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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Plasmid Sequence Analysis from Long Reads Resource Report Resource Website |
David Eccles | 10.17504/protocols.io.bqu3mwyn | This protocol demonstrates how to assemble reads from plasmid DNA, and generate a circularised and non-repetitive consensus sequenceAt the moment, this protocol uses Canu to de-novo assemble high-quality single-cut reads.Input(s): demultiplexed fastq files (see protocol Demultiplexing Nanopore reads with LAST). I've noticed that the default demultiplexing carried out by Guppy (at least up to v4.2.2, as used in the first version of this protocol) has issues with chimeric reads, which can affect assembly.Output(s):Consensus sequence per barcode as a fasta fileOutput(s): | Malaghan Institute of Medical Research (NZ) | 4 | 2020 | David Eccles 2020. Plasmid Sequence Analysis from Long Reads. protocols.io dx.doi.org/10.17504/protocols.io.bqu3mwyn | 2021-03-29 03:08:51 | ||||
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Using the Tecan Infinite M200 Pro plate reader for Symbiodiniaceae Biomass/Growth Estimates Resource Report Resource Website |
Samantha Coy | 10.17504/protocols.io.bkpqkvmw | Samantha R Coy's Protocols | This is a protocol for estimating Symbiodiniaceae biomass and growth based on fluorescence (chlorphyll-a). This is not directly comparable to cell counts, as fluorescence might vary depending on culturing conditions. | Rice University | 2 | 2020 | Samantha Coy 2020. Using the Tecan Infinite M200 Pro plate reader for Symbiodiniaceae Biomass/Growth Estimates. protocols.io dx.doi.org/10.17504/protocols.io.bkpqkvmw | 2021-03-29 03:08:51 | |||
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Running PCPipe (protein clustering) in iPlant Resource Report Resource Website |
Bonnie Hurwitz, Ken Youens-Clark | 10.17504/protocols.io.ef8bbrw | VERVE Net, Hurwitz Lab | Hurwitz, Bonnie L., and Matthew B. Sullivan. "The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology." PLoS One 8.2 (2013): e57355. | University of Arizona, University of Arizona | 1 | 2016 | Bonnie Hurwitz, Ken Youens-Clark 2016. Running PCPipe (protein clustering) in iPlant. protocols.io dx.doi.org/10.17504/protocols.io.ef8bbrw | 2021-03-29 03:08:52 | |||
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Colloidal Coomassie Blue Stain: Recipe and Protocol Resource Report Resource Website |
Jeremy Kamil | 10.17504/protocols.io.bmmtk46n | I learned this Colloidal Coomassie Blue staining recipe and protocol when I was a postdoc at Harvard Medical School.. Rumor has it, a postdoc reverse engineered a “safe stain” from a leading commercial supplier. It’s a really great recipe: much more sensitive, faster, and easier to use than traditional methanol based coomassie staining protocols you see in Cold Spring Harbor books, like by Maniatis etc.. Saves a ton of money compared to buying this stuff from commercial vendors. It is downstream compatible with mass spec and most other things you'd want to do with gel slices. | Louisiana State University Health Sciences Center Shreveport | 1 | 2020 | Jeremy Kamil 2020. Colloidal Coomassie Blue Stain: Recipe and Protocol. protocols.io dx.doi.org/10.17504/protocols.io.bmmtk46n | 2021-03-29 03:08:52 | ||||
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Hydrochloric Acid-Potassium Chloride Buffer (HCl-KCl) Resource Report Resource Website |
Neilier Junior | 10.17504/protocols.io.bfycjpsw | A buffer solution has the function of resisting changes in pH even when adding powerful acids or bases. However, in the physiological environment the buffered system also provides cofactors for enzymatic reactions, critical salts and even essential nutrients for cells and tissues. Therefore, when trying to reproduce biological conditions in vitro, we must make the appropriate choice of the buffer. After all, it will provide the appropriate medium in which reactions will occur. | Universidade Federal de Viçosa | 1 | 2020 | Neilier Junior 2020. Hydrochloric Acid-Potassium Chloride Buffer (HCl-KCl). protocols.io dx.doi.org/10.17504/protocols.io.bfycjpsw | 2021-03-29 03:08:51 | ||||
