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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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AAV Purification by Iodixanol Gradient Ultracentrifugation Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.bawqifdw | This protocol goes through AAV purification by Iodixanol gradient ultracentrifugation. To see the full abstract and additional resources, visit the Addgene protocol page.Sample Data | Addgene | https://www.addgene.org/protocols/aav-purification-iodixanol-gradient-ultracentrifugation/ | 2 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. AAV Purification by Iodixanol Gradient Ultracentrifugation. protocols.io https://dx.doi.org/10.17504/protocols.io.bawqifdw | 2021-04-15 09:14:44 | |||
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Protein Expression & Isolation & Purification Resource Report Resource Website |
Caroline Green | DOI:10.17504/protocols.io.fwvbpe6 | 1 | 2016 | Caroline Green 2016. Protein Expression & Isolation & Purification. protocols.io https://dx.doi.org/10.17504/protocols.io.fwvbpe6 | 2021-04-15 09:14:42 | ||||||
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Fluorescent caspase-3 staining to assess induction of apoptosis in A6 cells (Plos One) Resource Report Resource Website |
Elin Verbrugghe | DOI:10.17504/protocols.io.8tihwke | The largest current disease-induced loss of vertebrate biodiversity is due to chytridiomycosis and despite the increasing understanding of the pathogenesis, knowledge unravelling the early host-pathogen interactions remains limited. Batrachochytrium dendrobatidis (Bd)zoospores attach to and invade the amphibian epidermis, with subsequent invasive growth in the host skin. Availability of an in vitro assay would facilitate in depth study of this interaction while reducing the number of experimental animals needed. We describe a fluorescent cell-based in vitro infection model that reproduces host-Bd interactions. Using primary keratinocytes from Litoria caerulea and the epithelial cell line A6 from Xenopus laevis, we reproduced different stages of host cell infection and intracellular growth of Bd, resulting in host cell death, a key event in chytridiomycosis. The presented in vitro models may facilitate future mechanistic studies of host susceptibility and pathogen virulence. | Verbrugghe E, Rooij PV, Favoreel H, Martel A, Pasmans F (2019) In vitro modeling of Batrachochytrium dendrobatidis infection of the amphibian skin. PLoS ONE 14(11): e0225224. doi: 10.1371/journal.pone.0225224 | Ghent University, Faculty of Veterinary Medicine, Wildlife Health Ghent | https://doi.org/10.1371/journal.pone.0225224 | 1 | 2019 | Elin Verbrugghe 2019. Fluorescent caspase-3 staining to assess induction of apoptosis in A6 cells (Plos One). protocols.io https://dx.doi.org/10.17504/protocols.io.8tihwke | 2021-04-15 09:14:32 | ||
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Isolated astrocyte culture - protocol 2 Resource Report Resource Website |
Yasmin Bar El | DOI:10.17504/protocols.io.tqcemsw | An alternative protocol for isolated astrocyte cell culture preparation. Dissociation, preparation and plating of mice cortex neurons and glia cells on flasks. Isolatioin process of the culture from neurons, to obtain an isolated astrocyte culture. Plating isolated astrocytes on MEA. | School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv, Israel | 1 | 2018 | Yasmin Bar El 2018. Isolated astrocyte culture - protocol 2. protocols.io https://dx.doi.org/10.17504/protocols.io.tqcemsw | 2021-04-15 09:14:44 | ||||
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DNA extraction from plants Resource Report Resource Website |
Remco Stam | DOI:10.17504/protocols.io.eusbewe | Plantae, Stam Lab | Widely used protocol to extract DNA from plant leaves.Many versions circulate on the web, this is the version as we use it.It works well on maize, tomato and probably many other plants. | Technical University of Munich | 1 | 2016 | Remco Stam 2016. DNA extraction from plants. protocols.io https://dx.doi.org/10.17504/protocols.io.eusbewe | 2021-04-15 09:14:42 | |||
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Trace Metal Solution for ESAW Media Resource Report Resource Website |
Ashley Humphrey | DOI:10.17504/protocols.io.ge8bthw | Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | Trace metals solution to be used in ESAW Media for Marine Phytoplankton | University of Tennessee, Knoxville | 2 | 2016 | Ashley Humphrey 2016. Trace Metal Solution for ESAW Media. protocols.io https://dx.doi.org/10.17504/protocols.io.ge8bthw | 2021-04-15 09:14:44 | |||
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FLAVONOID PROFILING BY LIQUID CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY (LC/MS) Resource Report Resource Website |
