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Authors: J. Ashley Ezzell, Nicole A. Pelot, Kara A. Clissold, Warren M. Grill
Group: SPARC
Summary: Protocol for collection, histological processing, and imaging of rat vagus nerves.
Proper citation: J. Ashley Ezzell, Nicole A. Pelot, Kara A. Clissold, Warren M. Grill 2019. SPARC_Duke_Grill_OT2-OD025340_RatVagusNerveCollectionHistologyMicroscopy. protocols.io dx.doi.org/10.17504/protocols.io.ww3ffgn Copy
Authors: Vincent Bielinski, Chris Dupont
Group: Protist Research to Optimize Tools in Genetics (PROT-G), JCVI West Protocols
Summary: This protocol is the adaptation of previously published methods for use in isolating intact high molecular weight DNA from stramenopiles for long-read sequencing. The advantages here are minimal amount of centrifugation steps on isolated DNA, as well as the long-term storage of the DNA while in plugs to allow experimental flexibility.
Proper citation: Vincent Bielinski, Chris Dupont 2018. Modified HMW DNA Isolation from Stramenopiles with Agar Plugs. protocols.io dx.doi.org/10.17504/protocols.io.wenfbde Copy
Authors: Audrey Lapinaite, Sam Sternberg, Brett Staahl
Group: The Center for Genome Editing and Recording
Summary: This is a protocol from the Doudna Lab for His10-MBP-Cas9 purification.
Proper citation: Audrey Lapinaite, Sam Sternberg, Brett Staahl 2018. His10-MBP-Cas9 purification. protocols.io dx.doi.org/10.17504/protocols.io.ssseeee Copy
Authors: Jingrong Ye
Summary: We analyzed the demographic, clinical, and virological data of residents newly diagnosed with HIV in Beijing. We did population-based sequencing of the pol gene on plasma specimens and identified drug resistance mutations using the World Health Organization (WHO) list for surveillance of drug resistance mutations. HIV-1 subtype analyses utilized the automated subtyping tool COMET.
Proper citation: Jingrong Ye 2019. Protocol of HIV TDR and Subtype test in Beijing. protocols.io dx.doi.org/10.17504/protocols.io.8ahhsb6 Copy
Authors: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
Summary: This recepe is used in the following protocols:- PBMC- 01a - Isolation of Human PBMC from Buffy Coat- PBMC- 01b - Isolation of Human PBMC from Whole Blood- PBMC- 02 - CD4+ T cell Isolation from PBMC with “Dynabeads CD4 Positive Isolation Kit”- PBMC- 03 - TEFF+TREG Isolation from PBMC with “Miltenyi CD4+CD25+ Regulatory T cell Isolation Kit”- PMN- 01a - Isolation of Human PMN from Buffy Coat- PMN- 01b - Isolation of Human PMN from Whole Blood
Proper citation: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino 2020. SOLUTION- 09 - Trypan Blue solution. protocols.io dx.doi.org/10.17504/protocols.io.biwwkffe Copy
Authors: Angel Justiz-Vaillant, Monica F. Smikle
Group: University of the West Indies, [email protected]
Proper citation: Angel Justiz-Vaillant, Monica F. Smikle 2020. Universal sandwich ELISA for investigating the binding of Protein-LA (SpLA) to avian immunoglobulins using a peroxidase-labeled -anti-IgY conjugate.. protocols.io dx.doi.org/10.17504/protocols.io.bjq2kmye Copy
Authors: Chin Yee Tan
Proper citation: Chin Yee Tan 2019. 1. RNA isolation for tissue. protocols.io dx.doi.org/10.17504/protocols.io.zfyf3pw Copy
Authors: Jennifer B Treweek, Ken Y Chan, Nicholas C Flytzanis, Bin Yang, Benjamin E Deverman, Alon Greenbaum, Antti Lignell, Cheng Xiao, Long Cai, Mark S Ladinsky, Pamela J Bjorkman, Charless C Fowlkes, Viviana Gradinaru
Group: Optical Clearing of Tissue, Neurodegeneration Method Development Community
Summary: To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1–2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity. Furthermore, the macromolecule permeability of PACT- and PARS-processed tissue hybrids supports the diffusion of immunolabels throughout intact tissue, whereas RIMS (refractive index matching solution) grants high-resolution imaging at depth by further reducing light scattering in cleared and uncleared samples alike. These methods are adaptable to difficult-to-image tissues, such as bone (PACT-deCAL), and to magnified single-cell visualization (ePACT). Together, these protocols and solutions enable phenotyping of subcellular components and tracing cellular connectivity in intact biological networks.