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Screening of compounds for inhibition of Sporothix spp. growth Resource Report Resource Website |
luanaborba | 10.17504/protocols.io.bje9kjh6 | L. P. Borba-Santos | Borba-Santos LP, Vila T, Rozental S (2020) Identification of two potential inhibitors of Sporothrix brasiliensis and Sporothrix schenckii in the Pathogen Box collection. PLoS ONE 15(10): e0240658. doi: 10.1371/journal.pone.0240658 | Universidade Federal do Rio de Janeiro | https://doi.org/10.1371/journal.pone.0240658 | 1 | 2020 | luanaborba 2020. Screening of compounds for inhibition of Sporothix spp. growth. protocols.io dx.doi.org/10.17504/protocols.io.bje9kjh6 | 2021-03-29 03:08:51 | ||
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ESAW Media for Marine Phytoplankton Resource Report Resource Website |
Ashley Humphrey | 10.17504/protocols.io.f36bqre | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | University of Tennessee, Microbiology. | 1 | 2016 | Ashley Humphrey 2016. ESAW Media for Marine Phytoplankton. protocols.io dx.doi.org/10.17504/protocols.io.f36bqre | 2021-03-29 03:08:53 | ||||
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Production of AAV Virus by Iodixanol Gradient Ultracentrifugation Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.8dmhs46 | BICCN, Allen Institute for Brain Science | This protocol is used to produce AAV of any serotype with high purity and high titer. | Allen Institute | 2 | 2019 | Allen Institute for Brain Science 2019. Production of AAV Virus by Iodixanol Gradient Ultracentrifugation. protocols.io dx.doi.org/10.17504/protocols.io.8dmhs46 | 2021-03-29 03:08:53 | |||
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Protocol for DNA extraction from clay-rich subsoils Resource Report Resource Website |
Lukas Beule | 10.17504/protocols.io.bhmjj44n | Georg-August Universität Göttingen | 1 | 2020 | Lukas Beule 2020. Protocol for DNA extraction from clay-rich subsoils. protocols.io dx.doi.org/10.17504/protocols.io.bhmjj44n | 2021-03-29 03:08:52 | |||||
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Generation of DNA fragments by DNase digestion Resource Report Resource Website |
William H. Wilson and Declan Schroeder | 10.17504/protocols.io.dy47yv | VERVE Net | Generation of DNA fragments by DNase digestion involves digesting DNA for a range of times, then picking the time that gives optimal-sized DNA fragments (typically 1000–4000 bp). | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_134.pdf | 1 | 2016 | William H. Wilson and Declan Schroeder 2016. Generation of DNA fragments by DNase digestion. protocols.io dx.doi.org/10.17504/protocols.io.dy47yv | 2021-03-29 03:08:53 | ||
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Effect of ActiGraph’s LFE for estimating steps and physical activity intensity Resource Report Resource Website |
Yuri Feito, Lyndsey M. Hornbuckle, Lauren A. Reid, Scott E. Crouter | 10.17504/protocols.io.jfacjie | This study examined the effects of the ActiGraph’s (AG) low-frequency extension (LFE) filter on steps and physical activity classification in the free-living environment. Thirty-four African-American women (age, 24.5±5.2 years; BMI, 24.9±4.5 kg/m2) had daily activity measured simultaneously with an AG-GT3X+ accelerometer and a New Lifestyles NL-800 pedometer for seven days. Steps per day (steps/d) and time (minutes/day) spent in sedentary, light, and moderate-to-vigorous physical activity (MVPA) were examined with and without the LFE filter (AG-LFE and AG-N, respectively). The AG-LFE recorded more total steps (13,723±4,983 steps/d) compared to AG-N and NL-800 (6,172±2,838 and 5,817±3,037 steps/d, respectively; pppp | Kennesaw State University, University of Tennessee - Knoxville, University of South Carolina, University of Tennessee - Knoxville | 1 | 2017 | Yuri Feito, Lyndsey M. Hornbuckle, Lauren A. Reid, Scott E. Crouter 2017. Effect of ActiGraph’s LFE for estimating steps and physical activity intensity. protocols.io dx.doi.org/10.17504/protocols.io.jfacjie | 2021-03-29 03:08:52 | ||||
