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Authors: Alba Balletbó
Group: iGEM Wageningen 2019
Summary: This is the protocol for DNA Assembly using the NEBuilder® HiFi DNA Assembly Master Mix.
Proper citation: Alba Balletbó 2019. HiFi Gibson Assembly (Protocol for the NEBuilder® HiFi DNA Assembly Master Mix). protocols.io dx.doi.org/10.17504/protocols.io.7kchksw Copy
Authors: Bryon Drown, Caroline DeHart, Kelleher Research Group
Summary: Immunoprecipitation with non-covalent capture of antibodies is a rapid and effective method for enriching samples with desired antigens. Interference by the antibody in down-stream analysis of intact proteins by mass spectrometry can be eliminated by covalent linkage of antibodies to magnetic beads. While several amine-reactive bifunctional linkers have been used for this application, dimethyl pimelimidate (DMP) are particularly advantageous due to its water-solubility, stability of resulting amidines at low pH, and retention of positive charge at reaction sites. By cross-linking to Protein A/G magnetic beads, a greater portion of antibodies are correctly oriented and able to engage their antigen. Cross-linking antibodies to Protein A/G beads with DMP is a quick and effective method that mitigates interference from heavy and light chain IgG in down-stream mass spectrometry applications.
Proper citation: Bryon Drown, Caroline DeHart, Kelleher Research Group 2021. Crosslinking Immunoprecipitation Beads. protocols.io dx.doi.org/10.17504/protocols.io.bdhki34w Copy
Authors: Seham Hazem El-Ayouti, Heba Mahmoud Dahmoush, Hatem Wael Amer
Proper citation: Seham Hazem El-Ayouti, Heba Mahmoud Dahmoush, Hatem Wael Amer 2018. Immunohistochemical Expression of FAK and PCNA in Odontogenic Keratocyst, Orthokeratinized Odontogenic Cyst, Dentigerous Cyst and Glandular Odontogenic Cyst (In-vitro study). protocols.io dx.doi.org/10.17504/protocols.io.t5teq6n Copy
Authors: Noreen Wauford
Proper citation: Noreen Wauford 2016. PCSK9 gRNA amplification template PCR. protocols.io dx.doi.org/10.17504/protocols.io.e86bhze Copy
Authors: Ian Mackay, Judy Northill
Group: Public Health Virology, Forensic and Scientific Services
Summary: The protocol aims to specifically amplify Nipah viruses (NiV) and not other viruses.This is a modified version of a published assay. Modifications were to account for mismatches underneath oligo target sites.The assay targets the nucleoprotein (N) gene region and is designed as a qualitative test for investigating NiV infection of humans.
Proper citation: Ian Mackay, Judy Northill 2019. Nipah virus real-time RT-PCR (NiV-TM2018). protocols.io dx.doi.org/10.17504/protocols.io.rs5d6g6 Copy
Authors: Mandy Xu, Troy Ketela
Group: Human Cell Atlas Method Development Community, CZI START Project
Summary: This protocol has been developed by the Princess Margaret Genomics Centre specifically for Nuc-Seq, both at the bulk and single-cell levels.
Proper citation: Mandy Xu, Troy Ketela 2019. Nuclei-seq. protocols.io dx.doi.org/10.17504/protocols.io.8b8hsrw Copy
Authors: Zhonghua Qi, Matthew D. Breyer
Group: Diabetic Complications Consortium
Summary: This protocol describes the procedures for estimating glomerular filtration rate in conscious mice based on Fluorescein Isothiocyanate-inulin (FITC-inulin) clearance following a single bolus intravenous injection. Diabetic Complication:Reference:1. Hem, A., Smith, A.J., and Solberg, P. 1998. Saphenous vein puncture for blood sampling of the mouse, rat, hamster, gerbil, guinea pig, ferret and mink. Lab Anim 32:364-368. 2. Sturgeon, C., Sam, A.D., 2nd, and Law, W.R. 1998. Rapid determination of glomerular filtration rate by single-bolus inulin: a comparison of estimation analyses. J Appl Physiol 84:2154-2162. 3. Qi, Z., Whitt, I., Mehta, A., Jin, J., Zhao, M., Harris, R.C., Fogo, A.B., and Breyer, M.D. 2003. Serial Determination of Glomerular Filtration Rate in Conscious Mice Using FITC-Inulin Clearance. Am J Physiol Renal Physiol.
