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: Leigh Monahan, Kay Anantanawat, Joyce To, Aaron Darling
Group: Coronavirus Method Development Community
Summary: Managing the current COVID-19 pandemic requires diagnostic testing at an unprecedented scale. However, the crisis has revealed severe deficiencies in our capacity to perform such testing. Here we build on the work of others (1-3) to develop a protocol that not only enables many thousand diagnostic tests to be run in parallel, but also provides near-whole genome sequencing data to facilitate phylogenetic analysis and contact tracing. One of the key features of our protocol is a magnetic bead-based strategy for RNA capture that may circumvent the need for SARS-CoV-2 RNA extraction, currently one of the major bottlenecks in both reagent supply and hands-on sample processing time. This approach also eliminates the requirement for per-sample reverse transcription, significantly reducing per-sample costs. The major steps in our wet lab workflow can be summarised as follows. First, we generate a collection of bead-bound, single-stranded DNA probes tiling the entire SARS-CoV-2 genome. Multiple uniquely barcoded probe sets are prepared, each of which are used to capture viral RNA directly from patient swab samples via DNA/RNA hybridisation. Samples are combined together at this stage, enabling cDNA synthesis to be performed in a single pooled reaction. Finally, multiplex PCR is used to generate a library of overlapping amplicons ready for Illumina sequencing. A schematic overview of the workflow is attached below, along with a more detailed figure depicting the various stages of library preparation.Referenceshttps://docs.google.com/document/d/1kP2w_uTMSep2UxTCOnUhh1TMCjWvHEY0sUUpkJHPYV4/previewhttps://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w/abstracthttps://www.biorxiv.org/content/10.1101/2020.03.20.001008v1.full.pdf
Proper citation: Leigh Monahan, Kay Anantanawat, Joyce To, Aaron Darling 2020. A protocol for massively parallel diagnosis and genome sequencing of SARS-CoV-2. protocols.io dx.doi.org/10.17504/protocols.io.betrjem6 Copy
Authors: Deepak Nanjappa and Kathryn Coyne
Summary: This protocol was developed for the glass bead-mediated transformation of Heterosigma akashiwo. This species does not grow on solid medium, so transformants are grown "in bulk" and should not be considered clonal. We have repeated this protocol with success and have been able to maintain transformants on selection medium for several months.
Proper citation: Deepak Nanjappa and Kathryn Coyne 2019. Glass bead transformation of Heterosigma akashiwo. protocols.io dx.doi.org/10.17504/protocols.io.4qhgvt6 Copy
Authors: Kirstyn Brunker
Summary: This protocol details the steps involved to perform RNA extraction on rabies virus brain tissue samples collected by the WHO recommended "straw method" in the field (Meslin F-X, Kaplan MM, Koprowski H. Laboratory techniques in rabies. World Health Organization; 1996.[10]). The protocol is field-friendly and can be performed using portable, battery powered equipment.
Proper citation: Kirstyn Brunker 2020. RNA extraction from field-collected brain tissue samples from suspect rabid animals. protocols.io dx.doi.org/10.17504/protocols.io.bdcei2te Copy
Authors: Andrija S. Grustam, Nasuh Buyukkaramikli, Ron Koymans, Hubertus J.M. Vrijhoef, Johan L. Severens
Summary: Figure 1 - Single loop Monte Carlo scheme for computing overall individual Expected Value of Perfect Information (EVPI). andFigure 2 - Sampling algorithm for the calculation of Expected Value of Partially Perfect Information (EVPPI) with double loop.
Proper citation: Andrija S. Grustam, Nasuh Buyukkaramikli, Ron Koymans, Hubertus J.M. Vrijhoef, Johan L. Severens 2019. Value of Information in Telehealth for Chronic Heart Failure. protocols.io dx.doi.org/10.17504/protocols.io.xqdfms6 Copy
Authors: Nancy R. Buchan, Gianluca Grimalda, Marilynn Brewer, Enrique Fatas, Margaret Foddy, Rick Wilson
Summary: We present the protocol of international economics experiments conducted to study the relationship between globalisation, social identity and propensity to cooperate. We developed a scale of individual-level globalisation and three scales of local, social and global social identity. Three experimental decisions in social dilemmas measured the propensity to cooperate at the local, national and global level. Participants were about 200 adults from six countries (the US, Italy, Russia, Argentina, South Africa and Iran).Articles from this research have been published as:- Grimalda G, Buchan N, Brewer M (2018). Social identity mediates the positive effect of globalization on individual cooperation: Results from international experiments. PLoS ONE 13(12): e0206819. https://doi.org/10.1371/journal.pone.0206819. - Buchan N, Brewer M, Grimalda G, Wilson R, Fatas E, Foddy M (2011). “Global Social Identity and Global Cooperation”, Psychological Science, 22(6): 821-828. Doi: 10.1177/0956797611409590. - Buchan N, Grimalda G, Wilson R, Brewer M, Fatas E, Foddy M (2009) “Globalization and Human Cooperation”, Proceedings of the National Academy of Sciences of the USA, 106 (11): 4138-4142. (doi: 10.1073/pnas.0809522106).
