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| Name | Authors | DOI | Group |
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RRIDs used | ||||||
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Restriction Digest Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.chkt4v | New England Biolabs (NEB) | The following is a "typical" restriction endonuclease reaction. Please see the "guidelines" tab below for the NEB tips on optimizing restriction digests. | New England Biolabs | https://www.neb.com/protocols/2012/12/07/optimizing-restriction-endonuclease-reactions | 1 | 2014 | New England Biolabs 2014. Restriction Digest. protocols.io dx.doi.org/10.17504/protocols.io.chkt4v | 2021-03-29 03:11:59 | ||
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Installation and Getting Started Resource Report Resource Website |
Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. | 10.17504/protocols.io.d5k84v | VERVE Net, Hurwitz Lab | Motivation: An important step of "metagenomics" analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines employ a single-genome assembler with carefully optimized parameters and post-process the resulting scaffolds to correct assembly errors. Limitations of the use of a single-genome assembler for de novo metagenome assembly are that highly conserved sequences shared between different species often causes chimera contigs, and sequences of highly abundant species are likely mis-identified as repeats in a single genome.Methods:We modified and extended a single-genome and de Bruijn-graph based assembler, Velvet, for de novo metagenome assembly. Our fundamental ideas are first decomposing de Bruijn graph constructed from mixed short reads into individual sub-graphs and second building scaffolds based on every decomposed de Bruijn sub-graph as isolate species genome. | Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab | http://metavelvet.dna.bio.keio.ac.jp/MV.html | 1 | 2016 | Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2016. Installation and Getting Started. protocols.io dx.doi.org/10.17504/protocols.io.d5k84v | 2021-03-29 03:11:59 | ||
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Immunohistochemistry Protocol for Paraffin-Embedded Sections Resource Report Resource Website |
Kelsey Knight | 10.17504/protocols.io.tkjekun | BioLegend | BioLegend | https://www.biolegend.com/protocols/immunohistochemistry-protocol-for-paraffin-embedded-sections/4256/ | 2 | 2018 | Kelsey Knight 2018. Immunohistochemistry Protocol for Paraffin-Embedded Sections. protocols.io dx.doi.org/10.17504/protocols.io.tkjekun | 2021-03-29 03:12:00 | |||
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ChroPlate - ProteinA Resource Report Resource Website |
Alexandra Ehl, David Frommholz, Nadine Stefanczyk | 10.17504/protocols.io.uycexsw | Purification Guide for the Isolation of Antibodies with ChroPlate Filtration Plates by DALEX Biotech.Easy and quick high throughput antibody purification from various sources and species.Each well of the ChroPlate has a binding capacity of > 1 mg (tested with human polyclonal Ig, binding varies between species and clones).The proprietary resin does not shrink or swell in aqueous buffers.High pressure stability.pH stability short term 2 - 8, long term 3 - 8.Excellent thermal stability up to 15 minutes at 80 °C in aqueous buffers at neutral pH.Can be dried for long term storage (80 °C for > 2 h). | DALEX Biotech, DALEX Biotech, DALEX Biotech | https://dalex-biotech.com/ | 1 | 2018 | Alexandra Ehl, David Frommholz, Nadine Stefanczyk 2018. ChroPlate - ProteinA. protocols.io dx.doi.org/10.17504/protocols.io.uycexsw | 2021-03-29 03:12:00 | |||
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Bioinformatics: A rational combine approach used for the identification and in-vitro activity evaluation of potent β-Glucuronidase inhibitors Resource Report Resource Website |
Dr.maria Yousuf | 10.17504/protocols.io.q6pdzdn | Yousuf M, Shaikh NN, Ul-Haq Z, Choudhary MI (2018) Bioinformatics: A rational combine approach used for the identification and in-vitro activity evaluation of potent β-Glucuronidase inhibitors. PLoS ONE 13(12): e0200502. doi: 10.1371/journal.pone.0200502 | ICCBS University of Karachi, Dow University of Health sciences Karachi | https://doi.org/10.1371/journal.pone.0200502 | 1 | 2018 | Dr.maria Yousuf 2018. Bioinformatics: A rational combine approach used for the identification and in-vitro activity evaluation of potent β-Glucuronidase inhibitors. protocols.io dx.doi.org/10.17504/protocols.io.q6pdzdn | 2021-03-29 03:12:00 | |||
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Brooks Lab Western Blotting Protocol Resource Report Resource Website |
