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Authors: Kristine Dye

Proper citation: Kristine Dye 2018. MCPyV Co-Immunoprecipitation Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.v6ke9cw Copy   

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Authors: Helle Glud Binderup, Jonna Skov Madsen, Kim Houlind, Rikke Fredslund Andersen, Claus Lohman Brasen
Summary: 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

Proper citation: 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 Copy   

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Authors: Callum Macgregor
Group: EvoHull

Proper citation: Callum Macgregor 2018. DNA metabarcoding of pollen transported by moths. protocols.io https://dx.doi.org/10.17504/protocols.io.mygc7tw Copy   

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Authors: Yuan Yao

Proper citation: Yuan Yao 2018. Western blotting. protocols.io https://dx.doi.org/10.17504/protocols.io.qaddsa6 Copy   

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Authors: Marzia Ognibene

Proper citation: Marzia Ognibene 2020. Anchorage-independent growth assay or Soft Agar assay. protocols.io https://dx.doi.org/10.17504/protocols.io.bgeajtae Copy   

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Authors: Emil Boros, Marina Kolpakova
Summary: 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).

Proper citation: 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 Copy   

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Authors: Miriam Schalamun
Group: High molecular weight DNA extraction from all kingdoms
Summary: 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 

Proper citation: Miriam Schalamun 2017. High molecular weight DNA extraction after Bolger et al.. protocols.io https://dx.doi.org/10.17504/protocols.io.hhqb35w Copy   

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Authors: Janga H, Aznaourova M, Boldt F, Damm K, Grünweller A, Schulte LN
Summary: 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.

Proper citation: 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 Copy   

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Authors: 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
Summary: In this protocol, we aimed to show the step-by.step procedures used to develop, evaluate and validate (CVD) risk charts.

Proper citation: 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 Copy   

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Authors: Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Raffaele Adolfo Calogero, Francesca Cordero, Marco Beccuti, Michele De Bortoli
Group: Q-Bio Turin
Summary: 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.

Proper citation: 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 Copy   

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Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: This is the quick protocol for the Q5® Site-Directed Mutagenesis Kit (E0554)

Proper citation: New England Biolabs 2015. Q5® Site-Directed Mutagenesis Kit Quick Protocol (E0554). protocols.io https://dx.doi.org/10.17504/protocols.io.cpyvpv Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Last optimized January 2006, updated by Matt on March 16 2009

Proper citation: Matthew Sullivan 2016. Large Volume Marine Cyanophage Phage Purification. protocols.io https://dx.doi.org/10.17504/protocols.io.c3iykd Copy   

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Authors: Kelsey Miller
Group: BioLegend

Proper citation: Kelsey Miller 2016. Immunohistochemistry Protocol for Sternberger Monoclonal Antibodies. protocols.io https://dx.doi.org/10.17504/protocols.io.e2jbgcn Copy   

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Authors: Fausto Ciccacci, Francesca Lucaroni, Roberto Latagliata, Laura Morciano, Elisa Mondlane, Moises Balama, Dyna Tembo, Jane Gondwe, Stefano Orlando, Leonardo Palombi, Maria Cristina Marazzi
Summary: 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%; }

Proper citation: 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 Copy   

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Authors: Xiong Xinwei
Summary: This protocol provided the detail of in situ hybridization in the mantle tissue of Pinctada fucata martensii.

Proper citation: Xiong Xinwei 2019. In situ hybridization . protocols.io https://dx.doi.org/10.17504/protocols.io.9qhh5t6 Copy   

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Authors: Yanmin Wang, Hans Gregersen
Summary: 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.

Proper citation: Yanmin Wang, Hans Gregersen 2020. Performance Study of Wireless Fecobionics Device in Canine. protocols.io https://dx.doi.org/10.17504/protocols.io.bpzfmp3n Copy   

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Authors: Zhichao Zhao Shenao Biotechnology Company, wang jiang
Summary: 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.

Proper citation: 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 Copy   

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Authors: Harley King
Group: Harley King Workspace, USG Fall 2020 BSCI:414, protocols.io for Educators

Proper citation: 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:// Copy   

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Authors: New England Biolabs
Group: New England Biolabs (NEB)

Proper citation: New England Biolabs 2015. Adaptor Ligation Mixture (E7370). protocols.io https://dx.doi.org/10.17504/protocols.io.cg6tzd Copy   

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Authors: Lisa Sudek, Alexandra Worden, Manny Ares
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Worden Lab
Summary: 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.

Proper citation: 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 Copy   

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