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| Name | Authors | DOI | Group |
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Associated Publications |
RRIDs used | ||||||
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NGFR-mNG2 sorting protocol Resource Report Resource Website |
Benjamin Emert | 10.17504/protocols.io.rh6d39e | RajLab | Protocol for preparing NGFR-mNG2 tagged WM989 A6-G3 melanoma cells for sorting. | University of Pennsylvania | 1 | 2018 | Benjamin Emert 2018. NGFR-mNG2 sorting protocol. protocols.io dx.doi.org/10.17504/protocols.io.rh6d39e | 2021-03-29 03:10:16 | |||
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Target Guide Sequence Cloning Protocol Resource Report Resource Website |
Skye Waterland, Yang Li | 10.17504/protocols.io.bij2kcqe | Dr. Shen's Lab Group | Create single gRNA vectors for targeted cloning utilizing CRISPR or CRISPR-based systems. | Baylor College of Medicine, Baylor College of Medicine | 1 | 2020 | Skye Waterland, Yang Li 2020. Target Guide Sequence Cloning Protocol . protocols.io dx.doi.org/10.17504/protocols.io.bij2kcqe | 2021-03-29 03:10:16 | |||
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MojoSort™ Isolation Kits Column Protocol - 3 Resource Report Resource Website |
Sam Li | 10.17504/protocols.io.7behije | 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 and less antibody cocktail that with other commercial suppliers. We recommend a titration to find the best dilution factor. However, as a general rule, dilutions ranging from 1:2 to 1:10 for the antibody cocktail can be used. Dilutions ranging from 1:5 to 1:20 for the Streptavidin Nanobeads can be used. Please contact BioLegend Technical Service ([email protected]) if further assistance is needed. | BioLegend | https://www.biolegend.com/protocols/mojosort-isolation-kits-column-protocol-3/4591/ | 1 | 2019 | Sam Li 2019. MojoSort™ Isolation Kits Column Protocol - 3. protocols.io dx.doi.org/10.17504/protocols.io.7behije | 2021-03-29 03:10:16 | ||
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Tn5 Library Prep for Deep Sequencing Loci of CRISPR/Cas9 Edited Cells. Single gene specific primer amplification (UDiTaS protocol with alterations) Resource Report Resource Website |
Eric Danner | 10.17504/protocols.io.7k2hkye | This is the Tn5 gDNA prep published in the supplementary file of the UDiTaS paper (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4561-9).Usage: measuring chromosome fusions, InDels, mRNA splicing, structural variants, large resection, off target integration. -> Some of these DNA repair outcomes are demonstrated using such a sample preparation in this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6455975/ ). My protocol is a modified version of UDiTaS but with a few tweaks like using nested primers. You will need a protein facility to produce the recombinant Tn5.Software for analysis is on https://github.com/ericdanneror https://github.com/editasmedicine/uditas | Max Delbrück Center | 1 | 2020 | Eric Danner 2020. Tn5 Library Prep for Deep Sequencing Loci of CRISPR/Cas9 Edited Cells. Single gene specific primer amplification (UDiTaS protocol with alterations). protocols.io dx.doi.org/10.17504/protocols.io.7k2hkye | 2021-03-29 03:10:15 | ||||
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Evaluating probabilistic programming languages for simulating quantum correlations Resource Report Resource Website |
Abdul Obeid, Peter WIttek, Peter D. Bruza | 10.17504/protocols.io.u79ezr6 | Co-Author, Co-Author, Co-Author | 1 | 2018 | Abdul Obeid, Peter WIttek, Peter D. Bruza 2018. Evaluating probabilistic programming languages for simulating quantum correlations. protocols.io dx.doi.org/10.17504/protocols.io.u79ezr6 | 2021-03-29 03:10:24 | |||||
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Setting $PATH on UA HPC Resource Report Resource Website |
Ken Youens-Clark | 10.17504/protocols.io.fribm4e | MetaFunc Course | University of Arizona | 1 | 2016 | Ken Youens-Clark 2016. Setting $PATH on UA HPC. protocols.io dx.doi.org/10.17504/protocols.io.fribm4e | 2021-03-29 03:10:24 | ||||
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Extraction of PLFA from wood debris Resource Report Resource Website |
