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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Thawing and Seeding Frozen Cells Resource Report Resource Website |
Kenneth Schackart | DOI:10.17504/protocols.io.xkmfku6 | Yoon Lab | How to thaw cells from the liquid nitrogen storage and seed into a tissue culture flask | University of Arizona | 1 | 2019 | Kenneth Schackart 2019. Thawing and Seeding Frozen Cells. protocols.io https://dx.doi.org/10.17504/protocols.io.xkmfku6 | 2021-04-15 09:14:36 | |||
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PBMC- 03 - TEFF+TREG Isolation from PBMC with “Miltenyi CD4+CD25+ Regulatory T cell Isolation Kit” Resource Report Resource Website |
Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | DOI:10.17504/protocols.io.bjabkian | List of published work using this procedure: | Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy) | 1 | 2020 | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino 2020. PBMC- 03 - TEFF+TREG Isolation from PBMC with “Miltenyi CD4+CD25+ Regulatory T cell Isolation Kit”. protocols.io https://dx.doi.org/10.17504/protocols.io.bjabkian | 2021-04-15 09:14:36 | ||||
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Isolation of plasmid DNA from E. coli (Alkaline lysis method) Resource Report Resource Website |
Anna Behle | DOI:10.17504/protocols.io.gtbbwin | Axmann Lab | Isolation of plasmid DNA from E. coli using the alkaline lysis method modified from Birnboim et al., 1979. This protocol is suitable for fast, cheap recovery of large amounts of plasmid, e.g. for cloning purposes or restriction analysis. However, the purity of plasmid is insufficient for sequencing. | Institute for Synthetic Microbiology, Heinrich-Heine-University, Düsseldorf | 1 | 2017 | Anna Behle 2017. Isolation of plasmid DNA from E. coli (Alkaline lysis method). protocols.io https://dx.doi.org/10.17504/protocols.io.gtbbwin | 2021-04-15 09:14:36 | |||
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In vivo Nanopool: Pooled sgRNA competition assays to evaluate in vivo cancer dependencies Resource Report Resource Website |
Thomas Skipper, Daniel Bondeson, Brenton Paolella, Francisca Vazquez | Cancer Dependency Map Target Validation | Broad Institute, Broad Institute, Broad Institute, Broad Institute | 1 | 2020 | Thomas Skipper, Daniel Bondeson, Brenton Paolella, Francisca Vazquez 2020. In vivo Nanopool: Pooled sgRNA competition assays to evaluate in vivo cancer dependencies. protocols.io https:// | 2021-04-15 09:14:51 | |||||
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Enrichment of minor allele of SNPs and genetic prediction of type 2 diabetes risk in British population Resource Report Resource Website |
Xiaoyun Lei, Shi Huang | DOI:10.17504/protocols.io.j7icrke | Lei X, Huang S (2017) Enrichment of minor allele of SNPs and genetic prediction of type 2 diabetes risk in British population. PLoS ONE 12(11): e0187644. doi: 10.1371/journal.pone.0187644 | Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, Changsha, Hunan, China, Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, Changsha, Hunan, China | https://doi.org/10.1371/journal.pone.0187644 | 1 | 2017 | Xiaoyun Lei, Shi Huang 2017. Enrichment of minor allele of SNPs and genetic prediction of type 2 diabetes risk in British population. protocols.io https://dx.doi.org/10.17504/protocols.io.j7icrke | 2021-04-15 09:14:35 | |||
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Vandy - Hyperinsulinemic-euglycemic Clamp Resource Report Resource Website |
Li Kang | DOI:10.17504/protocols.io.yyafxse | Mouse Metabolic Phenotyping Centers | Summary:Mice with catheters implanted in the jugular vein (infusions) and carotid artery (sampling) are used for this procedure (V3002). The hyperinsulinemic, euglycemic clamp or “insulin clamp” has been used in a variety of species to assess insulin action. In an insulin clamp, the rate of glucose infused to maintain euglycemia is an index of whole body insulin sensitivity. Isotopes can be used during an insulin clamp to distinguish between insulin’s effects on endogenous glucose production and glucose utilization, or to examine insulin’s