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Authors: Jorge Fernandez Mendez
Group: AEGIS - Madrid iGEM 2019
Summary: Adaptated version of the crosslinking bioconjugation protocol depicted in https://doi.org/10.1177/1087057106292138 publication. The following protocol depicts the steps to follow for proper crosslinking of amino modified DNA aptamers with carboxyl surface functionalized latex beads..
Proper citation: Jorge Fernandez Mendez 2019. Aptamer 1-step conjugation protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.8h4ht8w Copy
Authors: Alba Balletbó, Sebastiaan Kuiper
Summary: Gel electrophoresis is the standard lab procedure for separating DNA by size (e.g., length in base pairs) for visualization and purification. Electrophoresis uses an electrical field to move the negatively charged DNA through an agarose gel matrix toward a positive electrode. Shorter DNA fragments migrate through the gel more quickly than longer ones. Thus, you can determine the approximate length of a DNA fragment by running it on an agarose gel alongside a DNA ladder (a collection of DNA fragments of known lengths).
Proper citation: Alba Balletbó, Sebastiaan Kuiper 2019. Agarose Gel Electrophoresis. protocols.io https://dx.doi.org/10.17504/protocols.io.7zmhp46 Copy
Authors: Christos-Georgios Kontovazainitis, Georgios Mitsiakos, Dimitra Gialamprinou
Proper citation: Christos-Georgios Kontovazainitis, Georgios Mitsiakos, Dimitra Gialamprinou 2020. The combination of LMWH (Low-Molecular-Weight Heparin) and Aspirin as a prophylaxis treatment for pre-eclampsia and SGA (Small-for-Gestational Age) neonates in medium- and high-risk women: protocol for a Systematic Review and Meta-Analysis.. protocols.io https://dx.doi.org/10.17504/protocols.io.bhdtj26n Copy
Authors: Tadeusz Dębniak1, Rodney J Scott, Bohdan Górski, Bartłomiej Masojć, Andrzej Kram, Romuald Maleszka, Cezary Cybulski, Katarzyna Paszkowska-Szczur, Aniruddh Kashyap, Dawid Murawa, Karolina Malińska, Magdalena Kiedrowicz, Emilia Rogoża-Janiszewska, Helena Rudnicka, Jakub Deptuła, Paweł Domagała, Wojciech Kluźniak, Marcin R. Lener, Jan Lubiński
Summary: In the study we have used a standard Thermo Fisher Scientific Sanger sequencing protocol which can be found under this link:
http://www.ramaciotti.unsw.edu.au/wp-content/uploads/2016/08/sequencing_handbook_FLR.pdf
Proper citation: Tadeusz Dębniak1, Rodney J Scott, Bohdan Górski, Bartłomiej Masojć, Andrzej Kram, Romuald Maleszka, Cezary Cybulski, Katarzyna Paszkowska-Szczur, Aniruddh Kashyap, Dawid Murawa, Karolina Malińska, Magdalena Kiedrowicz, Emilia Rogoża-Janiszewska, Helena Rudnicka, Jakub Deptuła, Paweł Domagała, Wojciech Kluźniak, Marcin R. Lener, Jan Lubiński 2018. Sanger sequencing protocol - BRCA1/2 mutations are not a common cause of malignant melanoma in the Polishpopulation. protocols.io https://dx.doi.org/10.17504/protocols.io.ta7eihn Copy
Authors: Snehadri Sinha
Group: Aalto-Helsinki 2016
Summary: Protocol for LiAc S. cerevisiae competent cell preparation and transformation, from Aalto University Molecular Biotechnology group.
Proper citation: Snehadri Sinha 2017. Yeast competent yeast cells + LiAc transformation from liquid culture. protocols.io https://dx.doi.org/10.17504/protocols.io.gzrbx56 Copy
Authors: Seth Currlin, Marda Jorgensen, Jerelyn Nick
Group: Optical Clearing of Tissue, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This document covers the CLARITY protocol for volumetric tissue clearing. This method can be applied to many tissue types and is easily modified. The link below is very useful and should be reviewed before beginning any CLARITY process. http://wiki.claritytechniques.org/index.php/CLARITY_Technique
Proper citation: Seth Currlin, Marda Jorgensen, Jerelyn Nick 2020. Tissue Clearing Using CLARITY Method. protocols.io https://dx.doi.org/10.17504/protocols.io.bppimmke Copy
Authors: Rochelle Lieberstein Stern
Summary: Abstract: Are there evidenced-based, reviews, articles of scientific validity, and/or clinical studies that imply other actions, in addition to WHO, NIH, and CDC recommendations, which could help, safeguard, or improve immunity response while home with or without COVID-19? This may include anything that would be accessible via home items, mail online orders, food, or over-the-counter items in the drug store. This review is exclusively based on scientific literature or medical professional observation
Proper citation: Rochelle Lieberstein Stern 2020. Preventative at Home COVID-19 Based on Literature. protocols.io https://dx.doi.org/10.17504/protocols.io.bf9ijr4e Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Proper citation: New England Biolabs 2015. BioBrick E0546 Upstream Reaction. protocols.io https://dx.doi.org/10.17504/protocols.io.cpivkd Copy
Authors: Eliab Estrada Cortés, Peter Hansen
Group: University of Florida Bovine Embryo Lab
Summary: This is a protocol to describe how to ship non-frozen embryos
Proper citation: Eliab Estrada Cortés, Peter Hansen 2021. Shipping Embryos in a Portable Incubator. protocols.io https://dx.doi.org/10.17504/protocols.io.bth4nj8w Copy
Authors: Judy Northill, Mitchell Finger, Michael Lyon, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services
Summary: A real-time RT-PCR using an MGB probe, this assay detects Japanese encephalitis virus (JEV) from human and mosquito samples.The assay targets the 3'UTR region of known JEV strains.
