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.
Authors: Lily Johanna Toro, Germán Alberto Téllez Ramírez, Diana Carolina Henao, Jhon Carlos Castaño Osorio
Group: Grupo de inmunología molecular
Summary: Evaluación de la capacidad de neutralización del efecto del Lipopolisacarido (LPS) de inducir la producción de Factor de Necrosis Tumoral (TNFalfa) en Células Mononucleares de Sangre Periférica (PBMCs) tratadas con peptidos cationicos.
Proper citation: Lily Johanna Toro, Germán Alberto Téllez Ramírez, Diana Carolina Henao, Jhon Carlos Castaño Osorio 2017. Evaluación la producción de TNF alfa por PBMCs estimulados con LPS tratados con péptidos. protocols.io dx.doi.org/10.17504/protocols.io.jb6cire Copy
Authors: Kelsey Miller
Group: BioLegend
Summary: Cell Fixation and Permeabilization Protocol Using 70% Ethanol
Proper citation: Kelsey Miller 2016. Ethanol Fixation Protocol. protocols.io dx.doi.org/10.17504/protocols.io.e24bggw Copy
Authors: Loreen Sommermann, Joerg Geistlinger, Jessica Zwanzig, Ingo Schellenberg
Summary: This protocol was used for the molecular profiling of the soil fungal community of two winter wheat fields as a part of a long-term field trial in Germany with following Illumina Amplicon Sequencing. Besides different pre-crops, the effects of soil management and fertilization on the fungal communities were investigated. Due to different aspects of our protocol, we wanted to ensure reproducing a realistic ratio of the different fungal communities in the soils. The most important steps to conform this demand being the frequently measurements of DNA concentrations at different steps of the protocol, the high numbers of PCRs of each soil sample and the use of the qPCR setting a cut-off for the PCR cycles to avoid an over-amplification of certain PCR-fragments and a loss of detectable biodiversity. The use of the two DNA isolation kits based on the cooperation with our project partner and the exchange of DNAs.
Proper citation: Loreen Sommermann, Joerg Geistlinger, Jessica Zwanzig, Ingo Schellenberg 2018. Preparation of Fungal ITS Amplicons from Soil Samples for Illumina Amplicon Sequencing. protocols.io dx.doi.org/10.17504/protocols.io.nmgdc3w Copy
Authors: Julie Huber, Caroline Fortunato
Group: Center for Dark Energy Biosphere Investigations, Huber Lab
Summary: These were developed to measure potential microbial activity for uptake of acetate and bicarbonate by microbes in venting hydrothermal fluids. The protocol was designed for Axial Seamount diffusely venting fluids, but can be applied to other fluid systems (e.g. cold, oxic fluids, seawater, etc). Concentrations of label will depend on environment of interest.
Proper citation: Julie Huber, Caroline Fortunato 2017. Potential Rate Measurements for Uptake of Bicarbonate and Acetate by Microbes in Crustal Fluids. protocols.io dx.doi.org/10.17504/protocols.io.iutcewn Copy
Authors: Kevin Nee, Quy Nguyen, Kai Kessenbrock
Group: Human Cell Atlas Method Development Community
Summary: Breast cancer originates in the mammary gland epithelium, however growing evidence demonstrates that the diverse array of stromal tissues influence the behavior of breast epithelium and has key roles in the pathogenesis of breast cancer. Despite increased recognition and research, the heterogeneity of the breast stroma (endothelium, fibroblasts, and adipocytes) poses challenges in elucidating which stromal populations are responsible for the complex interactions of the breast microenvironment. To this end, we have employed single cell RNA sequencing (scRNAseq) of the stromal populations within the breast. However adipose tissue, due to its delicate and lipid filled nature is not amenable to these methods of interrogation. To overcome this obstacle, we have developed a method for isolation of adipose nuclei for 10x sequencing. Together, we will use these approaches to investigate the heterogeneity of stroma and adipocytes, and determine the interactions of the breast microenvironment at single-cell resolution.
