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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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The reconstruction of a single lens microscope. Reviving the Leeuwenhoek’s microscope. Resource Report Resource Website |
Daniela Flores, Timothy Marzullo | Laboratory of Ontogeny and Phylogeny, University of Chile, Santiago, Chile., BackyardBrains, Ann Harbor, Michigan, USA, and Santiago, Chile. | https://backyardbrains.com/experiments/Leeuwenhoek | 1 | 2018 | Daniela Flores, Timothy Marzullo 2018. The reconstruction of a single lens microscope. Reviving the Leeuwenhoek’s microscope. . protocols.io https:// | 2021-04-15 09:15:35 | |||||
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Plasmid DNA Mini Kit I- Spin Protocol Resource Report Resource Website |
Alex Zegarra | BYU | 1 | 2020 | Alex Zegarra 2020. Plasmid DNA Mini Kit I- Spin Protocol . protocols.io https:// | 2021-04-15 09:15:09 | ||||||
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Media recipes for Synechococcus isolates Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c9jz4m | VERVE Net, Sullivan Lab | The following are media recipes necessary for isolating and maintaining Synechococcus isolates. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Media recipes for Synechococcus isolates. protocols.io https://dx.doi.org/10.17504/protocols.io.c9jz4m | 2021-04-15 09:15:09 | |||
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Propidium Iodide Cell Cycle Staining Protocol Resource Report Resource Website |
Sam Li | DOI:10.17504/protocols.io.bacyiaxw | BioLegend | BioLegend | https://www.biolegend.com/protocols/propidium-iodide-cell-cycle-staining-protocol/4303/ | 3 | 2019 | Sam Li 2019. Propidium Iodide Cell Cycle Staining Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bacyiaxw | 2021-04-15 09:15:09 | |||
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Y Choice test invertebrate Resource Report Resource Website |
Freddie-Jeanne Richard | DOI:10.17504/protocols.io.vpfe5jn | Y choice test designed for terrestrial invertebrase | Fortin M, Vitet C, Souty-Grosset C, Richard F (2018) How do familiarity and relatedness influence mate choice in Armadillidium vulgare?. PLoS ONE 13(12): e0209893. doi: 10.1371/journal.pone.0209893 | Universtié de Poitiers | https://doi.org/10.1371/journal.pone.0209893 | 2 | 2019 | Freddie-Jeanne Richard 2019. Y Choice test invertebrate. protocols.io https://dx.doi.org/10.17504/protocols.io.vpfe5jn | 2021-04-15 09:15:35 | ||
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Isolation of axenic Symbiodinium cultures Resource Report Resource Website |
Tingting Xiang | DOI:10.17504/protocols.io.qxzdxp6 | Aiptasia-Symbiodiniaceae Model System | University of North Carolina at Charlotte | 1 | 2018 | Tingting Xiang 2018. Isolation of axenic Symbiodinium cultures. protocols.io https://dx.doi.org/10.17504/protocols.io.qxzdxp6 | 2021-04-15 09:15:35 | ||||
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Single cell isolation from human fetal thigh Resource Report Resource Website |
Hongbo Zhang | DOI:10.17504/protocols.io.ta8eihw | This protocol can be used to isolate single cells from human fetal thigh from age GA6-GA11. | Welcome Sanger Institute | 1 | 2018 | Hongbo Zhang 2018. Single cell isolation from human fetal thigh. protocols.io https://dx.doi.org/10.17504/protocols.io.ta8eihw | 2021-04-15 09:15:38 | ||||
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RNA Isolation from Plant Tissue Protocol 1: Qiagen RNeasy Plant Mini Kit Resource Report Resource Website |
Jim Leebens-Mack, Charlotte Carrigan | DOI:10.17504/protocols.io.4vxgw7n | GigaScience Press | Protocol implemented by: Jim Leebens-Mack and Charlotte Carrigan The first protocol used for isolation of total RNA was Qiagen’s RNeasy Plant Mini Kit (Qiagen, Valencia, CA). These kits are commercially available and widely used in RNA isolation. For detailed methods associated with this kit we refer readers to the “RNeasy Mini Handbook” available for download at www.qiagen.com. This protocol is part of a collection of eighteen protocols used to isolate total RNA from plant tissue. (RNA Isolation from Plant Tissue Collection: https://www.protocols.io/view/rna-isolation-from-plant-tissue-439gyr6) | , | 1 | 2019 | Jim Leebens-Mack, Charlotte Carrigan 2019. RNA Isolation from Plant Tissue Protocol 1: Qiagen RNeasy Plant Mini Kit. protocols.io https://dx.doi.org/10.17504/protocols.io.4vxgw7n | 2021-04-15 09:15:38 | |||
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Electrode cleaning solution Resource Report Resource Website |
