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RRIDs used | ||||||
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Aptamer 1-step conjugation protocol Resource Report Resource Website |
Jorge Fernandez Mendez | DOI:10.17504/protocols.io.8h4ht8w | AEGIS - Madrid iGEM 2019 | 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.. | Universidad Complutense de Madrid | 1 | 2019 | Jorge Fernandez Mendez 2019. Aptamer 1-step conjugation protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.8h4ht8w | 2021-04-15 09:15:39 | |||
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Agarose Gel Electrophoresis Resource Report Resource Website |
Alba Balletbó, Sebastiaan Kuiper | DOI:10.17504/protocols.io.7zmhp46 | 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). | Wageningen University, Wageningen University | 1 | 2019 | Alba Balletbó, Sebastiaan Kuiper 2019. Agarose Gel Electrophoresis. protocols.io https://dx.doi.org/10.17504/protocols.io.7zmhp46 | 2021-04-15 09:15:41 | ||||
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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. Resource Report Resource Website |
Christos-Georgios Kontovazainitis, Georgios Mitsiakos, Dimitra Gialamprinou | DOI:10.17504/protocols.io.bhdtj26n | Medical School, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece, 2nd Neonatal Department and Neonatal Intensive Care Unit (NICU), Aristotle University of Thessaloniki, Papageorgiou Hospital, Ring Road Nea Efkarpia, 56403, Thessaloniki, Greece, 2nd Neonatal Department and Neonatal Intensive Care Unit (NICU), Aristotle University of Thessaloniki, Papageorgiou Hospital, Ring Road Nea Efkarpia, 56403, Thessaloniki, Greece | 1 | 2020 | 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 | 2021-04-15 09:15:39 | |||||
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Sanger sequencing protocol - BRCA1/2 mutations are not a common cause of malignant melanoma in the Polishpopulation Resource Report Resource Website |
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 | DOI:10.17504/protocols.io.ta7eihn | 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 | Dębniak T, Scott RJ, Górski B, Masojć B, Kram A, Maleszka R, Cybulski C, Paszkowska-Szczur K, Kashyap A, Murawa D, Malińska K, Kiedrowicz M, Rogoża-Janiszewska E, Rudnicka H, Deptuła J, Domagała P, Kluźniak W, Lener MR, Lubiński J (2018) BRCA1/2 mutations are not a common cause of malignant melanoma in the Polish population. PLoS ONE 13(10): e0204768. doi: 10.1371/journal.pone.0204768 | Pomeranian Medical University in Szczecin, University of Newcastle and the Hunter Medical Research Institute, Pomeranian Medical University in Szczecin, West Pomeranian Oncology Cente, Pomeranian Medical University in Szczecin, Pomeranian Medical University in Szczecin, Pomeranian Medical University in Szczecin, Pomeranian Medical University in Szczecin, Pomeranian Medical University in Szczecin, Greater Poland Cancer Center, Pomeranian Medical University in Szczecin, Pomeranian Medical University in Szczecin, Pomeranian Medical University in Szczecin, Pomeranian Medical University in Szczecin, Pomeranian Medical University in Szczecin, Pomeranian Medical University in Szczecin, Pomeranian Medical University in Szczecin, Pomeranian Medical University in Szczecin, Pomeranian Medical University in Szczecin | https://doi.org/10.1371/journal.pone.0204768 | 1 | 2018 | 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 | 2021-04-15 09:15:54 | ||
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Yeast competent yeast cells + LiAc transformation from liquid culture Resource Report Resource Website |
Snehadri Sinha | DOI:10.17504/protocols.io.gzrbx56 | Aalto-Helsinki 2016 | Protocol for LiAc S. cerevisiae competent cell preparation and transformation, from Aalto University Molecular Biotechnology group. | 1 | 2017 | Snehadri Sinha 2017. Yeast competent yeast cells + LiAc transformation from liquid culture. protocols.io https://dx.doi.org/10.17504/protocols.io.gzrbx56 | 2021-04-15 09:15:39 | ||||
