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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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SDS-PAGE Cracking Buffer Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.erpbd5n | VERVE Net | Recipe to make 10ml of 2x stock | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. SDS-PAGE Cracking Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.erpbd5n | 2021-04-15 09:15:40 | |||
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Multiple Alignments and Weblogo Resource Report Resource Website |
Nicolas Schmelling | DOI:10.17504/protocols.io.gscbwaw | Axmann Lab | This protocol show you how to create a sequence alignment with multiple sequences using CLUSTAL Omega and to futher modify it with Jalview and visualize it with Weblogo. | Schmelling NM, Lehmann R, Chaudhury P, Beck C, Albers S, Axmann IM, Wiegard A, Minimal tool set for a prokaryotic circadian clock. BMC Evolutionary Biology doi: 999 | Institute of Synthetic Microbiology, Heinrich Heine University Düsseldorf | https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-017-0999-7 | 1 | 2016 | Nicolas Schmelling 2016. Multiple Alignments and Weblogo. protocols.io https://dx.doi.org/10.17504/protocols.io.gscbwaw | 2021-04-15 09:15:13 | |
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Fungal CTAB DNA Extraction Resource Report Resource Website |
Derreck Carter-House, Jason Stajich, Sarah Unruh, Tania Kurbessoian | DOI:10.17504/protocols.io.bhx8j7rw | High molecular weight DNA extraction from all kingdoms, Chytrid Fungi - Molecular and Genomic Techniques, stajichlab | This protocol is a CTAB DNA extraction method for filamentous fungi. Its purpose is to extract high molecular weight genomic DNA for genome sequencing. | UC Riverside, UC Riverside, UC Riverside, UC Riverside | 1 | 2020 | Derreck Carter-House, Jason Stajich, Sarah Unruh, Tania Kurbessoian 2020. Fungal CTAB DNA Extraction . protocols.io https://dx.doi.org/10.17504/protocols.io.bhx8j7rw | 2021-04-15 09:15:39 | |||
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Chlorophyll Extraction in Cyanobacteria Resource Report Resource Website |
Nicolas Schmelling | DOI:10.17504/protocols.io.fuvbnw6 | Axmann Lab, CyanoWorld, iGEM Duesseldorf 2018 | This protocol should be used for chlorophyll extraction in cyanobacteria. The equation for calculating the exact chlorophyll content can be found at the end of this document.You might want to measure the optical density (OD) of you cyanobacteria culture at 750 nm. Use BG11 medium or water as the reference solution. You need the OD of your culture to normalize the cholorphyll concentration to the number of cyanobacteria.Calculate chlorophyll content (adapted from Lichtenthaler 1978)Chl [µg/ml] = OD665nm x 13.9 [µg/ml] x dilution factor of cultureYou can take less than 1 ml, but note the dilution factor for the calculation later on, e.g. :1 ml sample = dilution factor of 1500 µl sample = dilution factor of 2100 µl sample = dilution factor of 10 | Institute of Synthetic Microbiology Heinrich Heine University | 2 | 2016 | Nicolas Schmelling 2016. Chlorophyll Extraction in Cyanobacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.fuvbnw6 | 2021-04-15 09:15:14 | |||
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V-CHEK Coronavirus (SARS-CoV-2) Antigen Detection Kit Resource Report Resource Website |
bill , covidtesting | DOI:10.17504/protocols.io.bkwukxew | XPRIZE Rapid Covid Testing | Reliable-LFC, LLC, XPRIZE Foundation | 1 | 2020 | bill , covidtesting 2020. V-CHEK Coronavirus (SARS-CoV-2) Antigen Detection Kit. protocols.io https://dx.doi.org/10.17504/protocols.io.bkwukxew | 2021-04-15 09:15:39 | ||||
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Inmunohistoquímica rápida Resource Report Resource Website |