effects on specific tissues and metabolic pathways. The insulin infusion rate used in a study depends on a number of factors such as whether the experiment requires a sensitive analysis of endogenous glucose production, or whether the mouse is known to be unusually insulin resistant (e.g. ob/ob). Finally the insulin clamp technique, especially when isotopes are involved, is most quantitative under steady state conditions. Therefore, clamps should be of a duration (~2 h) that is sufficient for the actions of insulin to obtain steady state. The section that follows describes, a) the technical procedures used on the day of a clamp experiment; b) preparation of insulin and tracer infusates; and c) analyses of plasma and tissue radioactivity. Familiarity with these procedures combined with laboratory demonstration provides the investigator with the necessary background to clamp the conscious mouse. | Vanderbilt University | https://mmpc.org/shared/document.aspx?id=239&docType=Protocol | 1 | 2019 | Li Kang 2019. Vandy - Hyperinsulinemic-euglycemic Clamp. protocols.io https://dx.doi.org/10.17504/protocols.io.yyafxse | 2021-04-15 09:14:35 | ||
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Microbiome Assay with 96WP Updated April 2020 Resource Report Resource Website |
Priota Islam | DOI:10.17504/protocols.io.bfrqjm5w | Behavioural Genomics | Imperial College London | 1 | 2020 | Priota Islam 2020. Microbiome Assay with 96WP Updated April 2020. protocols.io https://dx.doi.org/10.17504/protocols.io.bfrqjm5w | 2021-04-15 09:14:49 | ||||
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Single-step purification by heat shock Resource Report Resource Website |
Hossein Tarrahimofrad, Amir Meimandipour, Sareh Arjmand, Mohammadtaghi Beigi Nassiri, Ehsan Jahangirian, Hossein Tavana, Javad Zamani, Somayyeh Rahimnahal, Saeed Aminzadeh | DOI:10.17504/protocols.io.bgbsjsne | After the cultivation period, cells were collected by centrifugation at 3500 × g for 30 min at 4 °C and resuspended in 4 ml lysis buffer (50 mM NaH2PO4, 300 mM NaCl, 10 mM Imidazole and 0.05% Tween 20 at a pH of 7). The mixture was sonicated with 4 × 40 sec pulses followed by 20 sec rest between cycles at 4 °C. The crude extracts were then centrifuged at 9000 × g for 30 min at 4 °C, and the resulting supernatant was heat-treated in a hot water bath at 90 °C for 15 min. Insoluble material was separated by centrifugation at 13000 × g for 10 min, and the supernatant, containing the enzyme, was analyzed on a 12% SDS–polyacrylamide. The purified elution fractions were dialysed overnight in a 50 mM potassium-phosphate buffer (pH=7) at 4 °C. | Tarrahimofrad H, Meimandipour A, Arjmand S, Nassiri MB, Jahangirian E, Tavana H, Zamani J, Rahimnahal S, Aminzadeh S (2020) Structural and biochemical characterization of a novel thermophilic Coh01147 protease. PLoS ONE 15(6): e0234958. doi: 10.1371/journal.pone.0234958 | Bioprocess engineering group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran, Bioprocess engineering group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran, Protein Research Center, Shahid Beheshti University, G. C., Tehran, Iran, Department of Animal Science and Food Technology, Agriculture Science and Natural Resources University Khouzestan, Ahwaz, Iran, Bioprocess engineering group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran, Department of Biomedical Engineering, The University of Akron, Akron, OH 44325, USA, Bioprocess engineering group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran, Bioprocess engineering group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran, Bioprocess engineering group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran | https://doi.org/10.1371/journal.pone.0234958 | 1 | 2020 | Hossein Tarrahimofrad, Amir Meimandipour, Sareh Arjmand, Mohammadtaghi Beigi Nassiri, Ehsan Jahangirian, Hossein Tavana, Javad Zamani, Somayyeh Rahimnahal, Saeed Aminzadeh 2020. Single-step purification by heat shock. protocols.io https://dx.doi.org/10.17504/protocols.io.bgbsjsne | 2021-04-15 09:14:35 | ||
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Flag M2 immunoprecipitation and Western Blot in Drosophila Resource Report Resource Website |
