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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Audiovisual stimuli creation Resource Report Resource Website |
HansRutger.Bosker | 10.17504/protocols.io.bmv3k68n | This protocol describes three ways of creating audiovisual stimuli that include (1) manipulations of the suprasegmental cues to lexical stress and (2) two different gestural alignments. These methods were used in Bosker & Peeters (submitted; https://doi.org/10.1101/2020.07.13.200543). | Max Planck Institute for Psycholinguistics | 1 | 2020 | HansRutger.Bosker 2020. Audiovisual stimuli creation. protocols.io dx.doi.org/10.17504/protocols.io.bmv3k68n | 2021-03-29 03:10:23 | ||||
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Learn Partial Correlation Disease-Specific Networks Resource Report Resource Website |
Lillian Thistlethwaite | 10.17504/protocols.io.bk7xkzpn | Metabolomics Protocols & Workflows | This protocol describes how to construct disease-specific network structures as described in Thistlethwaite et al. (2020). Thistlethwaite L.R., Petrosyan V., Li X., Miller M.J., Elsea S.H., Milosavljevic A. (2020). CTD: an information-theoretic method to interpret multivariate perturbations in the context of graphical models with applications in metabolomics and transcriptomics. In review. | Baylor College of Medicine | 2 | 2020 | Lillian Thistlethwaite 2020. Learn Partial Correlation Disease-Specific Networks. protocols.io dx.doi.org/10.17504/protocols.io.bk7xkzpn | 2021-03-29 03:10:26 | |||
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NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®) E7660 Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.btcenite | Coronavirus Method Development Community | This protocol details methods for the NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®), NEB #E7660S/L 24/96 reactions. | New England Biolabs | https://www.neb.com/-/media/nebus/files/manuals/manuale7660.pdf?rev=48c42313dcb64b0dbb16c4bfd1563a27 | 3 | 2021 | New England Biolabs 2021. NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®) E7660. protocols.io dx.doi.org/10.17504/protocols.io.btcenite | 2021-03-29 03:10:27 | ||
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How to make a 25-50 mg/ml Chloramphenicol Stock Solution Resource Report Resource Website |
Sean Seaver | 10.17504/protocols.io.ci5ug5 | How to make a 25-50 mg/ml Chloramphenicol Stock Solution | P212121 | http://store.p212121.com/chloramphenicol/ | 1 | 2014 | Sean Seaver 2014. How to make a 25-50 mg/ml Chloramphenicol Stock Solution. protocols.io dx.doi.org/10.17504/protocols.io.ci5ug5 | 2021-03-29 03:10:27 | |||
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DAB Detection of Biocytin Labeled Tissue Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bctbiwin | BICCN, Allen Institute for Brain Science | This protocol describes the process for diaminobenzidine (DAB) detection of biocytin filled cells. This protocol is optimized for use with brain slices cut at 350 µm thick, in which cells are first filled with biocytin (i.e., post-electrophysiological recording), fixed in 4% PFA/2.5% glutaraldehyde, and transferred to PBS until ready to stain. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. DAB Detection of Biocytin Labeled Tissue. protocols.io dx.doi.org/10.17504/protocols.io.bctbiwin | 2021-03-29 03:10:27 | |||
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Qiagen- RNeasy Mini Kit for tissue Resource Report Resource Website |
Maysa Silva, Maryana Branquinho, Maria Cármen Sales | 10.17504/protocols.io.ssceeaw | Protocol for extraction of tissue RNA by Qiagen Mini Kit. | Universidade de São Paulo, Universidade de São Paulo, Universidade de São Paulo | 1 | 2018 | Maysa Silva, Maryana Branquinho, Maria Cármen Sales 2018. Qiagen- RNeasy Mini Kit for tissue. protocols.io dx.doi.org/10.17504/protocols.io.ssceeaw | 2021-03-29 03:10:26 | ||||
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Conjugation of Keyhole limpet haemocynin to Peptide 254-274 of HIV gp-120 as immunogen. Resource Report Resource Website |