Antonio Hartley | DOI:10.17504/protocols.io.h2bb8an | Universidad Central de Chile | 1 | 2017 | Antonio Hartley 2017. Inmunohistoquímica rápida. protocols.io https://dx.doi.org/10.17504/protocols.io.h2bb8an | 2021-04-15 09:15:14 | |||||
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Determination of total glutathione (GSH) and oxidized glutathione (GSSG) levels of RBCs infected with Plasmodium falciparum (Pf RBCs) Resource Report Resource Website |
Hiroko Asahi | DOI:10.17504/protocols.io.i35cgq6 | Asahi H, Inoue S, Niikura M, Kunigo K, Suzuki Y, Kobayashi F, Sendo F (2017) Profiling molecular factors associated with pyknosis and developmental arrest induced by an opioid receptor antagonist and dihydroartemisinin in Plasmodium falciparum. PLoS ONE 12(9): e0184874. doi: 10.1371/journal.pone.0184874 | https://doi.org/10.1371/journal.pone.0184874 | 1 | 2017 | Hiroko Asahi 2017. Determination of total glutathione (GSH) and oxidized glutathione (GSSG) levels of RBCs infected with Plasmodium falciparum (Pf RBCs). protocols.io https://dx.doi.org/10.17504/protocols.io.i35cgq6 | 2021-04-15 09:15:40 | ||||
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Modified ZN Staining Protocol Resource Report Resource Website |
Asar Khan, Sumaira Shams, Saima Khan, Muhammad Iftikhar Khan, Sardar Khan, Abid Ali | DOI:10.17504/protocols.io.tb2eiqe | The Modified Ziehl-Neelsen stain (mZN stain) is a type of differential bacteriological stain used to identify acid-fast organisms, mainly Mycobacteria. Acid fast organisms are those which are capable of retaining the primary stain when treated with an acid (fast=holding capacity). Members of the Actinomycetes, genus Nocardia (N. brasiliensis and N. asteroides are opportunistic pathogens) are partially acid-fast. Oocysts of coccidian parasites, such as Cryptosporidium and Isospora, are also acid-fast. Hence they can also be detected and identified through mZN staining procedure. | Department of Zoology Abdul Wali Khan University Mardan, KPK Pakistan, Department of Zoology Abdul Wali Khan University Mardan, KPK Pakistan, Department of Zoology Abdul Wali Khan University Mardan, KPK Pakistan, Centre for Biotechnology and Microbiology University of Swat, Pakistan, Department of Environmental Science, University of Peshawar, Department of Zoology Abdul Wali Khan University Mardan, KPK Pakistan | 2 | 2018 | Asar Khan, Sumaira Shams, Saima Khan, Muhammad Iftikhar Khan, Sardar Khan, Abid Ali 2018. Modified ZN Staining Protocol . protocols.io https://dx.doi.org/10.17504/protocols.io.tb2eiqe | 2021-04-15 09:15:13 | ||||
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Measles Vaccine Virus Taqman-MGB Resource Report Resource Website |
Mitchell Finger, Michael Lyon, Judy Northill, Ian Mackay | DOI:10.17504/protocols.io.suceesw | Public Health Virology, Forensic and Scientific Services | This previously unpublished protocol aims to amplify genotype A measles virus (MeV) strains but not non-mealses viruses.Mitchell Finger and Michael Lyon developed this in-house test in 2010.The assay targets the intergenic region between the M (matrix) and F (fusion) genes, designed as a qualitative test for investigating measles vaccine virus (MVV) strains.Numbering indicates the oligonucleotide location on the sequence with MeV strain Edmonston (Moraten vaccine), complete genome, GenBank accession number AF266287. | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 2 | 2018 | Mitchell Finger, Michael Lyon, Judy Northill, Ian Mackay 2018. Measles Vaccine Virus Taqman-MGB. protocols.io https://dx.doi.org/10.17504/protocols.io.suceesw | 2021-04-15 09:15:13 | |||
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Basic Protocol 3: Testing auxin-mediated degradation of the AID-tagged protein Resource Report Resource Website |