Brooks Lab University of California, Eva Robinson, Alison Tang | 10.17504/protocols.io.bcsmiwc6 | BrooksLabUCSC | This is a Western Blotting Protocol for Brooks Lab, Department of Biomolecular Engineering, University of California, Santa Cruz. | University of California, Santa Cruz, University of California, Santa Cruz, University of California, Santa Cruz | 1 | 2020 | Brooks Lab University of California, Eva Robinson, Alison Tang 2020. Brooks Lab Western Blotting Protocol. protocols.io dx.doi.org/10.17504/protocols.io.bcsmiwc6 | 2021-03-29 03:12:00 | |||
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Enzymatic Assay of Trypsin Inhibition Resource Report Resource Website |
Neilier Junior | 10.17504/protocols.io.9a4h2gw | This protocol has been standardized for analysis of protease inhibitors in soybean leaf extract, but can be easily adjusted for other biological samples. | Universidade Federal de Viçosa | 1 | 2019 | Neilier Junior 2019. Enzymatic Assay of Trypsin Inhibition. protocols.io dx.doi.org/10.17504/protocols.io.9a4h2gw | 2021-03-29 03:12:00 | ||||
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Sampling for qEXT and MPN assays: Large-scale One-step Phage Infection of Cyanobacteria Resource Report Resource Website |
Sarah Giuliani | 10.17504/protocols.io.fh3bj8n | Coleman Lab | 15 Hourly Timepoints: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14Sampling is for qPCR assay to determine total extracellular phage (qEXT) and MPN (most probable number) assay to determine % phage infectivity.For qEXT and MPN sampling, 250 µL of sample in duplicates were collected and filtered through a 0.2 µm, 96-well filter plate, for each time point. (Flow through filtrate containing phage is the sample to analyze). | Coleman Lab - University of Chicago, Department of the Geophysical Sciences | 1 | 2016 | Sarah Giuliani 2016. Sampling for qEXT and MPN assays: Large-scale One-step Phage Infection of Cyanobacteria. protocols.io dx.doi.org/10.17504/protocols.io.fh3bj8n | 2021-03-29 03:12:00 | |||
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potato anthocyanin extraction and purification Resource Report Resource Website |
Yuanjun Yang, Fang Liu | 10.17504/protocols.io.k4mcyu6 | Potato tubers (250 g) were washed with distilled water and smashed in 500 mL of a mixture containing 50% alcohol and 1.6% citric acid. The resulting mixture was filtrated twice and centrifuged at 4000 rpm. The supernatant was transferred into a column filled with the pretreated macroporous resin AB-8 for 6 h, and the pigments absorbed in AB-8 were eluted with 95% alcohol. The eluate was concentrated with rotary evaporator at 30 °C and dried in vacuo for 12 h. Two biological replicates were used in this study. | Shandong agriculture academic sciencies, Shandong agriculture academic sciencies | 1 | 2017 | Yuanjun Yang, Fang Liu 2017. potato anthocyanin extraction and purification. protocols.io dx.doi.org/10.17504/protocols.io.k4mcyu6 | 2021-03-29 03:12:00 | ||||
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Sea stars bacterial sampling Resource Report Resource Website |
Andrew Loudon | 10.17504/protocols.io.f7abrie | ParfreyLab | 1 | 2016 | Andrew Loudon 2016. Sea stars bacterial sampling. protocols.io dx.doi.org/10.17504/protocols.io.f7abrie | 2021-03-29 03:12:01 | |||||
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Plate Pouring Resource Report Resource Website |
Priota Islam | 10.17504/protocols.io.3yygpxw | Behavioural Genomics | C. elegans is maintained in the laboratory on Nematode Growth Medium (NGM) agar which has been aseptically poured into petri plates. Smaller plates (35 mm diameter) are useful for mating or when using expensive drugs. Medium size plates (60 mm diameter) are useful for general strain maintenance, and larger plates (100 mm diameter) are useful for growing larger quantities of worms, such as for certain mutant screens. The NGM agar medium can be poured into petri plates easily and aseptically using a peristaltic pump. This pump can be adjusted so that a constant amount of NGM agar is dispensed into each petri plate. A constant amount of agar in the plates reduces the need for refocusing the microscope when you switch from one plate to another. Reference: http://www.wormbook.org/ | Imperial College London | 2 | 2019 | Priota Islam 2019. Plate Pouring. protocols.io dx.doi.org/10.17504/protocols.io.3yygpxw | 2021-03-29 03:12:01 | |||
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Polarity Hybrid Chemical Tag & IHC for Adult CNS Resource Report Resource Website |
