen, J., Obst, M., Lopez-Legentil, S., and Schramm, A. (2016) Endozoicomonasare specific, facultative symbionts of sea squirts. Front. Microbiol. 7: 1–15.Yang, C.-S., Chen, M.-H., Arun, A.B., Chen, C.A., Wang, J.-T., and Chen, W.-M. (2010) Endozoicomonas montiporaesp. nov., isolated from the encrusting pore coral Montipora aequituberculata. Int. J. Syst. Evol. Microbiol.60: 1158–1162. | University of Konstanz, King Abdullah University of Science and Technology | 1 | 2018 | Claudia Pogoreutz, Christian Voolstra 2018. Isolation, culturing, and cryopreservation of Endozoicomonas (Gammaproteobacteria: Oceanospirillales: Endozoicomonadaceae) from reef-building corals. protocols.io https://dx.doi.org/10.17504/protocols.io.t2aeqae | 2021-04-15 09:14:30 | |||
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Gait analysis using augmented reality markers Resource Report Resource Website |
Gergely Nagymáté, Rita M Kiss | DOI:10.17504/protocols.io.qkzdux6 | The protocol provides guidelines, preparation and execution instructions to perform and process a gait analysis trial by a novel motion capture method using virtually calibrated anatomical points tracked by augmented reality (AR) markers. | Department of Mechatronics, Optics and Mechanical Engineering Informatics, Budapest University of Technology and Economics, Department of Mechatronics, Optics and Mechanical Engineering Informatics, Budapest University of Technology and Economics | 1 | 2018 | Gergely Nagymáté, Rita M Kiss 2018. Gait analysis using augmented reality markers. protocols.io https://dx.doi.org/10.17504/protocols.io.qkzdux6 | 2021-04-15 09:14:30 | ||||
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Pour plating of Thalassiosira pseudonana (Tp) Resource Report Resource Website |
Jernej Turnsek, Chris Dupont | DOI:10.17504/protocols.io.jfncjme | Protist Research to Optimize Tools in Genetics (PROT-G) | Here we present an efficient way to grow Tp colonies inside a 0.25% superclean agar matrix. This protocol could possibly be applicable to other marine microeukaryotes that are problematic to grow on fully solid support. | University of California, Berkeley, J. Craig Venter Institute | 3 | 2017 | Jernej Turnsek, Chris Dupont 2017. Pour plating of Thalassiosira pseudonana (Tp). protocols.io https://dx.doi.org/10.17504/protocols.io.jfncjme | 2021-04-15 09:14:30 | |||
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ChroSpin - ProteinA/G Resource Report Resource Website |
David Frommholz, Alexandra Ehl, Nadine Stefanczyk | DOI:10.17504/protocols.io.vvte66n | Purification Guide for the Isolation of Antibodies with ChroSpin Columns by DALEX Biotech.Easy and quick small scale antibody purification from various sources and species.Each ChroSpin column has a binding capacity of > 2 mg (tested with human polyclonal Ig, binding varies between species and clones).The proprietary resin does not shrink or swell in aqueous buffers.High pressure stability.pH stability short term 2 - 8, long term 3 - 8.Excellent thermal stability up to 15 minutes at 80 °C in aqueous buffers at neutral pH.Can be dried for long term storage (80 °C for > 2 h). | DALEX Biotech, DALEX Biotech, DALEX Biotech | https://dalex-biotech.com/ | 1 | 2018 | David Frommholz, Alexandra Ehl, Nadine Stefanczyk 2018. ChroSpin - ProteinA/G. protocols.io https://dx.doi.org/10.17504/protocols.io.vvte66n | 2021-04-15 09:14:25 | |||
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Modified 1D Native Barcoding genomic DNA protocol from the Temperton Lab (University of Exeter) Resource Report Resource Website |
Michael Henson, Ben Temperton, Cameron Thrash | DOI:10.17504/protocols.io.bixskfne | Thrash Lab | Modified 1D Native Barcoding genomic DNA protocol (v. NBE_9006_v103_revO_21Dec2016 for SQK-LSK108) from the Temperton Lab (University of Exeter) | University of Chicago, University of Exeter, University of Southern California | 1 | 2020 | Michael Henson, Ben Temperton, Cameron Thrash 2020. Modified 1D Native Barcoding genomic DNA protocol from the Temperton Lab (University of Exeter). protocols.io https://dx.doi.org/10.17504/protocols.io.bixskfne | 2021-04-15 09:14:24 | |||
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cGAS Enzymatic Assay – cGAMP Fluorescence Polarization Format Resource Report Resource Website |
Fabien Vincent | DOI:10.17504/protocols.io.jaycifw | Hall J, Brault A, Vincent F, Weng S, Wang H, Dumlao D, Aulabaugh A, Aivazian D, Castro D, Chen M, Culp J, Dower K, Gardner J, Hawrylik S, Golenbock D, Hepworth D, Horn M, Jones L, Jones P, Latz E, Li J, Lin L, Lin W, Lin D, Lovering F, Niljanskul N, Nistler R, Pierce B, Plotnikova O, Schmitt D, Shanker S, Smith J, Snyder W, Subashi T, Trujillo J, Tyminski E, Wang G, Wong J, Lefker B, Dakin L, Leach K (2017) Discovery of PF-06928215 as a high affinity inhibitor of cGAS enabled by a novel fluorescence polarization assay. PLoS ONE 12(9): e0184843. doi: 10.1371/journal.pone.0184843 | https://doi.org/10.1371/journal.pone.0184843 | 1 | 2017 | Fabien Vincent 2017. cGAS Enzymatic Assay – cGAMP Fluorescence Polarization Format. protocols.io https://dx.doi.org/10.17504/protocols.io.jaycifw | 2021-04-15 09:14:24 | ||||
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Home-made TOP10 competent heat-shock cells Resource Report Resource Website |
Magdalena Julkowska | DOI:10.17504/protocols.io.pbtdinn | Salt Lab KAUST | The standard protocol to propagate TOP10 Competent cells for Heatshock transformation method | King Abdullah University of Science and Technology | 1 | 2020 | Magdalena Julkowska 2020. Home-made TOP10 competent heat-shock cells. protocols.io https://dx.doi.org/10.17504/protocols.io.pbtdinn | 2021-04-15 09:14:28 | |||
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Addition of the adaptor to RNA substrates for 5′ RACE Resource Report Resource Website |
Matus Valach | DOI:10.17504/protocols.io.xsrfnd6 | Simple protocol for mapping 5′-P RNA termini by RT-PCR after the addition of a 5′ adaptor using T4 RNA ligase 1. | Université de Montréal, Montreal, Quebec, Canada | 1 | 2019 | Matus Valach 2019. Addition of the adaptor to RNA substrates for 5′ RACE. protocols.io https://dx.doi.org/10.17504/protocols.io.xsrfnd6 | 2021-04-15 09:14:28 |
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