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| Name | Authors | DOI | Group |
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True-Nuclear™ Transcription Factor Staining Protocol for 96-Well, U-Bottom Plate Resource Report Resource Website |
BioLegend, Inc. | 10.17504/protocols.io.gq5bvy6 | BioLegend | , | http://www.biolegend.com/media_assets/support_protocol/True-Nuclear_Trademark_Transcription_Factor_Staining_Protocol.pdf | 2 | 2016 | BioLegend, Inc. 2016. True-Nuclear™ Transcription Factor Staining Protocol for 96-Well, U-Bottom Plate. protocols.io dx.doi.org/10.17504/protocols.io.gq5bvy6 | 2021-03-29 03:10:20 | |||
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Hello (bash) Resource Report Resource Website |
Ken Youens-Clark | 10.17504/protocols.io.jvgcn3w | Metafunc Course 2017 | University of Arizona | 1 | 2017 | Ken Youens-Clark 2017. Hello (bash). protocols.io dx.doi.org/10.17504/protocols.io.jvgcn3w | 2021-03-29 03:10:26 | ||||
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Purification of pooled PCR amplicon libraries using SPRI beads Resource Report Resource Website |
Kiran B | 10.17504/protocols.io.fnvbme6 | 1 | 2017 | Kiran B 2017. Purification of pooled PCR amplicon libraries using SPRI beads. protocols.io dx.doi.org/10.17504/protocols.io.fnvbme6 | 2021-03-29 03:10:26 | ||||||
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ADBS Whole Exome Sequencing (WES) Analysis Pipeline Resource Report Resource Website |
Ravi More | 10.17504/protocols.io.vrhe536 | Integrated Whole Exome Sequencing (WES) analysis pipline using various tools and databases, developed as part of the Accelerator program for Discovery in Brain disorders using Stem cells (ADBS) program at National Centre for Biological Sciences (NCBS), Bangalore. | University of Cambridge | 1 | 2018 | Ravi More 2018. ADBS Whole Exome Sequencing (WES) Analysis Pipeline. protocols.io dx.doi.org/10.17504/protocols.io.vrhe536 | 2021-03-29 03:10:26 | ||||
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Immunofluorescence Microscopy Protocol Resource Report Resource Website |
BioLegend, Inc. | 10.17504/protocols.io.eyubfww | BioLegend | , | http://www.biolegend.com/media_assets/support_protocol/Immunofluorescence_Microscopy_Protocol_050514.pdf | 1 | 2016 | BioLegend, Inc. 2016. Immunofluorescence Microscopy Protocol. protocols.io dx.doi.org/10.17504/protocols.io.eyubfww | 2021-03-29 03:10:20 | |||
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Yale - Blood Glucose Resource Report Resource Website |
John Stack, Gary Cline | 10.17504/protocols.io.y2kfycw | Mouse Metabolic Phenotyping Centers | Procedure used to measure glucose concentrations. Glucose is measured by the enzymatically coupled reactions of hexokinase and glucose-6-P dehydrogenase. The rate of NADH formation is monitored by the change in absorbance at 340 nm. | Yale University, Yale University | https://mmpc.org/shared/document.aspx?id=202&docType=Protocol | 1 | 2019 | John Stack, Gary Cline 2019. Yale - Blood Glucose. protocols.io dx.doi.org/10.17504/protocols.io.y2kfycw | 2021-03-29 03:10:20 | ||
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PCTE filter staining Resource Report Resource Website |
Ken Stedman | 10.17504/protocols.io.eavbae6 | VERVE Net | For use in "PCTE Protocol for VLP enumeration" | Stedman Lab | 1 | 2016 | Ken Stedman 2016. PCTE filter staining. protocols.io dx.doi.org/10.17504/protocols.io.eavbae6 | 2021-03-29 03:10:20 | |||
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Postural stability, body weight distribution, and foot typology of sportsmen Resource Report Resource Website |