Chenhui Chang | 10.17504/protocols.io.ixmcfk6 | Chang C, Wu F, Yang W, Xu Z, Cao R, He W, Tan B, Justine MF (2017) The microbial community in decaying fallen logs varies with critical period in an alpine forest. PLoS ONE 12(8): e0182576. doi: 10.1371/journal.pone.0182576 | https://doi.org/10.1371/journal.pone.0182576 | 1 | 2017 | Chenhui Chang 2017. Extraction of PLFA from wood debris. protocols.io dx.doi.org/10.17504/protocols.io.ixmcfk6 | 2021-03-29 03:10:23 | ||||
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Simple DNA Extraction for Phytoplankton Using Chelex 100 Resource Report Resource Website |
G Jason Smith | 10.17504/protocols.io.h58b89w | Protist Research to Optimize Tools in Genetics (PROT-G), Environmental Biotechnology Lab | This is a modification of the origianl Chelex 100 extraction described by Walsh, Metzger and Higuchi (1991 BioTechniques 10(4):506). Adding PVPP facilitates working with environmental samples as well as pure cultures hi in phenolics or other contaminants. | Moss Landing Marine Laboratories | 2 | 2017 | G Jason Smith 2017. Simple DNA Extraction for Phytoplankton Using Chelex 100. protocols.io dx.doi.org/10.17504/protocols.io.h58b89w | 2021-03-29 03:10:24 | |||
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Bioluminescence Resonance Energy Transfer at various ratios of expressed proteins Resource Report Resource Website |
Benoit Besson, Florian Sonthonnax, Magalie Duchateau, Youcef Ben Khalifa, Florence Larrous, Hyeju Eun, Véronique Hourdel, Mariette Matondo, Julia Chamot-Rooke, Regis Grailhe, Hervé Bourhy | 10.17504/protocols.io.jepcjdn | Besson B, Sonthonnax F, Duchateau M, Khalifa YB, Larrous F, Eun H, Hourdel V, Matondo M, Chamot-Rooke J, Grailhe R, Bourhy H (2017) Regulation of NF-κB by the p105-ABIN2-TPL2 complex and RelAp43 during rabies virus infection. PLoS Pathog 13(10): e1006697. doi: 10.1371/journal.ppat.1006697 | Institut Pasteur, Institut Pasteur, Institut Pasteur, Institut Pasteur, Institut Pasteur, Institut Pasteur Korea, Institut Pasteur, Institut Pasteur, Institut Pasteur, Institut Pasteur Korea, Institut Pasteur | https://doi.org/10.1371/journal.ppat.1006697 | 1 | 2017 | Benoit Besson, Florian Sonthonnax, Magalie Duchateau, Youcef Ben Khalifa, Florence Larrous, Hyeju Eun, Véronique Hourdel, Mariette Matondo, Julia Chamot-Rooke, Regis Grailhe, Hervé Bourhy 2017. Bioluminescence Resonance Energy Transfer at various ratios of expressed proteins. protocols.io dx.doi.org/10.17504/protocols.io.jepcjdn | 2021-03-29 03:10:23 | |||
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Blasticidin titration of cancer cell lines Resource Report Resource Website |
Emily Souster, Verity Goodwin, Adam Jackson, Charlotte Beaver, Rizwan Ansari, Fiona Behan, Mathew Garnett | 10.17504/protocols.io.bgz6jx9e | Cellular Generation and Phenotyping | This protocol is used to identify the optimum blasticidin concentration for the selection of Cas9 positive cancer cell lines. Process diagram: | Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute | 1 | 2020 | Emily Souster, Verity Goodwin, Adam Jackson, Charlotte Beaver, Rizwan Ansari, Fiona Behan, Mathew Garnett 2020. Blasticidin titration of cancer cell lines. protocols.io dx.doi.org/10.17504/protocols.io.bgz6jx9e | 2021-03-29 03:10:25 | |||
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Applying vContact to Viral Sequences and Visualizing the Output (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | 10.17504/protocols.io.ev8be9w | Sullivan Lab | 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. | 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: 10.1038/ismej.2016.89 | The Ohio State University | https://dx.doi.org/10.1038/ismej.2016.89 | 1 | 2016 | Benjamin Bolduc 2016. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.ev8be9w | 2021-03-29 03:10:25 | |
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DNA extraction, amplification, and sequencing of Ophiothrix (Echinodermata: Ophiuroidea) Resource Report Resource Website |
