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Authors: Maria Jimenez Gonzalez, Sarah Stanley, Rosemary Li
Summary: This is a protocol for iDISCO Clearing and immunostaining of pancreata/intrapancreatic ganglia in mice.
Proper citation: Maria Jimenez Gonzalez, Sarah Stanley, Rosemary Li 2020. iDISCO Clearing and Staining of Pancreas. protocols.io dx.doi.org/10.17504/protocols.io.baxbifin Copy
Authors: G-Biosciences
Group: G-Biosciences
Summary: 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.
Proper citation: G-Biosciences 2016. MegaLong™ Protocols Collection for Isolation of >100kb Genomic DNA. protocols.io dx.doi.org/10.17504/protocols.io.e7kbhkw Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. Mouse Cardiac Perfusion Fixation and Brain Collection. protocols.io dx.doi.org/10.17504/protocols.io.beudjes6 Copy
Authors: Betty San Martín, Lisette Lapierre, Marcela Fresno, Javiera Cornejo
Proper citation: 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 Copy
Authors: Roey Angel, Ana Lara-Rodriguez
Group: SoWa RI Anaerobic and Molecular Microbiology (public)
Summary: For the diferential isolation of Clostridium sp.
Proper citation: Roey Angel, Ana Lara-Rodriguez 2020. WILLIS -HOBBS AGAR. protocols.io dx.doi.org/10.17504/protocols.io.3exgjfn Copy
Authors: Jakub Nedbal
Summary: 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.
Proper citation: Jakub Nedbal 2020. Autoclaving Erlenmeyer Flasks for Sterile Algal Cultures. protocols.io dx.doi.org/10.17504/protocols.io.bd2di8a6 Copy
Authors: Henri Brunengraber
Group: Mouse Metabolic Phenotyping Centers
Summary: During the course of development or during a diet study the amount of food and body weights are measured 1-2 times per week.
Proper citation: Henri Brunengraber 2019. Case - Measurement of Food Consumption and Body Weight. protocols.io dx.doi.org/10.17504/protocols.io.yeqftdw Copy
Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: 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.
Proper citation: Angel Justiz-Vaillant 2020. ELISA for quantification of IL-5 in human serum.. protocols.io dx.doi.org/10.17504/protocols.io.bj25kqg6 Copy
Authors: BioLegend, Inc.
Group: BioLegend
Summary: 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.
Proper citation: BioLegend, Inc. 2016. Polarization of Mouse CD4+ Cells. protocols.io dx.doi.org/10.17504/protocols.io.ezsbf6e Copy
Authors: Julie Haendiges, Ruth Timme, Padmini Ramachandran, Maria Balkey
Group: GenomeTrakr
Summary: 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
Proper citation: 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 Copy
Authors: philippe.bechtold
Group: XPRIZE Rapid Covid Testing
Proper citation: philippe.bechtold 2020. Sample preparation. protocols.io dx.doi.org/10.17504/protocols.io.bjygkptw 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 avian immunoglobulins to Staphylococcal protein-A (SpA) using anti-IgY-peroxidase conjugate.. protocols.io dx.doi.org/10.17504/protocols.io.bjqxkmxn Copy
Authors: Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Jake E. Cariello, Kara A. Clissold, Warren M. Grill
Group: SPARC
Summary: The protocol describes immunohistochemistry with anti-claudin-1, imaging, image segmentation, and image analysis methods to quantify human vagus nerve morphology.
Proper citation: 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 Copy
Authors: Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger
Group: Laboratory of Systems Pharmacology, NCIHTAN
Summary: 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).
Proper citation: 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 Copy
Authors: Regina Hoo, Roser Vento-Tormo, Carmen Sancho
Group: Vento-Tormo
Summary: This protocol is for enrichment of fetal gonadal cells
Proper citation: 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 Copy
Authors: Nick Tang
Group: VERVE Net, Upton-Lab
Summary: 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
Proper citation: Nick Tang 2016. VBRC Base By Base: Align entire sequences or subsequence regions. protocols.io dx.doi.org/10.17504/protocols.io.ecybaxw Copy
Authors: Angel Justiz-Vaillant, Norma McFarlane-Anderson
Group: University of the West Indies, [email protected]
Summary: 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.
Proper citation: 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 Copy
Authors: Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N.
Group: GigaScience Press
Summary: 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
Proper citation: 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 Copy
Authors: Xiong Xinwei
Summary: This protocol provides details on RNA isolation of the tissue of Pinctada fucata martensii.
Proper citation: Xiong Xinwei 2019. RNA isolation of Pinctada fucata martensii. protocols.io dx.doi.org/10.17504/protocols.io.9qgh5tw Copy
Authors: G-Biosciences
Group: G-Biosciences
Summary: 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.
Proper citation: G-Biosciences 2016. OmniPrep™ Protocol Collection for High Quality Genomic DNA Extraction. protocols.io dx.doi.org/10.17504/protocols.io.e7rbhm6 Copy
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