Jitka Marencakova, Frantisek Zahalka | 10.17504/protocols.io.qp8dvrw | The protocol describes guidelines and steps for taking repeated measurements of sportive population: postural stability, body weight distribution during quiet stance, and the foot type diagnostic. The parameters calculated from repeated measurements can be used for separate analyses: analysis of center of pressure displacement, represented by total travelled way parameter; analysis of body weight distribution and loading of the lower limbs; and foot typology. The guidelines are mostly based on recommendations of the literature, partly on our own research experiences. It is important to remain consistent during all of the measurements and follow the guidelines as they control important aspects of the measurements. Any changes of any aspects can signifficantly alter the final results. | Marencakova J, Maly T, Sugimoto D, Gryc T, Zahalka F (2018) Foot typology, body weight distribution, and postural stability of adolescent elite soccer players: A 3-year longitudinal study. PLoS ONE 13(9): e0204578. doi: 10.1371/journal.pone.0204578 | Research Sport Centre, Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic, Research Sport Centre, Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic | https://doi.org/10.1371/journal.pone.0204578 | 1 | 2018 | Jitka Marencakova, Frantisek Zahalka 2018. Postural stability, body weight distribution, and foot typology of sportsmen . protocols.io dx.doi.org/10.17504/protocols.io.qp8dvrw | 2021-03-29 03:10:20 | ||
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Qant-iT™ PicoGreen® dsDNA Quantification Resource Report Resource Website |
Roey Angel, Eva Petrova | 10.17504/protocols.io.bftfjnjn | SoWa RI Anaerobic and Molecular Microbiology (public) | The following protocol is intended for the quantification of double-stranded DNA using Quant-iT™PicoGreen® dsDNA Assay Kit (ThermoFisher). This protocol is a simplified and condensed version of the full protocol from the manufacturer. The procedure described here is for 96 reactions. If samples are run in duplicates, then this should allow quantifying 40 samples. | Soil and Water Research Inrastructure, Soil and Water Research Inrastructure | https://www.thermofisher.com/order/catalog/product/P11496 | 2 | 2020 | Roey Angel, Eva Petrova 2020. Qant-iT™ PicoGreen® dsDNA Quantification. protocols.io dx.doi.org/10.17504/protocols.io.bftfjnjn | 2021-03-29 03:10:20 | ||
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Root nitrate influx Resource Report Resource Website |
Prajakta Bendre, Vanessa Melino | 10.17504/protocols.io.biibkcan | Nitrogen (N) in the form of nitrate (NO3-) can move radially from roots to the vascular tissue from where it is transported to the above-ground organs. Roots are the first to sense the scarcity of nitrogen in the soil. The following protocol describes the step-wise procedure for performing unidirectional root NO3- influx with the use of 15N labelled NO3- at a concentration that stimulates the inducible high-affinity nitrate transporters. Stable isotopes such as 15N can be used to trace the movement of NO3- through the plant. This protocol uses a split-root design where only embryonic roots are treated with the 15N label. The remaining, non-embryonic roots are not labelled but similarly treated. this split-root design can be modified to select and label specific root types based on your interest. .justify:after { content: ""; display:inline-block; width: 100%; } | [The University of Melbourne], [The University of Melbourne], [King Abdullah University for Science and Technology] | 1 | 2020 | Prajakta Bendre, Vanessa Melino 2020. Root nitrate influx . protocols.io dx.doi.org/10.17504/protocols.io.biibkcan | 2021-03-29 03:10:20 | ||||
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Ultrasensitive hybridization capture of short tuberculosis cell-free DNA from urine Resource Report Resource Website |
Amy Oreskovic, Barry Lutz | 10.17504/protocols.io.bep4jdqw | Overview: This protocol describes a method for highly sensitive sequence-specific purification of short tuberculosis (TB) urine cell-free DNA (cfDNA) from large-volume (10 mL) urine samples. Biotinylated oligonucleotide capture probes complementary to the target of interest are immobilized on streptavidin-coated magnetic beads and used to capture, concentrate, and purify target DNA via hybridization. This protocol improves upon the analytical performance of both existing silica-based extraction methods for urine cfDNA and previous hybridization capture protocols, and meets several previously unmet design