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| Name | Authors | DOI | Group |
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RRIDs used | ||||||
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iDISCO Clearing and Staining of Pancreas Resource Report Resource Website |
Maria Jimenez Gonzalez, Sarah Stanley, Rosemary Li | 10.17504/protocols.io.baxbifin | This is a protocol for iDISCO Clearing and immunostaining of pancreata/intrapancreatic ganglia in mice. | Icahn School of Medicine at Mount Sinai, Icahn School of Medicine at Mount Sinai, Icahn School of Medicine at Mount Sinai | 1 | 2020 | Maria Jimenez Gonzalez, Sarah Stanley, Rosemary Li 2020. iDISCO Clearing and Staining of Pancreas. protocols.io dx.doi.org/10.17504/protocols.io.baxbifin | 2021-03-29 03:08:36 | ||||
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MegaLong™ Protocols Collection for Isolation of >100kb Genomic DNA Resource Report Resource Website |
G-Biosciences | 10.17504/protocols.io.e7kbhkw | G-Biosciences | This is a collection of G-Biosciences MegaLong™ protocols for the isolation of >100kb Genomic DNA .MegaLong™ isolates high molecular weight (>100kb) genomic DNA from a variety of samples, including animal tissues, cultured cells, whole blood, bacterial and yeast. Please refer to the appropriate protocol below, depending on your application. | https://www.gbiosciences.com/image/pdfs/protocol/786-146_protocol.pdf | 1 | 2016 | G-Biosciences 2016. MegaLong™ Protocols Collection for Isolation of >100kb Genomic DNA. protocols.io dx.doi.org/10.17504/protocols.io.e7kbhkw | 2021-03-29 03:08:36 | |||
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Mouse Cardiac Perfusion Fixation and Brain Collection Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.beudjes6 | BICCN, Allen Institute for Brain Science | This protocol describes the procedures for intracardiac perfusion fixation of postnatal mice, including anesthesia, exsanguination, fixation, brain removal and post-fixation storage. Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 3 | 2020 | Allen Institute for Brain Science 2020. Mouse Cardiac Perfusion Fixation and Brain Collection. protocols.io dx.doi.org/10.17504/protocols.io.beudjes6 | 2021-03-29 03:08:36 | |||
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Determination of florfenicol and florfenicol amine in fish plasma (Salmo salar) through HPLC MS/MS Resource Report Resource Website |
Betty San Martín, Lisette Lapierre, Marcela Fresno, Javiera Cornejo | 10.17504/protocols.io.zhdf326 | Martín BS, Fresno M, Cornejo J, Godoy M, Ibarra R, Vidal R, Araneda M, Anadón A, Lapierre L (2019) Optimization of florfenicol dose against Piscirickettsia salmonis in Salmo salar through PK/PD studies. PLoS ONE 14(5): e0215174. doi: 10.1371/journal.pone.0215174 | Universidad de Chile, Universidad de Chile, Universidad de Chile, Universidad de Chile | https://doi.org/10.1371/journal.pone.0215174 | 1 | 2019 | Betty San Martín, Lisette Lapierre, Marcela Fresno, Javiera Cornejo 2019. Determination of florfenicol and florfenicol amine in fish plasma (Salmo salar) through HPLC MS/MS. protocols.io dx.doi.org/10.17504/protocols.io.zhdf326 | 2021-03-29 03:08:37 | |||
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WILLIS -HOBBS AGAR Resource Report Resource Website |
Roey Angel, Ana Lara-Rodriguez | 10.17504/protocols.io.3exgjfn | SoWa RI Anaerobic and Molecular Microbiology (public) | For the diferential isolation of Clostridium sp. | Soil and Water Research Infrastructure, Soil and Water Research Infrastructure | http://himedialabs.com/TD/M1375.pdf | 1 | 2020 | Roey Angel, Ana Lara-Rodriguez 2020. WILLIS -HOBBS AGAR. protocols.io dx.doi.org/10.17504/protocols.io.3exgjfn | 2021-03-29 03:08:37 | ||
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Autoclaving Erlenmeyer Flasks for Sterile Algal Cultures Resource Report Resource Website |
Jakub Nedbal | 10.17504/protocols.io.bd2di8a6 | This protocol describes autoclaving the Erlenmeyer flasks for sterile microalgae culture. It describes the cleaning and preparation of flasks for autoclaving. In the second part, the protocol describes the method of autoclaving. | King's College London | https://app.labstep.com/sharelink/8251a76e-d779-469b-8d01-e4627440d4b0 | 1 | 2020 | Jakub Nedbal 2020. Autoclaving Erlenmeyer Flasks for Sterile Algal Cultures. protocols.io dx.doi.org/10.17504/protocols.io.bd2di8a6 | 2021-03-29 03:08:37 | |||
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Case - Measurement of Food Consumption and Body Weight Resource Report Resource Website |
