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Authors: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino

Proper citation: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino 2020. SOLUTION- 11 - CD4+T cells isolation buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.bi79khr6 Copy   

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Authors: Sam Li
Group: BioLegend

Proper citation: Sam Li 2019. Cell Fixation and Permeabilization Protocol using 70% Ethanol. protocols.io https://dx.doi.org/10.17504/protocols.io.bacziax6 Copy   

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Authors: Takao Ito, Ryoji Nakaune
Group: Plantae
Summary: In the STEPS, we describe TaqMan multiplex real-time PCR to universally detect phytoplasmas (PP) and Xylella spp. (XL) with plant internal control (IC) from crude extracts. A protocol file uploaded in the DESCRIPTION shows further details of the protocol in Japanese and English.

Proper citation: Takao Ito, Ryoji Nakaune 2017. A protocol of molecular detection of phytoplasmas and Xylella spp. in post-entry quarantine for plants.. protocols.io https://dx.doi.org/10.17504/protocols.io.kvvcw66 Copy   

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Authors: David Frommholz, Nadine Stefanczyk, Alexandra Ehl
Summary: Purification Guide for the Isolation of Antibodies with ChroDrip Columns by DALEX Biotech.Easy and quick small scale antibody purification from various sources and species.Each ChroDrip column has a binding capacity of > 10 mg/ml (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).

Proper citation: David Frommholz, Nadine Stefanczyk, Alexandra Ehl 2018. ChroDrip - ProteinA/G. protocols.io https://dx.doi.org/10.17504/protocols.io.vufe6tn Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the capture of 20X multi-channel images using human and mouse tissue.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Proper citation: Allen Institute for Brain Science 2020. Zeiss AxioImager Multi Channel 20X Image Capture. protocols.io https://dx.doi.org/10.17504/protocols.io.bdpki5kw Copy   

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Authors: Manuela De Las Casas
Group: AEGIS - Madrid iGEM 2019
Summary: The aim of this protocol is to check the efficiency of the detection system that will be present in the strips. Like the qualitative assay, this is a dot blot performed with streptavidin and aptamers, also named paper ELONA.The expected result is a good binding between the streptavidin and the aptamers (knowing already that the streptavidin binds correctly to the nitrocellulose membrane thanks to previous experiments), great hybridization between both aptamers and a clear visible result when yielding with the ABTS. In order to make this experiment quantitative, several concentrations are made from the same mix, to test the minimum concentration with a detectable change of color.

Proper citation: Manuela De Las Casas 2019. Quantitative paper ELONA. protocols.io https://dx.doi.org/10.17504/protocols.io.8hdht26 Copy   

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Authors: mrwick
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, BVS, Inc, mrwick
Summary: IVDS is uniquely suited to large volume sampling.Collection from saliva or sputum are straightforward – collection in disposable pipette and transfer to a small vial, dilute as needed, filter, and test, all at under 5 minutes including results.Sample collection, storage and processing are straightforward, not requiring sensitive or unstable solutions.

Proper citation: mrwick 2020. Integrated Virus Detection System - sample collection - prep - processing. protocols.io https://dx.doi.org/10.17504/protocols.io.bktkkwkw Copy   

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Authors: Carezza Botto-Mahan, Antonella Bacigalupo, Viviana Estadella, Berenice Cornejo-Villar, Juana P. Correa, Pedro E. Cattan
Summary: Includes a list of materials, baits, references, and recommended procedures to capture the hematophagous bugs of the subfamily Triatominae, vectors of Chagas disease in semi-arid areas.

Proper citation: Carezza Botto-Mahan, Antonella Bacigalupo, Viviana Estadella, Berenice Cornejo-Villar, Juana P. Correa, Pedro E. Cattan 2019. Baited live-trapping of triatomines in semi-arid environments. protocols.io https://dx.doi.org/10.17504/protocols.io.wnpfddn Copy   

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Authors: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
Group: University of the West Indies, [email protected]

Proper citation: Angel Justiz-Vaillant, Belkis Ferrer-Cosme 2020. ELISA for quantification of human C4 in serum or plasma.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj75krq6 Copy   

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Authors: Aaron Meyer
Summary: We use this process to create our own Luminex assays from standard ELISA reagents.

Proper citation: Aaron Meyer 2015. Luminex Bead Coupling. protocols.io https://dx.doi.org/10.17504/protocols.io.ctmwk5 Copy   

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Authors: Rachel Aronoff, Guy Aidelberg
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, Guy Aidelberg
Summary: Corona Detective is based upon a molecular amplification strategy inspired by the ‘GMO Detective’ method, in order to detect the virus causing Covid-19. Done not only without complicated equipment, but with a simple +/- fluorescent readout, the Corona Detective is very specific. Furthermore, controls to ensure sensitive detection, without false positives or negatives, are intrinsic to this solution. The final product, strips/plates of tubes with dry reagents, specific for Corona and a control gene (extraction control), can be shipped anywhere, without cold-chain dependence. Critically, monitoring tests could be run by ordinary people, by following this protocol. (Even kids have successfully participated in GMO detective workshops, also soldering their own fluor detectors.)This user guide will allow you to test samples with this system, provided as freeze-dried reaction components in 0.2ml tubes made by this protocol (other formats possible e.g. 8-tube strips, 96-well plates, 1000 reactions, etc.).Human or clinical samples should only be run in settings with access to appropriate biosafety facilities, of course.Acknowledging the JOGL Open Covid 19 Initiative and all the #proj nucleic-acid-amplification team for support.

