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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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SPARC_Duke_Grill_OT2-OD025340_RatVagusNerveCollectionHistologyMicroscopy Resource Report Resource Website |
J. Ashley Ezzell, Nicole A. Pelot, Kara A. Clissold, Warren M. Grill | 10.17504/protocols.io.ww3ffgn | SPARC | Protocol for collection, histological processing, and imaging of rat vagus nerves. | University of North Carolina, Duke University, University of North Carolina, Duke University | 1 | 2019 | 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 | 2021-03-29 03:09:08 | |||
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Modified HMW DNA Isolation from Stramenopiles with Agar Plugs Resource Report Resource Website |
Vincent Bielinski, Chris Dupont | 10.17504/protocols.io.wenfbde | Protist Research to Optimize Tools in Genetics (PROT-G), JCVI West Protocols | 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. | J. Craig Venter Institute, Synthetic Biology & Bioenergy Group, J. Craig Venter Institute, Synthetic Biology & Bioenergy Group | 1 | 2018 | Vincent Bielinski, Chris Dupont 2018. Modified HMW DNA Isolation from Stramenopiles with Agar Plugs. protocols.io dx.doi.org/10.17504/protocols.io.wenfbde | 2021-03-29 03:09:08 | |||
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His10-MBP-Cas9 purification Resource Report Resource Website |
Audrey Lapinaite, Sam Sternberg, Brett Staahl | 10.17504/protocols.io.ssseeee | The Center for Genome Editing and Recording | This is a protocol from the Doudna Lab for His10-MBP-Cas9 purification. | University of California, Berkeley, University of California, Berkeley, University of California, Berkeley | 2 | 2018 | Audrey Lapinaite, Sam Sternberg, Brett Staahl 2018. His10-MBP-Cas9 purification. protocols.io dx.doi.org/10.17504/protocols.io.ssseeee | 2021-03-29 03:09:08 | |||
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Protocol of HIV TDR and Subtype test in Beijing Resource Report Resource Website |
Jingrong Ye | 10.17504/protocols.io.8ahhsb6 | 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. | Ye J, Hao M, Xing H, Wang Y, Wang J, Feng Y, Xin R, Zeng J, Zhao S, Hao Y, Chen J, Ruan Y, Li X, Shao Y, Lu H (2020) Characterization of subtypes and transmitted drug resistance strains of HIV among Beijing residents between 2001-2016. PLoS ONE 15(3): e0230779. doi: 10.1371/journal.pone.0230779 | Beijing Center for Disease Prevention and Control(CDC), Beijing, China. | https://doi.org/10.1371/journal.pone.0230779 | 2 | 2019 | Jingrong Ye 2019. Protocol of HIV TDR and Subtype test in Beijing. protocols.io dx.doi.org/10.17504/protocols.io.8ahhsb6 | 2021-03-29 03:09:19 | ||
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SOLUTION- 09 - Trypan Blue solution Resource Report Resource Website |
Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | 10.17504/protocols.io.biwwkffe | 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 | Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy) | 1 | 2020 | 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 | 2021-03-29 03:09:19 | ||||
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Universal sandwich ELISA for investigating the binding of Protein-LA (SpLA) to avian immunoglobulins using a peroxidase-labeled -anti-IgY conjugate. Resource Report Resource Website |
Angel Justiz-Vaillant, Monica F. Smikle | 10.17504/protocols.io.bjq2kmye | University of the West Indies, [email protected] | University of the West Indies St. Augustine, University of the West Indies. Mona Campus | 1 | 2020 | 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 | 2021-03-29 03:09:19 | ||||
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1. RNA isolation for tissue Resource Report Resource Website |
Chin Yee Tan | 10.17504/protocols.io.zfyf3pw | Duke University | 1 | 2019 | Chin Yee Tan 2019. 1. RNA isolation for tissue. protocols.io dx.doi.org/10.17504/protocols.io.zfyf3pw | 2021-03-29 03:09:18 | |||||
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Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping Resource Report Resource Website |
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 | 10.17504/protocols.io.8xehxje | Optical Clearing of Tissue, Neurodegeneration Method Development Community | 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. | Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA., Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA, Department of Computer Science, University of California, Irvine, California, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA | https://www.nature.com/articles/nprot.2015.122 | 1 | 2019 | 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 | 2021-03-29 03:09:21 | ||
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In vitro transcription of guide RNAs Resource Report Resource Website |
Mark Dewitt, Julia Wong | 10.17504/protocols.io.exabfie | Innovative Genomics Institute, CornLab | sgRNA template assembly, in vitro T7 transcription, and SPRI bead cleanup | UC BERKELEY-IGI, UC BERKELEY-IGI | 5 | 2016 | Mark Dewitt, Julia Wong 2016. In vitro transcription of guide RNAs. protocols.io dx.doi.org/10.17504/protocols.io.exabfie | 2021-03-29 03:09:19 | |||
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SOB Media Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.pnfdmbn | Grupo de Estudos de Leveduras Cervejeiras | New England Biolabs | https://www.neb.com/protocols/2012/06/21/making-your-own-electrocompetent-cells | 1 | 2018 | New England Biolabs 2018. SOB Media. protocols.io dx.doi.org/10.17504/protocols.io.pnfdmbn | 2021-03-29 03:09:19 | |||