Humberto J O Ramos | DOI:10.17504/protocols.io.udqes5w | Flavonoids play a variety of biological activities in plants, animals and bacteria range from physiological development to plant responses for abiotic and biotic stresses, as well as health-promoting effects of pharmaceutical interest. The following protocol describes the steps and details to generation of qualitative and quantitative broad-range profiles of flavonoids from plant tissues by ultra-high-performance liquid chromatograph (UHPLC) coupled to mass spectrometry | Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa - UFV, BIOAGRO/INCT-IPP, Viçosa-MG, Brazil | 1 | 2018 | Humberto J O Ramos 2018. FLAVONOID PROFILING BY LIQUID CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY (LC/MS). protocols.io https://dx.doi.org/10.17504/protocols.io.udqes5w | 2021-04-15 09:14:32 | ||||
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Cell Surface Immunofluorescence Staining Protocol Resource Report Resource Website |
BioLegend, Inc. | DOI:10.17504/protocols.io.excbfiw | BioLegend | , | http://www.biolegend.com/media_assets/support_protocol/BioLegend_Surface_Staining_Flow_Protocol_060215.pdf | 1 | 2016 | BioLegend, Inc. 2016. Cell Surface Immunofluorescence Staining Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.excbfiw | 2021-04-15 09:14:44 | |||
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THP1 cell line differentiation Resource Report Resource Website |
Rabia Khan | DOI:10.17504/protocols.io.fhubj6w | 1 | 2016 | Rabia Khan 2016. THP1 cell line differentiation. protocols.io https://dx.doi.org/10.17504/protocols.io.fhubj6w | 2021-04-15 09:14:31 | ||||||
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1% Agarose Gel Electrophoresis Prep Resource Report Resource Website |
Claire Rycroft, Ben Sutherland | DOI:10.17504/protocols.io.m9qc95w | Ararose (1%) gel electrophoresis for genomic DNA quality checking.This protocol comes with no guarantees from the authors. | University of British Columbia, Dalhousie Universtiy, University of British Columbia | 1 | 2019 | Claire Rycroft, Ben Sutherland 2019. 1% Agarose Gel Electrophoresis Prep. protocols.io https://dx.doi.org/10.17504/protocols.io.m9qc95w | 2021-04-15 09:14:33 | ||||
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Cell lysis, detergent-free Resource Report Resource Website |
Queenie Chan | DOI:10.17504/protocols.io.k79czr6 | Detergents are generally not compatible with mass spectrometers, so this is a detergent-free method of cell lysis that is compatible with mass spectrometry. Since this protocol does not have a precipitation step, it saves time and minimizes sample loss as well. | UBC | 1 | 2018 | Queenie Chan 2018. Cell lysis, detergent-free. protocols.io https://dx.doi.org/10.17504/protocols.io.k79czr6 | 2021-04-15 09:14:33 | ||||
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Adult mouse testis cell dissociation (on ice) Resource Report Resource Website |
Robert Mahoney | DOI:10.17504/protocols.io.smkec4w | Human Cell Atlas Method Development Community | This protocol is used to dissociate adult (8-10 week) mouse testis into a single cell suspension. The entire procedure is carried out 'on ice', reducing artifact gene expression changes. The yield is 5.4 million cells from 25 mg tissue and the viability is ~99%. | CCHMC | 1 | 2018 | Robert Mahoney 2018. Adult mouse testis cell dissociation (on ice). protocols.io https://dx.doi.org/10.17504/protocols.io.smkec4w | 2021-04-15 09:14:45 | |||
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Coronavirus Lateral Flow Assay (LFA) sample preparation protocol Resource Report Resource Website |
peijun he | DOI:10.17504/protocols.io.bksfkwbn | Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, Highfield Diagnostics | Coronavirus Lateral Flow Assay (LFA) sample preparation protocol | Highfield Diagnostics, UK | 1 | 2020 | peijun he 2020. Coronavirus Lateral Flow Assay (LFA) sample preparation protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bksfkwbn | 2021-04-15 09:14:44 | |||
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Haematoxylin Eosin (H&E) staining Resource Report Resource Website |
Yongbo Cui | DOI:10.17504/protocols.io.ihxcb7n | Haematoxylin Eosin (H&E) staining of mouse intestinal tissue | 1 | 2017 | Yongbo Cui 2017. Haematoxylin Eosin (H&E) staining. protocols.io https://dx.doi.org/10.17504/protocols.io.ihxcb7n | 2021-04-15 09:14:34 | |||||
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Ribosome profiling of Drosophila third instar larvae body wall muscle (with ribosome affinity purification) Resource Report Resource Website |