Proper citation: Kevin Nee, Quy Nguyen, Kai Kessenbrock 2018. Single Nuclei RNA Sequencing of Breast Adipose Tissue (10x Nuclei-Seq) . protocols.io dx.doi.org/10.17504/protocols.io.tdwei7e Copy
Authors: Sien Ombelet
Proper citation: Sien Ombelet 2019. Salmonella blood culture surveillance: Antibiotic susceptibility testing. protocols.io dx.doi.org/10.17504/protocols.io.9q9h5z6 Copy
Authors: Maria Rubio-Brotons
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Multicellgenomelab
Proper citation: Maria Rubio-Brotons 2016. How to culture corallochytrean Corallochytrium limacisporum, a unicellular relative to animals. protocols.io dx.doi.org/10.17504/protocols.io.gqmbvu6 Copy
Authors: Nina Dar, Long Cai
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: Once a tissue is received, it should be frozen using the following protocol:
Proper citation: Nina Dar, Long Cai 2019. Tissue Freezing for seqFISH. protocols.io dx.doi.org/10.17504/protocols.io.7mdhk26 Copy
Authors: Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa
Proper citation: Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa 2019. Preparation of primary chicken embryo liver (CEL) cells. protocols.io dx.doi.org/10.17504/protocols.io.7zchp2w Copy
Authors: William Rooney, Janet Laird (University of Glasgow), Mechna Chowdhury (University of Glasgow), Catriona MacIntosh (University of Glasgow), Xiaoyi Deng (University of Glasgow), Phoebe McBride (University of Glasgow), Joel Milner (University of Glasgow)
Summary: Seed contamination represents a critical route for the transmission of bacterial plant diseases. Here we have created a step-by-step protocol for in vitro seed infections of Pseudomonas syringae. This protocol provides a robust method for P. syringae infection in cucumber. This synthetic seed infection assay is generally applicable for P. syringae as we have successfully adapted it for both tomato and soybean.
Proper citation: William Rooney, Janet Laird (University of Glasgow), Mechna Chowdhury (University of Glasgow), Catriona MacIntosh (University of Glasgow), Xiaoyi Deng (University of Glasgow), Phoebe McBride (University of Glasgow), Joel Milner (University of Glasgow) 2021. Pseudomonas syringae seed infections. protocols.io dx.doi.org/10.17504/protocols.io.bhwhj7b6 Copy
Authors: Nafiul Huda, Md. Ismail Hosen, Pankaj Kumar Sarkar, A.K.M. Mahbub Hasan, A.H.M. Nurun Nabi
Summary: To amplify the target regions of GATA3 for studying rs3824662 polymorphism, a web-based primer designing tool available at http://bioinfo.ut.ee/primer3-0.4.0 facilitates crafting the set of outer primers [forward outer primer: 5’-TTGCAAATGGAAGAGGGTCT-3’ and reverse outer primer: 5’-ACCCTGCAAATGAGAGGAAA-3’] and inner primers [G specific primer: 5’-TGAGATTAAACACAAACACGtTG-3’ and T specific primer: 5’-CTGAGATTAAACACAAACACGaTT-3’] to perform allele-specific PCR that specifically amplify the GATA3 gene. G/T allele-specific primer is very sensitive and binds only with the DNA fragments containing G/T nucleotide template DNA. Forward outer and reverse outer primers will amplify a specific 691 base pair region of GATA3. This 691 base pair region contains the desired polymorphic site of interest. Allele-specific primers produce 506 bp products upon the presence of either a G allele or T allele. PCR reaction in a total volume of 15 μL with an initial denaturing step of 5 min at 95°C, followed by 40 cycles of 30 s at 95°C, 45 s at 55°C, and 1 min at 72°C, and a final extension step of 5 min at 72°C will produce better reproducible result. The reaction mixture contains both forward outer and reverse outer primers and contains either the G allele-specific forward inner primer or the T allele-specific forward inner primer. Primer concentration used was 200 nM each. When the G allele is present in a specific DNA sequence, only the 506 base pair band will be found upon gel electrophoresis of PCR amplicons with the G allele-specific primer. In this case, no such 506 base pair band will be obtained upon gel electrophoresis with the T allele-specific primer. On the other hand, for mutant TT genotypes, the opposite phenomenon will occur when the T allele is present, which will be reflected by the presence of the 506 base pair DNA band. In the case of the heterozygous genotype (GT), both inner primers for G and T alleles will bind with specific DNA sequences to produce 506 base pair bands.
