Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Determining Chlorophyll Concentration using CuSO4 Magnesium-Copper Exchange Titration Resource Report Resource Website |
Victor Rodriguez | DOI:10.17504/protocols.io.7xrhpm6 | This protocol is designed to be able to extract and analyze the concentration of chlorophyll within a sample on a molecular level. The procedures of this protocol require using copper II sulfate and hydrochloric acid as a means of trituration to determine the approximate level a chlorophyll within a given sample. | Independent Researcher | 1 | 2019 | Victor Rodriguez 2019. Determining Chlorophyll Concentration using CuSO4 Magnesium-Copper Exchange Titration. protocols.io https://dx.doi.org/10.17504/protocols.io.7xrhpm6 | 2021-04-15 09:14:36 | ||||
|
CviJI Assay Conditions Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.esqbedw | VERVE Net | For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviJI Assay Conditions. protocols.io https://dx.doi.org/10.17504/protocols.io.esqbedw | 2021-04-15 09:14:36 | ||||
|
Basic Molecular Biology Resource Report Resource Website |
Ken Christensen | DOI:10.17504/protocols.io.bc64izgw | A collection of public protocols used in the Christensen Lab. | Brigham Young University | 2 | 2020 | Ken Christensen 2020. Basic Molecular Biology. protocols.io https://dx.doi.org/10.17504/protocols.io.bc64izgw | 2021-04-15 09:14:48 | ||||
|
Dundee neutrophil isolation protocol (from whole blood) Resource Report Resource Website |
Ying Fan, Andrew J.M. Howden, Dario R. Alessi, Esther M. Sammler | DOI:10.17504/protocols.io.bnhtmb6n | asap | We describe a fast and efficient immunomagnetic negative isolation method to purify peripheral blood neutrophils for LRRK2 kinase pathway analysis in humans .justify:after { content: ""; display:inline-block; width: 100%; } Gain of kinase function mutations in the Leucine rich repeat kinase 2 (LRRK2) are associated with causing Parkinson’s disease. LRRK2 phosphorylates a subgroup of Rab GTPases and their phosphorylation levels mirror LRRK2 kinase activation status. Here, we describe a facile and robust method for isolating peripheral blood neutrophils by immunomagnetic negative selection, subsequent treatment with and without the specific LRRK2 kinase inhibitor MLi-2 to ensure that any effect seen is LRRK2 kinase dependent and cell lysis. Neutrophil lysates can then be used to quantify LRRK2 kinase pathway activity by measuring LRRK2-mediated phosphorylation of its endogenous Rab GTPase substrates either by quantitative immunoblotting or targeted mass-spectrometry. The benefit of using peripheral blood neutrophils is that they are an abundant and homogenous white blood cell population that express relatively high levels of LRRK2, Rab10 and other Rab GTPases. The downside is their high intrinsic elastase serine protease activity that necessitates using the neurotoxic, but efficient serine protease inhibitor Diisopropyl fluorophosphate (DIFP) when lysing the cells. Using this assay, we have demonstrated significantly elevated LRRK2 kinase pathway activity in human peripheral blood neutrophils of patients carrying specific mutations such as LRRK2 R1441G (doi:https://doi.org/10.1101/2021.01.28.21249614) and VPS35 D620N (PMID:29743203). This assay can also be used for pharmacodynamic and target engagement studies of small molecule LRRK2 kinase inhibitors. .justify:after { content: ""; display:inline-block; width: 100%; } | Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK, Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK, Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK, Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK | 1 | 2021 | Ying Fan, Andrew J.M. Howden, Dario R. Alessi, Esther M. Sammler 2021. Dundee neutrophil isolation protocol (from whole blood). protocols.io https://dx.doi.org/10.17504/protocols.io.bnhtmb6n | 2021-04-15 09:14:35 | |||
|
Doctor Vida Pocket - COVID-19 assay - Instructions for Use Resource Report Resource Website |
goncalo.doria | DOI:10.17504/protocols.io.bkc8kszw | XPRIZE Rapid Covid Testing | Instruction of use for Doctor Vida pocket - COVID-19 assay | STAB VIDA Lda | 1 | 2020 | goncalo.doria 2020. Doctor Vida Pocket - COVID-19 assay - Instructions for Use. protocols.io https://dx.doi.org/10.17504/protocols.io.bkc8kszw | 2021-04-15 09:14:48 | |||