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Viral isolation for SAR11 and OM43 hosts Resource Report Resource Website |
Holger Buchholz, Michelle Michelsen, Michael Allen, Ben Temperton | 10.17504/protocols.io.bb73irqn | Temperton Lab | Working protocol | University of Exeter, University of Exeter, University of Exeter; Plymouth Marine Laboratory, University of Exeter | 1 | 2020 | 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 | 2021-03-29 03:09:21 | |||
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Identification of different EEC types and nerve fiber types in human gastric mucosa Resource Report Resource Website |
Madeleine Di Natale, Josiane Fakhry, Martin Stebbing, Billie Hunne, John B. Furness | 10.17504/protocols.io.8u7hwzn | 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. |
RRID:AB_2783525 RRID:AB_2314960 RRID:AB_2783534 RRID:AB_572268 RRID:AB_2783533 RRID:AB_2814842 RRID:AB_2762851 RRID:AB_2783523 RRID:AB_2767291 RRID:AB_2315530 |
University of Melbourne, University of Melbourne, University of Melbourne, University of Melbourne, University of Melbourne | 1 | 2019 | 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 | 2021-03-29 03:09:21 | |||
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Genomic DNA extraction from mosquitoes Resource Report Resource Website |
Fabio Gomes | 10.17504/protocols.io.d7h9j5 | 1 | 2015 | Fabio Gomes 2015. Genomic DNA extraction from mosquitoes. protocols.io dx.doi.org/10.17504/protocols.io.d7h9j5 | 2021-03-29 03:09:21 | ||||||
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First-strand synthesis and touchdown PCR for SARS-CoV-2 Resource Report Resource Website |
Leonardo Caserta | 10.17504/protocols.io.br54m88w | Coronavirus Method Development Community, Diel Lab | Cornell University | 2 | 2021 | Leonardo Caserta 2021. First-strand synthesis and touchdown PCR for SARS-CoV-2. protocols.io dx.doi.org/10.17504/protocols.io.br54m88w | 2021-03-29 03:09:19 | ||||
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DNA quantification using the Quantus fluorometer Resource Report Resource Website |
Josh Quick | 10.17504/protocols.io.7pzhmp6 | Diaz-Munoz Lab, Coronavirus Method Development Community, Szentagothai Research Centre Virology | Pattabiraman C, Habib F, K. HP, Rasheed R, Prasad P, Reddy V, Dinesh P, Damodar T, Hosallimath K, George AK, Reddy NVK, John B, Pattanaik A, Kumar N, Mani RS, Venkataswamy MM, Hameed SKS, G. PKB, Desai A, Vasanthapuram R (2020) Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka. PLoS ONE 15(12): e0243412. doi: 10.1371/journal.pone.0243412 | University of Birmingham | https://doi.org/10.1016/j.remle.2020.05.007 | 1 | 2019 | Josh Quick 2019. DNA quantification using the Quantus fluorometer . protocols.io dx.doi.org/10.17504/protocols.io.7pzhmp6 | 2021-03-29 03:09:19 | ||
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Molecular Assessment of Kallikrein 3 in Ameloblastoma and Odontogenic Keratocyst (In-vitro Study) Resource Report Resource Website |
Kholoud Refaat Ahmed, Amal Hassan Abdel Rahman, Manar Abdul Waniss Mohammed Abdul Aziz | 10.17504/protocols.io.uazesf6 | Assistant Lecturer at at Oral Pathology Department Faculty of Oral and Dental Medicine, Ahram Canadian University., Professor of Oral and Maxillofacial Pathology, Faculty of Dentistry, Cairo University., Lecturer of Oral and Maxillofacial Pathology, Faculty of Dentistry, Cairo University | 1 | 2018 | 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 | 2021-03-29 03:09:19 | |||||
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Digestion for BioBrick Assembly Kit (E0546) Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.cphvj5 | New England Biolabs (NEB) | 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. | New England Biolabs | https://www.neb.com/protocols/1/01/01/digestion-protocol-e0546 | 1 | 2015 | New England Biolabs 2015. Digestion for BioBrick Assembly Kit (E0546). protocols.io dx.doi.org/10.17504/protocols.io.cphvj5 | 2021-03-29 03:09:19 | ||
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Lysate titer Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | 10.17504/protocols.io.dqn5vd | VERVE Net | For use in "Obtaining pure cyanophage stocks (liquid assay)" | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Lysate titer. protocols.io dx.doi.org/10.17504/protocols.io.dqn5vd | 2021-03-29 03:09:19 | |||
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Total RNA extraction Resource Report Resource Website |
Izabela Rezende, Lívia Sacchetto | 10.17504/protocols.io.pw7dphn | MRCA | For purification of viral RNA from serum and cell-culture supernatants. | Federal University of Minas Gerais - Laboratório de Vírus, Federal University of Minas Gerais - Laboratório de Vírus | 1 | 2019 | Izabela Rezende, Lívia Sacchetto 2019. Total RNA extraction. protocols.io dx.doi.org/10.17504/protocols.io.pw7dphn | 2021-03-29 03:09:19 | |||
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Electroporation of Thalassiosira pseudonana Resource Report Resource Website |
Joshua Bugge, Deborah Robertson | 10.17504/protocols.io.yvqfw5w | Protist Research to Optimize Tools in Genetics (PROT-G), Robertson Lab | 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. | Clark University, Clark University | 1 | 2019 | Joshua Bugge, Deborah Robertson 2019. Electroporation of Thalassiosira pseudonana. protocols.io dx.doi.org/10.17504/protocols.io.yvqfw5w | 2021-03-29 03:09:21 |
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