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MCPyV Co-Immunoprecipitation Protocol Resource Report Resource Website |
Kristine Dye | DOI:10.17504/protocols.io.v6ke9cw | Dye KN, Welcker M, Clurman BE, Roman A, Galloway DA (2019) Merkel cell polyomavirus Tumor antigens expressed in Merkel cell carcinoma function independently of the ubiquitin ligases Fbw7 and β-TrCP. PLoS Pathog 15(1): e1007543. doi: 10.1371/journal.ppat.1007543 | University of Washington | https://doi.org/10.1371/journal.ppat.1007543 | 2 | 2018 | Kristine Dye 2018. MCPyV Co-Immunoprecipitation Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.v6ke9cw | 2021-04-15 09:15:28 | |||
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Quantification of circulating microRNA using single TaqMan assays Resource Report Resource Website |
Helle Glud Binderup, Jonna Skov Madsen, Kim Houlind, Rikke Fredslund Andersen, Claus Lohman Brasen | DOI:10.17504/protocols.io.q9edz3e | A protocol for quantification of circulating microRNA using TaqMan assays.MicroRNAs are purified from platelet-poor plasma using Nucleospin columnsDuring the purification step samples are spiked with cel-miR-39 as a mean of technical normalizationNormalization is performed using the ΔCt-method | Binderup HG, Madsen JS, Heegaard NHH, Houlind K, Andersen RF, Brasen CL (2018) Quantification of microRNA levels in plasma – Impact of preanalytical and analytical conditions. PLoS ONE 13(7): e0201069. doi: 10.1371/journal.pone.0201069 | Biochemistry and Immunology, Lillebaelt Hospital, Kolding and Vejle, Denmark, Biochemistry and Immunology, Lillebaelt Hospital, Kolding and Vejle, Denmark, Department of Vascular Surgery, Lillebaelt Hospital, Kolding, Denmark, Biochemistry and Immunology, Lillebaelt Hospital, Kolding and Vejle, Denmark, Biochemistry and Immunology, Lillebaelt Hospital, Kolding and Vejle, Denmark | https://doi.org/10.1371/journal.pone.0201069 | 1 | 2018 | Helle Glud Binderup, Jonna Skov Madsen, Kim Houlind, Rikke Fredslund Andersen, Claus Lohman Brasen 2018. Quantification of circulating microRNA using single TaqMan assays. protocols.io https://dx.doi.org/10.17504/protocols.io.q9edz3e | 2021-04-15 09:15:28 | ||
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DNA metabarcoding of pollen transported by moths Resource Report Resource Website |
Callum Macgregor | DOI:10.17504/protocols.io.mygc7tw | EvoHull | University of York | 2 | 2018 | Callum Macgregor 2018. DNA metabarcoding of pollen transported by moths. protocols.io https://dx.doi.org/10.17504/protocols.io.mygc7tw | 2021-04-15 09:15:28 | ||||
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Western blotting Resource Report Resource Website |
Yuan Yao | DOI:10.17504/protocols.io.qaddsa6 | Yao Y, Ma Y, Chen X, Bade R, Lv C, Zhu R (2018) Absence of RstA results in delayed initiation of DNA replication in Escherichia coli. PLoS ONE 13(7): e0200688. doi: 10.1371/journal.pone.0200688 | Inner Mongolia People`s Hospital | https://doi.org/10.1371/journal.pone.0200688 | 1 | 2018 | Yuan Yao 2018. Western blotting. protocols.io https://dx.doi.org/10.17504/protocols.io.qaddsa6 | 2021-04-15 09:15:28 | |||
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Anchorage-independent growth assay or Soft Agar assay Resource Report Resource Website |
Marzia Ognibene | DOI:10.17504/protocols.io.bgeajtae | Ognibene M, Pezzolo A (2020) Ezrin interacts with the tumor suppressor CHL1 and promotes neuronal differentiation of human neuroblastoma. PLoS ONE 15(12): e0244069. doi: 10.1371/journal.pone.0244069 | Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, IRCCS Istituto Gaslini, Genova, Italy | https://doi.org/10.1371/journal.pone.0244069 | 1 | 2020 | Marzia Ognibene 2020. Anchorage-independent growth assay or Soft Agar assay. protocols.io https://dx.doi.org/10.17504/protocols.io.bgeajtae | 2021-04-15 09:15:28 | |||
