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Name Authors DOI Group Summary Associated Publications RRIDs used Affiliations External URL Version Publication Date Proper Citation Record Last Update
A protocol for massively parallel diagnosis and genome sequencing of SARS-CoV-2
 
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Leigh Monahan, Kay Anantanawat, Joyce To, Aaron Darling 10.17504/protocols.io.betrjem6 Coronavirus Method Development Community 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 University of Technology Sydney, University of Technology Sydney, University of Technology Sydney, University of Technology Sydney 1 2020 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 2021-03-29 03:08:50
Glass bead transformation of Heterosigma akashiwo
 
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Deepak Nanjappa and Kathryn Coyne 10.17504/protocols.io.4qhgvt6 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.  University of Delaware 3 2019 Deepak Nanjappa and Kathryn Coyne 2019. Glass bead transformation of Heterosigma akashiwo. protocols.io dx.doi.org/10.17504/protocols.io.4qhgvt6 2021-03-29 03:08:50
RNA extraction from field-collected brain tissue samples from suspect rabid animals
 
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Kirstyn Brunker 10.17504/protocols.io.bdcei2te 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. University of Glasgow 1 2020 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 2021-03-29 03:08:50
Value of Information in Telehealth for Chronic Heart Failure
 
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Andrija S. Grustam, Nasuh Buyukkaramikli, Ron Koymans, Hubertus J.M. Vrijhoef, Johan L. Severens 10.17504/protocols.io.xqdfms6 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. Erasmus School of Health Policy & Management, Erasmus University Rotterdam, The Netherlands, iMTA, Institute of Medical Technology Assessment, Erasmus University Rotterdam, The Netherlands, Professional Health Solutions & Services Department, Philips Research, The Netherlands, Department of Patient & Care, Maastricht UMC, The Netherlands, Erasmus School of Health Policy & Management, Erasmus University Rotterdam, The Netherlands 1 2019 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 2021-03-29 03:08:50
"Globalization, Cooperation & Social Identity" project
 
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Nancy R. Buchan, Gianluca Grimalda, Marilynn Brewer, Enrique Fatas, Margaret Foddy, Rick Wilson 10.17504/protocols.io.wmhfc36 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). University of South Carolina, Kiel Institute for the World Economy, Ohio State University, Columbus, Loughborough University, University of Pennsylvania, Carleton University, Rice University https://doi.org/10.1371/journal.pone.0206819 3 2018 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 2021-03-29 03:08:50
NanoAmpli-Seq - Sample processing and sequencing library preparation workflow
 
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Szymon T Calus, Umer Zeeshan Ijaz, Ameet Pinto 10.17504/protocols.io.u26eyhe Pinto Lab Ex-Uni of Glasgow/Birmingham/Aberystwyth, University of Glasgow, Northeastern University https://www.biorxiv.org/content/early/2018/01/07/244517 1 2018 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 2021-03-29 03:08:49
Fixing Cell Pellets for Flow Cytometry
 
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Verity Goodwin, Emily Souster, Mathew Garnett, Fiona Behan, Charlotte Beaver, Rizwan Ansari, Adam Jackson 10.17504/protocols.io.bixakfie Cellular Generation and Phenotyping 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: Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute 2 2020 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 2021-03-29 03:08:49
S30-S30A-S30-Buffers- Haseloff Lab
 
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Fernando Guzman Chavez, Jim Haseloff 10.17504/protocols.io.bigckbsw 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 University of Cambridge, University of Cambridge 1 2020 Fernando Guzman Chavez, Jim Haseloff 2020. S30-S30A-S30-Buffers- Haseloff Lab. protocols.io dx.doi.org/10.17504/protocols.io.bigckbsw 2021-03-29 03:08:49
First strand cDNA synthesis (ThermoScientific RevertAid)
 