Geoffrey W. Meissner, Jonathan B. Grimm, Rebecca M. Johnston, Ben Sutcliffe, Julian Ng, Gregory S.X.E. Jefferis, Sebastian Cachero, Luke D. Lavis, Oz Malkesman | 10.17504/protocols.io.nycdfsw | The use of genetically encoded ‘self-labeling tags’ with chemical fluorophore ligands enables rapid labeling of specific cells in neural tissue. To improve the chemical tagging of neurons, we synthesized and evaluated new fluorophore ligands based on Cy, Janelia Fluor, Alexa Fluor, and ATTO dyes and tested these with recently improved Drosophila melanogaster transgenes. We found that tissue clearing and mounting in DPX substantially improves signal quality when combined with specific non-cyanine fluorophores. We compared and combined this labeling technique with standard immunohistochemistry in the Drosophila brain. | Meissner GW, Grimm JB, Johnston RM, Sutcliffe B, Ng J, Jefferis GSXE, Cachero S, Lavis LD, Malkesman O (2018) Optimization of fluorophores for chemical tagging and immunohistochemistry of Drosophila neurons. PLoS ONE 13(8): e0200759. doi: 10.1371/journal.pone.0200759 | Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA, Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA | https://doi.org/10.1371/journal.pone.0200759 | 1 | 2018 | Geoffrey W. Meissner, Jonathan B. Grimm, Rebecca M. Johnston, Ben Sutcliffe, Julian Ng, Gregory S.X.E. Jefferis, Sebastian Cachero, Luke D. Lavis, Oz Malkesman 2018. Polarity Hybrid Chemical Tag & IHC for Adult CNS. protocols.io dx.doi.org/10.17504/protocols.io.nycdfsw | 2021-03-29 03:12:01 | ||
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Go game as metaphor of cancer metastasis Resource Report Resource Website |
Didier Barradas-Bautista, Matias Alvarado, Mark Agostino, Germinal Cocho | 10.17504/protocols.io.nqddds6 | This work aims for modeling and simulating the metastasis of cancer, via the analogy between the cancer process and the board game Go. In the game of Go, black stones that play first could correspond to a metaphor of the birth, growth, and metastasis of cancer. Moreover, playing white stones on the second turn could correspond the inhibition of cancer invasion. Mathematical modeling and algorithmic simulation of Go may, therefore, benefit the efforts to deploy therapies to surpass cancer illness by providing insight into the cellular growth and expansion over a tissue area. We use the Ising Hamiltonian, that models the energy exchange in interacting particles, for modeling the cancer dynamics. Parameters in the energy function refer the biochemical elements that induce cancer birth, growth, and metastasis; as well as the biochemical immune system process of defense. | Barradas-Bautista D, Alvarado-Mentado M, Agostino M, Cocho G (2018) Cancer growth and metastasis as a metaphor of Go gaming: An Ising model approach. PLoS ONE 13(5): e0195654. doi: 10.1371/journal.pone.0195654 | Centro de Investigación y de Estudios Avanzados del IPN, Centro de Investigación y de Estudios Avanzados del IPN, Curtin University, Universidad Nacional Autónoma de México | https://doi.org/10.1371/journal.pone.0195654 | 1 | 2018 | Didier Barradas-Bautista, Matias Alvarado, Mark Agostino, Germinal Cocho 2018. Go game as metaphor of cancer metastasis. protocols.io dx.doi.org/10.17504/protocols.io.nqddds6 | 2021-03-29 03:12:01 | ||
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Eisen Lab, Fresh Cow Dung Resource Report Resource Website |
Emily E. Hare, Brant K. Peterson, Venky N. Iyer, Rudolph Meier, Michael B. Eisen | 10.17504/protocols.io.ebebaje | VERVE Net | This protocol is from:Hare EE, Peterson BK, Iyer VN, Meier R, Eisen MB (2008) Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation. PLoS Genet 4(6): e1000106. doi:10.1371/journal.pgen.1000106Please see the full manuscript for additional details.(Image: calf, Jim Champion, CC BY-SA) | Eisen Lab, Eisen Lab, Eisen Lab, Eisen Lab, Eisen Lab | http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000106 | 1 | 2015 | Emily E. Hare, Brant K. Peterson, Venky N. Iyer, Rudolph Meier, Michael B. Eisen 2015. Eisen Lab, Fresh Cow Dung. protocols.io dx.doi.org/10.17504/protocols.io.ebebaje | 2021-03-29 03:12:01 | ||
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Before Data Acquisition Resource Report Resource Website |
Tinka Beemsterboer, Lukas Snoek | 10.17504/protocols.io.jk5cky6 | Spinoza Centre, REC-L | Dear researcher,This protocol gives you the steps to start an MRI project at the Spinoza Centre Roeterseiland. If you haven't had contact with Steven Scholte or Tinka Beemsterboer, make sure to contact them before completing this protocol. You can reach us by email:Steven Scholte: [email protected] Beemsterboer: [email protected] you have any suggestions for improving the workflow, don't hesitate to add comments to the steps in the protocol.Hope to see you soon!Spinoza REC Team!Steven Scholte, Tinka Beemsterboer en Lukas Snoek | Spinoza Centre, REC-L, Spinoza Centre, REC-L | 1 | 2018 | Tinka Beemsterboer, Lukas Snoek 2018. Before Data Acquisition. protocols.io dx.doi.org/10.17504/protocols.io.jk5cky6 | 2021-03-29 03:12:01 | |||