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An assessment on a large geographic scale of Eurasian inland saline surface waters Resource Report Resource Website |
Emil Boros, Marina Kolpakova | DOI:10.17504/protocols.io.ptidnke | The major ion concentration data of sodium (Na), potassium (K), calcium (Ca), magnesium (Mg), chloride (Cl), sulphate (SO4), bicarbonate (HCO3), carbonate (CO3) and pH (if it was coupled with ion data) were input into the database. The data were drawn from a large geographic scale across Eurasia (Austria, China, Hungary, Kazakhstan, Mongolia, Russia, Serbia, Turkey) and from a large number of saline lakes and pans (N=220) with minimum a 1.0 g L–1 salinity threshold. The 1.0 g L–1 salinity threshold was selected based on a former study (Boros et al., 2014), where this threshold was experimentally found to be the characteristic boundary of soda ecosystems. Salinity was estimated by the sum of measured concentrations of eight major ions (Na, K, Ca, Mg, Cl, SO4, HCO3, CO3). As generally known, sodium is by far the most common cation in saline lakes and necessarily the dominant cation in soda type lakes. Therefore, sites were excluded from the dataset if Na was not the most abundant ion. If seasonal or annual water data were available, mean values were put into database. Most of the data came from papers (sources are indicated in the table). | Balaton Limnological Institute, Centre for Ecological Research, Hungarian Academy of Sciences (MTA), Sobolev Institute of Geology and Mineralogy, Siberian Branch of Russian Academy of Sciences | 2 | 2018 | Emil Boros, Marina Kolpakova 2018. An assessment on a large geographic scale of Eurasian inland saline surface waters. protocols.io https://dx.doi.org/10.17504/protocols.io.ptidnke | 2021-04-15 09:15:26 | ||||
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High molecular weight DNA extraction after Bolger et al. Resource Report Resource Website |
Miriam Schalamun | DOI:10.17504/protocols.io.hhqb35w | High molecular weight DNA extraction from all kingdoms | Extraction of high molecular weight DNA after Bolger et al. Carried out for eucalyptus grandis. DNA fragments were ranging up to 270 kb on a Pulsfield Electrophoresis Gel | 1 | 2017 | Miriam Schalamun 2017. High molecular weight DNA extraction after Bolger et al.. protocols.io https://dx.doi.org/10.17504/protocols.io.hhqb35w | 2021-04-15 09:15:26 | ||||
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Mammalian non-coding RNA knockout through epigenetic start signature excision Resource Report Resource Website |
Janga H, Aznaourova M, Boldt F, Damm K, Grünweller A, Schulte LN | DOI:10.17504/protocols.io.mmic44e | This protocol describes how to knockout mammalian non-coding RNA genes through excision of an epigenetic transcriptional start site (TSS) signature. To this end two guideRNAs are cloned onto the pX458 CRISPR vector to induce DNA cleavage right up- and downstream of the TSS element.The protocol describes how to generate homozygous knockout cell clones. Optionally, successful target DNA excision by the dual guideRNA pX458 construct may be pre-validated by transfection into an easy-to-transfect cell line (e.g. Hek293) and genomic PCR without prior single cell clonal expansion. | Janga H, Aznaourova M, Boldt F, Damm K, Grünweller A, Schulte LN (2018) Cas9-mediated excision of proximal DNaseI/H3K4me3 signatures confers robust silencing of microRNA and long non-coding RNA genes. PLoS ONE 13(2): e0193066. doi: 10.1371/journal.pone.0193066 | Institute for Lung Research, Philipps University, Marburg, Germany, Institute for Lung Research, Philipps University, Marburg, Germany, Institute for Lung Research, Philipps University, Marburg, Germany, Institute for Pharmaceutical Chemistry, Philipps University, Marburg, Germany, Institute for Pharmaceutical Chemistry, Philipps University, Marburg, Germany, Institute for Lung Research, Philipps University, Marburg, Germany | https://doi.org/10.1371/journal.pone.0193066 | 2 | 2018 | Janga H, Aznaourova M, Boldt F, Damm K, Grünweller A, Schulte LN 2018. Mammalian non-coding RNA knockout through epigenetic start signature excision. protocols.io https://dx.doi.org/10.17504/protocols.io.mmic44e | 2021-04-15 09:15:26 | ||