Renata Alitto, Michela Borges, Letícia Dias de Oliveira, Karin Regina Seger | 10.17504/protocols.io.tz7ep9n | DNA extraction, amplification, and sequencing, particularly for the brittel star Ophiothrix. | Alitto RAdS, Amaral ACZ, Oliveira LDd, Serrano H, Seger KR, Guilherme PDB, Domenico MD, Christensen AB, Lourenço LB, Tavares M, Borges M (2019) Atlantic West Ophiothrix spp. in the scope of integrative taxonomy: Confirming the existence of Ophiothrix trindadensis Tommasi, 1970. PLoS ONE 14(1): e0210331. doi: 10.1371/journal.pone.0210331 | UNICAMP, UNICAMP, UNICAMP, UNICAMP | https://doi.org/10.1371/journal.pone.0210331 | 1 | 2019 | Renata Alitto, Michela Borges, Letícia Dias de Oliveira, Karin Regina Seger 2019. DNA extraction, amplification, and sequencing of Ophiothrix (Echinodermata: Ophiuroidea). protocols.io dx.doi.org/10.17504/protocols.io.tz7ep9n | 2021-03-29 03:10:21 | ||
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Isolation of Haloviruses from Natural Waters Resource Report Resource Website |
Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith | 10.17504/protocols.io.ebcbaiw | VERVE Net | This is a protocol from: Stedman, K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6: The isolation of viruses infecting Archaea. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7Please see the published manuscript for additional information. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_057.pdf | 1 | 2016 | Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith 2016. Isolation of Haloviruses from Natural Waters. protocols.io dx.doi.org/10.17504/protocols.io.ebcbaiw | 2021-03-29 03:10:21 | ||
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Adapter ligation with AMII Resource Report Resource Website |
Josh Quick | 10.17504/protocols.io.bdp9i5r6 | Diaz-Munoz Lab, Coronavirus Method Development Community, Szentagothai Research Centre Virology | This is a subprotocol for performing adapter ligation with AMII | Pattabiraman C, Habib F, K. HP, Rasheed R, Prasad P, Reddy V, Dinesh P, Damodar T, Hosallimath K, George AK, Reddy NVK, John B, Pattanaik A, Kumar N, Mani RS, Venkataswamy MM, Hameed SKS, G. PKB, Desai A, Vasanthapuram R (2020) Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka. PLoS ONE 15(12): e0243412. doi: 10.1371/journal.pone.0243412 | University of Birmingham | http://lab.loman.net/protocols/ | 1 | 2020 | Josh Quick 2020. Adapter ligation with AMII. protocols.io dx.doi.org/10.17504/protocols.io.bdp9i5r6 | 2021-03-29 03:10:21 | |
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SensingSelf S1 Rapid Antigen Test (Saliva/Sputum/Stool) Resource Report Resource Website |
Shripal Gandhi, Santo Purnama, Keyur Patel, Praveen Sukumara, Dr Rinu R Ravi | 10.17504/protocols.io.bj6ykrfw | Coronavirus Method Development Community, SensingSelfMission, XPRIZE Rapid Covid Testing | Summary:The S1 COVID-19 Rapid Antigen test kit developed by Sensing Self Pte. Ltd. can quickly and qualitatively detect the spike glycoprotein of novel coronavirus (SARS-COV-2) in human saliva/sputum/stool samples. It can be used as an aid for COVID-19 diagnosis.Objective:According to the clinical trial plan, the S1 COVID-19 Rapid Antigen test kit or “test reagent”, is to test saliva/sputum/stool samples from healthy subjects and confirmed COVID-19 patients. Test results are compared with another commercial SARS-COV-2 nucleic acid detection kit with CFDA approval, which is defined as the “gold standard”. The sensitivity, specificity, and total agreement rate are used to evaluate the feasibility of the test reagent in clinical applications.Method:A collection of clinical samples were examined by the S1 COVID-19 Rapid Antigen test kit and the gold standard SARS-COV-2 nucleic acid detection kit in parallel, to calculate the clinical sensitivity, clinical specificity and total agreement rate of the test reagent.Results:Compared to the gold standard, the clinical sensitivity of test reagent reached 90.0%, the clinical specificity reached 100.0%, and the total coincidence rate reached 95.0%.Conclusions:The performance of test reagent has a high agreement rate with the gold standard, proving its good feasibility in diagnosing suspected COVID-19 cases. | Sensing Self Pte Ltd, Singapore, Sensingself pte. ltd., Sensingself pte. ltd., Sensingself pte. ltd., Sensingself pte. ltd. | http://www.sensingself.me | 1 | 2020 | Shripal Gandhi, Santo Purnama, Keyur Patel, Praveen Sukumara, Dr Rinu R Ravi 2020. SensingSelf S1 Rapid Antigen Test (Saliva/Sputum/Stool). protocols.io dx.doi.org/10.17504/protocols.io.bj6ykrfw | 2021-03-29 03:10:21 | ||