Proper citation: Nafiul Huda, Md. Ismail Hosen, Pankaj Kumar Sarkar, A.K.M. Mahbub Hasan, A.H.M. Nurun Nabi 2018. Genotyping of rs3824662 polymorphism in GATA3 gene by allele-specific PCR. protocols.io dx.doi.org/10.17504/protocols.io.k45cyy6 Copy
Authors: Adolfo Maria Tambella, Stefano Martin, Anna Rita Attili, Cecilia Vullo, Luca Omini
Summary: This protocol describes a radiographic procedure to objectively quantifyin vivothe cranial tibial translation using a simple device in dogs.
.justify:after {
content: "";
display:inline-block;
width: 100%;
}
.justify:after {
content: "";
display:inline-block;
width: 100%;
}
This protocol was used in the following publication:
.justify:after {
content: "";
display:inline-block;
width: 100%;
}
https://doi.org/10.1371/journal.pone.0228621
.justify:after {
content: "";
display:inline-block;
width: 100%;
}
Tambella AM, Omini L, Attili AR, Vullo C, Martin S (2020) Evaluation of cranial tibial translation in dogs: Diagnostic accuracy of radiographic method using a simple device. PLoS ONE 15(2): e0228621. (ISSN: 1932-6203) (DOI: 10.1371/journal.pone.0228621)
.justify:after {
content: "";
display:inline-block;
width: 100%;
}
Proper citation: Adolfo Maria Tambella, Stefano Martin, Anna Rita Attili, Cecilia Vullo, Luca Omini 2020. Radiographic protocol to quantify cranial tibial translation in dogs. protocols.io dx.doi.org/10.17504/protocols.io.bc48iyzw Copy
Authors: Benjamin Bolduc
Group: VERVE Net, Sullivan Lab, iVirus
Summary: A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user uses actual reads from Ocean Sampling Day (2014) and processes them entirely within Cyverse, a NSF-supported cyberinfrastructure.
Proper citation: Benjamin Bolduc 2019. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.x5xfq7n Copy
Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: Peroxidase labeled anti-human IgG is a conjugated secondary antibody that can be used to detect specific antibodies against millions of antigens in humans. This reagent is usually used in enzyme-linked immunosorbent assay, immunoblot analysis and dot blot [1,2]. Reference1. Stubenrauch K, Wessels U, Essig U, Kowalewsky F, Vogel R, Heinrich J. Characterization of murine anti-human Fab antibodies for use in an immunoassay for generic quantification of human Fab fragments in non-human serum samples including cynomolgus monkey samples.J Pharm Biomed Anal. 2013;72:208-215. doi:10.1016/j.jpba.2012.08.0232.Justiz Vaillant AA, McFarlane-Anderson N, Akpaka PE, Smikle MP, Ramirez N, et al. (2013) Use of Dot Blots Analysis in the Separation of Anti-HIV Antibodies in Animals. J Chromat Separation Techniq 4: 181. doi:10.4172/2157- 7064.1000181
Proper citation: Angel Justiz-Vaillant 2020. Protocol of preparation of horseradish peroxidase (HRP) conjugated to anti-human IgG to be used as secondary antibody in immunoassays. . protocols.io dx.doi.org/10.17504/protocols.io.bjmxkk7n Copy
Authors: Luciano Bonilla, Peter Hansen
Group: University of Florida Bovine Embryo Lab
Summary: The following protocol is derived from the protocol described by Genicot et al. (Theriogenology 63: 1181- 1194, 2005) and is based on the fluorescence emitted by Nile Red when in association with lipid (see Fowler and Greenspan, J Histochem Cytochem 33: 833-836, 1985).