criteria for urine cfDNA: (1) high recovery of short fragments, (2) large sample input volume, and (3) . There are two key innovations that contribute to the robustness and unprecedented sensitivity of this method: dual biotinylated capture probes, which increase recovery compared to single biotinylated probes by moderating probe density on the bead surface (a key variable affecting efficiency of surface-based hybridization), improving thermostability of the bead-probe linkage, and eliminating interference by endogenous biotin in urine, and a two-probe system for each target region, which enables recovery of both strands of double-stranded DNA. We designed this hybridization method for capture of short, dilute TB cfDNA fragments from urine, but anticipate that it will be versatile and may be useful for other applications and sample types requiring sensitive and efficient purification of DNA from large sample volumes. Design of primer and probe sequences for new targets is straightforward (see "Materials" tab).Expected performance:Near 100% recovery (95% CI: 82.6 - 117.6%) of synthetic ssDNA or dsDNA spiked into 10 mL urine samples, verified across concentrations of at least 1 – 10,000 copies/mL and fragment lengths of at least 25 – 150 bpLimit of detection of ≤5 copies of dsDNA in 10 mL urine (0.5 copies/mL)Enables amplification of DNA from 10 mL urine in a single PCR well (500X concentration factor)Tolerant to variations in sample composition, including pH (5 – 8), salt (0 – 500 mM), and non-target DNA (0 – 10 µg)Graphic abstract: (A) Schematic of capture probe design. (B) Overview of workflow. | Oreskovic A, Lutz BR (2021) Ultrasensitive hybridization capture: Reliable detection of <1 copy/mL short cell-free DNA from large-volume urine samples. PLoS ONE 16(2): e0247851. doi: 10.1371/journal.pone.0247851 | University of Washington, Department of Bioengineering , University of Washington, Department of Bioengineering | https://doi.org/10.1371/journal.pone.0247851 | 1 | 2021 | Amy Oreskovic, Barry Lutz 2021. Ultrasensitive hybridization capture of short tuberculosis cell-free DNA from urine. protocols.io dx.doi.org/10.17504/protocols.io.bep4jdqw | 2021-03-29 03:10:20 | ||
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Valence-space associations in vertical touchscreen interactions Resource Report Resource Website |
Sergio Cervera-Torres, Susana Ruiz Fernández, Martin Lachmair, Peter Gerjets | 10.17504/protocols.io.qagdsbw | Embodied cognition research suggests that bodily experiences might ground mental representations of emotional valence in the vertical dimension of space (i.e., positive is up and negative is down). Accordingly, recent studies show that upward and downward arm movements may also influence the evaluation of valence-laden stimuli, suggesting that upward (downwards) movements lead to more positive (negative) evaluations. Interestingly, these studies typically did not investigate paradigms that require a direct hand interaction with the stimuli. With the advent of touchscreen devices and their use for experimental environments, however, a direct and more natural hand interaction with the stimuli has come to the fore. In this regard, the goal of the present study is to examine how direct hand interaction with valence-laden stimuli on a touchscreen monitor affects their perceived valence. To do so, participants evaluated emotional pictures after touching and moving them either upwards or downwards across a vertically mounted touchscreen. In contrast to previous findings, the results suggest that positive pictures were evaluated as more positive after downward movements while negative pictures were evaluated as less negative following upward movements. This finding may indicate that a matching between the pictures’ valence and the valence associated with their vertical touch location leads to more positive evaluations. Thus, the present study extends earlier results by an important point: Touching the emotional pictures during movement may influence their valence processing. | Cervera-Torres S, Fernández SR, Lachmair M, Gerjets P (2018) Valence-space associations in touchscreen interactions: Valence match between emotional pictures and their vertical touch location leads to pictures' positive evaluation. PLoS ONE 13(7): e0199972. doi: 10.1371/journal.pone.0199972 | Leibniz-Institut für Wissensmedien (IWM), Leibniz-Institut für Wissensmedien (IWM), Leibniz-Institut für Wissensmedien (IWM), Leibniz-Institut für Wissensmedien (IWM) | https://doi.org/10.1371/journal.pone.0199972 | 1 | 2018 | Sergio Cervera-Torres, Susana Ruiz Fernández, Martin Lachmair, Peter Gerjets 2018. Valence-space associations in vertical touchscreen interactions. protocols.io dx.doi.org/10.17504/protocols.io.qagdsbw | 2021-03-29 03:10:20 | ||
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Case selection and causal inferences in qualitative comparative research Resource Report Resource Website |
Thomas Plümper, Vera Troeger, Eric Neumayer | 10.17504/protocols.io.kjccuiw | Traditionally, social scientists perceived causality as regularity. As a consequence, qualitative comparative case study research was regarded as unsuitable for drawing causal inferences. Apparently, few cases cannot establish regularity. The dominant perception of causality has changed, however. Nowadays, social scientists define and identify causality through the counterfactual effect of a treatment. This brings causal inference in qualitative comparative research back on the agenda since obviously comparative case studies can identify treatment effects. We argue that the validity of causal inferences from the comparative study of cases depends on the employed case-selection algorithm. We employ Monte Carlo techniques to demonstrate that different case-selection rules strongly differ in their ex ante reliability for making valid causal inferences and identify the most and the least reliable case selection rules. | Vienna University of Economics and Business, University of Warwick, London School of Economics and Political Science | 1 | 2017 | Thomas Plümper, Vera Troeger, Eric Neumayer 2017. Case selection and causal inferences in qualitative comparative research. protocols.io dx.doi.org/10.17504/protocols.io.kjccuiw | 2021-03-29 03:10:27 | ||||
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CODEX Oligo-labeled Antibody Conjugation Resource Report Resource Website |
Yury Goltsev, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black, Garry Nolan | 10.17504/protocols.io.3fugjnw | Human Cell Atlas Method Development Community | CODEX is a technology that uses oligo labeled antibodies, specialized fluorescent probes, and a companion instrument along-side a standard fluorescence microscope to create single-cell resolution fluorescence data across a multitude of parameters within spatial context in a single tissue. CODEX was developed by Yury Goltsev and Nikolay Samusik in the laboratory of Garry Nolan at Stanford. The technology is being commercialized by Akoya Biosciences. | Stanford University, Stanford University, Stanford University, Stanford University, Stanford University, Stanford University, Stanford University, Stanford University | https://www.cell.com/cell/pdf/S0092-8674(18)30904-8.pdf | 2 | 2019 | Yury Goltsev, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black, Garry Nolan 2019. CODEX Oligo-labeled Antibody Conjugation. protocols.io dx.doi.org/10.17504/protocols.io.3fugjnw | 2021-03-29 03:10:27 | ||
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SOC Media Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.pngdmbw | Grupo de Estudos de Leveduras Cervejeiras | New England Biolabs | https://www.neb.com/protocols/2012/06/21/making-your-own-electrocompetent-cells | 1 | 2018 | New England Biolabs 2018. SOC Media. protocols.io dx.doi.org/10.17504/protocols.io.pngdmbw | 2021-03-29 03:10:26 | |||
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Quantifying Fluorescent Cells in Mammalian Cell Tissue Culture Resource Report Resource Website |