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Standardized procedures for thoracentesis / pleural biopsy at Pleural Diseases Outpatient Clinic - HUPE / UERJ Resource Report Resource Website |
Ana Paula Santos, Thiago Mafort, Rogério Rufino | 10.17504/protocols.io.saceaaw | Thoracentesis is a procedure in which a needle is inserted into the pleural space between the lungs and the chest wall. This procedure is done to remove excess fluid from the pleural space or to determine the cause of the pleural effusion. The aim of this protocol is to spread to the cientific community the standard procedures to perform thoracentesis and pleural biopsy at HUPE / UERJ. | Santos AP, Corrêa RdS, Ribeiro-Alves M, Silva ACOSd, Mafort TT, Leung J, Pereira GMB, Rodrigues LS, Rufino R (2018) Application of Venn's diagram in the diagnosis of pleural tuberculosis using IFN-γ, IP-10 and adenosine deaminase. PLoS ONE 13(8): e0202481. doi: 10.1371/journal.pone.0202481 | Pedro Ernesto University Hospital - UERJ, Pedro Ernesto University Hospital - UERJ, Pedro Ernesto University Hospital - UERJ | https://doi.org/10.1371/journal.pone.0202481 | 1 | 2018 | Ana Paula Santos, Thiago Mafort, Rogério Rufino 2018. Standardized procedures for thoracentesis / pleural biopsy at Pleural Diseases Outpatient Clinic - HUPE / UERJ. protocols.io dx.doi.org/10.17504/protocols.io.saceaaw | 2021-03-29 03:10:22 | ||
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River biofilms sampling for both downstream DNA analysis and microscopic counts Resource Report Resource Website |
Frederic Rimet, Marine Vautier, Rainer Kurmayer, Nico Salmaso, Camilla Capelli, Agnès Bouchez, Peter Hufnagl, Isabelle Domaizon | 10.17504/protocols.io.ben6jdhe | EcoALpsWater | The objective of this protocol is to provide a reliable and replicable method for the sampling of river micro-phytobenthos and associated microbes in biofilms, to be used in both downstream DNA analysis and algal microscopic counts. .justify:after { content: ""; display:inline-block; width: 100%; } The filed protocol is optimized for routine sampling and is in agreement with CEN guidance (NF EN 13946) and CEN technical report (CEN/TR 17245) for the analysis of benthic diatoms from rivers and lakes. .justify:after { content: ""; display:inline-block; width: 100%; } The application proposed here in the context of EcoAlpsWater aims in comparing DNA inventories to traditional inventories (microscopy). .justify:after { content: ""; display:inline-block; width: 100%; } This protocol is part of the deliverables provided by the WP1 of the Eco-AlpsWater project. All members of the EcoAlpsWater consortium (involving 12 partners : http://www.alpine-space.eu/projects/eco-alpswater/en/home) have contributed to the optimization of this protocol. .justify:after { content: ""; display:inline-block; width: 100%; } .justify:after { content: ""; display:inline-block; width: 100%; } Phytobenthos-based ecological assessment of running waters is part of the EU Water Framework Directive 2000/60/EC (European Commission) allowing to evaluate the level of nutrients and organic matter pollution in rivers. According to the countries, phytobenthos assessment includes all groups of algae or is based only on diatoms communities. Other periphytic organisms such as fungi, bacteria or microbial eukaryotes as cilates or planktonic (metaphytic) algae are not considered in this assessment method. Further the group of charophytes is covered by the macrophyte ecology method assessment. .justify:after { content: ""; display:inline-block; width: 100%; } The recent development of DNA metabarcoding has the potential to complement the traditional biological monitoring based on the direct observation of the organisms, both by reducing sample-processing cost and time and by offering the opportunity to consider a larger taxonomic diversity (e.g. bacteria, heterotrophic micro-eukaryotes …). .justify:after { content: ""; display:inline-block; width: 100%; } The protocol described here is dedicated to the sampling of