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Tissue Clearing Using CLARITY Method Resource Report Resource Website |
Seth Currlin, Marda Jorgensen, Jerelyn Nick | DOI:10.17504/protocols.io.bppimmke | Optical Clearing of Tissue, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | 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 | University of Florida, University of Florida, University of Florida | 1 | 2020 | Seth Currlin, Marda Jorgensen, Jerelyn Nick 2020. Tissue Clearing Using CLARITY Method. protocols.io https://dx.doi.org/10.17504/protocols.io.bppimmke | 2021-04-15 09:15:39 | |||
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Preventative at Home COVID-19 Based on Literature Resource Report Resource Website |
Rochelle Lieberstein Stern | DOI:10.17504/protocols.io.bf9ijr4e | 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 | MLIS, Medical Librarian | https://documentcloud.adobe.com/link/track?uri=urn%3Aaaid%3Ascds%3AUS%3A1a11b741-b1e9-460c-8283-52998acb5501 | 1 | 2020 | Rochelle Lieberstein Stern 2020. Preventative at Home COVID-19 Based on Literature. protocols.io https://dx.doi.org/10.17504/protocols.io.bf9ijr4e | 2021-04-15 09:15:42 | |||
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BioBrick E0546 Upstream Reaction Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.cpivkd | New England Biolabs (NEB) | New England Biolabs | https://www.neb.com/protocols/1/01/01/digestion-protocol-e0546 | 1 | 2015 | New England Biolabs 2015. BioBrick E0546 Upstream Reaction. protocols.io https://dx.doi.org/10.17504/protocols.io.cpivkd | 2021-04-15 09:15:40 | |||
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Shipping Embryos in a Portable Incubator Resource Report Resource Website |
Eliab Estrada Cortés, Peter Hansen | DOI:10.17504/protocols.io.bth4nj8w | University of Florida Bovine Embryo Lab | This is a protocol to describe how to ship non-frozen embryos | University of Florida, University of Florida | 1 | 2021 | Eliab Estrada Cortés, Peter Hansen 2021. Shipping Embryos in a Portable Incubator. protocols.io https://dx.doi.org/10.17504/protocols.io.bth4nj8w | 2021-04-15 09:15:54 | |||
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Japanese encephalitis virus real-time RT-PCR Resource Report Resource Website |
Judy Northill, Mitchell Finger, Michael Lyon, Ian Mackay | DOI:10.17504/protocols.io.kr9cv96 | Public Health Virology, Forensic and Scientific Services | 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. | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | https://doi.org/10.1089/vbz.2013.1373 | 2 | 2017 | 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 | 2021-04-15 09:15:41 | ||
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Three-dimensional computerized forensic craniofacial reconstruction (CCFR) Resource Report Resource Website |
Geraldo Elias Miranda, Caroline Wilkinson, Mark Roughley, Thiago Leite Beaini, Rodolfo Francisco Haltenhoff Melani | DOI:10.17504/protocols.io.m4xc8xn | 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. | Universidade Federal de São Paulo, Liverpool John Moores University, Liverpool John Moores University, Universidade Federal de Uberlândia, Universidade Federal de São Paulo | 1 | 2018 | 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 | 2021-04-15 09:15:41 | ||||
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Identifying Viral Sequences Using VirSorter (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.eyjbfun | Sullivan Lab, iVirus | Identifying putative viral sequences from SPAdes-assembled data from the Ocean Sampling Day (2014) metagenomic datasets using VirSorter. | Bolduc B, Youens-Clark K, Roux S, Hurwitz BL, Sullivan MB, iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. The ISME Journal 11(1). doi: ismej201689 | The Ohio State University | https://www.nature.com/articles/ismej201689.pdf?origin=ppub | 2 | 2016 | Benjamin Bolduc 2016. Identifying Viral Sequences Using VirSorter (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.eyjbfun | 2021-04-15 09:15:41 | |
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microC: A 3D virtual microenvironment for perturbation biology Resource Report Resource Website |