Henri Brunengraber | 10.17504/protocols.io.yeqftdw | Mouse Metabolic Phenotyping Centers | During the course of development or during a diet study the amount of food and body weights are measured 1-2 times per week. | Case Western Reserve University | https://mmpc.org/shared/document.aspx?id=269&docType=Protocol | 1 | 2019 | Henri Brunengraber 2019. Case - Measurement of Food Consumption and Body Weight. protocols.io dx.doi.org/10.17504/protocols.io.yeqftdw | 2021-03-29 03:08:38 | ||
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ELISA for quantification of IL-5 in human serum. Resource Report Resource Website |
Angel Justiz-Vaillant | 10.17504/protocols.io.bj25kqg6 | University of the West Indies, [email protected] | Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. They play essential roles in the activation and differentiation of immune cells, as well as proliferation, maturation, migration, and adhesion. They also have pro-inflammatory and anti-inflammatory properties. The primary function of interleukins is, therefore, to modulate growth, differentiation, and activation during inflammatory and immune responses. Interleukins consist of a large group of proteins that can elicit many reactions in cells and tissues by binding to high-affinity receptors in cell surfaces. They have both paracrine and autocrine function. Interleukins are also used in animal studies to investigate aspect related to clinical medicine.T cells and stem cells make IL-3. It functions as a multilineage colony-stimulating factor. CD4+T cells (Th2) produce IL-5, and its principal targets are B cells. It causes B-cell growth factor and differentiation and IgA selection. Besides, causes eosinophil activation and increased production of these innate immune cells [1]Reference1. Justiz Vaillant AA, Qurie A. Interleukin. In:StatPearls. Treasure Island (FL): StatPearls Publishing; June 12, 2019. | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. ELISA for quantification of IL-5 in human serum.. protocols.io dx.doi.org/10.17504/protocols.io.bj25kqg6 | 2021-03-29 03:08:38 | |||
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Polarization of Mouse CD4+ Cells Resource Report Resource Website |
BioLegend, Inc. | 10.17504/protocols.io.ezsbf6e | BioLegend | This is collection of BioLegend protocols for polarization of mouse CD4+ cells. Please make sure you refer to the correct protocol, depending on whether you are using Th1, Th2, Th17, or Treg. | , | 1 | 2016 | BioLegend, Inc. 2016. Polarization of Mouse CD4+ Cells. protocols.io dx.doi.org/10.17504/protocols.io.ezsbf6e | 2021-03-29 03:08:38 | |||
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DNA Quantification using the Qubit Fluorometer Resource Report Resource Website |
Julie Haendiges, Ruth Timme, Padmini Ramachandran, Maria Balkey | 10.17504/protocols.io.bi8dkhs6 | GenomeTrakr | This procedure outlines the protocol for quantitation of gDNA for subsequent WGS. This document applies to all laboratory personnel in the Division of Microbiology (DM) as well as laboratories in the GenomeTrakr Network.Complete in order:1. DNA Extraction (Manual DNA Extraction or Automated DNA Extraction using the Qiacube)Step-by-step procedures to obtain high quality DNA from isolates in TSB for whole genome sequencing2. DNA Quantitation (included SOP)Quantitation of extracted DNA using the Qubit Flourometer 3. Library Preparation for WGS (Library preparation using Illumina DNA Prep or Library Preparation using Illumina Nextera XT )Library preparation using NexteraXT or Illumina DNA Prep (previously Nextera DNA Flex)2. DNA Quantitation (included SOP)Quantitation of extracted DNA using the Qubit Flourometer 3. Library Preparation for WGS (Library preparation using Illumina DNA Prep or Library Preparation using Illumina Nextera XT )Library preparation using NexteraXT or Illumina DNA Prep (previously Nextera DNA Flex)3. Library Preparation for WGS (Library preparation using Illumina DNA Prep or Library Preparation using Illumina Nextera XT )4. Sequencing using Illumina MiSeq5. Data Quality Checks and NCBI Submission | US Food and Drug Administration, US Food and Drug Administration, US Food and Drug Administration, US Food and Drug Administration | 1 | 2020 | Julie Haendiges, Ruth Timme, Padmini Ramachandran, Maria Balkey 2020. DNA Quantification using the Qubit Fluorometer. protocols.io dx.doi.org/10.17504/protocols.io.bi8dkhs6 | 2021-03-29 03:08:38 | |||