Caroline Grabbe, Ingrid Dacklin, Behzad Khoshnood | DOI:10.17504/protocols.io.jivcke6 | Khoshnood B, Dacklin I, Grabbe C (2017) A proteomics approach to identify targets of the ubiquitin-like molecule Urm1 in Drosophila melanogaster. PLoS ONE 12(9): e0185611. doi: 10.1371/journal.pone.0185611 | Umeå University, Umeå University, Umeå University | https://doi.org/10.1371/journal.pone.0185611 | 1 | 2017 | Caroline Grabbe, Ingrid Dacklin, Behzad Khoshnood 2017. Flag M2 immunoprecipitation and Western Blot in Drosophila. protocols.io https://dx.doi.org/10.17504/protocols.io.jivcke6 | 2021-04-15 09:14:50 | |||
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Anesthetizing Sea Cucumbers Resource Report Resource Website |
Jon Eilers | DOI:10.17504/protocols.io.5nyg5fw | This protocol is for anesthetizing sea cucumbers. After soaking the sea cucumber in the menthol/ethanol/saltwaer solution for 30-60 minutes the sea cucumber should be flacid and relatively unresponsive to poking. No sea cucumber has eviscerated during surgery after being anesthetized although they do contract and appear like they are trying. The anesthestia wears off quickly after being placed back in salt water. This protocol is based on the method for anesthetizing Apostichopus japonicus as published in the citation below | Walla Walla College | 1 | 2019 | Jon Eilers 2019. Anesthetizing Sea Cucumbers. protocols.io https://dx.doi.org/10.17504/protocols.io.5nyg5fw | 2021-04-15 09:14:36 | ||||
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Protein Synthesis Reaction using PURExpress (E6800) Resource Report Resource Website |
New England Biolabs | New England Biolabs | https://www.neb.com/protocols/0001/01/01/protein-synthesis-reaction-using-purexpress-e6800 | 1 | 2020 | New England Biolabs 2020. Protein Synthesis Reaction using PURExpress (E6800). protocols.io https:// | 2021-04-15 09:14:50 | |||||
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Growing and harvesting Electro Competent E-coli Cells Resource Report Resource Website |
Leo Blondel | DOI:10.17504/protocols.io.gc7bszn | for 500ml (2x250ml) | Harvard University | 1 | 2016 | Leo Blondel 2016. Growing and harvesting Electro Competent E-coli Cells. protocols.io https://dx.doi.org/10.17504/protocols.io.gc7bszn | 2021-04-15 09:14:35 | ||||
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Transformation of Aureococcus anophagefferens by Electroporation Resource Report Resource Website |
Eric Gann | DOI:10.17504/protocols.io.g2vbye6 | Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | 1 | 2017 | Eric Gann 2017. Transformation of Aureococcus anophagefferens by Electroporation. protocols.io https://dx.doi.org/10.17504/protocols.io.g2vbye6 | 2021-04-15 09:14:49 | |||||
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EpiTect Plus Bisulfite Conversion Resource Report Resource Website |
Bing Yang | DOI:10.17504/protocols.io.3bfgijn | Jarrard WE, Schultz A, Etheridge T, Damodaran S, Allen GO, Jarrard D, Yang B (2019) Screening of urine identifies PLA2G16 as a field defect methylation biomarker for prostate cancer detection. PLoS ONE 14(6): e0218950. doi: 10.1371/journal.pone.0218950 | University of Wisconsin-Madison | https://doi.org/10.1371/journal.pone.0218950 | 1 | 2019 | Bing Yang 2019. EpiTect Plus Bisulfite Conversion. protocols.io https://dx.doi.org/10.17504/protocols.io.3bfgijn | 2021-04-15 09:14:35 | |||
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Copy of ELISA for quantification of IL-7 in human serum. Resource Report Resource Website |
Angel Justiz-Vaillant | DOI:10.17504/protocols.io.bj28kqhw | 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. Th9, Th2, Th17, mast cells, NKT cells, and regulatory T cells produce interleukin-9. It enhances T-cell survival, mast cell activation and synergy with erythropoietin.[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. Copy of ELISA for quantification of IL-7 in human serum.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj28kqhw | 2021-04-15 09:14:48 | ||||