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Plasmid Cloning by PCR Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | 10.17504/protocols.io.43rgym6 | This protocol describes plasmid cloning by Polymerase Chain Reaction (PCR). To see the full abstract and additional resources, please visit the Addgene protocol page. | Addgene | https://www.addgene.org/protocols/pcr-cloning/ | 1 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. Plasmid Cloning by PCR. protocols.io dx.doi.org/10.17504/protocols.io.43rgym6 | 2021-03-29 03:08:53 | |||
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Mulheres na praça, saúde de graça: relato de experiência da equipe multiprofissional do grupo de mulheres do bairro Tamarindo Resource Report Resource Website |
Elis Sales Muniz Lima, Ana Cesarina Silva Gomes, Hyara Brena Oliveira Rufino, Jamile Xavier de Oliveira | 10.17504/protocols.io.bay4ifyw | , , , | 1 | 2020 | Elis Sales Muniz Lima, Ana Cesarina Silva Gomes, Hyara Brena Oliveira Rufino, Jamile Xavier de Oliveira 2020. Mulheres na praça, saúde de graça: relato de experiência da equipe multiprofissional do grupo de mulheres do bairro Tamarindo. protocols.io dx.doi.org/10.17504/protocols.io.bay4ifyw | 2021-03-29 03:08:53 | |||||
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Patch-Seq Internal Solution with Biocytin Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.9gih3ue | BICCN, Allen Institute for Brain Science | This SOP provides instruction to prepare Internal Solution which is used for patch clamp electrophysiology, modified for cleanliness and mRNA capture and sustainability. | Allen Institute | 1 | 2019 | Allen Institute for Brain Science 2019. Patch-Seq Internal Solution with Biocytin. protocols.io dx.doi.org/10.17504/protocols.io.9gih3ue | 2021-03-29 03:08:53 | |||
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Effect of Multiple Biofortified Food Crops-based Meals on Micronutrient Status and Immune Function in The First 1000 Days of Life in India: Study Protocol for a Randomized Controlled Feeding Trial Resource Report Resource Website |
Saurabh Mehta, Bryan Gannon, Camille E. Jones, Laura S. Hackl, Shoba A. Udipi, Varsha Thakker, Aparna Thorat, Wesley Bonam, Jere D. Haas, Julia Finkelstein | 10.17504/protocols.io.bqcmmsu6 | Mehta Research Group @ Cornell | Division of Nutritional Sciences, Cornell University, Ithaca NY 14853; Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca NY 14853, Division of Nutritional Sciences, Cornell University, Ithaca NY 14853; Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca NY 14853, Division of Nutritional Sciences, Cornell University, Ithaca NY 14853, Division of Nutritional Sciences, Cornell University, Ithaca NY 14853, Shreemati Nathibai Damodar Thackersey (SNDT) Women’s University, Mumbai, India; Kasturba Health Society, Medical Research Centre, Mumbai, India, Shreemati Nathibai Damodar Thackersey (SNDT) Women’s University, Mumbai, India; Kasturba Health Society, Medical Research Centre, Mumbai, India, Shreemati Nathibai Damodar Thackersey (SNDT) Women’s University, Mumbai, India; Kasturba Health Society, Medical Research Centre, Mumbai, India, Arogyavaram Medical Centre, Madanapalle, Andhra Pradesh, India, Division of Nutritional Sciences, Cornell University, Ithaca NY 14853, Division of Nutritional Sciences, Cornell University, Ithaca NY 14853; Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca NY 14853 | 1 | 2020 | Saurabh Mehta, Bryan Gannon, Camille E. Jones, Laura S. Hackl, Shoba A. Udipi, Varsha Thakker, Aparna Thorat, Wesley Bonam, Jere D. Haas, Julia Finkelstein 2020. Effect of Multiple Biofortified Food Crops-based Meals on Micronutrient Status and Immune Function in The First 1000 Days of Life in India: Study Protocol for a Randomized Controlled Feeding Trial. protocols.io dx.doi.org/10.17504/protocols.io.bqcmmsu6 | 2021-03-29 03:08:53 | ||||