Angel Justiz-Vaillant | 10.17504/protocols.io.bjh7kj9n | University of the West Indies, [email protected] | Chemical synthesis facilitates the generation of peptides which are difficult to express in bacteria. The fragment 254-274 of the human immunodeficiency virus (HIV) is critical for infectivity of the virus and induction of antibody neutralization (Ho et al, 1988). Boudet et al, 1995 demonstrated that a synthetic peptide derived from the third variable domain of the HIV-1 gp-120 when used as immunogen was able to induce an antibody response to multiple (up to six) HIV strains. ReferenceHo DD, Kaplan JC, Rackauskas IE, Gurney ME. Second conserved domain of gp120 is important for HIV infectivity and antibody neutralization.Science. 1988;239(4843):1021-1023. doi:10.1126/science.2830667.Boudet F, Keller H, Kieny MP, Thèze J. Single peptide and anti-idiotype based immunizations can broaden the antibody response against the variable V3 domain of HIV-1 in mice.Mol Immunol. 1995;32(7):449-457. doi:10.1016/0161-5890(95)00007-2 | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. Conjugation of Keyhole limpet haemocynin to Peptide 254-274 of HIV gp-120 as immunogen.. protocols.io dx.doi.org/10.17504/protocols.io.bjh7kj9n | 2021-03-29 03:10:26 | |||
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CasX GFP-Targeting gRNA IVT Resource Report Resource Website |
Connor Tsuchida, Liz O'Brien | 10.17504/protocols.io.8uwhwxe | The Center for Genome Editing and Recording | This protocol explains how to transcribe gRNA in vitro. | University of California at Berkeley, University of California, Berkeley | 1 | 2019 | Connor Tsuchida, Liz O'Brien 2019. CasX GFP-Targeting gRNA IVT. protocols.io dx.doi.org/10.17504/protocols.io.8uwhwxe | 2021-03-29 03:10:21 | |||
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C_HW7 (hamming) Resource Report Resource Website |
Ken Youens-Clark | 10.17504/protocols.io.f7wbrpe | MetaFunc Course | University of Arizona | 1 | 2016 | Ken Youens-Clark 2016. C_HW7 (hamming). protocols.io dx.doi.org/10.17504/protocols.io.f7wbrpe | 2021-03-29 03:10:21 | ||||
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Fecal DNA extraction by bead beating Resource Report Resource Website |
Chin Yee Tan | 10.17504/protocols.io.zvrf656 | From Surana Lab protocolsThis protocol is suitable for extracting DNA from either human or mouse feces. Best results will be obtained with 10-60 mg of starting material | Duke University | 2 | 2019 | Chin Yee Tan 2019. Fecal DNA extraction by bead beating. protocols.io dx.doi.org/10.17504/protocols.io.zvrf656 | 2021-03-29 03:10:21 | ||||
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Feeding bacteria to house flies for microbe fate and gene expression analysis. Resource Report Resource Website |
Dana Nayduch, Hayley Meier, Christine Mccoy | 10.17504/protocols.io.vhde326 | ESA MUVE | Objective: To feed individual house flies a specific amount of bacteria in order to determine bacteria “fate” (persistence, via enumeration; spatiotemporal location, via microscopy) and house fly immune response (whole fly or tissue-specific, via downstream mRNA or protein expression analyses) | USDA-ARS, Arthropod-Borne Animal Diseases Research Unit, USDA-ARS, Arthropod-Borne Animal Diseases Research Unit, USDA-ARS, Arthropod-Borne Animal Diseases Research Unit | 2 | 2018 | Dana Nayduch, Hayley Meier, Christine Mccoy 2018. Feeding bacteria to house flies for microbe fate and gene expression analysis.. protocols.io dx.doi.org/10.17504/protocols.io.vhde326 | 2021-03-29 03:10:25 | |||
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High-efficiency S. cerevisiae lithium acetate transformation Resource Report Resource Website |
Carl De Boer | 10.17504/protocols.io.j4tcqwn | A protocol for lithium acetate transformation of yeast that can be used to generate highly complex plasmid libraries (O(1E8) if starting with ~1L of culture) and can get over 1 million transformants from a single transformation (as described here). Optimized using yeast strain Y8203. Based on a protocol originally by Supipi Kaluarachchi Duffy. | Broad Institute | 1 | 2017 | Carl De Boer 2017. High-efficiency S. cerevisiae lithium acetate transformation. protocols.io dx.doi.org/10.17504/protocols.io.j4tcqwn | 2021-03-29 03:10:25 | ||||
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Biolistic transformation of Emiliania huxleyi Resource Report Resource Website |