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Assessment of safety and effectiveness for pediatric patients of cryoanalgesia compared to epidural for the Nuss procedure in real-world data from Electronic Health Records: a protocol and statistical analysis plan Resource Report Resource Website |
Benjamin S. Glicksberg, Roberto Mora, Stefano Rensi, Vivek A. Rudrapatna, Andrew M. Bishara, Elizabeth Gress, Rohit Vashisht, Michael Zobel, Benjamin Padilla, Benjamin Padilla, Atul J. Butte | DOI:10.17504/protocols.io.bbpaimie | Randomized control trials (RCTs) are the gold standard for clinical trials to evaluate effectiveness and safety of interventions. Conducting RCTs, however, is not always feasible, particularly for rare conditions. Real-world data (RWD), including clinical information from Electronic Health Records (EHR), are utilized for similar analyses in retrospective data. The United States Food and Drug Administration are increasingly receptive of accepting such analyses as evidence as long as the studies are designed and conducted robustly. EHR work suffers from a reproducibility crisis due to such factors such as hospital-specific biases, among others. Akin to preregistration of RCTs, devising, detailing, and publishing protocols of RWD before conducting analyses can enhance reproducibility and fidelity of results. In the current work, we release a detailed protocol to assess effectiveness and safety of a cryoablation intervention compared to epidural for pain control in adolescent patients undergoing the Nuss procedure in the retrospective EHRs of a major hospital system. | Bakar Computational Health Sciences Institute, University of California, San Francisco, USA; Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Department of Surgery, University of California, San Francisco, USA, Department of Surgery, University of California, San Francisco, USA; Department of Bioengineering, Stanford University, USA, Bakar Computational Health Sciences Institute, University of California, San Francisco, USA, Bakar Computational Health Sciences Institute, University of California, San Francisco, USA; 5. Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, USA, Department of Surgery, University of California, San Francisco, USA; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, USA , Bakar Computational Health Sciences Institute, University of California, San Francisco, USA, Department of Surgery, University of California, San Francisco, USA, Department of Surgery, University of California, San Francisco, USA; Department of Surgery, Phoenix Children’s Hospital, USA, Department of Surgery, University of California, San Francisco, USA; Department of Surgery, Phoenix Children’s Hospital, USA, Bakar Computational Health Sciences Institute, University of California, San Francisco, USA | 1 | 2020 | Benjamin S. Glicksberg, Roberto Mora, Stefano Rensi, Vivek A. Rudrapatna, Andrew M. Bishara, Elizabeth Gress, Rohit Vashisht, Michael Zobel, Benjamin Padilla, Benjamin Padilla, Atul J. Butte 2020. Assessment of safety and effectiveness for pediatric patients of cryoanalgesia compared to epidural for the Nuss procedure in real-world data from Electronic Health Records: a protocol and statistical analysis plan. protocols.io https://dx.doi.org/10.17504/protocols.io.bbpaimie | 2021-04-15 09:14:35 | ||||
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Guide for Supporting Diverse Career Exploration of Trainees Resource Report Resource Website |
Lenny Teytelman, Liz Silva, Joanne Kamens, Lex Flagel | DOI:10.17504/protocols.io.8mwhu7e | Academic Career Forum | [Please use the commenting functionality to suggest edits and additional resources. Also, please feel free to use the “copy/fork” button to make a different version of this for your field/institute/students.]In the 1960s, 60% of biomedical PhDs went on to tenure track faculty positions. Today, that fraction is estimated to be 10%-15% of graduate students. Similar trends exist across the biological sciences. This shift means that over the years, many of the students and postdocs in your lab will also explore different career options, and as a good mentor, being able to support them is important, no