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Sample preparation Resource Report Resource Website |
philippe.bechtold | 10.17504/protocols.io.bjygkptw | XPRIZE Rapid Covid Testing | ETHZ - ETH Zurich | 1 | 2020 | philippe.bechtold 2020. Sample preparation. protocols.io dx.doi.org/10.17504/protocols.io.bjygkptw | 2021-03-29 03:08:37 | ||||
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Universal sandwich ELISA for investigating the binding of avian immunoglobulins to Staphylococcal protein-A (SpA) using anti-IgY-peroxidase conjugate. Resource Report Resource Website |
Angel Justiz-Vaillant, Monica F. Smikle | 10.17504/protocols.io.bjqxkmxn | 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 avian immunoglobulins to Staphylococcal protein-A (SpA) using anti-IgY-peroxidase conjugate.. protocols.io dx.doi.org/10.17504/protocols.io.bjqxkmxn | 2021-03-29 03:08:42 | ||||
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SPARC_Duke_PelotGrill_OT2-OD025340_HumanVagusNerve_Claudin1IHC_Morphology Resource Report Resource Website |
Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Jake E. Cariello, Kara A. Clissold, Warren M. Grill | 10.17504/protocols.io.bh4dj8s6 | SPARC | The protocol describes immunohistochemistry with anti-claudin-1, imaging, image segmentation, and image analysis methods to quantify human vagus nerve morphology. | Duke University, Duke University, Duke University, Duke University, Duke University, Duke University | 4 | 2020 | Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Jake E. Cariello, Kara A. Clissold, Warren M. Grill 2020. SPARC_Duke_PelotGrill_OT2-OD025340_HumanVagusNerve_Claudin1IHC_Morphology. protocols.io dx.doi.org/10.17504/protocols.io.bh4dj8s6 | 2021-03-29 03:08:42 | |||
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FFPE Tissue Pre-treatment Before t-CyCIF on Leica Bond RX Resource Report Resource Website |
Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger | 10.17504/protocols.io.bji2kkge | Laboratory of Systems Pharmacology, NCIHTAN | Tissue-based cyclic immunofluorescence (t-CyCIF) is optimized for FFPE specimens mounted on glass slides. Dewaxing and antigen retrieval are important steps to remove wax and expose antigenic sites. This protocol describes dewaxing and antigen retrieval on a Leica Bond RX automated slide processor; similar instruments are manufactured by Ventana or Dako and are commonly found in histopathology core facilities. t-CyCIF can also be performed following manual de-waxing and antigen retrieval (e.g. microwaving slides in citrate buffer or using a pressure cooker). | Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA;Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA;Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA;Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA;Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA;Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA;Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA;Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA;Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA | www.cycif.org | 2 | 2020 | Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger 2020. FFPE Tissue Pre-treatment Before t-CyCIF on Leica Bond RX. protocols.io dx.doi.org/10.17504/protocols.io.bji2kkge | 2021-03-29 03:08:42 | ||
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Human embryonic gonad dissociation with Trypsin-EDTA Resource Report Resource Website |
Regina Hoo, Roser Vento-Tormo, Carmen Sancho | 10.17504/protocols.io.66fhhbn | Vento-Tormo | This protocol is for enrichment of fetal gonadal cells | Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute | 1 | 2021 | Regina Hoo, Roser Vento-Tormo, Carmen Sancho 2021. Human embryonic gonad dissociation with Trypsin-EDTA. protocols.io dx.doi.org/10.17504/protocols.io.66fhhbn | 2021-03-29 03:08:39 | |||
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VBRC Base By Base: Align entire sequences or subsequence regions Resource Report Resource Website |
