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Authors: Ken Christensen
Summary: The ZR Plasmid Miniprep-Classic kit is designed for efficient isolation of plasmid DNA from E. coli cell lysates using a procedure that is simple, rapid, user-friendly, and reliable. It features a modified alkaline lysis protocol together with a unique Fast Spin column to yield high-quality plasmid DNA in minutes. The ZR Plasmid Miniprep-Classic features color-coded (red, green, yellow) reagents for easy determination of complete cell lysis. The Zymo-Spin llN columns facilitate high yield plasmid DNA that is endotoxin-free. Plasmid DNA purified using the ZR Plasmid Miniprep-Classic kit is well suited for use in restriction endonuclease digestion, sequencing, DNA ligation, cloning, PCR, bacterial transformation, transfection, etc.
Proper citation: Ken Christensen 2020. Zymo Plasmid Miniprep - Classic - CHEM 584. protocols.io dx.doi.org/10.17504/protocols.io.bj5bkq2n Copy
Authors: Jaclyn Winter
Proper citation: Jaclyn Winter 2019. Advanced Marfey's. protocols.io dx.doi.org/10.17504/protocols.io.8f6htre Copy
Authors: Alise Ponsero
Group: iMicrobe, Metafunc course 2018
Summary: How to run Centrifuge version 1.0.4-beta (Kim et al. 2016) through the iMicrobe plaform.Centrifuge is a microbial classification engine that enables rapid, accurate, and sensitive taxonomic labeling of metagenomic reads and quantification of species. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. More informations about centrifuge can be found here : https://ccb.jhu.edu/software/centrifuge/manual.shtml
Proper citation: Alise Ponsero 2018. Run Centrifuge using iMicrobe. protocols.io dx.doi.org/10.17504/protocols.io.spuednw Copy
Authors: Trina Knotts
Group: Mouse Metabolic Phenotyping Centers
Summary: Behaviorally, meals are defined as periods of intense feeding and drinking separated by periods of activity, grooming, and rest. A “meal” is the primary data unit for characterizing food intake behavior. Changes in the patterning of meals (number, size or duration) may affect food intake and energy balance indirectly. "Meal", in our SOP, is defined by a minimum food intake of 0.02g and at least 10 min between food bout events. Detailed analysis of food intake behavior includes an assessment of average meal duration, average meal size, number of meals, average inter-meal interval (IMI), as well as calculation of satiety ratio. In addition, the diurnal (light cycle/dark cycle) patterns of food intake behavior are also calculated to examine temporal shifts in feeding behavior. Meal pattern and food intake behavior is measured in the Columbus Instruments Oxymax system within a temperature and light controlled cabinet. Animals are acclimated to the facility for at least 1 week. Animals are then acclimated to the CLAMS cages and powdered diet for 48 hours and to the light and temperature-controlled chamber for 24 hours prior to testing. Analyzed data constitutes data collected from 48 hours of continuous measurement (2 light/2 dark cycles).
Proper citation: Trina Knotts 2019. UC Davis - Meal Pattern Analysis. protocols.io dx.doi.org/10.17504/protocols.io.yrwfv7e Copy
Authors: Livia Tenuta, Tarcísio Leitão, Jaime A. Cury
Proper citation: Livia Tenuta, Tarcísio Leitão, Jaime A. Cury 2018. Kinetics of calcium binding and release from S. mutans. protocols.io dx.doi.org/10.17504/protocols.io.mamc2c6 Copy
Authors: Dr. Steven Wilhelm, Maddie Denney
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Great Lakes Center for Fresh Waters and Human Health
Summary: Please contact Dr. Steven Wilhelm ([email protected]) or Maddie Denney ([email protected]) for additional information regarding this protocol.Modified from Guan, Riezman, Wenk & Riezman, 2010Please note that there are two versions of this protocol. Use the one that corresponds to your sample.
Proper citation: Dr. Steven Wilhelm, Maddie Denney 2017. Cyanobacteria Total Lipid Extraction. protocols.io dx.doi.org/10.17504/protocols.io.ibkcakw Copy
Authors: Alan Cone
Group: Ju Lab
Proper citation: Alan Cone 2017. 4% / 10% Stacking and Separating Protein Gel. protocols.io dx.doi.org/10.17504/protocols.io.kqgcvtw Copy
Authors: Wolfgang Teufl, Markus Miezal, Bertram Taetz, Michael Fröhlich, Gabriele Bleser
Summary: The attached file contains a detailed description of the methods used in the manuscript "Validity of inertial sensor based 3D joint kinematics of static and dynamic sport and physiotherapy specific movements" for the calculation of 3D joint angles incorporating inertial sensor data and optical motion capture data.