Proper citation: Nancy R. Buchan, Gianluca Grimalda, Marilynn Brewer, Enrique Fatas, Margaret Foddy, Rick Wilson 2018. "Globalization, Cooperation & Social Identity" project. protocols.io dx.doi.org/10.17504/protocols.io.wmhfc36 Copy
Authors: Szymon T Calus, Umer Zeeshan Ijaz, Ameet Pinto
Group: Pinto Lab
Proper citation: Szymon T Calus, Umer Zeeshan Ijaz, Ameet Pinto 2018. NanoAmpli-Seq - Sample processing and sequencing library preparation workflow. protocols.io dx.doi.org/10.17504/protocols.io.u26eyhe Copy
Authors: Verity Goodwin, Emily Souster, Mathew Garnett, Fiona Behan, Charlotte Beaver, Rizwan Ansari, Adam Jackson
Group: Cellular Generation and Phenotyping
Summary: This protocol is designed to outline the process of fixing cell pellets in 1.5ml tubes. It has been developed within the Cellular Generation and Phenotyping Group at the Wellcome Sanger Institute.Process diagram:
Proper citation: Verity Goodwin, Emily Souster, Mathew Garnett, Fiona Behan, Charlotte Beaver, Rizwan Ansari, Adam Jackson 2020. Fixing Cell Pellets for Flow Cytometry. protocols.io dx.doi.org/10.17504/protocols.io.bixakfie Copy
Authors: Fernando Guzman Chavez, Jim Haseloff
Summary: Following this recipe, you will obtain 1L of S30, S30A and S30B BuffersS30 Buffer is a standard solution to wash cell pellets previous to lysis. Likewise, it is used during the cell lysis.NOTE :The protocol described here is an adaptation from these papers:Adam D. Silverman, Nancy Kelley-Loughnane, Julius B. Lucks, and Michael C. Jewett (2019).Deconstructing Cell-Free Extract Preparation for in Vitro Activation of Transcriptional Genetic Circuitry. ACS Synthetic Biology, 403-414. DOI: 10.1021/acssynbio.8b00430.Yang WC, Patel KG, Wong HE, Swartz JR.(2012). Simplifying and streamlining Escherichia coli-based cell-free protein synthesis.Biotechnol Prog. 28(2):413-420. DOI:10.1002/btpr.1509.https://www.protocols.io/researchers/anibal-arce-medinaYang WC, Patel KG, Wong HE, Swartz JR.(2012). Simplifying and streamlining Escherichia coli-based cell-free protein synthesis.Biotechnol Prog. 28(2):413-420. DOI:10.1002/btpr.1509.https://www.protocols.io/researchers/anibal-arce-medina
Proper citation: Fernando Guzman Chavez, Jim Haseloff 2020. S30-S30A-S30-Buffers- Haseloff Lab. protocols.io dx.doi.org/10.17504/protocols.io.bigckbsw Copy
Authors: Sebastian Triesch, Maximilian Dietsch
Group: Axmann Lab, CyanoWorld, M4455 - Synthetische Biologie und Biotechnologie
Summary: The following protocol is optimized to generate first-strand cDNA for use in two step-PCR.
Proper citation: Sebastian Triesch, Maximilian Dietsch 2019. First strand cDNA synthesis (ThermoScientific RevertAid). protocols.io dx.doi.org/10.17504/protocols.io.ze3f3gn Copy
Authors: Kelsey Miller, 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 and less antibody 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: Kelsey Miller, Sam Li 2019. MojoSort™ Streptavidin Nanobeads Column Protocol - Positive Selection. protocols.io dx.doi.org/10.17504/protocols.io.692hh8e Copy
Authors: Bao Thai
Group: Stephen Floor Lab
Proper citation: Bao Thai 2018. PBS (1L of 10X). protocols.io dx.doi.org/10.17504/protocols.io.mpec5je Copy
Authors: Kameran Lashkari, Gianna Teague, Ursula Beattie, Joanna Betts, Megan M McLaughlin, Francisco J Lopez
Proper citation: Kameran Lashkari, Gianna Teague, Ursula Beattie, Joanna Betts, Megan M McLaughlin, Francisco J Lopez 2020. PONE-S-20-05322-2 DATA SETS, BOX PLOTS and GRAPHS. protocols.io dx.doi.org/10.17504/protocols.io.bhwuj7ew Copy
Authors: Kelsey Miller
Group: BioLegend
Proper citation: Kelsey Miller 2018. Th9 Polarization of Mouse CD4+ Cells. protocols.io dx.doi.org/10.17504/protocols.io.tnnemde Copy
Authors: Masahito Yamagata
Group: RANbody forum
Summary: Each P-RANbody consists of a HRP reporter and a nanobody that binds to antigen(s). This is a protocol to stain cells and tissues with P-RANbodies. The method is similar to common immunostaining protocols. However, this protocol focuses on some important tips.
Proper citation: Masahito Yamagata 2018. Staining with P-RANbodies. protocols.io dx.doi.org/10.17504/protocols.io.pqadmse Copy
Authors: Meru J. Sadhu, Joshua S. Bloom, Laura Day, Leonid Kruglyak
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.