Nick Tang | 10.17504/protocols.io.ecybaxw | VERVE Net, Upton-Lab | Viral Bioinformatic Resource CentreProvide databases of viral genomic information. Please check the Organisms menu to see which viruses we support: we’re now focusing on large DNA viruses The VOCs (Virus Orthologous Clusters) database is at the heart of our system. The database links directly to integrated tools for comparative analyses. VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval. Provide easy access to the genes, gene families, and genomes of the different virus families. via a unique series of powerful Java tools that support multiple computer platforms (see VBRC Tools menu). design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists. Rally the research community to provide expert curation of these viral genomes by: Adding value to GenBank sequences through enhancing and updating genome annotations Linking to research reviews/papers for the research community. Collaborate with researchers to help on specific bioinformatics problems, e.g. Custom searches of the databases Building new features into our tools Help with genome annotation | University of Victoria: Department of Biochemistry and Microbiology | 1 | 2016 | Nick Tang 2016. VBRC Base By Base: Align entire sequences or subsequence regions. protocols.io dx.doi.org/10.17504/protocols.io.ecybaxw | 2021-03-29 03:08:41 | |||
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Enzyme linked immunosorbent assay for investigating the binding of protein-LG (SpLG) to immunoglobulins. Resource Report Resource Website |
Angel Justiz-Vaillant, Norma McFarlane-Anderson | 10.17504/protocols.io.bjpmkmk6 | University of the West Indies, [email protected] | This SpLG ELISA can be used to detect specific antibodies in various animal species including human, mouse, rat, dog, rabbit, chicken, monkey, pig and hamster [1].1. Kihlberg BM, Sjöbring U, Kastern W, Björck L. Protein LG: a hybrid molecule with unique immunoglobulin binding properties.J Biol Chem. 1992;267(35):25583-25588. | University of the West Indies St. Augustine, University of West Indies. Mona Campus | 1 | 2020 | Angel Justiz-Vaillant, Norma McFarlane-Anderson 2020. Enzyme linked immunosorbent assay for investigating the binding of protein-LG (SpLG) to immunoglobulins.. protocols.io dx.doi.org/10.17504/protocols.io.bjpmkmk6 | 2021-03-29 03:08:39 | |||
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Reference transcriptome sequence resource for the study of the Cestode Schistocephalus solidus, a threespine stickleback parasite. Resource Report Resource Website |
Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N. | 10.17504/protocols.io.ew9bfh6 | GigaScience Press | These methods accompany the following publication:Hebert, F, O; Grambauer, S; Barber, I; Landry, C, R; Aubin-Horth, N (2016): Reference transcriptome sequence resource for the study of the Cestode Schistocephalus solidus, a threespine stickleback parasite. GigaScience Database. http://dx.doi.org/10.5524/100197 | Hébert FO, Grambauer S, Barber I, Landry CR, Aubin-Horth N, Transcriptome sequences spanning key developmental states as a resource for the study of the cestode , a threespine stickleback parasite. GigaScience doi: 128 | , , , , | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891850/ | 1 | 2016 | Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N. 2016. Reference transcriptome sequence resource for the study of the Cestode Schistocephalus solidus, a threespine stickleback parasite.. protocols.io dx.doi.org/10.17504/protocols.io.ew9bfh6 | 2021-03-29 03:08:41 | |
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RNA isolation of Pinctada fucata martensii Resource Report Resource Website |
Xiong Xinwei | 10.17504/protocols.io.9qgh5tw | This protocol provides details on RNA isolation of the tissue of Pinctada fucata martensii. | Xiong X, Li C, Zheng Z, Du X, Novel globular C1q domain-containing protein (PmC1qDC-1) participates in shell formation and responses to pathogen-associated molecular patterns stimulation in . Scientific Reports doi: 10.1038/s41598-020-80295-0 | Guangdong Ocean University | https://doi.org/10.1371/journal.pone.0226367 | 1 | 2019 | Xiong Xinwei 2019. RNA isolation of Pinctada fucata martensii. protocols.io dx.doi.org/10.17504/protocols.io.9qgh5tw | 2021-03-29 03:08:39 | ||
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OmniPrep™ Protocol Collection for High Quality Genomic DNA Extraction Resource Report Resource Website |
G-Biosciences | 10.17504/protocols.io.e7rbhm6 | G-Biosciences | This is a collection of protocols for high quality genomic DNA extraction using the OmniPrep™ kit. Please refer to the appropriate protocol below depending on your application. | https://www.gbiosciences.com/image/pdfs/protocol/786-136_protocol.pdf | 1 | 2016 | G-Biosciences 2016. OmniPrep™ Protocol Collection for High Quality Genomic DNA Extraction. protocols.io dx.doi.org/10.17504/protocols.io.e7rbhm6 | 2021-03-29 03:08:41 |
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