Dimitrios Voukantsis, Kenneth Kahn, Martin Hadley, Rowan Wilson, Francesca M Buffa | DOI:10.17504/protocols.io.vx3e7qn | 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 | Computational Biology and Integrative Genomics, MRC/CRUK Oxford Institute, University of Oxford, Oxford, Oxfordshire, OX3 7DQ, UK, Academic Information Technology Research Team, University of Oxford, Oxford, Oxfordshire, OX2 6NN, UK, Academic Information Technology Research Team, University of Oxford, Oxford, Oxfordshire, OX2 6NN, UK, Academic Information Technology Research Team, University of Oxford, Oxford, Oxfordshire, OX2 6NN, UK, Computational Biology and Integrative Genomics, MRC/CRUK Oxford Institute, University of Oxford, Oxford, Oxfordshire, OX3 7DQ, UK | http://microc.org | 1 | 2018 | 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 | 2021-04-15 09:15:54 | |||
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Protocols for Primer Design Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Protocols for Primer Design. protocols.io https:// | 2021-04-15 09:15:41 | ||||||
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Chlorovirus DNA Miniprep Procedure Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.erzbd76 | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Chlorovirus DNA Miniprep Procedure. protocols.io https://dx.doi.org/10.17504/protocols.io.erzbd76 | 2021-04-15 09:15:41 | ||||
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Acrolein + PFA perfusion for immunocytochemistry Resource Report Resource Website |
Cleyde Helena | DOI:10.17504/protocols.io.tb9eir6 | 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. | ASC group | 1 | 2018 | Cleyde Helena 2018. Acrolein + PFA perfusion for immunocytochemistry . protocols.io https://dx.doi.org/10.17504/protocols.io.tb9eir6 | 2021-04-15 09:15:41 | ||||
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Dephosphorylation using rSAP in Restriction Enzyme Reaction(M0371) Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.nkxdcxn | New England Biolabs (NEB) | This protocol is for dephosphorylation of 5´-ends of DNA using rSAP in restriction enzyme reaction (M0371) | NEB, Ipswich MA | https://www.neb.com/protocols/2013/06/10/protocol-for-dephosphorylation-of-5-ends-of-dna-in-restriction-enzyme-reaction-m0371 | 3 | 2018 | New England Biolabs 2018. Dephosphorylation using rSAP in Restriction Enzyme Reaction(M0371). protocols.io https://dx.doi.org/10.17504/protocols.io.nkxdcxn | 2021-04-15 09:15:53 | ||
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qRT-PCR Resource Report Resource Website |
Ning Chen | DOI:10.17504/protocols.io.ixecfje | 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. | Chen N, Du B, Zhou H, Shen F, Li J, Xie Z (2017) Abnormal expression of Nrf2 may play an important role in the pathogenesis and development of adenomyosis. PLoS ONE 12(8): e0182773. doi: 10.1371/journal.pone.0182773 | Women’s Hospital, School of Medicine, Zhejiang University | https://doi.org/10.1371/journal.pone.0182773 | 1 | 2017 | Ning Chen 2017. qRT-PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.ixecfje | 2021-04-15 09:15:54 | ||
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MojoSort™ Human anti-APC Nanobeads Column Protocol Resource Report Resource Website |
Sam Li | DOI:10.17504/protocols.io.7afhibn | BioLegend | 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. | BioLegend | https://www.biolegend.com/protocols/mojosort-human-anti-apc-nanobeads-column-protocol/4758/ | 1 | 2019 | Sam Li 2019. MojoSort™ Human anti-APC Nanobeads Column Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.7afhibn | 2021-04-15 09:15:41 | ||
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Protein expression in yeast Resource Report Resource Website |
Jaclyn Winter | DOI:10.17504/protocols.io.8gahtse | University of Utah | 1 | 2019 | Jaclyn Winter 2019. Protein expression in yeast. protocols.io https://dx.doi.org/10.17504/protocols.io.8gahtse | 2021-04-15 09:15:39 |
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