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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Cambridge Fetal Thymus Dissociation Resource Report Resource Website |
Jongeun Park | DOI:10.17504/protocols.io.wedfba6 | Human Cell Atlas Method Development Community | This is protocol for fetal thymus dissociation. (Can be applied to other fetal tissues)Can be also adapted to adult thymus or lymphoid organs. (Volume of solution needs to be adjusted to take account of larger tissue size, also consider multiple rounds of digestion in this case) | Wellcome Sanger Institute | 1 | 2018 | Jongeun Park 2018. Cambridge Fetal Thymus Dissociation. protocols.io https://dx.doi.org/10.17504/protocols.io.wedfba6 | 2021-04-15 09:15:51 | |||
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Host Range Protocols Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dew3fd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Host Range Protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.dew3fd | 2021-04-15 09:15:36 | ||||
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Transformation Resource Report Resource Website |
Rengin Yamur Akbiyik, Sevval Uysalcan | DOI:10.17504/protocols.io.2nwgdfe | Transformation is a direct modification of the genotype of a cell from a different one by extracellular applications using recombinant DNA techniques. Transformation refers generally to the integration of exogenous DNA into the cell and its integration into the genome. Before starting the transformation process, the gene of interest is ligated with the plasmid vector via the ligase enzyme. This process is called ligation. Generally, nucleic acids or plasmids cannot enter into bacterial cells by themselves. The stimulatory effect is required for that purpose. This means that the cell membranes to be transformed must be pre-arranged. Bacteria that can contain free DNA are called competent bacteria. Some bacteria are highly competitive in normal growth conditions; but some must be treated with chemical or physical methods to gain competitive properties. Competent cells which are cells are generally stimulated with calcium chloride about chemically and the cell membranes are arranged such that the plasmid vector containing the gene of interest can harbor the vector.Some bacterial cells are lasting competent, however; most of them need to be influenced forbeing competent. There are two ways about this transformation process that;• Chemical Transformation• Electrical Transformation (Electroporation)In general, chemical transformation is used. In chemical way, some special chemicals are used to open the pores which are found in cell membrane. This is because, opening the pores represents the availability of being permeable. Most of the time, divalent ions like Ca++ are used with assistance of heat-shock. | Istanbul Bilgi University, Istanbul Bilgi University | 4 | 2019 | Rengin Yamur Akbiyik, Sevval Uysalcan 2019. Transformation. protocols.io https://dx.doi.org/10.17504/protocols.io.2nwgdfe | 2021-04-15 09:15:39 | ||||
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Immunohistochemical staining of Syndecan-1 (Sdc-1) core proteins in islet beta cells of formalin-fixed human pancreas Resource Report Resource Website |
Lora Starrs, Debra Brown, Sarah Popp, Charmaine Simeonovic | DOI:10.17504/protocols.io.bkqxkvxn | Paraffin sections (4 μm thickness) of formalin-fixed human pancreases were treated with heat/citrate buffer for antigen retrieval. Sdc-1core proteins were detected immunohistochemically using rat anti-mouse CD138 (Sdc-1) mAb (BD Biosciences), with horseradish peroxidase-conjugated rabbit anti-rat Ig (Dako). Background staining was checked using the corresponding isotype control Ig instead of the primary antibody. 3-amino-9-ethylcarbazole (AEC) was used as the chromogen. For morphometry, stained sections were imaged using a light microscope with attached camera (Olympus BX41). Image J software with color deconvolution plugin was used for the quantitative analysis of the % of islet area stained. | The John Curtin School of Medical Research, The Australian National University, The John Curtin School of Medical Research, The Australian National University, The John Curtin School of Medical Research, The Australian National University, The John Curtin School of Medical Research, The Australian National University | https://doi.org/10.1371/journal.pone.0191360 | 2 | 2020 | Lora Starrs, Debra Brown, Sarah Popp, Charmaine Simeonovic 2020. Immunohistochemical staining of Syndecan-1 (Sdc-1) core proteins in islet beta cells of formalin-fixed human pancreas. protocols.io https://dx.doi.org/10.17504/protocols.io.bkqxkvxn | 2021-04-15 09:15:53 | |||