biofilms in rivers both for microscopic enumeration of the phytobenthic community and for downstream DNA analyses of microbial assemblages. .justify:after { content: ""; display:inline-block; width: 100%; } This field protocol is based on routine methods used for biofilms sampling and is in agreement with: .justify:after { content: ""; display:inline-block; width: 100%; } - CEN, 2014. Water quality - NF EN 13946 - Guidance for the routine sampling and preparation of benthic diatoms from rivers and lakes. Afnor, 1-23. .justify:after { content: ""; display:inline-block; width: 100%; } - CEN 2018. Water quality - CEN/TR 17245 - Technical report for the routine sampling of benthic diatoms from rivers and lakes adapted for metabarcoding analyses. CEN, 1-8. .justify:after { content: ""; display:inline-block; width: 100%; } | INRAE, CARRTEL, Pole R&D ECLA, 74200 Thonon les bains, France, INRAE, CARRTEL, Pole R&D ECLA, 74200 Thonon les bains, France, University of Innsbruck, Research Dep. for Limnology, Innsbruck, Austria , Edmund Mach Foundation, San Michele all’Adige, Trento, Italy , University of Applied Sciences Southern Switzerland, SUPSI, Cannobio, Switzerland , INRAE, CARRTEL, Pole R&D ECLA, 74200 Thonon les bains, France, Austrian Agency for Health and Food Safety Ltd.(AGES), Austria, INRAE, CARRTEL, Pole R&D ECLA, 74200 Thonon les bains, France | 1 | 2020 | Frederic Rimet, Marine Vautier, Rainer Kurmayer, Nico Salmaso, Camilla Capelli, Agnès Bouchez, Peter Hufnagl, Isabelle Domaizon 2020. River biofilms sampling for both downstream DNA analysis and microscopic counts. protocols.io dx.doi.org/10.17504/protocols.io.ben6jdhe | 2021-03-29 03:10:22 | |||
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Amplicon sequencing using MinION optimized from 1D native barcoding genomic DNA Resource Report Resource Website |
Yiheng Hu, Benjamin Schwessinger | 10.17504/protocols.io.mhkc34w | High molecular weight DNA extraction from all kingdoms, Team Schwessinger | This is a protocol optimized from Oxford Nanopore Technology 1D native barcoding genomic DNA (with EXP-NBD103 and SQK-LSK108) for sequencing amplicons of fungal marker genes (ITS, EF1a) using PCR.Thanks to Dr. Benjamin Schwesinger for his suggestions about the protocol.Thanks to Dr. Leon Smith (ANU, Linde lab), Prof. Wieland Meyer (USydney) and Dr. Laszlo Irinyi for their contribution of fungal samples. | Australian National University, Australian National University | 1 | 2018 | Yiheng Hu, Benjamin Schwessinger 2018. Amplicon sequencing using MinION optimized from 1D native barcoding genomic DNA. protocols.io dx.doi.org/10.17504/protocols.io.mhkc34w | 2021-03-29 03:10:27 | |||
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An easy chromatographic method for purification of Immunoglobulin Y (IgY) using HiTrap™ Columns. Resource Report Resource Website |
Angel Justiz-Vaillant | 10.17504/protocols.io.bju7knzn | University of the West Indies, [email protected] | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. An easy chromatographic method for purification of Immunoglobulin Y (IgY) using HiTrap™ Columns.. protocols.io dx.doi.org/10.17504/protocols.io.bju7knzn | 2021-03-29 03:10:27 | ||||
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Preparing biological samples for metabarcoding Resource Report Resource Website |
Tim Regan | 10.17504/protocols.io.bms8k6hw | This protocol describes the preparation of biological samples (specifically from a marine environment e.g. hatchery or RAS unit) for amplicon sequencing. Starting with a biological sample stored in Qiagen buffer ATL, or similar, it begins with a bead beating process to homogenise the sample. Enzymatic lysis using Metapolyzyme and Proteinase K are emplyed to ensure efficient DNA release. The Qiagen DNeasy kit is used to column extract DNA from lysates. Following concentration estimates of DNA elutions, samples are diluted >1:10 to avoid PCR inhibition during amplicon library preparation. | The Roslin Institute, University of Edinburgh | 2 | 2020 | Tim Regan 2020. Preparing biological samples for metabarcoding. protocols.io dx.doi.org/10.17504/protocols.io.bms8k6hw | 2021-03-29 03:10:26 |
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