|
Canary VOC testing protocol Resource Report Resource Website |
Charlie Mize, Raj Reddy, Purav Badani | DOI:10.17504/protocols.io.bkm4ku8w | Canary, XPRIZE Rapid Covid Testing | Canary Health Technologies, Canary Health Technologies, Canary Health Technologies | 1 | 2020 | Charlie Mize, Raj Reddy, Purav Badani 2020. Canary VOC testing protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bkm4ku8w | 2021-04-15 09:14:34 | ||||
|
Competition among Aedes aegypti larvae in microcosms Resource Report Resource Website |
Kurt Steinwascher | DOI:10.17504/protocols.io.tcweixe | Female larvae of the Aedes aegypti mosquito outcompete male larvae for food. Male larvae pupate earlier and at smaller masses in vials where competition is most intense. Competition at the higher densities causes the food/larva to appear lower than the equivalent mg/larva at lower densities for both sexes. The total food per vial appears to change the nature of the exploitative competition among females, which affects the competition among males. No interference competition was observed; females may dominate the competition by their larger size (increased filtering ability) and by retaining food particles within their guts to extract a larger fraction of their nutrients. Pupal mass for both sexes is primarily affected by food/larva; density affects the pupal mass through competition and the total food/vial (the interaction between food and density) and this interaction is different for the two sexes. Age at pupation is more affected by density than by food/larva and the interaction between food and density also differs across the two sexes for this variable. The nature of competition between and within the sexes at various food levels and densities is described. The implications of this complex response to food level and density among larvae on the ecology of this species is considered. | Steinwascher K (2018) Competition among Aedes aegypti larvae. PLoS ONE 13(11): e0202455. doi: 10.1371/journal.pone.0202455 | retired | https://doi.org/10.1371/journal.pone.0202455 | 1 | 2018 | Kurt Steinwascher 2018. Competition among Aedes aegypti larvae in microcosms. protocols.io https://dx.doi.org/10.17504/protocols.io.tcweixe | 2021-04-15 09:14:34 | ||
|
10Xv3.1 Genomics Sample Processing Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.brt5m6q6 | BICCN, Allen Institute for Brain Science | This protocol is used for the rapid generation of 3’ transcriptomic-NGS-ready- single-cell-libraries from pools of cells.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number's 1U01MH114812-01 and 1U19MH114830-01. 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 | https://community.brain-map.org/ | 1 | 2021 | Allen Institute for Brain Science 2021. 10Xv3.1 Genomics Sample Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.brt5m6q6 | 2021-04-15 09:14:47 | ||
|
Encasing LAMP mixture in paraffin Resource Report Resource Website |
Niels Appelman | DOI:10.17504/protocols.io.8jbhuin | iGEM Wageningen 2019 | This protocol can be used to encase LAMP mastermix and primers in paraffin. | Wageningen University | 1 | 2019 | Niels Appelman 2019. Encasing LAMP mixture in paraffin. protocols.io https://dx.doi.org/10.17504/protocols.io.8jbhuin | 2021-04-15 09:14:34 | |||
|
Multiplexed scNOMe-seq protocol based on isolated single nuclei Resource Report Resource Website |
Sebastian Pott, Michael Wasney, Nadia Khan | DOI:10.17504/protocols.io.bgfvjtn6 | Single_Cell_Uchicago | What follows is the protocol for performing single-cell Nucleosome Occupancy and Methylome sequencing on single nuclei (scNOMe-seq). This plate-based method, which can be used to simultaneously assess nucleosome occupancy and DNA methylation in single nuclei, draws upon the approach laid out in Luo et al., 2018. Everything from the initial nuclei sorting step to the final library preparation that directly precedes sequencing is included in this protocol. This protocol is optimized for non-neuronal nuclei and can be applied to a range of different cell types (e.g., intestinal organoid, fibroblasts).This is the method we are using and it is working.Adapted from "Robust single-cell DNA methylome profiling with snmC-seq2," by C. Luo et al., 2018, Nature Communications 9(1), pp. 1-6. Copyright 2018 by the authors. | Department of Medicine, University of Chicago, Department of Medicine, University of Chicago, Department of Medicine, University of Chicago | 2 | 2020 | Sebastian Pott, Michael Wasney, Nadia Khan 2020. Multiplexed scNOMe-seq protocol based on isolated single nuclei. protocols.io https://dx.doi.org/10.17504/protocols.io.bgfvjtn6 | 2021-04-15 09:14:47 | |||