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In vitro digestion of DNA with Cas9 Nuclease, S. pyogenes (M0386) Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.ch2t8d | New England Biolabs (NEB) | Cas9 Nuclease, S. pyogenes (Cas9), is a double-stranded DNA endonuclease that is guided to its target by sequence complementarity of a small RNA loaded into the protein. This protocol describes how to digest double-stranded DNA in vitro using Cas9 and a single guide RNA (sgRNA). | New England Biolabs | https://www.neb.com/protocols/2014/05/01/in-vitro-digestion-of-dna-with-cas9-nuclease-s-pyogenes-m0386 | 1 | 2014 | New England Biolabs 2014. In vitro digestion of DNA with Cas9 Nuclease, S. pyogenes (M0386). protocols.io https://dx.doi.org/10.17504/protocols.io.ch2t8d | 2021-04-15 09:15:38 | ||
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In vitro digestion of DNA with Cas9 Nuclease, S. pyogenes (M0386) Resource Report Resource Website |
Binnypreet Kaur | DOI:10.17504/protocols.io.rmud46w | Protist Research to Optimize Tools in Genetics (PROT-G), Julius Lukes | Cas9 Nuclease, S. pyogenes, (Cas9) is a double-stranded DNA endonuclease that is guided to its target by sequence complementarity of a small RNA loaded into the protein. This protocol describes how to digest double-stranded DNA in vitro using Cas9 and a single guide RNA (sgRNA). | 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic | 1 | 2018 | Binnypreet Kaur 2018. In vitro digestion of DNA with Cas9 Nuclease, S. pyogenes (M0386). protocols.io https://dx.doi.org/10.17504/protocols.io.rmud46w | 2021-04-15 09:15:38 | |||
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Isolation of Extracellular Vesicles from Cell Culture Media by Differential Ultracentrifugation Resource Report Resource Website |
Dima Ter-Ovanesyan, Wendy Trieu , Maia Norman, Roey Lazarovits, George Church, David Walt | DOI:10.17504/protocols.io.bnr3md8n | Walt Lab | Extracellular vesicles (EVs) are released by all mammalian cells and are thought to be important mediators ofintercellular communication. There are many methods for isolating EVs from cell culture media, but one of themost commonly used methods continues to be purification based on ultracentrifugation. This approach has the advantage of allowing a large input volume of cell culture media. Here, we provide a detailedprotocol for isolating EVs by differential ultracentrifugation. | Wyss Institute for Biologically Inspired Engineering, Wyss Institute for Biologically Inspired Engineering, Wyss Institute for Biologically Inspired Engineering, Brigham and Women's Hospital, Wyss Institute for Biologically Inspired Engineering, Wyss Institute for Biologically Inspired Engineering, Harvard Medical School Department of Genetics, Wyss Institute for Biologically Inspired Engineering, Brigham and Women's Hospital | 1 | 2020 | Dima Ter-Ovanesyan, Wendy Trieu , Maia Norman, Roey Lazarovits, George Church, David Walt 2020. Isolation of Extracellular Vesicles from Cell Culture Media by Differential Ultracentrifugation . protocols.io https://dx.doi.org/10.17504/protocols.io.bnr3md8n | 2021-04-15 09:15:53 | |||
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Appraisal of clinical practice guidelines for the management of attention deficithyperactivity disorder (ADHD) using the AGREE II Instrument: a systematic review Resource Report Resource Website |