Harley King | 10.17504/protocols.io.y2nfyde | Quantifying the change in fluorescent status of cells over time can be an important data point in experimental analysis. Optimally, quantification can be accomplished with flow cytometers. However, these instruments are not available to every lab. Routine analysis and multi-sample preparation can be both time and cost prohibitive.Fluorescent cell quantifcation in cell culture requires a fluorescent microscope and freely available imaging software like Image J. | LuminUltra | 1 | 2019 | Harley King 2019. Quantifying Fluorescent Cells in Mammalian Cell Tissue Culture. protocols.io dx.doi.org/10.17504/protocols.io.y2nfyde | 2021-03-29 03:10:25 | ||||
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Gamma radiation of Drosophila suzukii under hypoxia and normoxia atmosphere conditions. Resource Report Resource Website |
Fabiana Sassu, Katerina Nikolouli, Rui Pereira, Marc Vreysen, Christian Stauffer, Carlos Cáceres | 10.17504/protocols.io.76whrfe | The sterile insect technique (SIT) is an environmentally friendly control tactic based on the sequential, inundative releases of sterile insects in a targeted area. Recently, this technique has been suggested as a potential complementary control method as part of an area-wide insect pest management program (AW-IPM) against D. suzukii. One of the key issues for the SIT application is to determine the radiation dose since the doses used to induce reproductive sterility can vary between sexes and among species. Treating insects with a lower oxygen atmosphere before and during exposure to radiation can mitigate some of the negative physiological effects due to the irradiation. The irradiation of pupae under the oxygen-reduced environments such as hypoxia is routinely used in the SIT operational programs of some tephritid species as it provides radiological protection. This treatment allows to have the sterile pupae already in sealed containers to facilitate their shipment. Therefore, it is crucial to study the effects of irradiation on the reproductive sterility in D. suzukii males and females under low-oxygen atmosphere (hypoxia) compare to normal oxygen level conditions (normoxia). .justify:after { content: ""; display:inline-block; width: 100%; } This protocol describes step-by-step the irradiation of D. suzukii pupae under hypoxia and normoxia atmosphere conditions. This protocol may be utilized for a further assessment concerning the quality of the sterile versus non-sterile D. suzukii adults such as laboratory and/or field behavioral studies. Additionally, the description of the hypoxia treatment in this protocol may allow for the evaluation of the handling and release processes of the sterile males. The adoption of this protocol by different laboratories should increase further studies for the applicability of SIT on D. suzukii or for continuing assessments to improve SIT technology and decrease the variability in data between different studies. .justify:after { content: ""; display:inline-block; width: 100%; } | Sassù F, Nikolouli K, Pereira R, Vreysen MJB, Stauffer C, Cáceres C (2019) Irradiation dose response under hypoxia for the application of the sterile insect technique in Drosophila suzukii. PLoS ONE 14(12): e0226582. doi: 10.1371/journal.pone.0226582 | Universität für Bodenkultur Wien, Insect Pest Control Subprogramme, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture; Universität für Bodenkultur Wien, Insect Pest Control Subprogramme, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Insect Pest Control Subprogramme, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Universität für Bodenkultur Wien, Insect Pest Control Subprogramme, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture | https://doi.org/10.1371/journal.pone.0226582 | 1 | 2019 | Fabiana Sassu, Katerina Nikolouli, Rui Pereira, Marc Vreysen, Christian Stauffer, Carlos Cáceres 2019. Gamma radiation of Drosophila suzukii under hypoxia and normoxia atmosphere conditions.. protocols.io dx.doi.org/10.17504/protocols.io.76whrfe | 2021-03-29 03:10:26 | ||
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Protocol G: Preparation of reporter DNA Resource Report Resource Website |