Proper citation: Luciano Bonilla, Peter Hansen 2019. Determining Lipid Content in Embryos using Nile Red Fluorescence. protocols.io dx.doi.org/10.17504/protocols.io.8qwhvxe Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: Artificial Cerebrospinal Fluid IX (ACSF.IX) is used for applications including tissue bath solution during electrophysiological recording for probing synaptic connections under physiological conditions.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. Artificial Cerebrospinal Fluid IX (ACSF.IX). protocols.io dx.doi.org/10.17504/protocols.io.bdn9i5h6 Copy
Authors: Geoff Baldwin, Traci Haddock-Angelli, Jacob Beal, Ari Dwijayanti, Marko Storch, Natalie Farny, Richard Tennant, Paul Rutten
Group: iGEM Measurement
Summary: Plate readers report fluorescence values in arbitrary units that vary widely from instrument to instrument. Therefore absolute fluorescence values cannot be directly compared from one instrument to another. In order to compare fluorescence output of test devices between teams, it is necessary for each team to create a standard fluorescence curve. Although distribution of a known concentration of GFP protein would be an ideal way to standardize the amount of GFP fluorescence in our E. coli cells, the stability of the protein and the high cost of its purification are problematic. We therefore use the small molecule fluorescein, which has similar excitation and emission properties to GFP, but is cost-effective and easy to prepare. (The version of GFP used in the devices, GFP mut3b, has an excitation maximum at 501 nm and an emission maximum at 511 nm; fluorescein has an excitation maximum at 494 nm and an emission maximum at 525nm).You will prepare a dilution series of fluorescein in four replicates and measure the fluorescence in a 96 well plate in your plate reader. By measuring these in your plate reader, you will generate a standard curve of fluorescence for fluorescein concentration. You will be able to use this to convert your cell based readings to an equivalent fluorescein concentration. Before beginning this protocol, ensure that you are familiar with the GFP settings and measurement modes of your instrument. You will need to know what filters your instrument has for measuring GFP, including information about the bandpass width (530 nm / 30 nm bandpass, 25-30 nm width is recommended), excitation (485 nm is recommended) and emission (520-530 nm is recommended) of this filter.Note: The iGEM Abs600 (OD) calibration protocol with microspheres calibration method is a pre-requisite for carrying out this protocol. You will need data from that calibration to analyse the results of this protocol.
Proper citation: Geoff Baldwin, Traci Haddock-Angelli, Jacob Beal, Ari Dwijayanti, Marko Storch, Natalie Farny, Richard Tennant, Paul Rutten 2019. Calibration Protocol - Plate Reader Fluorescence Calibration with Fluorescein. protocols.io dx.doi.org/10.17504/protocols.io.548g8zw Copy
Authors: Sandra L. Ross, Marika Sherman, Patricia L. McElroy, Julie A. Lofgren, Gordon Moody, Patrick A. Baeuerle, Angela Coxon, Tara Arvedson
Summary: This protocol describes the use of neutralizing antibodies to block receptrs for assessing involvement in bystander killing by BiTE®-activated T cells.
Proper citation: Sandra L. Ross, Marika Sherman, Patricia L. McElroy, Julie A. Lofgren, Gordon Moody, Patrick A. Baeuerle, Angela Coxon, Tara Arvedson 2017. Bystander Receptor Blockade: IFN?R1, TNFRSF1A, ICAM-1 and FAS. protocols.io dx.doi.org/10.17504/protocols.io.hw8b7hw Copy
Authors: Miyuki Takasu
Proper citation: Miyuki Takasu 2019. Protocol. protocols.io dx.doi.org/10.17504/protocols.io.bavbie2n Copy
Authors: James Thornton Jr.
Group: Hurwitz Lab, iMicrobeOutreach
Summary: Centrifuge is a classification software used on whole genome shotgun (WGS) reads. It uses a reference database to determine what organisms are found in your sample. This protocol will show you how to access the data on CyVerse and walk you through some questions to help in the analysis of the plots.
Proper citation: James Thornton Jr. 2017. Centrifuge Report of Normal vs Dermatitis Skin Microbiome. protocols.io dx.doi.org/10.17504/protocols.io.g9gbz3w Copy
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:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
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 sources that were queried against in your search that you can investigate further.
Here are the categories present within dkNET that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
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