Proper citation: Zhonghua Qi, Matthew D. Breyer 2019. Determination of Glomerular Filtration Rate in Conscious Mice using FITC-inulin. protocols.io dx.doi.org/10.17504/protocols.io.3fngjme Copy
Authors: Xu Min
Proper citation: Xu Min 2018. The method to measure one side surface area of the seaweed. protocols.io dx.doi.org/10.17504/protocols.io.m6yc9fw Copy
Authors: Johannes Debler
Summary: Adapted from Chi, M. H., Park, S. Y., & Lee, Y. H. (2009).Colony PCR on fungal colonies grown on plates does not work as well as it does for bacteria (it usually doesn't work at all). DNA therefore needs to be extracted first. As this DNA will only be used as a PCR template to check for presence / absence of individual genes I am not too concerend about high molecular weight or purity.This protocol is quick and can be used to process several samples at the same time.
Proper citation: Johannes Debler 2018. Quick Fungal DNA extraction from colonies on plates. protocols.io dx.doi.org/10.17504/protocols.io.snzedf6 Copy
Authors: Lukas Snoek, Tinka Beemsterboer
Group: Spinoza Centre, REC-L
Summary: This protocol lists all the steps necessary to run your MRI experiment/data acquisition safely and in a way that yields high-quality data. Moreover, if you use the centre's QC/preprocessing service, it lists the steps necessary to make sure we can convert the data into BIDS and run them through the QC/preprocessing pipelines.
Proper citation: Lukas Snoek, Tinka Beemsterboer 2018. During data acquisition. protocols.io dx.doi.org/10.17504/protocols.io.nz2df8e Copy
Authors: Junyan Qian
Group: iGEM EPFL
Summary: General toehold assemble method using NEB Q5 High-Fidelity 2x Master Mix. Here we took Boir Noir toeholds as an example, it has four candidates we wanted to test. In order to have a higher yield, run 5 reactions for each candidates.
Proper citation: Junyan Qian 2019. Toehold switch assembly. protocols.io dx.doi.org/10.17504/protocols.io.72bhqan Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol is used to prepare 30% Sucrose Solution in 0.1M phosphate buffer. 30% Sucrose in 0.1M phosphate buffer is used for the cryoprotection of mice brains post perfusion.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. 30% Sucrose for Cryoprotection of brains after Perfusions. protocols.io dx.doi.org/10.17504/protocols.io.bg5ujy6w Copy
Authors: Kami Ahmad, Steven Henikoff
Summary: This is a modification of the Benchtop CUT&Tag method (dx.doi.org/10.17504/protocols.io.bcuhiwt6) for epigenomic profiling of histone modifications and chromatin proteins in dissected Drosophila tissues. Intact unfixed tissues are permeabilized and incubated under conditions where a factor-specific antibody can infiltrate and bind a chromatin protein in situ. This antibody is then decorated with a secondary antibody, and this is used to tether a protein AG-Tn5 fusion protein loaded with sequencing adapters. Upon transposome activation by adding Mg2+ ions, DNA is tagmented around the chromatin binding site. Here, dissected imaginal discs are coated with magnetic beads for handling, and about 5 imaginal discs provides high-quality data for histone modifications or for chromatin factor for which high-quality antibodies are available. The protocol is scaled for 8 samples. Performing CUT&Tag takes 2 days from larvae to sequencing-ready libraries.