Michael Economo | DOI:10.17504/protocols.io.8pwhvpe | How to make a cleaning solution for cleaning silicon probes | Boston University | 1 | 2019 | Michael Economo 2019. Electrode cleaning solution. protocols.io https://dx.doi.org/10.17504/protocols.io.8pwhvpe | 2021-04-15 09:15:13 | ||||
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Transfection of O. marina using particle bombardment Resource Report Resource Website |
Pia Elustondo, Claudio Slamovits | DOI:10.17504/protocols.io.ui7euhn | Protist Research to Optimize Tools in Genetics (PROT-G) | Dalhousie University, Dalhousie University | 1 | 2018 | Pia Elustondo, Claudio Slamovits 2018. Transfection of O. marina using particle bombardment. protocols.io https://dx.doi.org/10.17504/protocols.io.ui7euhn | 2021-04-15 09:15:38 | ||||
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Immunoprecipitation / coimmunoiprecipitation (IP / Co-IP) {biochemistry} Resource Report Resource Website |
Kevin Bonham | DOI:10.17504/protocols.io.ccisud | For purifying proteins from mammalian cells for analysis by western blot. | Harvard | 1 | 2014 | Kevin Bonham 2014. Immunoprecipitation / coimmunoiprecipitation (IP / Co-IP) {biochemistry}. protocols.io https://dx.doi.org/10.17504/protocols.io.ccisud | 2021-04-15 09:15:39 | ||||
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OptoPlate Calibration protocol Resource Report Resource Website |
Edvard Grødem, Kieran Sweeney, Megan N. McClean | DOI:10.17504/protocols.io.bivmke46 | Optogenetic systems use light to precisely control and investigate cellular processes. Until recently, there had been few instruments available for applying controlled light doses to cultures of cells. The optoPlate, a programmable array of 192 LEDs, was developed to meet this need. However, LED performance varies and without calibration there are substantial brightness differences between LEDs on an optoPlate. Here we present a method for calibrating an optoPlate that uses a programmable microscope stage and optical power meter to automatically measure all 192 LEDs of an optoPlate. The resulting brightness measurements are used to calculate calibration values that tune the electrical current supplied to each optoPlate LED to reduce brightness variation in optogenetic experiments. | Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI USA, Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI USA, Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI USA | 1 | 2020 | Edvard Grødem, Kieran Sweeney, Megan N. McClean 2020. OptoPlate Calibration protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bivmke46 | 2021-04-15 09:15:13 | ||||
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RNA extraction for plant samples using CTAB-pBIOZOL Resource Report Resource Website |
Weixue Mu, Jinpu Wei, Ting Yang, Yannan Fan, Le Cheng, Jinlong Yang, Ranchang Mu, Jie Liu, Jianming Zhao, Weibang Sun, Xun Xu, Xin Liu, Radoje Drmanac, Huan Liu | DOI:10.17504/protocols.io.gsnbwde | Bauhinia Genome, Plantae, BGI | RNA extraction of plant tissues (in our case Bauhinia leaves) using a pBIOZOL/CTAB lysis buffer | State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China, State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China, State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China, State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China, BGI-Yunnan, BGI-Shenzhen, Kunming, 650106, China, BGI-Yunnan, BGI-Shenzhen, Kunming, 650106, China, Forestry Bureau of Ruili, Yunnan Dehong, Ruili 678600, China, Forestry Bureau of Ruili, Yunnan Dehong, Ruili 678600, China, Forestry Bureau of Ruili, Yunnan Dehong, Ruili 678600, China, Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, Yunnan, China, State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China, State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China, State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China, State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China | 1 | 2017 | Weixue Mu, Jinpu Wei, Ting Yang, Yannan Fan, Le Cheng, Jinlong Yang, Ranchang Mu, Jie Liu, Jianming Zhao, Weibang Sun, Xun Xu, Xin Liu, Radoje Drmanac, Huan Liu 2017. RNA extraction for plant samples using CTAB-pBIOZOL. protocols.io https://dx.doi.org/10.17504/protocols.io.gsnbwde | 2021-04-15 09:15:39 | |||
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Step-by-Step guide for downloading very large datasets to a supercomputer using the SRA Toolkit
Resource Report Resource Website |