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Sebastian Triesch, Maximilian Dietsch 10.17504/protocols.io.ze3f3gn Axmann Lab, CyanoWorld, M4455 - Synthetische Biologie und Biotechnologie The following protocol is optimized to generate first-strand cDNA for use in two step-PCR. Institute for Synthetic Microbiology, HHU Düsseldorf, Institute for Synthetic Microbiology, HHU Düsseldorf 1 2019 Sebastian Triesch, Maximilian Dietsch 2019. First strand cDNA synthesis (ThermoScientific RevertAid). protocols.io dx.doi.org/10.17504/protocols.io.ze3f3gn 2021-03-29 03:08:49
MojoSort™ Streptavidin Nanobeads Column Protocol - Positive Selection
 
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Kelsey Miller, Sam Li 10.17504/protocols.io.692hh8e 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 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, BioLegend https://www.biolegend.com/protocols/mojosort-streptavidin-nanobeads-column-protocol-positive-selection/4773/ 2 2019 Kelsey Miller, Sam Li 2019. MojoSort™ Streptavidin Nanobeads Column Protocol - Positive Selection. protocols.io dx.doi.org/10.17504/protocols.io.692hh8e 2021-03-29 03:08:49
PBS (1L of 10X)
 
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Bao Thai 10.17504/protocols.io.mpec5je Stephen Floor Lab University of California, San Francisco 1 2018 Bao Thai 2018. PBS (1L of 10X). protocols.io dx.doi.org/10.17504/protocols.io.mpec5je 2021-03-29 03:08:49
PONE-S-20-05322-2 DATA SETS, BOX PLOTS and GRAPHS
 
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Kameran Lashkari, Gianna Teague, Ursula Beattie, Joanna Betts, Megan M McLaughlin, Francisco J Lopez 10.17504/protocols.io.bhwuj7ew Lashkari K, Teague GC, Beattie U, Betts J, Kumar S, McLaughlin MM, López FJ (2020) Plasma biomarkers of the amyloid pathway are associated with geographic atrophy secondary to age-related macular degeneration. PLoS ONE 15(8): e0236283. doi: 10.1371/journal.pone.0236283 Schepens Eye Research Institute, Schepens Eye Research Institute, Schepens Eye Research Institute, Computational Biology, GlaxoSmithKline, GlaxoSmithKline, Allergan (Abbvie) https://doi.org/10.1371/journal.pone.0236283 1 2020 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 2021-03-29 03:08:49
Th9 Polarization of Mouse CD4+ Cells
 
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Kelsey Miller 10.17504/protocols.io.tnnemde BioLegend BioLegend https://www.biolegend.com/protocols/th9-polarization-of-mouse-cd4--cells-protocol/4243/ 2 2018 Kelsey Miller 2018. Th9 Polarization of Mouse CD4+ Cells. protocols.io dx.doi.org/10.17504/protocols.io.tnnemde 2021-03-29 03:08:52
Staining with P-RANbodies
 
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Masahito Yamagata 10.17504/protocols.io.pqadmse RANbody forum 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.   Harvard University https://www.ncbi.nlm.nih.gov/pubmed/29440485 1 2018 Masahito Yamagata 2018. Staining with P-RANbodies. protocols.io dx.doi.org/10.17504/protocols.io.pqadmse 2021-03-29 03:08:52
CRISPR-Directed Mitotic Recombination Enables Genetic Mapping Without Crosses
 
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Meru J. Sadhu, Joshua S. Bloom, Laura Day, Leonid Kruglyak 10.17504/protocols.io.hu7b6zn Protist Research to Optimize Tools in Genetics (PROT-G) Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol. , , , http://science.sciencemag.org/content/352/6289/1113.full 1 2017 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 2021-03-29 03:08:51
unexpected perturbations while walking in virtual reality environment
 