Kizhakke Mattada Sathyan, Thomas G. Scott, Michael J. Guertin | DOI:10.17504/protocols.io.bdyfi7tn | Please refer to the description section of the protocol collection. | Biochemistry and Molecular Genetics Department, University of Virginia, Biochemistry and Molecular Genetics Department, University of Virginia, Biochemistry and Molecular Genetics Department, University of Virginia ; Center for Public Health Genomics, University of Virginia; Cancer Center, University of Virginia | 1 | 2020 | Kizhakke Mattada Sathyan, Thomas G. Scott, Michael J. Guertin 2020. Basic Protocol 3: Testing auxin-mediated degradation of the AID-tagged protein. protocols.io https://dx.doi.org/10.17504/protocols.io.bdyfi7tn | 2021-04-15 09:15:39 | ||||
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Regular non-enzymatic splitting of human pluripotent stem cells Resource Report Resource Website |
Ralitsa Madsen | DOI:10.17504/protocols.io.4rtgv6n | This protocol describes the non-enzymatic splitting of human pluripotent stem cells with ReLeSR (Stem Cell Technologies) and RevitaCell (Thermo Fisher Scientific). This method allows pluripotent stem cells to preserve their undifferentiated state and enhances their survival. Success will hinge upon: Ensuring the right size of colony clumps following ReLeSR treatment, which requires optimal pipetting (speed and number of mixing steps)Sticking to a consistent maintenance schedule (splitting the cells at regular intervals, preferrably at roughly the same time of day) | University of Edinburgh | 1 | 2019 | Ralitsa Madsen 2019. Regular non-enzymatic splitting of human pluripotent stem cells . protocols.io https://dx.doi.org/10.17504/protocols.io.4rtgv6n | 2021-04-15 09:15:14 | ||||
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Aiptasia spawning and embryo/larvae handling - Pringle Lab Resource Report Resource Website |
Pringle Lab, Santiago Perez, Olivia Barry | DOI:10.17504/protocols.io.ru2d6ye | Aiptasia-Symbiodiniaceae Model System | This protocol seeks to provide all information needed to allow regular spawning of Aiptasia and safe handling of the spawn.It is based on the protocol described in Grawunder et al., 2015. | Stanford University, Stanford University, now Portland Community College, Stanford University | 1 | 2018 | Pringle Lab, Santiago Perez, Olivia Barry 2018. Aiptasia spawning and embryo/larvae handling - Pringle Lab. protocols.io https://dx.doi.org/10.17504/protocols.io.ru2d6ye | 2021-04-15 09:15:39 | |||
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CviJI Purification From IL-3A Virus Infected NC64A Chlorella Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.er3bd8n | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. CviJI Purification From IL-3A Virus Infected NC64A Chlorella. protocols.io https://dx.doi.org/10.17504/protocols.io.er3bd8n | 2021-04-15 09:15:14 | ||||
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MtDNA copy number Resource Report Resource Website |
Wen Aw | DOI:10.17504/protocols.io.rtdd6i6 | Cage Studies | Aw WC, Towarnicki SG, Melvin RG, Youngson NA, Garvin MR, Hu Y, Nielsen S, Thomas T, Pickford R, Bustamante S, Vila-Sanjurjo A, Smyth GK, Ballard JWO (2018) Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness. PLoS Genet 14(11): e1007735. doi: 10.1371/journal.pgen.1007735 | [email protected] | https://doi.org/10.1371/journal.pgen.1007735 | 1 | 2018 | Wen Aw 2018. MtDNA copy number. protocols.io https://dx.doi.org/10.17504/protocols.io.rtdd6i6 | 2021-04-15 09:15:40 | ||
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Ensayo angiogénesis in vitro Resource Report Resource Website |