Yasser Amer, Turki Albatti, Fahad Bashiri, Muddathir Hamad, Haya Al-Joudi, Saleh Al Salehi, Hadeel Daghash, Jeremy Varnham | DOI:10.17504/protocols.io.q27dyhn | PROSPERO protocolLink: http://www.crd.york.ac.uk/PROSPERO/display_record.php?ID=CRD42017078712 | Amer YS, Al-Joudi HF, Varnham JL, Bashiri FA, Hamad MH, Salehi SMA, Daghash HF, Albatti TH, oboTSAS (2019) Appraisal of clinical practice guidelines for the management of attention deficit hyperactivity disorder (ADHD) using the AGREE II Instrument: A systematic review. PLoS ONE 14(7): e0219239. doi: 10.1371/journal.pone.0219239 | King Saud University, King Saud University, King Saud University, King Saud University, King Faisal Specialist Hospital and Research Center, Princess Noura bint Abdulrahman University, Ministry of Health, SA, Saudi ADHD Society | https://doi.org/10.1371/journal.pone.0219239 | 1 | 2018 | Yasser Amer, Turki Albatti, Fahad Bashiri, Muddathir Hamad, Haya Al-Joudi, Saleh Al Salehi, Hadeel Daghash, Jeremy Varnham 2018. Appraisal of clinical practice guidelines for the management of attention deficithyperactivity disorder (ADHD) using the AGREE II Instrument: a systematic review. protocols.io https://dx.doi.org/10.17504/protocols.io.q27dyhn | 2021-04-15 09:15:38 | ||
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RNA extraction with trizol for tissues Resource Report Resource Website |
Maysa Silva, Maryana Branquinho, Maria Cármen Sales | DOI:10.17504/protocols.io.stmeek6 | , , Universidade de São Paulo | 1 | 2018 | Maysa Silva, Maryana Branquinho, Maria Cármen Sales 2018. RNA extraction with trizol for tissues. protocols.io https://dx.doi.org/10.17504/protocols.io.stmeek6 | 2021-04-15 09:15:38 | |||||
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ChroDrip - IMAC Resource Report Resource Website |
David Frommholz, Nadine Stefanczyk, Alexandra Ehl | DOI:10.17504/protocols.io.uvvew66 | Purification Guide for the Isolation of Histidine-tagged Proteins with ChroDrip Columns by DALEX Biotech.ChroSpin-IMAC by DALEX Biotech offers a robust and convenient way to isolate polyhistidine-tagged protein from bacterial, mamalian, and insect cell cultures.Immobilized metal affinity chromatography (IMAC) is based on the interaction of the imidazole ring of histidine with transition metal ions immobilized on a solid support. Recombinant proteins with a 3 - 10 histidine fusion tag bind to these metal ions while unwanted proteins are removed by washing with excess binding buffer. Elution of the target protein is achieved by the addition of imidazole, EDTA or a low pH. Easy and quick small scale fusion protein purification from various sources.Low metal leaching from column.Tolerates reducing reagents (e.g. DTT up to 10 mM).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 120 °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 | David Frommholz, Nadine Stefanczyk, Alexandra Ehl 2018. ChroDrip - IMAC. protocols.io https://dx.doi.org/10.17504/protocols.io.uvvew66 | 2021-04-15 09:15:53 | |||
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Neural rosette banking Resource Report Resource Website |
Celeste Karch, Rita Martinez, Jacob Marsh | DOI:10.17504/protocols.io.x87frzn | Neurodegeneration Method Development Community | Washington University in St Louis, Washington University in St Louis, Washington University in St Louis | 1 | 2019 | Celeste Karch, Rita Martinez, Jacob Marsh 2019. Neural rosette banking. protocols.io https://dx.doi.org/10.17504/protocols.io.x87frzn | 2021-04-15 09:15:51 | ||||
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Labyrinthulomycete DNA extraction protocol Resource Report Resource Website |
Jackie L. Collier | DOI:10.17504/protocols.io.n83dhyn | Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab | Modified from Lippmeier et al. 2009 | Stony Brook University | 1 | 2018 | Jackie L. Collier 2018. Labyrinthulomycete DNA extraction protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.n83dhyn | 2021-04-15 09:15:38 | |||
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Correlative Light-Electron Microscopy of α-synuclein Aggregates in Primary Neurons Resource Report Resource Website |
Felix Kraus, vtrinkaus , Ruben Fernandez Busnadiego | DOI:10.17504/protocols.io.btyinpue | This protocol details methods for correlative light-electron microscopy of α-synuclein aggregates in primary neurons. | Harvard Medical School, Department of Cell Biology, Harvard Medical School, Department of Cell Biology, Harvard Medical School, Department of Cell Biology | 1 | 2021 | Felix Kraus, vtrinkaus , Ruben Fernandez Busnadiego 2021. Correlative Light-Electron Microscopy of α-synuclein Aggregates in Primary Neurons. protocols.io https://dx.doi.org/10.17504/protocols.io.btyinpue | 2021-04-15 09:15:38 | ||||