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Human Parechovirus A real-time RT-PCR ["Nix assay"; 2017-] Resource Report Resource Website |
Ian Mackay | 10.17504/protocols.io.k2kcycw | This version is based on a recipe (see forked version) my team and I used this assay between 2008-2015; we dubbed it the 'Nix assay'. It targets the 5'UTR and employs quite degenerate oligos.In silico sequence alignments indicated the olignucleotides could theoretically detect aft least HPeV 1-7, 17 and 18. Further validation of this recipe is ongoing.However during a period of assay comparison, another assay (see link below), the 'Benschop assay' (J.Clin.Virol. 2008. 41(2):69-74), was found to produce more sigmoidal and higher curves and 1-5 cycle improvements to CT values when compared among the sample sampe extract set. | The University of Queensland | 4 | 2017 | Ian Mackay 2017. Human Parechovirus A real-time RT-PCR ["Nix assay"; 2017-]. protocols.io dx.doi.org/10.17504/protocols.io.k2kcycw | 2021-03-29 03:08:53 | ||||
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The Nanopore libraries preparation for the Scapharca broughtonii Resource Report Resource Website |
Chang-Ming Bai | 10.17504/protocols.io.z8bf9sn | This protocol is used to outline the process of Nanopore library preparation for Scapharca broughtonii genome. | Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences | 1 | 2019 | Chang-Ming Bai 2019. The Nanopore libraries preparation for the Scapharca broughtonii. protocols.io dx.doi.org/10.17504/protocols.io.z8bf9sn | 2021-03-29 03:08:53 | ||||
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Fermentor Growth of Streptococcus sanguinis Resource Report Resource Website |
Tanya Puccio, Todd Kitten | 10.17504/protocols.io.bkayksfw | Streptococcus sanguinis is a lactic acid-forming bacterium that can be cultured in both aerobic and anaerobic conditions. It is a primary colonizer of the oral cavity but can also cause a heart disease called infective endocarditis. Our main objective for this protocol was to grow large, controlled cultures before and after manganese depletion for various analyses. In order to obtain large scale, reproducible growth of S. sanguinis, a biostat was used to maintain controlled conditions. After optimization, it was determined that traditional chemostat conditions (Burne and Chen, 1998) were not appropriate for these experiments. Thus, we decided on this modified protocol. Using this method, we were able to identify a concentration of the non-specific metal chelator, EDTA, that would lead to a decreased growth rate in a manganese transporter mutant but not in the wild-type strain. | Philips Institute for Oral Health Research, Virginia Commonwealth University, Philips Institute for Oral Health Research, Virginia Commonwealth University | 1 | 2020 | Tanya Puccio, Todd Kitten 2020. Fermentor Growth of Streptococcus sanguinis. protocols.io dx.doi.org/10.17504/protocols.io.bkayksfw | 2021-03-29 03:08:52 | ||||
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Priming and loading a MinION flowcell Resource Report Resource Website |
Josh Quick | 10.17504/protocols.io.7q5hmy6 | 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. Priming and loading a MinION flowcell. protocols.io dx.doi.org/10.17504/protocols.io.7q5hmy6 | 2021-03-29 03:08:52 | ||
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Real-time Reverse Transcription Polymerase Chain Reaction (RT- qPCR) Resource Report Resource Website |
Izabela Rezende, Lívia Sacchetto | 10.17504/protocols.io.pw8dphw | MRCA | For investigate the presence of YFV genome by quantitative PCR assays in the hydrolysis probe detection format. The target is the 5’-noncoding region (5’-NC) of the YFV genome (Domingo et al., 2012). | Federal University of Minas Gerais - Laboratório de Vírus, Federal University of Minas Gerais - Laboratório de Vírus | 1 | 2018 | Izabela Rezende, Lívia Sacchetto 2018. Real-time Reverse Transcription Polymerase Chain Reaction (RT- qPCR). protocols.io dx.doi.org/10.17504/protocols.io.pw8dphw | 2021-03-29 03:08:52 |
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