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(CVD) risk chart development, evaluation, and validation Resource Report Resource Website |
Nizal Sarrafzadegan, Razieh Hassannejad, Hamid Reza Marateb, Mohammad Talaei, Masoumeh Sadeghi, Hamid Reza Roohafza, Farzad Masoudkabir, Shahram OveisGharan, Marjan Mansourian, Mohammad Reza Mohebian, Miquel Angel Mañanas | DOI:10.17504/protocols.io.j7rcrm6 | In this protocol, we aimed to show the step-by.step procedures used to develop, evaluate and validate (CVD) risk charts. | Sarrafzadegan N, Hassannejad R, Marateb HR, Talaei M, Sadeghi M, Roohafza HR, Masoudkabir F, OveisGharan S, Mansourian M, Mohebian MR, Mañanas MA (2017) PARS risk charts: A 10-year study of risk assessment for cardiovascular diseases in Eastern Mediterranean Region. PLoS ONE 12(12): e0189389. doi: 10.1371/journal.pone.0189389 | Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran; School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada, Department of Epidemiology and Biostatistics, School of Public Health, Isfahan University of Medical Sciences, Isfahan, Iran, Biomedical Engineering Department, Engineering Faculty, University of Isfahan, Isfahan, Iran; Department of Automatic Control, Biomedical Engineering Research Center, Universitat Politècnica de Catalunya, BarcelonaTech (UPC), Barcelona, Spain, Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran, Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran, Department of Cardiology, School of Medicine, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran; Cardiac Primary Prevention Research Center, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran, Department of Neurology, School of Medicine, Tehran University of Medical Sciences; Tehran; Iran; Rush Alzheimer’s disease Center; Rush University Medical Center; Chicago; IL, USA, Department of Epidemiology and Biostatistics, School of Public Health, Isfahan University of Medical Sciences, Isfahan, Iran, Biomedical Engineering Department, Engineering Faculty, University of Isfahan, Isfahan, Iran, Department of Automatic Control, Biomedical Engineering Research Center, Universitat Politècnica de Catalunya, BarcelonaTech (UPC), Barcelona, Spain; Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBERBBN), Spain | https://doi.org/10.1371/journal.pone.0189389 | 1 | 2017 | Nizal Sarrafzadegan, Razieh Hassannejad, Hamid Reza Marateb, Mohammad Talaei, Masoumeh Sadeghi, Hamid Reza Roohafza, Farzad Masoudkabir, Shahram OveisGharan, Marjan Mansourian, Mohammad Reza Mohebian, Miquel Angel Mañanas 2017. (CVD) risk chart development, evaluation, and validation . protocols.io https://dx.doi.org/10.17504/protocols.io.j7rcrm6 | 2021-04-15 09:15:26 | ||
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Protocol for a reproducible circRNA analysis using Docker4Circ Resource Report Resource Website |
Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Raffaele Adolfo Calogero, Francesca Cordero, Marco Beccuti, Michele De Bortoli | DOI:10.17504/protocols.io.xkcfksw | Q-Bio Turin | Despite many computational tools were developed to predict circular RNAs (circRNAs), a limited number of work-flows exists to fully analyse a circRNA set ensuring the computational reproducibility of the whole analysis.For this purpose, we designed Docker4Circ, a computational work-flow for a comprehensive circRNAs analysis of a circRNAs composed of four modules: the circRNAs prediction (module 1), the circRNAs classification and annotation (module 2), the