|
RNA Samples Steps Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dev3e5 | VERVE Net, Sullivan Lab | For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. RNA Samples Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.dev3e5 | 2021-04-15 09:14:34 | |||
|
Rearing of Drosophila on Holidic Media (HM) for feeding behavior assays Resource Report Resource Website |
Zita Santos, Patrícia Francisco, Margarida Anjos, Célia Baltazar, Ana Paula Elias, Gabriela Tondolo Fioreze, Pavel M. Itskov, Matthew D. W. Piper, Carlos Ribeiro | DOI:10.17504/protocols.io.hhcb32w | Ribeiro Lab | This protocol is part of the manuscript: Gonçalves et al. Commensal bacteria and essential amino acids control food choice behavior and reproduction. Plos Biology. 2017 Apr 18. | Leitão-Gonçalves R, Carvalho-Santos Z, Francisco AP, Fioreze GT, Anjos M, Baltazar C, Elias AP, Itskov PM, Piper MDW, Ribeiro C, Commensal bacteria and essential amino acids control food choice behavior and reproduction. PLoS Biology 15(4). doi: 10.1371/journal.pbio.2000862 | Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences | https://doi.org/10.1371/journal.pbio.2000862 | 1 | 2017 | Zita Santos, Patrícia Francisco, Margarida Anjos, Célia Baltazar, Ana Paula Elias, Gabriela Tondolo Fioreze, Pavel M. Itskov, Matthew D. W. Piper, Carlos Ribeiro 2017. Rearing of Drosophila on Holidic Media (HM) for feeding behavior assays. protocols.io https://dx.doi.org/10.17504/protocols.io.hhcb32w | 2021-04-15 09:14:47 | |
|
ELISA for quantification of IL-31 in human serum. Resource Report Resource Website |
Angel Justiz-Vaillant | DOI:10.17504/protocols.io.bkemktc6 | 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. IL-31 is produced mainly by Th2 cells and dendritic cells. It is a proinflammatory cytokine and a chemotactic factor that direct polymorphonuclear cells, monocytes, and T cells to inflammatory lesions. IL-31 induces chemokines production and synthesis of IL-6, IL-16, and IL-32. [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-31 in human serum.. protocols.io https://dx.doi.org/10.17504/protocols.io.bkemktc6 | 2021-04-15 09:14:47 | |||
|
2×CTAB Protocol for Isolation of predominantly Symbiodinium DNA from symbiotic anemones Resource Report Resource Website |
Pringle Lab, Christian Renicke | DOI:10.17504/protocols.io.kzqcx5w | Aiptasia-Symbiodiniaceae Model System | This protocol is kit-free and can be used to isolate high quality genomic DNA of predominantly Symbiodinium from symbiotic Aiptasia which can be used as e.g. PCR template for genotyping. It is based on the method described in Coffroth et al., 1992. | Stanford University, Stanford University | 1 | 2018 | Pringle Lab, Christian Renicke 2018. 2×CTAB Protocol for Isolation of predominantly Symbiodinium DNA from symbiotic anemones. protocols.io https://dx.doi.org/10.17504/protocols.io.kzqcx5w | 2021-04-15 09:14:47 | |||
|
ELISPOT Protocol Resource Report Resource Website |
Sam Li | DOI:10.17504/protocols.io.98yh9xw | BioLegend | BioLegend | https://www.biolegend.com/protocols/elispot-protocol/4249/ | 3 | 2019 | Sam Li 2019. ELISPOT Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.98yh9xw | 2021-04-15 09:14:34 | |||
|
Agar Plate Preparation Resource Report Resource Website |
Andrew Crowley | DOI:10.17504/protocols.io.4c3gsyn | Ackerman Lab | Default scale - 1 L (makes approx. 2.5 sleeves of plates) | Dartmouth College, Ackerman Lab | 2 | 2019 | Andrew Crowley 2019. Agar Plate Preparation. protocols.io https://dx.doi.org/10.17504/protocols.io.4c3gsyn | 2021-04-15 09:14:47 | |||
|