Jacob Heldenbrand, Yingxue Ren, Yan Asmann, Liudmila S. Mainzer | DOI:10.17504/protocols.io.kb6csre | National Center for Supercomputing Applications, University of Illinois at Urbana-champaign, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, National Center for Supercomputing Applications, University of Illinois at Urbana-champaign | 1 | 2017 | Jacob Heldenbrand, Yingxue Ren, Yan Asmann, Liudmila S. Mainzer 2017. Step-by-Step guide for downloading very large datasets to a supercomputer using the SRA Toolkit . protocols.io https://dx.doi.org/10.17504/protocols.io.kb6csre | 2021-04-15 09:15:13 | |||||
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C-SOP-901: Preparation of DNA Isolates for Domestic and Overseas Transport Resource Report Resource Website |
Mihir Kekre | The Centre for Genomic Pathogen Surveillance, Oxford, United Kingdom | 1 | 2021 | Mihir Kekre 2021. C-SOP-901: Preparation of DNA Isolates for Domestic and Overseas Transport. protocols.io https:// | 2021-04-15 09:15:39 | ||||||
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Trimble GPS Protocol Resource Report Resource Website |
Sabine St-Jean | DOI:10.17504/protocols.io.9zeh73e | Canadian Airborne Biodiversity Observatory | Here we describe the standardised protocol used by the Canadian Airborne Biodiversity Observatory (CABO) to use the Trimble GPS with the NTRIP centimeter-level precision subscription from Cansel to record the precise location of a plot (corner or center) or a plant. | Université de Sherbrooke | http://caboscience.org/ | 1 | 2020 | Sabine St-Jean 2020. Trimble GPS Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.9zeh73e | 2021-04-15 09:15:13 | ||
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Suggested field procedures for collecting soil/litter arthropods in a tropical rainforest for long-term monitoring with DNA metabarcoding Resource Report Resource Website |
Yves Basset | DOI:10.17504/protocols.io.bj9gkr3w | Suggested field procedures for collecting soil/litter arthropods in a tropical rainforest for long-term monitoring with DNA metabarcoding.Standardized field protocols to monitor the soil fauna exist but they are not tailored to surveys in tropical rainforests and not designated to obtain samples that can be later processed with metabarcoding. In general, the soil fauna is extracted by Berlese-Tullgren apparatus, while the litter-dwelling and more active fauna is better surveyed with Winkler extractors. Here, we used Berlese-Tullgren which represent the choice method for Collembola but included in our samples both soil and litter. | Smithsonian Tropical Research Institute | 1 | 2020 | Yves Basset 2020. Suggested field procedures for collecting soil/litter arthropods in a tropical rainforest for long-term monitoring with DNA metabarcoding. protocols.io https://dx.doi.org/10.17504/protocols.io.bj9gkr3w | 2021-04-15 09:15:39 | ||||
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Colony PCR Protocol Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c6czav | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Colony PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c6czav | 2021-04-15 09:15:39 | ||||
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Site directed mutagenesis by PCR Resource Report Resource Website |
Tobias von der Haar | DOI:10.17504/protocols.io.igucbww | University of Kent at Canterbury | 1 | 2019 | Tobias von der Haar 2019. Site directed mutagenesis by PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.igucbww | 2021-04-15 09:15:39 | |||||
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OmniPrep™ For High Quality Genomic DNA Extraction From Body Fluids Resource Report Resource Website |
G-Biosciences | DOI:10.17504/protocols.io.e6jbhcn | G-Biosciences | The OmniPrep™ kit isolates high quality genomic DNA from many different species and tissue types including animal, plant, bacteria, yeast, fungi, whole blood, and cells in culture. DNA can be isolated from samples high in polysaccharides or other contaminants that are difficult to remove from the DNA preparations.This protocol is for use with body fluids (including CSF, plasma, saliva, serum, sputum, synovial fluid, urine and whole blood). Please refer to the appropriate protocol depending on your application. | https://www.gbiosciences.com/image/pdfs/protocol/786-136_protocol.pdf | 1 | 2016 | G-Biosciences 2016. OmniPrep™ For High Quality Genomic DNA Extraction From Body Fluids. protocols.io https://dx.doi.org/10.17504/protocols.io.e6jbhcn | 2021-04-15 09:15:13 |
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