Germán Alberto Téllez Ramírez, Lily Johanna Toro, Jesica Palacio, Diana Carolina Henao, Jhon Carlos Castaño Osorio | DOI:10.17504/protocols.io.ju3cnyn | Grupo de inmunología molecular | Angionesis in vitro: Es la formación In vitro de tubos capilares por células endoteliales en la matriz de una membrana basal, es un metodo in vitro poderoso para evaluar varios factores que promueven o inhiben angiogenesis. Es para definir las rutas de señalización en angiogenesis, identificando los genes reguladores de angiogenesis y caracterizando las células endoteliales del progenitor.El ensayo puede ser hecho como primera valoración antes de una prueba costosa con animales y puede ser hecho como un proceso de alta tecnología. Este es un método in vitro privilegiado para evaluar reguladores angiogenicos.La realizacion de este protocolo fue posible gracias al apoyo del departamento administrativo de ciencia tecnología e innovacion, Colciencias a traves del proyecto 111356933173 convocatoria569-2012. | Centro de investigaciones biomédicas, Universidad del Quindío., Centro de Investigaciones Biomédicas - Universidad del Quindío, Centro de investigaciones biomédicas, Universidad del Quindío., Centro de investigaciones biomédicas, Universidad del Quindío., Centro de investigaciones biomédicas, Universidad del Quindío. | 1 | 2017 | Germán Alberto Téllez Ramírez, Lily Johanna Toro, Jesica Palacio, Diana Carolina Henao, Jhon Carlos Castaño Osorio 2017. Ensayo angiogénesis in vitro. protocols.io https://dx.doi.org/10.17504/protocols.io.ju3cnyn | 2021-04-15 09:15:14 | |||
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Targeted proteomic LC-MS/MS analysis Resource Report Resource Website |
Yan Chen, Jennifer Gin, Christopher Petzold | DOI:10.17504/protocols.io.bf9xjr7n | LBNL-omics | This protocol details steps in targeted proteomic data acquisition with a standard-flow UHPLC-QQQ system. It was adapted from Chen, Y. et al. “A rapid methods development workflow for high-throughput quantitative proteomic applications.” PloS ONE 14,2 e0211582. 14 Feb. 2019, doi:10.1371/journal.pone.0211582. | Lawrence Berkeley National Laboratory, Lawrence Berkeley National Laboratory, Lawrence Berkeley National Laboratory | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0211582 | 1 | 2020 | Yan Chen, Jennifer Gin, Christopher Petzold 2020. Targeted proteomic LC-MS/MS analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.bf9xjr7n | 2021-04-15 09:15:39 | ||
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PCLS Single Cell Suspension Resource Report Resource Website |
Morrisey Lab | LungMap2 Consortium | University of Pennsylvania | 1 | 2021 | Morrisey Lab 2021. PCLS Single Cell Suspension. protocols.io https:// | 2021-04-15 09:15:39 | |||||
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CviJI Buffer B, pH 8.5 Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.eskbecw | VERVE Net | For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviJI Buffer B, pH 8.5. protocols.io https://dx.doi.org/10.17504/protocols.io.eskbecw | 2021-04-15 09:15:13 | ||||
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Silver staining of SDS-page Resource Report Resource Website |
Brian Kenn Baltzar | DOI:10.17504/protocols.io.g8zbzx6 | Silver staining of a acrylamide gel. | DEPARTMENT OF BIOCHEMISTRY AND MOLECULAR BIOLOGY, UNIVERSITY OF SOUTHERN DENMARK, ODENSE, DENMARK | 1 | 2017 | Brian Kenn Baltzar 2017. Silver staining of SDS-page. protocols.io https://dx.doi.org/10.17504/protocols.io.g8zbzx6 | 2021-04-15 09:15:13 | ||||
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RNAi by feeding in Euplotes focardii (povisional) Resource Report Resource Website |
Francesca Papi, Angela Piersanti | DOI:10.17504/protocols.io.zk8f4zw | Protist Research to Optimize Tools in Genetics (PROT-G) | University of Camerino, University of Camerino | 1 | 2019 | Francesca Papi, Angela Piersanti 2019. RNAi by feeding in Euplotes focardii (povisional). protocols.io https://dx.doi.org/10.17504/protocols.io.zk8f4zw | 2021-04-15 09:15:39 |
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