circRNAs sequence analysis (module 3), and circRNAs expression analysis (module 4).To ensure reproducibility each function of Docker4Circ was embeded into a docker image following guideline provided by Reproducible Bioinformatics Project (RBP, http://reproducible-bioinformatics.org/). Each function is included in the Docker4Seq R package which already includes different solutions for reproducible bioinformatic analyses.This protocol describes the use of each function of Docker4Circ to analyse the circRNAs predicted from a set of RNA-Seq experiments performed in normal colon and colorectal cancer cell lines. Furthermore, the description of the functions required to compute the expression level of the analysed circRNAs in a set of RNA-Seq experiments of colorectal primary tumors is provided. | University of Turin, University of Turin, University of Turin, University of Turin, University of Turin, University of Turin, University of Turin, University of Turin, University of Turin | 2 | 2019 | Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Raffaele Adolfo Calogero, Francesca Cordero, Marco Beccuti, Michele De Bortoli 2019. Protocol for a reproducible circRNA analysis using Docker4Circ. protocols.io https://dx.doi.org/10.17504/protocols.io.xkcfksw | 2021-04-15 09:15:26 | |||
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Q5® Site-Directed Mutagenesis Kit Quick Protocol (E0554) Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.cpyvpv | New England Biolabs (NEB) | This is the quick protocol for the Q5® Site-Directed Mutagenesis Kit (E0554) | NEB | https://www.neb.com/protocols/2013/01/26/q5-site-directed-mutagenesis-kit-quick-protocol-e0554 | 1 | 2015 | New England Biolabs 2015. Q5® Site-Directed Mutagenesis Kit Quick Protocol (E0554). protocols.io https://dx.doi.org/10.17504/protocols.io.cpyvpv | 2021-04-15 09:15:28 | ||
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Large Volume Marine Cyanophage Phage Purification Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c3iykd | VERVE Net, Sullivan Lab | Last optimized January 2006, updated by Matt on March 16 2009 | Matthew Sullivan | 1 | 2016 | Matthew Sullivan 2016. Large Volume Marine Cyanophage Phage Purification. protocols.io https://dx.doi.org/10.17504/protocols.io.c3iykd | 2021-04-15 09:15:49 | |||
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Immunohistochemistry Protocol for Sternberger Monoclonal Antibodies Resource Report Resource Website |
Kelsey Miller | DOI:10.17504/protocols.io.e2jbgcn | BioLegend | BioLegend | http://www.biolegend.com/media_assets/support_protocol/Sternberger_Monoclonals_IHC_Protocol_using_USA_Kit_102914.pdf | 1 | 2016 | Kelsey Miller 2016. Immunohistochemistry Protocol for Sternberger Monoclonal Antibodies. protocols.io https://dx.doi.org/10.17504/protocols.io.e2jbgcn | 2021-04-15 09:15:26 | |||
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Hematologic alterations and early mortality in a cohort of HIV positive African patients Resource Report Resource Website |
Fausto Ciccacci, Francesca Lucaroni, Roberto Latagliata, Laura Morciano, Elisa Mondlane, Moises Balama, Dyna Tembo, Jane Gondwe, Stefano Orlando, Leonardo Palombi, Maria Cristina Marazzi | DOI:10.17504/protocols.io.bcdfis3n | Infection with Human Immunodeficiency Virus (HIV) is highly prevalent worldwide, especially in Sub-Saharan Africa, where anaemia is also widespread. HIV infection is known to be associated with anaemia and various other haematologic alterations, but little data on correlation with immunological and virologic conditions in treatment-naïve patients is available. To investigate these associations, we conducted a retrospective analysis of baseline data (general details, nutritional status, full blood count and HIV infection progress data) and 12 months follow-up status for HIV+ adult patients in 22 health facilities in Malawi and