matter which career track they choose.One of the challenges for professors is that they are deeply familiar with the academic track, but are often at a loss in recommending resources and steps for the trainees who are not 100% certain that they will become faculty as well.This guide is meant to be a starting point. It can be easily shared with the trainees and offers simple tips for career exploration. The goal is not to steer trainees away from academia, but to help them figure out whether academia is the right fit, and if not, how they can explore the many different options that are available to them to find a rewarding and satisfying path.(Image: Flazingo Photos, "Newspaper - Careers", CC BY-SA 2.0) | protocols.io, University of California, San Francisco, Addgene, Bayer Crop Science | 1 | 2020 | Lenny Teytelman, Liz Silva, Joanne Kamens, Lex Flagel 2020. Guide for Supporting Diverse Career Exploration of Trainees. protocols.io https://dx.doi.org/10.17504/protocols.io.8mwhu7e | 2021-04-15 09:14:49 | |||
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DAB Solutions Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bew7jfhn | BICCN, Allen Institute for Brain Science | 3, 3´ Diaminobenzidine (DAB) is a commonly used chromogen for histological staining. In the presence of peroxidase enzyme, DAB produces a brown precipitate that is insoluble in alcohol and xylene. Peroxidase catalyzes hydrogen peroxide oxidation of substrate DAB. This SOP provides instructions to prepare four different formulations of DAB. DAB for Immunohistochemical staining (IHC), DAB for Acetylcholinesterase (AChE) Staining, Nickel Enchanced DAB for Biocytin staining, and DAB for Biocytin staining.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 | 5 | 2020 | Allen Institute for Brain Science 2020. DAB Solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.bew7jfhn | 2021-04-15 09:14:49 | |||
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Finding the core vs flexible microbiome Resource Report Resource Website |
Bonnie Hurwitz | DOI:10.17504/protocols.io.d2y8fv | Hurwitz Lab, ABE487_HMP, ABE487_EMP | In a study comparing obese versus lean twins, Turnbaugh and colleagues found that there were "shared microbial genes among sampled individuals, comprising an extensive, identifiable 'core microbiome' at the gene, rather than at the organismal lineage level". This means that despite having differences in bacterial composition, the "core" functional repertoire of microbiome remains the same in obese versus lean twins. In this tutorial, we are going to explore these functional differences in two lean twins (TS1 and TS2) and two obese twins (TS19 and TS20) from this study. Turnbaugh, Peter J., et al. "A core gut microbiome in obese and lean twins."nature 457.7228 (2009): 480-484. | University of Arizona | 1 | 2015 | Bonnie Hurwitz 2015. Finding the core vs flexible microbiome. protocols.io https://dx.doi.org/10.17504/protocols.io.d2y8fv | 2021-04-15 09:14:35 | |||
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S.O.F protocol for nuclei isolation from fresh and frozen tissues using OptiPrep® discontinuous gradient Resource Report Resource Website |
Luciano Martelotto | DOI:10.17504/protocols.io.bsxhnfj6 | Human Cell Atlas Method Development Community, Single Cell Core, Harvard Medical School | This protocol is the result of the combination of various nuclei isolation protocols for single cell RNA-seq experiments using droplet-based methods, and is an extension of the Frankenstein (S.O.F means Son Of Frankenstein). Developed to prepare nuclei isolates from fresh and frozen material of small-to-large sizes. The good thing is that it does not uses FACS but OptiPrep® discontinuous gradient to remove debris. It is the alternative protocol when FACS is not available. | Harvard Medical School | https://singlecellcore.hms.harvard.edu/ | 4 | 2021 | Luciano Martelotto 2021. S.O.F protocol for nuclei isolation from fresh and frozen tissues using OptiPrep® discontinuous gradient . protocols.io https://dx.doi.org/10.17504/protocols.io.bsxhnfj6 | 2021-04-15 09:14:48 |
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