Proper citation: Judy Northill, Mitchell Finger, Michael Lyon, Ian Mackay 2017. Japanese encephalitis virus real-time RT-PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.kr9cv96 Copy
Authors: Geraldo Elias Miranda, Caroline Wilkinson, Mark Roughley, Thiago Leite Beaini, Rodolfo Francisco Haltenhoff Melani
Summary: A description of to how to produce and evaluate three-dimensional computerized forensic craniofacial reconstructions (CCFR) using Horos, Blender, Cloud Compare, MakeHuman and Picassa computer programs.
Proper citation: Geraldo Elias Miranda, Caroline Wilkinson, Mark Roughley, Thiago Leite Beaini, Rodolfo Francisco Haltenhoff Melani 2018. Three-dimensional computerized forensic craniofacial reconstruction (CCFR). protocols.io https://dx.doi.org/10.17504/protocols.io.m4xc8xn Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
Summary: Identifying putative viral sequences from SPAdes-assembled data from the Ocean Sampling Day (2014) metagenomic datasets using VirSorter.
Proper citation: Benjamin Bolduc 2016. Identifying Viral Sequences Using VirSorter (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.eyjbfun Copy
Authors: Dimitrios Voukantsis, Kenneth Kahn, Martin Hadley, Rowan Wilson, Francesca M Buffa
Summary: microC is a multiscale virtual microenvironment for perturbation biology. It enables experiments that link genotype to phenotype taking into account the surrounding microenvironment. microC has a modular architecture that enables a wide variety of experiment. Furthermore, it offers easy access to advanced computational modelling and supercomputing resources to the wider scientific community.microC combines agent-based and gene network modelling and uses partial differential equations to simulate interactions among cells. The tool itself does not require any installation on the user’s machine, as it can be accessed using a web browser. Experimental results and data are also available via a web interface. This protocol describes the process of preparing and submiting an experiment with microC, and interpreting the simulation results
Proper citation: Dimitrios Voukantsis, Kenneth Kahn, Martin Hadley, Rowan Wilson, Francesca M Buffa 2018. microC: A 3D virtual microenvironment for perturbation biology. protocols.io https://dx.doi.org/10.17504/protocols.io.vx3e7qn Copy
Authors:
Group: UCSC BME 22L
Proper citation: 2020. Protocols for Primer Design. protocols.io https:// Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. Chlorovirus DNA Miniprep Procedure. protocols.io https://dx.doi.org/10.17504/protocols.io.erzbd76 Copy
Authors: Cleyde Helena
Summary: Appropriate tissue fixation is essential for a good quality immunocytochemistry (ICC).There are several fixation methods, but "whole body" or "target" perfusion of the animal is one of the most efficient methods.Most perfusing protocols include only paraformaldehyde, but acrolein penetrates tissue more rapidly, improving final fixation of the tissue.
Proper citation: Cleyde Helena 2018. Acrolein + PFA perfusion for immunocytochemistry . protocols.io https://dx.doi.org/10.17504/protocols.io.tb9eir6 Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: This protocol is for dephosphorylation of 5´-ends of DNA using rSAP in restriction enzyme reaction (M0371)
Proper citation: New England Biolabs 2018. Dephosphorylation using rSAP in Restriction Enzyme Reaction(M0371). protocols.io https://dx.doi.org/10.17504/protocols.io.nkxdcxn Copy
Authors: Ning Chen
Summary: qRT- PCR for each gene was carried out using a thermal cycler (Bio-Rad, Hercules, CA, USA) and amplification conditions were 40 cycles of 30s at 95°C, 3 s at 95°C, and 30 s at 60°C.
Proper citation: Ning Chen 2017. qRT-PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.ixecfje Copy
Authors: Sam Li
Group: BioLegend
Summary: BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple protocol consists of following the MojoSort™ protocol to label the cells with pre-diluted MojoSort™ reagents and using the columns as indicated by the manufacturer.Note: Due to the properties of our beads, it may be possible to use far fewer beads than with other commercial suppliers. We recommend a titration to find the best dilution factor. However, as a general rule, dilutions ranging from 1:3 to 1:20 for the Nanobeads can be used. Please contact BioLegend Technical Service ([email protected]) if further assistance is needed.
Proper citation: Sam Li 2019. MojoSort™ Human anti-APC Nanobeads Column Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.7afhibn Copy
Authors: Jaclyn Winter
Proper citation: Jaclyn Winter 2019. Protein expression in yeast. protocols.io https://dx.doi.org/10.17504/protocols.io.8gahtse Copy
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