Proper citation: Jennifer B Treweek, Ken Y Chan, Nicholas C Flytzanis, Bin Yang, Benjamin E Deverman, Alon Greenbaum, Antti Lignell, Cheng Xiao, Long Cai, Mark S Ladinsky, Pamela J Bjorkman, Charless C Fowlkes, Viviana Gradinaru 2019. Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. protocols.io dx.doi.org/10.17504/protocols.io.8xehxje Copy
Authors: Mark Dewitt, Julia Wong
Group: Innovative Genomics Institute, CornLab
Summary: sgRNA template assembly, in vitro T7 transcription, and SPRI bead cleanup
Proper citation: Mark Dewitt, Julia Wong 2016. In vitro transcription of guide RNAs. protocols.io dx.doi.org/10.17504/protocols.io.exabfie Copy
Authors: New England Biolabs
Group: Grupo de Estudos de Leveduras Cervejeiras
Proper citation: New England Biolabs 2018. SOB Media. protocols.io dx.doi.org/10.17504/protocols.io.pnfdmbn Copy
Authors: Holger Buchholz, Michelle Michelsen, Michael Allen, Ben Temperton
Group: Temperton Lab
Summary: Working protocol
Proper citation: Holger Buchholz, Michelle Michelsen, Michael Allen, Ben Temperton 2020. Viral isolation for SAR11 and OM43 hosts. protocols.io dx.doi.org/10.17504/protocols.io.bb73irqn Copy
Authors: Madeleine Di Natale, Josiane Fakhry, Martin Stebbing, Billie Hunne, John B. Furness
Summary: Enteroendocrine cells are important regulators of gastrointestinal, digestive and metabolic function. Here we describe protocols for investigating nerve fiber populations that may innervate these cells, using immunohistochemistry and high resolution microscopy techniques in the human gastric mucosa and muscle.
Proper citation: Madeleine Di Natale, Josiane Fakhry, Martin Stebbing, Billie Hunne, John B. Furness 2019. Identification of different EEC types and nerve fiber types in human gastric mucosa. protocols.io dx.doi.org/10.17504/protocols.io.8u7hwzn Copy
Authors: Fabio Gomes
Proper citation: Fabio Gomes 2015. Genomic DNA extraction from mosquitoes. protocols.io dx.doi.org/10.17504/protocols.io.d7h9j5 Copy
Authors: Leonardo Caserta
Group: Coronavirus Method Development Community, Diel Lab
Proper citation: Leonardo Caserta 2021. First-strand synthesis and touchdown PCR for SARS-CoV-2. protocols.io dx.doi.org/10.17504/protocols.io.br54m88w Copy
Authors: Josh Quick
Group: Diaz-Munoz Lab, Coronavirus Method Development Community, Szentagothai Research Centre Virology
Proper citation: Josh Quick 2019. DNA quantification using the Quantus fluorometer . protocols.io dx.doi.org/10.17504/protocols.io.7pzhmp6 Copy
Authors: Kholoud Refaat Ahmed, Amal Hassan Abdel Rahman, Manar Abdul Waniss Mohammed Abdul Aziz
Proper citation: Kholoud Refaat Ahmed, Amal Hassan Abdel Rahman, Manar Abdul Waniss Mohammed Abdul Aziz 2018. Molecular Assessment of Kallikrein 3 in Ameloblastoma and Odontogenic Keratocyst (In-vitro Study). protocols.io dx.doi.org/10.17504/protocols.io.uazesf6 Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: The BioBrick® Assembly Kit was developed in partnership with Ginkgo BioWorks. What follows is an abbreviated set of protocols for the use of the BioBrick® Assembly Kit (to assemble an Upstream Part with a Downstream Part into a Destination Plasmid). For more details and for technical questions, please see here.
Proper citation: New England Biolabs 2015. Digestion for BioBrick Assembly Kit (E0546). protocols.io dx.doi.org/10.17504/protocols.io.cphvj5 Copy
Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net
Summary: For use in "Obtaining pure cyanophage stocks (liquid assay)"
Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Lysate titer. protocols.io dx.doi.org/10.17504/protocols.io.dqn5vd Copy
Authors: Izabela Rezende, Lívia Sacchetto
Group: MRCA
Summary: For purification of viral RNA from serum and cell-culture supernatants.
Proper citation: Izabela Rezende, Lívia Sacchetto 2019. Total RNA extraction. protocols.io dx.doi.org/10.17504/protocols.io.pw7dphn Copy
Authors: Joshua Bugge, Deborah Robertson
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Robertson Lab
Summary: An electroporation-mediated genetic transformation or the marine diatom Thalassiosira pseudonana was developed. Using a sorbitol-based buffer, T. pseudonana cells were successfully transformed with the Tpfcp/nat plasmid at an efficiency of 2820 per 108 cells. This represents a six-fold improvement compared with previously published methods.
Proper citation: Joshua Bugge, Deborah Robertson 2019. Electroporation of Thalassiosira pseudonana. protocols.io dx.doi.org/10.17504/protocols.io.yvqfw5w Copy
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