Xun Chen, Dion Dickman | DOI:10.17504/protocols.io.j89crz6 | Chen X, Dickman D (2017) Development of a tissue-specific ribosome profiling approach in Drosophila enables genome-wide evaluation of translational adaptations. PLoS Genet 13(12): e1007117. doi: 10.1371/journal.pgen.1007117 | University of Southern California, University of Southern California | https://doi.org/10.1371/journal.pgen.1007117 | 1 | 2017 | Xun Chen, Dion Dickman 2017. Ribosome profiling of Drosophila third instar larvae body wall muscle (with ribosome affinity purification). protocols.io https://dx.doi.org/10.17504/protocols.io.j89crz6 | 2021-04-15 09:14:46 | |||
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Isotopic labeling of freshwater mixotrophic algae using isotopic labeled heat-killed bacteria Resource Report Resource Website |
Ramon terrado | DOI:10.17504/protocols.io.ezdbf26 | Caron Lab - Protistan Ecology | This protocol aims to achieve an isotopic labeling of mixotrophic algae using 15N and 13C labeled heat-killed bacteria. It was developped to be used with the mixorophic chrysophyte Ochromonas to asses the sources of carbon and nitrogen of this algae when growing mixotrophically . Sources of nitrogen and carbon in the media used were reduced to 1 inorganic source (NH4Cl for nitrogen and bicarbonate for carbon) and 1 organic source (heat-killed bacteria); media used for Ochromonas growth was modified accordingly to reflect this.Downstream analysis of isotopic labeled Ochromonas include bulk IRMS measurements or nanoSIMS measurements. | University of Southern California (USC) | https://ncma.bigelow.org/media/pdf/NCMA-algal-medium-DY-V.pdf | 1 | 2016 | Ramon terrado 2016. Isotopic labeling of freshwater mixotrophic algae using isotopic labeled heat-killed bacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.ezdbf26 | 2021-04-15 09:14:45 | ||
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Preparation of Chemicals Resource Report Resource Website |
Nus Igem | DOI:10.17504/protocols.io.7pmhmk6 | National University of Singapore | 1 | 2019 | Nus Igem 2019. Preparation of Chemicals. protocols.io https://dx.doi.org/10.17504/protocols.io.7pmhmk6 | 2021-04-15 09:14:44 | |||||
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3' Azide labelling with TdT Resource Report Resource Website |
Benjamin Emert | DOI:10.17504/protocols.io.qnmdvc6 | Human Cell Atlas Method Development Community, RajLab | Protocol for add azide modified nucleotide to 3' end of unmodified DNA olgionucleotide using terminal transferase. Protocol adapted from Winz et al. 2015. | University of Pennsylvania | 1 | 2018 | Benjamin Emert 2018. 3' Azide labelling with TdT. protocols.io https://dx.doi.org/10.17504/protocols.io.qnmdvc6 | 2021-04-15 09:14:34 | |||
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Reovirus Plaque Assay Resource Report Resource Website |
Bernardo Mainou | DOI:10.17504/protocols.io.kghctt6 | Assay to obtain plaque forming units of mammalian orthoreovirus | Berger AK, Yi H, Kearns DB, Mainou BA (2017) Bacteria and bacterial envelope components enhance mammalian reovirus thermostability. PLoS Pathog 13(12): e1006768. doi: 10.1371/journal.ppat.1006768 | Emory University | https://doi.org/10.1371/journal.ppat.1006768 | 1 | 2017 | Bernardo Mainou 2017. Reovirus Plaque Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.kghctt6 | 2021-04-15 09:14:33 | ||
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Protein interaction analysis of KaiC3 with various Kai homologs via yeast two-hybrid experiments (β-Galactosidase Assay) Resource Report Resource Website |
Anika Wiegard, Christin Köbler, Katsuaki Oyama, Anja K. Dörrich, Chihiro Azai, Kazuki Terauchi, Annegret Wilde, Ilka Maria Axmann | DOI:10.17504/protocols.io.v7ve9n6 | CyanoWorld | This protocol can be used to investigate protein-protein interaction via yeast two-hybrid experiments. It describes the yeast-two hybrid method relying on a color change using β-galactosidase activity. | Wiegard A, Köbler C, Oyama K, Dörrich AK, Azai C, Terauchi K, Wilde A, Axmann IM, Array. Journal of Bacteriology 202(4). doi: 10.1128/JB.00478-19 | Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden, Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan, Institute for Microbiology and Molecular Biology, Justus-Liebig University, 35392 Giessen, Germany, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan, Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany, Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany | https://doi.org/10.1128/JB.00478-19 | 1 | 2019 | Anika Wiegard, Christin Köbler, Katsuaki Oyama, Anja K. Dörrich, Chihiro Azai, Kazuki Terauchi, Annegret Wilde, Ilka Maria Axmann 2019. Protein interaction analysis of KaiC3 with various Kai homologs via yeast two-hybrid experiments (β-Galactosidase Assay). protocols.io https://dx.doi.org/10.17504/protocols.io.v7ve9n6 | 2021-04-15 09:14:45 |
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