Subcellular localisation of newly synthesized viral RNA in coronavirus infection by EM autoradiography Resource Report Resource Website |
Ronald W.A.L. Limpens, Eric J. Snijder, Abraham J. Koster, Montserrat Bárcena | DOI:10.17504/protocols.io.bfrtjm6n | Coronavirus Method Development Community | This protocol allowed the subcellular localisation of viral RNA synthesis in coronavirus-infected cells by EM autoradiography, though it is largely applicable to other types of EM autoradiography samples. Newly synthesized viral RNA is metabolically labelled by providing the infected cells with tritiated uridine while arresting cellular transcription. Subsequently, the samples are processed for EM, sectioned and incubated with a photographic emulsion. Radioactive disintegrations from the labelled viral RNA generate signal around the radioactive source that, after development, becomes apparent as electron-dense grains that can be detected by transmission electron microscopy. The advantages of this approach are its high sensitivity and its compatibility with high-contrast EM sample preparation protocols. The protocol presented here is an adaptation of different methods and tips to EM autoradiography discussed in detail by Williams, in Glauert, 1977, Practical Methods in Electron Microscopy, Volume 6, Chapter 4. | Snijder EJ, Limpens RWAL, Wilde AHd, Jong AWMd, Zevenhoven-Dobbe JC, Maier HJ, Faas FFGA, Koster AJ, Bárcena M (2020) A unifying structural and functional model of the coronavirus replication organelle: Tracking down RNA synthesis. PLoS Biol 18(6): e3000715. doi: 10.1371/journal.pbio.3000715 | Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands, Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands, Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands, Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands | https://www.kosterlab.nl/virus-replication-18 | 1 | 2020 | Ronald W.A.L. Limpens, Eric J. Snijder, Abraham J. Koster, Montserrat Bárcena 2020. Subcellular localisation of newly synthesized viral RNA in coronavirus infection by EM autoradiography. protocols.io https://dx.doi.org/10.17504/protocols.io.bfrtjm6n | 2021-04-15 09:14:47 | |
|
Immunocytochemistry Staining Protocol Resource Report Resource Website |
Simeng Li | DOI:10.17504/protocols.io.thwej7e | University College Dublin | http://www.biolegend.com/media_assets/support_protocol/Immunofluorescence_Microscopy_Protocol_050514.pdf | 1 | 2018 | Simeng Li 2018. Immunocytochemistry Staining Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.thwej7e | 2021-04-15 09:14:48 | ||||
|
Mixture for PCR Amplification (E7370) Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.cg7tzm | New England Biolabs (NEB) | New England Biolabs | https://www.neb.com/protocols/2012/11/19/pcr-amplification-e7370 | 1 | 2015 | New England Biolabs 2015. Mixture for PCR Amplification (E7370). protocols.io https://dx.doi.org/10.17504/protocols.io.cg7tzm | 2021-04-15 09:14:35 | |||
|
2100 Bioanalyzer Operation for PCR, GTP and IVT Products Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bfzjjp4n | BICCN, Allen Institute for Brain Science | This protocol describes bioanalyzer operation. The Agilent Bioanalyzer is used as a quality control step for PCR and IVT products. Peak size, shape, and sample concentration are recorded and used to evaluate samples on a pass/fail level.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 | 1 | 2020 | Allen Institute for Brain Science 2020. 2100 Bioanalyzer Operation for PCR, GTP and IVT Products. protocols.io https://dx.doi.org/10.17504/protocols.io.bfzjjp4n | 2021-04-15 09:14:51 |
Can't find your Protocol?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. If you want to find a specific protocol and you know the DOI of the protocol already, it's easier to enter a DOI to search. You can refine the search results using Facets on the left side of the search results page. If you are on the table view, you can also search in a specific column by clicking the column title and enter the keywords.
If you still could not find your protocol in the search results, please help us by adding it into the system — it's easy. Create and publish your protocols at Protocols.io.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