Mozambique. .justify:after { content: ""; display:inline-block; width: 100%; } Among the 22.657 patients included, we found associations of sex, nutritional status, CD4 count, and VL with anaemia, leukopenia, and thrombocytopenia. Also, any cytopenia was present in 1/3 of patients with normal nutritional status and less advanced HIV infection, and it wouldn’t be diagnosed in a basic HIV care setting. .justify:after { content: ""; display:inline-block; width: 100%; } Moreover anaemia, lower Red blood cells and platelets counts correlated with mortality in the first year of care, independently by BMI, Hb, CD4 count and VL. .justify:after { content: ""; display:inline-block; width: 100%; } Our results emphasize the need for including a full blood count in the routine HIV care services in Sub-Saharan Africa. .justify:after { content: ""; display:inline-block; width: 100%; } | Ciccacci F, Lucaroni F, Latagliata R, Morciano L, Mondlane E, Balama M, Tembo D, Gondwe J, Orlando S, Palombi L, Marazzi MC (2020) Hematologic alterations and early mortality in a cohort of HIV positive African patients. PLoS ONE 15(11): e0242068. doi: 10.1371/journal.pone.0242068 | UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy, Department of Biomedicine and Prevention, University or Rome Tor Vergata, Rome, Italy, Hematology, Department of Translational and Precision Medicine, University ‘Sapienza' and Policlinico Umberto 1, Rome, Italy, Department of Biomedicine and Prevention, University or Rome Tor Vergata, Rome, Italy, DREAM program, Community of Sant’Egidio, Maputo, Mozambique, DREAM program, Community of Sant’Egidio, Beira, Mozambique, DREAM program, Community of Sant’Egidio, Blantyre, Malawi, DREAM program, Community of Sant’Egidio, Blantyre, Malawi, Department of Biomedicine and Prevention, University or Rome Tor Vergata, Rome, Italy, Department of Biomedicine and Prevention, University or Rome Tor Vergata, Rome, Italy, LUMSA, Rome, Italy | https://doi.org/10.1371/journal.pone.0242068 | 1 | 2020 | Fausto Ciccacci, Francesca Lucaroni, Roberto Latagliata, Laura Morciano, Elisa Mondlane, Moises Balama, Dyna Tembo, Jane Gondwe, Stefano Orlando, Leonardo Palombi, Maria Cristina Marazzi 2020. Hematologic alterations and early mortality in a cohort of HIV positive African patients. protocols.io https://dx.doi.org/10.17504/protocols.io.bcdfis3n | 2021-04-15 09:15:26 | ||
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In situ hybridization Resource Report Resource Website |
Xiong Xinwei | DOI:10.17504/protocols.io.9qhh5t6 | This protocol provided the detail of in situ hybridization in the mantle tissue of Pinctada fucata martensii. | Xiong X, Xie B, Zheng Z, Deng Y, Jiao Y, Du X (2019) PfmPif97-like regulated by Pfm-miR-9b-5p participates in shell formation in Pinctada fucata martensii. PLoS ONE 14(12): e0226367. doi: 10.1371/journal.pone.0226367 | Guangdong Ocean University | https://doi.org/10.1371/journal.pone.0226367 | 1 | 2019 | Xiong Xinwei 2019. In situ hybridization . protocols.io https://dx.doi.org/10.17504/protocols.io.9qhh5t6 | 2021-04-15 09:15:26 | ||
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Performance Study of Wireless Fecobionics Device in Canine Resource Report Resource Website |
Yanmin Wang, Hans Gregersen | DOI:10.17504/protocols.io.bpzfmp3n | We developed a novel wireless device (Fecobionics) for mapping colonic and anorectal neuromuscular function. The hypothesis of this protocol is that the Fecobionics device can test pressures, orientation, bending, shape, and cross-sectional area changes in colon and rectum. To validate our hypothesis, we inserted the device to the proximal colon, either through a cannula or colonoscopy, followed by data transmission and recording. | California Medical Innovations Institute, California Medical Innovations Institute | 1 | 2020 | Yanmin Wang, Hans Gregersen 2020. Performance Study of Wireless Fecobionics Device in Canine. protocols.io https://dx.doi.org/10.17504/protocols.io.bpzfmp3n | 2021-04-15 09:15:25 | ||||