Proper citation: Kami Ahmad, Steven Henikoff 2020. CUT&Tag with Drosophila tissues. protocols.io dx.doi.org/10.17504/protocols.io.bnx5mfq6 Copy
Authors: Roscoff Culture Collection
Group: Roscoff Culture Collection
Summary: How to prepare soil extract
Proper citation: Roscoff Culture Collection 2019. Soil extract for algal media. protocols.io dx.doi.org/10.17504/protocols.io.s28eghw Copy
Authors: Shaina Robbins, Alison Moss, Sean Nieves
Group: SPARC
Summary: This collection of protocols were used to obtain the current data for the Blackfynn Dataset Molecular Phenotype Distribution of Single Rate ICN Neurons, which we refer to as Rat Heart B.
Proper citation: Shaina Robbins, Alison Moss, Sean Nieves 2020. Molecular Phenotype Distribution of Single Rat ICN Neurons - Heart B. protocols.io dx.doi.org/10.17504/protocols.io.w56fg9e Copy
Authors: Angel Justiz-Vaillant, Monica F. Smikle
Group: University of the West Indies, [email protected]
Summary: Referencesst protein LA (SpLA) is an immunoglobulin-binding protein that interacts with the Fab and Fc regions of many mammalian immunoglobulins [1].References1.Vaillant AJ, McFarlane-Andersonv N, Wisdom B, Mohammed W, Vuma S, et al. (2013) Immunoglobulin-binding Bacterial Proteins (IBP) Conjugates and their Reactivity with Immunoglobulin in Enzyme-Linked Immunosorbent Assays (ELISA). J Anal Bioanal Tech 4: 175. doi:10.4172/2155-9872.1000175
Proper citation: Angel Justiz-Vaillant, Monica F. Smikle 2020. Direct ELISA for investigating the binding of recombinant Protein-LA to immunoglobulins.. protocols.io dx.doi.org/10.17504/protocols.io.bjxukpnw Copy
Authors: Nus Igem
Proper citation: Nus Igem 2019. Gel Extraction. protocols.io dx.doi.org/10.17504/protocols.io.7pthmnn 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. Direct ELISA for investigating the binding of Protein-A to immunoglobulins. . protocols.io dx.doi.org/10.17504/protocols.io.bjxqkpmw Copy
Authors: Bastien Castagneyrol, Elena Valdés-Correcher, Michèle Kaennel Dobbertin, Martin Gossner
Summary: The 'Oak bodyguards' citizen science project aimed to assess the effects of climate on two key biotic interactions occurring widely in natural and anthropized ecosystems, i.e., the top-down and bottom-up forces controlling insect herbivory on leaves of the English oak (Quercus robur) trees. We chose the English oak as a model species as it is one of the most common and most emblematic forest trees in Europe, with a geographic range spanning more than 19 degrees of latitude. It is also widespread in both rural, suburban and urban environments. We exposed dummy plasticine caterpillars in trees to estimate predation rates. We additionally estimated leaf insect herbivory as the percentage of leaf area removed or damaged by insect herbivores. The Oak bodyguards project involved professional scientists and school children throughout Europe. We designed a simple protocol that was applied by both partner types. The protocol was written by scientists in collaboration with science instructors and communication officers. It was available in five languages: French, English, German, Spanish and Portuguese. The present document is the English version of the protocol. It describes how to estimate insect herbivory on oak leaves as well as predation rate on artificial prey made with green modelling clay.
Proper citation: Bastien Castagneyrol, Elena Valdés-Correcher, Michèle Kaennel Dobbertin, Martin Gossner 2019. Predation assessment on fake caterpillars and leaf sampling: Protocol for partner schools. protocols.io dx.doi.org/10.17504/protocols.io.42pgydn Copy
Authors: Lev Tsypin, Yinon Bar-On, Scott Saunders, Jared R Leadbetter, Dianne K Newman
Summary: This is a protocol for the enrichment of phenazine-1-carboxylic acid oxidizing microbes from a soil sample.
Proper citation: Lev Tsypin, Yinon Bar-On, Scott Saunders, Jared R Leadbetter, Dianne K Newman 2020. Phenzine Oxidizer Enrichment and Isolation. protocols.io dx.doi.org/10.17504/protocols.io.bh4tj8wn Copy
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