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Q5® Site-Directed Mutagenesis (E0554) Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.cjpumm | New England Biolabs (NEB) | This is the protocol for the Q5® Site-Directed Mutagenesis Kit (E0554) | New England Biolabs | https://www.neb.com/protocols/2013/01/26/q5-site-directed-mutagenesis-kit-protocol-e0554 | 1 | 2014 | New England Biolabs 2014. Q5® Site-Directed Mutagenesis (E0554). protocols.io dx.doi.org/10.17504/protocols.io.cjpumm | 2021-03-29 03:12:01 | ||
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Chlorovirus Purification Resource Report Resource Website |
David Dunigan and Irina Agarkova | 10.17504/protocols.io.er2bd8e | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Chlorovirus Purification. protocols.io dx.doi.org/10.17504/protocols.io.er2bd8e | 2021-03-29 03:12:00 | ||||
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in situ hybridization performed on the peri-rhopalial tissue of a scyphozoan jellyfish Resource Report Resource Website |
Christelle Bouchard | 10.17504/protocols.io.3qngmve | Bouchard C, Boudko DY, Jiang RHY (2019) A SLC6 transporter cloned from the lion's mane jellyfish (Cnidaria, Scyphozoa) is expressed in neurons. PLoS ONE 14(6): e0218806. doi: 10.1371/journal.pone.0218806 | University of South Florida | https://doi.org/10.1371/journal.pone.0218806 | 1 | 2019 | Christelle Bouchard 2019. in situ hybridization performed on the peri-rhopalial tissue of a scyphozoan jellyfish. protocols.io dx.doi.org/10.17504/protocols.io.3qngmve | 2021-03-29 03:12:00 | |||
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Detection of viable Dichelobacter nodosus by real-time PCR using PMAxx™ Resource Report Resource Website |
Peter Kuhnert, Tobias Hidber | 10.17504/protocols.io.bbh9ij96 | Dichelobacter nodosus is a gram-negative fastidious anaerobic bacterium and the causative agent of ovine footrot. The disease has a global presence and is endemic in many countries. Clinical symptoms range from mild interdigital dermatitis in benign footrot to severe underrunning and separation of the hoof horn from the underlying tissue in virulent footrot. Clinical symptoms start as early as 2 weeks after first contact and the disease leads to pain, lameness, decreased meat and wool production as well as animal welfare issues. Diagnosis has improved significantly by the development of a real-time PCR to detect and discriminate virulent (aprV2-positive) and benign (aprB2-positive) D. nodosus strains. However, the real-time PCR also detects dead cells making its use for testing e.g. disinfecting agents limited. A PMA (propidium monoazid) real-time PCR using the improved dye PMAxx™ was therefore developed for virulent D. nodosus that allows discrimination of viable and dead bacteria. The distinction between viable and non-viable cells is possible, based on membrane integrity. For that purpose, the samples containing D. nodosus are treated with the improved nucleic acid intercalating PMA dye PMAxx™ that selectively enters cells with compromised cell membranes, whereas the intact cell membrane presents a natural barrier for this molecule. After exposure to strong light, it covalently binds to the DNA, preventing DNA from being amplified by PCR, thereby enabling differentiation of viable from non-viable cells. The PMA-qPCR proved to be a valid method for comparison of antimicrobial efficiency in ex vivo experiments. | Hidber T, Pauli U, Steiner A, Kuhnert P (2020) In vitro and ex vivo testing of alternative disinfectants to currently used more harmful substances in footbaths against Dichelobacter nodosus. PLoS ONE 15(2): e0229066. doi: 10.1371/journal.pone.0229066 | Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland | https://doi.org/10.1371/journal.pone.0229066 | 1 | 2020 | Peter Kuhnert, Tobias Hidber 2020. Detection of viable Dichelobacter nodosus by real-time PCR using PMAxx™. protocols.io dx.doi.org/10.17504/protocols.io.bbh9ij96 | 2021-03-29 03:12:00 | ||
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Standard iGEM Cell Measurement Protocol Resource Report Resource Website |
Richard Tennant, Paul Rutten | 10.17504/protocols.io.zgmf3u6 | iGEM Measurement | This is a protocol from the 2018 iGEM InterLab study which tests various 'standard' parts from the Registry. | Fedorec AJ, Robinson CM, Wen KY, Barnes CP, FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data. ACS Synthetic Biology 9(9). doi: 10.1021/acssynbio.0c00296 | iGEM Measurement Committee, iGEM Measurement Committee | https://2019.igem.org/Measurement | 1 | 2019 | Richard Tennant, Paul Rutten 2019. Standard iGEM Cell Measurement Protocol. protocols.io dx.doi.org/10.17504/protocols.io.zgmf3u6 | 2021-03-29 03:12:00 |
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