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PCR Reaction Optimization Resource Report Resource Website |
Kenneth Schackart | DOI:10.17504/protocols.io.ygqftvw | Yoon Lab | How to run nucleic acid amplification using the Thermo scientific PCR Master Mix kit.Each reaction produces 50 μL.For the original protocol, look at: . | University of Arizona | 3 | 2019 | Kenneth Schackart 2019. PCR Reaction Optimization. protocols.io https://dx.doi.org/10.17504/protocols.io.ygqftvw | 2021-04-15 09:15:34 | |||
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Primer ID MiSeq Library Prep for HIV-1 DR and diversity Resource Report Resource Website |
Shuntai Zhou | DOI:10.17504/protocols.io.6hchb2w | This is the protocol to prepare Primer ID MiSeq sequencing library. Viral RNA was first extracted using QIAamp viral RNA extraction kit. The block of random nucleotides (Ns) in the cDNA primers served as the Primer ID. The Superscript III kit was used for the cDNA synthesis. We used two rounds of PCR to amplify the cDNA and incorporate Illumina indexed adapters with KAPA2G Robust and KAPA HiFi PCR kits, respectively. | University of North Carolina at Chapel Hill | 1 | 2019 | Shuntai Zhou 2019. Primer ID MiSeq Library Prep for HIV-1 DR and diversity. protocols.io https://dx.doi.org/10.17504/protocols.io.6hchb2w | 2021-04-15 09:15:34 | ||||
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Protocol for Exonuclease III (NEB #M0206) Resource Report Resource Website |
New England Biolabs | New England Biolabs (NEB) | New England Biolabs | https://neb.com/protocols/2019/07/24/protocol-for-exonuclease-iii-m0206 | 1 | 2020 | New England Biolabs 2020. Protocol for Exonuclease III (NEB #M0206). protocols.io https:// | 2021-04-15 09:15:34 | ||||
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615.1 URMC HTC Non-Inflated Fresh-Frozen Embedded Lung and Associated Tissue Resource Report Resource Website |
Gloria Pryhuber, Heidie Huyck, Lisa Rogers, Cory Poole | DOI:10.17504/protocols.io.bjtnknme | Human Cell Atlas Method Development Community, Human BioMolecular Atlas Program (HuBMAP) Method Development Community, LungMap2 Consortium, URMC Pryhuber Lab | Purpose and Scope of the Procedure- Rapid blocking, embedding and freezing of human lung tissue in no freezing media, 100% OCT or 5% CMC - Rapid freezing of non-lung tissue in no freezing media, 100% OCT or 5% CMC | University of Rochester Medical Center, University of Rochester, University of Rochester Medical Center, University of Rochester | 1 | 2020 | Gloria Pryhuber, Heidie Huyck, Lisa Rogers, Cory Poole 2020. 615.1 URMC HTC Non-Inflated Fresh-Frozen Embedded Lung and Associated Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.bjtnknme | 2021-04-15 09:15:34 | |||
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Vezina Lab Mouse Kidney Capsule Implant Protocol Resource Report Resource Website |
Chad Vezina | UW- Madison | 1 | 2020 | Chad Vezina 2020. Vezina Lab Mouse Kidney Capsule Implant Protocol. protocols.io https:// | 2021-04-15 09:15:38 | ||||||
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Capture of Philaenus spumarius and Cicadella viridis Resource Report Resource Website |
Niels Appelman | DOI:10.17504/protocols.io.8jdhui6 | iGEM Wageningen 2019 | This protocol is used to capture spittlebugs (Philaenus spumarius) and Green Leafhoppers (Cicadella viridis) | Wageningen University | 1 | 2019 | Niels Appelman 2019. Capture of Philaenus spumarius and Cicadella viridis. protocols.io https://dx.doi.org/10.17504/protocols.io.8jdhui6 | 2021-04-15 09:15:38 | |||
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ssh to UA HPC Resource Report Resource Website |
Ken Youens-Clark | DOI:10.17504/protocols.io.fm7bk9n | MetaFunc Course | This describes setting up ssh keys and configuration to avoid having to use your NetID+ 2-factor authentication every time you log into the HPC. Windows users are encouraged to install Cygwin (http://www.cygwin.com), a free Unix-like environment that provides a terminal so as to avoid using an ssh client like Putty. Cygwin users must be sure to install the "ssh" tools which are not installed by default. | University of Arizona | 1 | 2016 | Ken Youens-Clark 2016. ssh to UA HPC. protocols.io https://dx.doi.org/10.17504/protocols.io.fm7bk9n | 2021-04-15 09:15:34 |
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