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Authors: Addgene The Nonprofit Plasmid Repository
Summary: 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

Proper citation: Addgene The Nonprofit Plasmid Repository 2019. AAV Purification by Iodixanol Gradient Ultracentrifugation. protocols.io https://dx.doi.org/10.17504/protocols.io.bawqifdw Copy   

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Authors: Caroline Green

Proper citation: Caroline Green 2016. Protein Expression & Isolation & Purification. protocols.io https://dx.doi.org/10.17504/protocols.io.fwvbpe6 Copy   

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Authors: Elin Verbrugghe
Summary: 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.

Proper citation: 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 Copy   

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Authors: Yasmin Bar El
Summary: 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.

Proper citation: Yasmin Bar El 2018. Isolated astrocyte culture - protocol 2. protocols.io https://dx.doi.org/10.17504/protocols.io.tqcemsw Copy   

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Authors: Remco Stam
Group: Plantae, Stam Lab
Summary: 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.

Proper citation: Remco Stam 2016. DNA extraction from plants. protocols.io https://dx.doi.org/10.17504/protocols.io.eusbewe Copy   

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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 https://dx.doi.org/10.17504/protocols.io.ge8bthw Copy   

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Authors: Humberto J O Ramos
Summary: 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

Proper citation: 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 Copy   

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Authors: BioLegend, Inc.
Group: BioLegend

Proper citation: BioLegend, Inc. 2016. Cell Surface Immunofluorescence Staining Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.excbfiw Copy   

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Authors: Rabia Khan

Proper citation: Rabia Khan 2016. THP1 cell line differentiation. protocols.io https://dx.doi.org/10.17504/protocols.io.fhubj6w Copy   

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Authors: Claire Rycroft, Ben Sutherland
Summary: Ararose (1%) gel electrophoresis for genomic DNA quality checking.This protocol comes with no guarantees from the authors.

Proper citation: Claire Rycroft, Ben Sutherland 2019. 1% Agarose Gel Electrophoresis Prep. protocols.io https://dx.doi.org/10.17504/protocols.io.m9qc95w Copy   

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Authors: Queenie Chan
Summary: 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.

Proper citation: Queenie Chan 2018. Cell lysis, detergent-free. protocols.io https://dx.doi.org/10.17504/protocols.io.k79czr6 Copy   

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Authors: Robert Mahoney
Group: Human Cell Atlas Method Development Community
Summary: 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%. 

Proper citation: Robert Mahoney 2018. Adult mouse testis cell dissociation (on ice). protocols.io https://dx.doi.org/10.17504/protocols.io.smkec4w Copy   

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Authors: peijun he
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, Highfield Diagnostics
Summary: Coronavirus Lateral Flow Assay (LFA) sample preparation protocol

Proper citation: peijun he 2020. Coronavirus Lateral Flow Assay (LFA) sample preparation protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bksfkwbn Copy   

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Authors: Yongbo Cui
Summary: Haematoxylin Eosin (H&E) staining of mouse intestinal tissue

Proper citation: Yongbo Cui 2017. Haematoxylin Eosin (H&E) staining. protocols.io https://dx.doi.org/10.17504/protocols.io.ihxcb7n Copy   

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Authors: Xun Chen, Dion Dickman

Proper citation: 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 Copy   

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Authors: Ramon terrado
Group: Caron Lab - Protistan Ecology
Summary: 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.

Proper citation: 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 Copy   

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Authors: Nus Igem

Proper citation: Nus Igem 2019. Preparation of Chemicals. protocols.io https://dx.doi.org/10.17504/protocols.io.7pmhmk6 Copy   

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Authors: Benjamin Emert
Group: Human Cell Atlas Method Development Community, RajLab
Summary: Protocol for add azide modified nucleotide to 3' end of unmodified DNA olgionucleotide using terminal transferase. Protocol adapted from Winz et al. 2015. 

Proper citation: Benjamin Emert 2018. 3' Azide labelling with TdT. protocols.io https://dx.doi.org/10.17504/protocols.io.qnmdvc6 Copy   

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Authors: Bernardo Mainou
Summary: Assay to obtain plaque forming units of mammalian orthoreovirus

Proper citation: Bernardo Mainou 2017. Reovirus Plaque Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.kghctt6 Copy   

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Authors: Anika Wiegard, Christin Köbler, Katsuaki Oyama, Anja K. Dörrich, Chihiro Azai, Kazuki Terauchi, Annegret Wilde, Ilka Maria Axmann
Group: CyanoWorld
Summary: 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.

Proper citation: 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 Copy   

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