David Booth | 10.17504/protocols.io.h8yb9xw | King Lab, Protist Research to Optimize Tools in Genetics (PROT-G) | University of California, San Francisco | 1 | 2018 | David Booth 2018. Protocol G: Preparation of reporter DNA. protocols.io dx.doi.org/10.17504/protocols.io.h8yb9xw | 2021-03-29 03:10:22 | ||||
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Collection of brain stem for post-mortem diagnosis of rabies in animals by the LN34 pan-lyssavirus real-time RT-PCR assay Resource Report Resource Website |
Crystal M. Gigante, Rene Edgar Condori, Lillian Orciari, Todd G. Smith, Yu Li | 10.17504/protocols.io.n4sdgwe | Patterns of rabies virus spread within the central nervous system suggest that a thorough examination of the brain stem is critical for rabies diagnosis. Viral RNA is widespread in the brain of most animals positive for rabies. However, because virus spread may be unilateral, especially in larger animals, a negative finding for rabies can be made only if a complete cross section of the brain stem is examined. Examination may be made at the level of the pons, medulla, or midbrain of the brain stem.While a negative finding for rabies can be made only if a full cross section of brain stem tissue is examined, incomplete or suboptimal specimens should be tested, if possible. Identification of rabies virus RNA in any tissue is diagnostic of rabies infection [1, 2]. Examples of samples that may be tested for rabies virus RNA to rule-in (but not rule-out) rabies infection are hippocampus, cerebellum, cortex, saliva, and nuchal skin biopsy. |
Gigante CM, Dettinger L, Powell JW, Seiders M, Condori REC, Griesser R, et al. (2018) Multi-site evaluation of the LN34 pan-lyssavirus real-time RT-PCR assay for post-mortem rabies diagnostics. PLoS ONE 13(5): e0197074. https://doi.org/10.1371/journal.pone.0197074 |
Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA | 1 | 2018 | Crystal M. Gigante, Rene Edgar Condori, Lillian Orciari, Todd G. Smith, Yu Li 2018. Collection of brain stem for post-mortem diagnosis of rabies in animals by the LN34 pan-lyssavirus real-time RT-PCR assay. protocols.io dx.doi.org/10.17504/protocols.io.n4sdgwe | 2021-03-29 03:10:23 | |||
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Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping Resource Report Resource Website |
Wei Tang, Xuepeng Sun, Junyang Yue, Xiaofeng Tang, Chen Jiao, Ying Yang, Xiangli Niu, Min Miao, Danfeng Zhang, Shenxiong Huang, Wei Shi, Mingzhang Li, Congbing Fang, Zhangjun Fei, Yongsheng Liu | 10.17504/protocols.io.vgse3we | This protocol includes a computational pipeline used in assembly and annotation of Kiwifruit Actinidia eriantha genome. | School of Horticulture, Anhui Agricultural University, Hefei 230036, China, Boyce Thompson Institute, Cornell University, Ithaca NY 14853, USA, School of Horticulture, Anhui Agricultural University, Hefei 230036, China, School of Horticulture, Anhui Agricultural University, Hefei 230036, China, Boyce Thompson Institute, Cornell University, Ithaca NY 14853, USA, School of Horticulture, Anhui Agricultural University, Hefei 230036, China, School of Horticulture, Anhui Agricultural University, Hefei 230036, China, School of Horticulture, Anhui Agricultural University, Hefei 230036, China, School of Horticulture, Anhui Agricultural University, Hefei 230036, China, School of Horticulture, Anhui Agricultural University, Hefei 230036, China, School of Horticulture, Anhui Agricultural University, Hefei 230036, China, School of Horticulture, Anhui Agricultural University, Hefei 230036, China, School of Horticulture, Anhui Agricultural University, Hefei 230036, China, Boyce Thompson Institute, Cornell University, Ithaca NY 14853, USA, School of Horticulture, Anhui Agricultural University, Hefei 230036, China | 2 | 2018 | Wei Tang, Xuepeng Sun, Junyang Yue, Xiaofeng Tang, Chen Jiao, Ying Yang, Xiangli Niu, Min Miao, Danfeng Zhang, Shenxiong Huang, Wei Shi, Mingzhang Li, Congbing Fang, Zhangjun Fei, Yongsheng Liu 2018. Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping. protocols.io dx.doi.org/10.17504/protocols.io.vgse3we | 2021-03-29 03:10:24 |
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