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Uri Rosenblum, Lotem Kribus-Shmiel, Gabi Zeilig, Yotam Bahat, Shani Kimel-Naor, Itshak Melzer, Meir Plotnik 10.17504/protocols.io.bdjvi4n6 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. Rosenblum U, Kribus-Shmiel L, Zeilig G, Bahat Y, Kimel-Naor S, Melzer I, Plotnik M (2020) Novel methodology for assessing total recovery time in response to unexpected perturbations while walking. PLoS ONE 15(6): e0233510. doi: 10.1371/journal.pone.0233510 Center of Advanced Technologies in Rehabilitation, Sheba Medical Center, Tel Hashomer, Israel; Department of Physical Therapy, Recanati School for Community Health Professions, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel, Center of Advanced Technologies in Rehabilitation, Sheba Medical Center, Tel Hashomer, Israel, Department of Neurological Rehabilitation, Sheba Medical Center, Tel HaShomer, Israel; Department of Physical and Rehabilitation Medicine, Sackler Faculty of Medicine, Tel Aviv University, Israel , Center of Advanced Technologies in Rehabilitation, Sheba Medical Center, Tel Hashomer, Israel, Center of Advanced Technologies in Rehabilitation, Sheba Medical Center, Tel Hashomer, Israel, Department of Physical Therapy, Recanati School for Community Health Professions, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel, Center of Advanced Technologies in Rehabilitation, Sheba Medical Center, Tel Hashomer, Israel; Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel https://doi.org/10.1371/journal.pone.0233510 1 2020 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 2021-03-29 03:08:51
Study protocols (in English)
 
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Daniel Hausmann, Vera Kiesel, Lukas Zimmerli, Narcisa Schlatter, Amandine von Gunten, Nadine Wattinger, Thomas Rosemann 10.17504/protocols.io.urvev66 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) Hausmann D, Kiesel V, Zimmerli L, Schlatter N, Gunten Av, Wattinger N, Rosemann T (2019) Sensitivity for multimorbidity: The role of diagnostic uncertainty of physicians when evaluating multimorbid video case-based vignettes. PLoS ONE 14(4): e0215049. doi: 10.1371/journal.pone.0215049 Department of Psychology, University of Zurich, Zurich, Switzerland, Department of Psychology, University of Zurich, Zurich, Switzerland, Department of Internal Medicine, University Hospital of Zurich, Zurich, Switzerland, Department of Psychology, University of Zurich, Zurich, Switzerland, Department of Psychology, University of Zurich, Zurich, Switzerland, Department of Psychology, University of Zurich, Zurich, Switzerland, Institute of Primary Care, University of Zurich, Zurich, Switzerland http://pone.edmgr.com/ 1 2018 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 2021-03-29 03:08:51
Platelet-rich plasma application in experimentally-induced skin wounds in animals: protocol for a systematic review and meta-analysis
 
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Adolfo Maria TAMBELLA, Anna Rita ATTILI 10.17504/protocols.io.mnrc5d6 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 School of Biosciences and Veterinary Medicine, University of Camerino, Matelica, MC, Italy, School of Biosciences and Veterinary Medicine, University of Camerino, Matelica, MC, Italy https://doi.org/10.1371/journal.pone.0191093 2 2018 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 2021-03-29 03:08:51
A computer animation based mating preference assessment protocol
 
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Bo-jian Chen, Kai Liu, Lin-jun Zhou, Guilherme Gomes-Silva, Carolin Sommer-Trembo, Martin Plath 10.17504/protocols.io.m67c9hn 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. Chen B, Liu K, Zhou L, Gomes-Silva G, Sommer-Trembo C, Plath M (2018) Personality differentially affects individual mate choice decisions in female and male Western mosquitofish (Gambusia affinis). PLoS ONE 13(5): e0197197. doi: 10.1371/journal.pone.0197197 College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P.R. China, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P.R. China, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P.R. China, Department of Geography (“Saude Ambiental”), Universidade Federal de Uberlândia, Minas Gerais, Brazil, Department of Ecology and Evolution, J.W. Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P.R. China https://doi.org/10.1371/journal.pone.0197197 1 2018 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 2021-03-29 03:08:51
MojoSort™ Mouse CD8a Selection Kit Column Protocol
 
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Sam Li 10.17504/protocols.io.bbugintw 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. BioLegend https://www.biolegend.com/en-us/protocols/mojosort-mouse-cd8a-selection-kit-column-protocol 1 2020 Sam Li 2020. MojoSort™ Mouse CD8a Selection Kit Column Protocol. protocols.io dx.doi.org/10.17504/protocols.io.bbugintw 2021-03-29 03:08:51

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