Glen Wheeler, Rowena Stern | 10.17504/protocols.io.8tzhwp6 | Marine Biological Association, Marine Biological Association | 1 | 2019 | Glen Wheeler, Rowena Stern 2019. Biolistic transformation of Emiliania huxleyi. protocols.io dx.doi.org/10.17504/protocols.io.8tzhwp6 | 2021-03-29 03:10:32 | |||||
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Low-Dose Streptozotocin Induction Protocol (mouse) Resource Report Resource Website |
Frank Brosius | 10.17504/protocols.io.8izhuf6 | Diabetic Complications Consortium | This protocol is used by DiaComp members to induce diabetes in a number of the animal models developed by the consortium. STZ is toxic to the insulinproducing beta cells of the pancreas and used to induce a diabetes similar to a type I diabetic (Reference). Some reports suggest cellular toxicity outside of the pancreas. STZ also exhibits broad spectrum antibacterial properties and alters the gut microbiota. Please ensure that appropriate controls are included in all studies and complementary models considered (e.g. the Ins2Akita mouse).Diabetic Complications: | University of Arizona | https://www.diacomp.org/shared/document.aspx?id=19&docType=Protocol | 2 | 2019 | Frank Brosius 2019. Low-Dose Streptozotocin Induction Protocol (mouse). protocols.io dx.doi.org/10.17504/protocols.io.8izhuf6 | 2021-03-29 03:10:32 | ||
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Single nick pCrispomyces 2 Resource Report Resource Website |
Jaclyn Winter | 10.17504/protocols.io.8f5htq6 | University of Utah | 1 | 2019 | Jaclyn Winter 2019. Single nick pCrispomyces 2. protocols.io dx.doi.org/10.17504/protocols.io.8f5htq6 | 2021-03-29 03:10:32 | |||||
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Internal Genomic DNA Standard for Quantitative Metagenome Analysis Resource Report Resource Website |
Brandon M. Satinsky, Scott M. Gifford, Byron C. Crump, Christa Smith, Mary Ann Moran, Moran Lab | 10.17504/protocols.io.ftgbnjw | Moran Lab | Satinsky, Brandon M., et al. 'Use of internal standards for quantitative metatranscriptome and metagenome analysis.' Methods in enzymology 531 (2012): 237-250. | University of Georgia, University of Georgia, University of Georgia, University of Georgia, University of Georgia, University of Georgia | http://www.sciencedirect.com/science/article/pii/B9780124078635000125 | 2 | 2016 | Brandon M. Satinsky, Scott M. Gifford, Byron C. Crump, Christa Smith, Mary Ann Moran, Moran Lab 2016. Internal Genomic DNA Standard for Quantitative Metagenome Analysis. protocols.io dx.doi.org/10.17504/protocols.io.ftgbnjw | 2021-03-29 03:10:32 | ||
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Chromatin Immunoprecipitation Lysis Buffer Sets Resource Report Resource Website |
Vivian Liu | 10.17504/protocols.io.dmh435 | 1 | 2015 | Vivian Liu 2015. Chromatin Immunoprecipitation Lysis Buffer Sets. protocols.io dx.doi.org/10.17504/protocols.io.dmh435 | 2021-03-29 03:10:32 | ||||||
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Stellaris® RNA FISH Sequential IF + FISH in Adherent Cells Protocol Resource Report Resource Website |
LGC Biosearch Technologies | 10.17504/protocols.io.ekzbcx6 | Stellaris RNA FISH protocol for sequential labeling with IF and RNA FISH in adherent cells. | Biosearch Technologies | https://biosearchassets.blob.core.windows.net/assets/bti_custom_stellaris_immunofluorescence_seq_protocol.pdf | 1 | 2016 | LGC Biosearch Technologies 2016. Stellaris® RNA FISH Sequential IF + FISH in Adherent Cells Protocol. protocols.io dx.doi.org/10.17504/protocols.io.ekzbcx6 | 2021-03-29 03:10:32 | |||
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03 Ligation Resource Report Resource Website |
Tjusls China | 10.17504/protocols.io.49igz4e | Tianjin University | 1 | 2019 | Tjusls China 2019. 03 Ligation. protocols.io dx.doi.org/10.17504/protocols.io.49igz4e | 2021-03-29 03:10:32 | |||||
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invertedClampFISH ligation Resource Report Resource Website |
Benjamin Emert | 10.17504/protocols.io.qnkdvcw | Human Cell Atlas Method Development Community, RajLab | Protocol for making invertedClampFISH probes. | University of Pennsylvania | 1 | 2018 | Benjamin Emert 2018. invertedClampFISH ligation. protocols.io dx.doi.org/10.17504/protocols.io.qnkdvcw | 2021-03-29 03:10:31 |
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