Proper citation: Wolfgang Teufl, Markus Miezal, Bertram Taetz, Michael Fröhlich, Gabriele Bleser 2019. Joint angle calculation from optical markers and IMUs attached to the lower body. protocols.io dx.doi.org/10.17504/protocols.io.vwye7fw Copy
Authors: Sarah Popp, Charmaine Simeonovic
Summary: Paraffin sections of formalin-fixed human pancreas and isolated human islets were treated with 0.05% pronase for antigen retrieval, blocked with 2% bovine serum albumin (BSA; Sigma)/phosphate buffered saline (PBS), incubated overnight (4°C) with 10E4 (anti-HS) mAb (1/10; US Biological/Amsbio), washed and stained with AlexaFluor 488-goat anti-mouse IgM (Thermo Fisher). The same sections were washed, incubated with rabbit anti-human glucagon IgG (Abcam) or guinea-pig anti-pig insulin Ig (Dako), washed and stained with Alexafluor 568-donkey anti-rabbit IgG or AlexaFluor 568-goat anti-guinea-pig IgG (Thermo Fisher). The specificity of HS staining was checked on serial sections using IgMκ isotype control (BD Biosciences), instead of 10E4 mAb, together with anti-glucagon or anti-insulin antibody. Nuclei were stained with DAPI (0.2 μg/ml; Sigma). Sections were photographed using an automated Axio Observer inverted fluorescence microscope (Zeiss). Merged images were prepared using ZEN (version 2.3) software (Zeiss).
Proper citation: Sarah Popp, Charmaine Simeonovic 2018. Immunofluorescence staining of heparan sulfate (HS) in islet beta cells of formalin-fixed human pancreas and isolated islets. protocols.io dx.doi.org/10.17504/protocols.io.kvycw7w Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the procedure for receiving human surgical tissue, followed by trimming, mounting, embedding, and slicing under sterile conditions in order to produce tissue suitable for both slice culture as well as acute slice electrophysiology recording.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U01MH114812. 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. Human Neurosurgical Tissue Processing. protocols.io dx.doi.org/10.17504/protocols.io.bf66jrhe Copy
Authors: Carolina Cadena
Group: VERVE Net
Summary: This protocol is based on the study done by two members of the Biological and Agricultural Engineering department at UC Davis which analyzes the ability of infrared spectroscopy to detect fungal infections in almonds. The methods section of this article was adapted to fit the protocols.io format.
Source: “Detection of fungal infection in almond kernels using near-infrared reflectance spectroscopy”. Pei-Shih Liang, David C. Slaughter, Alejandro Ortega-Beltran, Themis J. Michailides. Biosystems Engineering, Volume 137, September 2015, Pages 64–72
Proper citation: Carolina Cadena 2016. Detecting Fungal Infections in Almonds. protocols.io dx.doi.org/10.17504/protocols.io.etnbeme Copy
Authors: Marloes Van Splunter
Proper citation: Marloes Van Splunter 2019. FACS staining PBMCs for TLR and intracellular staining. protocols.io dx.doi.org/10.17504/protocols.io.87qhzmw Copy
Authors: Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, , Priscila Peña-Diaz1 and Julius Lukeš1, 2
Group: Julius Lukes
Proper citation: Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, , Priscila Peña-Diaz1 and Julius Lukeš1, 2 2018. Cell Counting using a haemocytometer (Neubauer cell chamber) with fixer. protocols.io dx.doi.org/10.17504/protocols.io.hfxb3pn Copy
Authors: Hannah Gunderman, Angelina Spotts, Emma Slayton
Summary: At CMU Libraries, each year we celebrate Love Data Week (LDW) with events, workshops, speakers, and activities to help engage campus in the world of data that surrounds us! Similar to Open Access Week, the purpose of LDW events is to raise awareness and build a community to engage on topics related to research data management, sharing, preservation, reuse, and library-based research data services. We share practical tips, resources, and stories to help researchers at any stage in their career use good data practices. We believe research data are the foundation of the scholarly record and crucial for advancing our knowledge of the world around us.CMU Libraries is proud to offer an institutional license to protocols.io, a collaborative platform for computational workflows, operational procedures, instructions/manuals, and more! It can even be used for cooking recipes! To highlight the research workflow capabilities of protocols.io, we are proud to offer several dessert recipes that are tried-and-true by our 2020 Love Data Week committee at CMU Libraries. Why not make them for a special someone this Valentine's Day?We hope you enjoy, and feel free to contact us at [email protected] if you'd like to use this platform for your research data needs!