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A protocol for rapid western-blot: shorten the time to 1-3 hours Resource Report Resource Website |
Zhichao Zhao Shenao Biotechnology Company, wang jiang | DOI:10.17504/protocols.io.bfyxjpxn | Western blot (WB) is a classical and powerful tool to detect the level of interested protein from among a mixture of proteins. Since its invention in 1979, WB is a time-consuming technique that usually needs 1 to 2 days to obtain the result. Here, being aware of the time spent by the researcher, we share a rapid protocol that shortens the time up to 1 hour for detecting the internal loading control protein actin (42kDa) when using the HRP-conjugated anti-actin antibody. Additionally, the time for detecting other (21kDa-100kDa) could be shortened to 3 hours when using the second HRP-conjugated antibody. In conclusion, this rapid protocol dramatically improved the efficiency of WB without increasing the experiment cost or losing its high data quality. | Shenao Biotechnology Company, University of Chinese Academy of Science | 2 | 2020 | Zhichao Zhao Shenao Biotechnology Company, wang jiang 2020. A protocol for rapid western-blot: shorten the time to 1-3 hours. protocols.io https://dx.doi.org/10.17504/protocols.io.bfyxjpxn | 2021-04-15 09:15:26 | ||||
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Understanding the Purpose of Every Nucleotide in the Comirnaty (Pfizer-BioNTech) Vaccine, a Hands-on Activity for Virtual Presentations Resource Report Resource Website |
Harley King | Harley King Workspace, USG Fall 2020 BSCI:414, protocols.io for Educators | LuminUltra | 1 | 2021 | Harley King 2021. Understanding the Purpose of Every Nucleotide in the Comirnaty (Pfizer-BioNTech) Vaccine, a Hands-on Activity for Virtual Presentations. protocols.io https:// | 2021-04-15 09:15:26 | |||||
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Adaptor Ligation Mixture (E7370) Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.cg6tzd | New England Biolabs (NEB) | New England Biolabs | https://www.neb.com/protocols/2012/11/15/adaptor-ligation-e7370 | 1 | 2015 | New England Biolabs 2015. Adaptor Ligation Mixture (E7370). protocols.io https://dx.doi.org/10.17504/protocols.io.cg6tzd | 2021-04-15 09:15:48 | |||
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Reporter titrations for transfection of Micromonas commoda CCMP2709 Resource Report Resource Website |
Lisa Sudek, Alexandra Worden, Manny Ares | DOI:10.17504/protocols.io.57rg9m6 | Protist Research to Optimize Tools in Genetics (PROT-G), Worden Lab | This protocol describes the method used to test various amounts (0, 0.3, 3, 10, 20 and 30 µg) of reporter (H3proMpo-LUC) DNA. The plasmid H3proMpo-LUC carries a codon optimized Nanoluc coding region, whose expression is driven by the histone H3 promoter and 3' mRNA end formation and termination sequences. Lumen per total number of cells (including transfected and non-transfected cells within a culture) is used as a proxy for relative transfection efficiencies. It is determined in each culture based on luminescence measurements performed 72 hrs after transfection using the Nano-Glo® Luciferase Assay System. | Monterey Bay Aquarium Research Institute, Moss Landing, USA, Monterey Bay Aquarium Research Institute, Moss Landing, USA; Ocean EcoSystems Biology Unit, Marine Ecology Division, Helmholtz Centre for Ocean Research, Kiel, Germany, University of California, Santa Cruz | 1 | 2019 | Lisa Sudek, Alexandra Worden, Manny Ares 2019. Reporter titrations for transfection of Micromonas commoda CCMP2709. protocols.io https://dx.doi.org/10.17504/protocols.io.57rg9m6 | 2021-04-15 09:15:26 |
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