Proper citation: Meru J. Sadhu, Joshua S. Bloom, Laura Day, Leonid Kruglyak 2017. CRISPR-Directed Mitotic Recombination Enables Genetic Mapping Without Crosses. protocols.io dx.doi.org/10.17504/protocols.io.hu7b6zn Copy
Authors: Uri Rosenblum, Lotem Kribus-Shmiel, Gabi Zeilig, Yotam Bahat, Shani Kimel-Naor, Itshak Melzer, Meir Plotnik
Summary: Walking perturbations are a well-established tool to study human performance of balance tasks. We aimed to characterize walking and balance reactions in adults with and without neurological disease. Participants walked on self-paced treadmill while being exposed to unexpected surface displacement Perturbations. these were introduced at different phases of the gait cycle, on both legs and in anterior-posterior or medio-lateral directions, in random order. Two types of perturbations were implemented: (1) medio-lateral platform perturbations were achieved by displacing the moving platform 15 cm, to the left or to the right, over 0.92 seconds. The platform held its new position for 30 seconds and then returned gradually to its original position over 3 seconds; (2) anterior-posterior treadmill belt perturbations were achieved by reducing the speed of one of the treadmill belts by 1.2 m/s with a deceleration of 5 m/s2.Relevant gait phase, gait parameters of step length and width as well as walking speed were detected and calculated from force plate and markers data in the sagittal plane. Force plate data was filtered using a low-pass filter with cutoff frequency of 5Hz and a force threshold of 25N is used; no filters were applied to the marker data.The protocol has two steps: (1) self-pace learning and (2) walking with unexpected surface displacement perturbations.
Proper citation: Uri Rosenblum, Lotem Kribus-Shmiel, Gabi Zeilig, Yotam Bahat, Shani Kimel-Naor, Itshak Melzer, Meir Plotnik 2020. unexpected perturbations while walking in virtual reality environment. protocols.io dx.doi.org/10.17504/protocols.io.bdjvi4n6 Copy
Authors: Daniel Hausmann, Vera Kiesel, Lukas Zimmerli, Narcisa Schlatter, Amandine von Gunten, Nadine Wattinger, Thomas Rosemann
Summary: Study Material for Manuscript: Sensitivity for Multimorbidity: The Role of Diagnostic Uncertainty of Physicians when Evaluating Multimorbid Video Case-based Vignettes (English version of study protocols)
Proper citation: Daniel Hausmann, Vera Kiesel, Lukas Zimmerli, Narcisa Schlatter, Amandine von Gunten, Nadine Wattinger, Thomas Rosemann 2018. Study protocols (in English). protocols.io dx.doi.org/10.17504/protocols.io.urvev66 Copy
Authors: Adolfo Maria TAMBELLA, Anna Rita ATTILI
Summary: Objective To determine whether the topical application of platelet-rich plasma (PRP) promotes healing in experimentally-induced full-thickness skin wounds in animals, a systematic review and meta-analysis will be performed.MethodsWeb of Science, Cochrane Library, PubMed, Research Gate, Cochrane Wounds Group, and Veterinary Information Network will be searched to identify randomised and not randomised controlled clinical trials comparing PRP with placebo or with other treatments in animals. Primary outcome: reduction of open wound area; secondary outcomes: healing time and number of healed cases. Effect sizes: Hedges’ g; odds ratio. This protocol was used in the following publication:https://doi.org/10.1371/journal.pone.0191093Tambella AM, Attili AR, Dupré G, Cantalamessa A, Martin S, Cuteri V, Marcazzan S, Del Fabbro M (2018) Platelet-rich plasma to treat experimentally-induced skin wounds in animals: A systematic review and meta-analysis. PLoS ONE 13(1): e0191093. doi: 10.1371/journal.pone.0191093
Proper citation: Adolfo Maria TAMBELLA, Anna Rita ATTILI 2018. Platelet-rich plasma application in experimentally-induced skin wounds in animals: protocol for a systematic review and meta-analysis. protocols.io dx.doi.org/10.17504/protocols.io.mnrc5d6 Copy
Authors: Bo-jian Chen, Kai Liu, Lin-jun Zhou, Guilherme Gomes-Silva, Carolin Sommer-Trembo, Martin Plath
Summary: In this protocol, we used computer animated stimuli for two mate choice tests of Gambusia affinis, such that stimulus pairs differed only by (a) body size and (b) locomotor activity, but not in other morphological or behavioural traits that could affect mate choice decisions.
Proper citation: Bo-jian Chen, Kai Liu, Lin-jun Zhou, Guilherme Gomes-Silva, Carolin Sommer-Trembo, Martin Plath 2018. A computer animation based mating preference assessment protocol. protocols.io dx.doi.org/10.17504/protocols.io.m67c9hn 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.
Proper citation: Sam Li 2020. MojoSort™ Mouse CD8a Selection Kit Column Protocol. protocols.io dx.doi.org/10.17504/protocols.io.bbugintw 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
