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Authors: HansRutger.Bosker
Summary: 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).
Proper citation: HansRutger.Bosker 2020. Audiovisual stimuli creation. protocols.io dx.doi.org/10.17504/protocols.io.bmv3k68n Copy
Authors: Lillian Thistlethwaite
Group: Metabolomics Protocols & Workflows
Summary: 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.
Proper citation: Lillian Thistlethwaite 2020. Learn Partial Correlation Disease-Specific Networks. protocols.io dx.doi.org/10.17504/protocols.io.bk7xkzpn Copy
Authors: New England Biolabs
Group: Coronavirus Method Development Community
Summary: This protocol details methods for the NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®), NEB #E7660S/L 24/96 reactions.
Proper citation: 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 Copy
Authors: Sean Seaver
Summary: How to make a 25-50 mg/ml Chloramphenicol Stock Solution
Proper citation: Sean Seaver 2014. How to make a 25-50 mg/ml Chloramphenicol Stock Solution. protocols.io dx.doi.org/10.17504/protocols.io.ci5ug5 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. DAB Detection of Biocytin Labeled Tissue. protocols.io dx.doi.org/10.17504/protocols.io.bctbiwin Copy
Authors: Maysa Silva, Maryana Branquinho, Maria Cármen Sales
Summary: Protocol for extraction of tissue RNA by Qiagen Mini Kit.
Proper citation: Maysa Silva, Maryana Branquinho, Maria Cármen Sales 2018. Qiagen- RNeasy Mini Kit for tissue. protocols.io dx.doi.org/10.17504/protocols.io.ssceeaw Copy
Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: 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
Proper citation: 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 Copy
Authors: Connor Tsuchida, Liz O'Brien
Group: The Center for Genome Editing and Recording
Summary: This protocol explains how to transcribe gRNA in vitro.
Proper citation: Connor Tsuchida, Liz O'Brien 2019. CasX GFP-Targeting gRNA IVT. protocols.io dx.doi.org/10.17504/protocols.io.8uwhwxe Copy
Authors: Ken Youens-Clark
Group: MetaFunc Course
Proper citation: Ken Youens-Clark 2016. C_HW7 (hamming). protocols.io dx.doi.org/10.17504/protocols.io.f7wbrpe Copy
Authors: Chin Yee Tan
Summary: 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
Proper citation: Chin Yee Tan 2019. Fecal DNA extraction by bead beating. protocols.io dx.doi.org/10.17504/protocols.io.zvrf656 Copy
Authors: Dana Nayduch, Hayley Meier, Christine Mccoy
Group: ESA MUVE
Summary: 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)
Proper citation: 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 Copy
Authors: Carl De Boer
Summary: 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.
Proper citation: Carl De Boer 2017. High-efficiency S. cerevisiae lithium acetate transformation. protocols.io dx.doi.org/10.17504/protocols.io.j4tcqwn Copy
Authors: Glen Wheeler, Rowena Stern
Proper citation: Glen Wheeler, Rowena Stern 2019. Biolistic transformation of Emiliania huxleyi. protocols.io dx.doi.org/10.17504/protocols.io.8tzhwp6 Copy
Authors: Frank Brosius
Group: Diabetic Complications Consortium
Summary: 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:
Proper citation: Frank Brosius 2019. Low-Dose Streptozotocin Induction Protocol (mouse). protocols.io dx.doi.org/10.17504/protocols.io.8izhuf6 Copy
Authors: Jaclyn Winter
Proper citation: Jaclyn Winter 2019. Single nick pCrispomyces 2. protocols.io dx.doi.org/10.17504/protocols.io.8f5htq6 Copy
Authors: Brandon M. Satinsky, Scott M. Gifford, Byron C. Crump, Christa Smith, Mary Ann Moran, Moran Lab
Group: Moran Lab
Summary: Satinsky, Brandon M., et al. 'Use of internal standards for quantitative metatranscriptome and metagenome analysis.' Methods in enzymology 531 (2012): 237-250.
Proper citation: 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 Copy
Authors: Vivian Liu
Proper citation: Vivian Liu 2015. Chromatin Immunoprecipitation Lysis Buffer Sets. protocols.io dx.doi.org/10.17504/protocols.io.dmh435 Copy
Authors: LGC Biosearch Technologies
Summary: Stellaris RNA FISH protocol for sequential labeling with IF and RNA FISH in adherent cells.
Proper citation: LGC Biosearch Technologies 2016. Stellaris® RNA FISH Sequential IF + FISH in Adherent Cells Protocol. protocols.io dx.doi.org/10.17504/protocols.io.ekzbcx6 Copy
Authors: Tjusls China
Proper citation: Tjusls China 2019. 03 Ligation. protocols.io dx.doi.org/10.17504/protocols.io.49igz4e Copy
Authors: Benjamin Emert
Group: Human Cell Atlas Method Development Community, RajLab
Summary: Protocol for making invertedClampFISH probes.
Proper citation: Benjamin Emert 2018. invertedClampFISH ligation. protocols.io dx.doi.org/10.17504/protocols.io.qnkdvcw Copy
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