Proper citation: Hannah Gunderman, Angelina Spotts, Emma Slayton 2020. Love Data Week 2020 at CMU Libraries - Valentine's Day Dessert Recipes. protocols.io dx.doi.org/10.17504/protocols.io.bcccissw Copy
Authors: Nicholas Boudreau
Summary: Purpose of this protocol is to assess the enzymatic activity of glycosidases using fluorophores conjugated to substrates of interest (such as cellobiose or xylobiose). Once the enzyme of interest cleaves substrate, the fluorophore is released enabling quantification of enzymatic activity.
Proper citation: Nicholas Boudreau 2018. Fluorophore Assessment of Glycosidase Activity. protocols.io dx.doi.org/10.17504/protocols.io.nvzde76 Copy
Authors: Thomas Dugé, Franziska Liesecke
Summary: This workflow described how to download RNA-seq raw data from NCBI or EBI and to process them to quantify transcript abundance.
Proper citation: Thomas Dugé, Franziska Liesecke 2018. RNA-seq quantification from published data. protocols.io dx.doi.org/10.17504/protocols.io.qxhdxj6 Copy
Authors: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
Group: Neurodegeneration Method Development Community
Proper citation: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward 2019. ASSESSING RTTA ACTIVITY (Support Protocol 6) . protocols.io dx.doi.org/10.17504/protocols.io.5w8g7hw Copy
Authors: LI-COR Biosciences
Group: LI-COR Biosciences
Summary: This is an In-Cell Western™ Assay protocol for the detection of Phospho-p53 in COS cells in response to Hydroxyurea.
Developed for:
Aerius,
Odyssey® Classic,
Odyssey CLx, and
Odyssey Sa
Infrared Imaging Systems
Please refer to your manual to confirm that this protocol is appropriate for the applications compatible with your Odyssey Imager model.
Proper citation: LI-COR Biosciences 2018. In-Cell Western™ Assay (COS Cells Phospho-p53 Detection in Response to Hydroxyurea). protocols.io dx.doi.org/10.17504/protocols.io.grtbv6n Copy
Authors: Integrated Islet Distribution Program
Group: Integrated Islet Distribution Program, Integrated Islet Distribution Program and Human Islet Phenotyping Program
Summary: This SOP defines the pancreas donor profile acceptable for use in the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) sponsored research in the Integrated Islet Distribution Program (IIDP). This SOP applies to all IIDP islet distribution centers using funds from the NIDDK to manufacture purified human pancreatic islets for basic research studies for IIDP approved investigators.The IIDP depends on the subcontracted human islet isolation centers to provide research investigators with human islets. It is the responsiblity of the human islet centers to obtain research quality pancreata from the Organ Procurement Organizations (OPO). Some criteria are stricter than those used by transplant centers for organ transplant donors. This protocol provides the inclusion and exclusion criteria in order to determine the proper parameters for research donors.The donor criteria also reflects the required 2020 testing for COVID-19. Positive testing for COVID-19, HIV, Hepatitis C, and Hepatitis B are examples of some exclusion criteria.References (attached)OPTN Policies Effective as of April 3 2020 [Emergency COVID-19 Policy Actions]Organ Procurement and Transplantation Network, 2020 Apr.2013 PHS Guideline for Reducing Human Immunodeficiency Virus, Hepatitis B Virus, and Hepatitis C Virus Transmission through Organ Transplantation1 Behavioral Risk Factors for Recent HIV, HBV, or HCV Infection. Organ Procurement and Transplantation Network, 2013 Nov.
Proper citation: Integrated Islet Distribution Program 2020. Determining IIDP Minimal Donor Criteria. protocols.io dx.doi.org/10.17504/protocols.io.bhdvj266 Copy
Authors: Alex Zegarra
Proper citation: Alex Zegarra 2020. Long Primer PCR (for Trypanosoma brucei) . protocols.io dx.doi.org/10.17504/protocols.io.bgcnjsve Copy
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