Proper citation: Rachel Aronoff, Guy Aidelberg 2020. Corona Detective User Protocol V2.0. protocols.io https://dx.doi.org/10.17504/protocols.io.bpwzmpf6 Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. FISH Protocol for FISH & FLOW. protocols.io https://dx.doi.org/10.17504/protocols.io.dfe3jd Copy   

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Authors: Ajit N Shah

Proper citation: Ajit N Shah 2019. Isolation of mononuclear cells using Septmate . protocols.io https://dx.doi.org/10.17504/protocols.io.88chzsw Copy   

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Authors: Adam Hunter
Group: Human Cell Atlas Method Development Community

Proper citation: Adam Hunter 2018. CGAP Dead cell removal EasySep kit with The Big Easy Magnet. protocols.io https://dx.doi.org/10.17504/protocols.io.qz6dx9e Copy   

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Authors: LI-COR Biosciences
Group: LI-COR Biosciences
Summary: The Odyssey Fc Imager, with 600 channel capabilities, can image agarose gels stained with popular DNA stains, such as ethidium bromide and SYBR Safe DNA stain, with sub-nanogram sensitivity. The Odyssey Fc Imager contains a 532 nm diffuse source with an excitation maximum of 520 nm and a detection maximum of 600 nm. These instrument parameters are within the range of the excitation and emission wavelengths of ethidium bromide (Ex/Em = 302 & 518/605 nm) and other visible fluorescent nucleic acid stains and provide a sensitive gel documentation option. Developed for: Odyssey Fc Imaging System

Proper citation: LI-COR Biosciences 2018. Imaging Nucleic Acid Gels on the Odyssey® Fc Imager. protocols.io https://dx.doi.org/10.17504/protocols.io.guvbww6 Copy   

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Authors: Alice Pawlowski
Group: Axmann Lab
Summary: RNA is denatured in 8 M Urea and separated in a polyacrylamide gel electrophoresis (PAGE) based on its molecular weight. Using this method, fragments between 2 to 500 nucleotids can be separated. The migration of the RNA depends on the concentration of PAA: the higher the PAA percentage, the better the resolution of low molecular weight fragments and vice versa. We used 10 % PAA to separate fragments between 50 - 200 nucleotides in 10 ml mini-gels (10.5 x 10 cm) using the Hoefer SE260 Mighty Small system. Subsequently, RNA is transfered from the gel to a nylon membrane (Northern blotting) by using aTrans-Blot SD Semi-Dry Electrophoretic Transfer Cell (BioRad).

Proper citation: Alice Pawlowski 2021. Denaturing RNA electrophoresis in urea polyacrylamide gels (Urea-PAGE) and semi-dry Northern Blot transfer. protocols.io https://dx.doi.org/10.17504/protocols.io.beemjbc6 Copy   

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Authors: Lawrence A. Klobutcher, Larry Klobutcher
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: This procedure was developed to investigate the possible use of RNAi through bacterial feeding as a means of knocking down expression of particular genes.While the utility of RNAi is still being investigated, the method is effective in growing Euplotes crassus to higher densities than is possible using algae alone. Using moderately dense cultures of algae, we typically achieve cell densities of 500-1,000 cells/ml, while with the E. coli supplemented cultures we describe here, Euplotes cell densities exceed 3,000 cells/ml. In fact, preliminary studies mixing a volume of a Euplotes culture with an equal volume of resuspended E. coli have produced a density of ~8,000 cells/ml.While the described procedure involves small cultures, it can likely be scaled up as required.For some species of Euplotes, long-term culture using bacteria as a food source has not been successful (C. Miceli, personal communication), suggesting that some essential nutrient is not being provided in sufficient quantitities

Proper citation: Lawrence A. Klobutcher, Larry Klobutcher 2019. Culturing Euplotes crassus to high densities using a combination of algae and bacteria as the food source.. protocols.io https://dx.doi.org/10.17504/protocols.io.2amgac6 Copy   

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Authors: G Jason Smith, April Woods
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Environmental Biotechnology Lab
Summary: This is a modified version of  'Conjugation of Thalassiosira pseudonana', publishedby J. Turnsek dx.doi.org/10.17504/protocols.io.f55bq86 .The protocol was modified to enhance viability in the diatom Pseudo-nitzschia multiseries. This version was used to transform Pseudo-nitzschia multiseries isolate 15091C3 with an episomal plasmid derived from pPtPUC3 to express a egfp gene under control of the P. multiseries actin promoter and termination domains. PLASMID INFOpPmAGFPC10 EPI : A P. multiseries derived expression cassette under control of P. multiseries ca 1000 bp of actin promoter and termination domains. Pm actPs::eGFP::actTs

Proper citation: G Jason Smith, April Woods 2019. Modified Bacterial Conjugation Protocol For Pseudo-nitzschia multiseries. protocols.io https://dx.doi.org/10.17504/protocols.io.7vhhn36 Copy   

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Authors: OSU Weis Lab
Group: Weis Lab Oregon State, Aiptasia-Symbiodiniaceae Model System
Summary: This protocol describes how Aiptasia stocks are cared for in the Weis lab. The protocol was last updated in 2018. Most students and postdocs tha have been in the Weis lab have contributed to this protocol in some form or another, and they are too numerous to list.

Proper citation: OSU Weis Lab 2018. General Aiptasia husbandry - Weis Lab. protocols.io https://dx.doi.org/10.17504/protocols.io.rihd4b6 Copy   

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Authors: Liz McDonough
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research
Summary: This is an overview of all protocols currently in use for the GE/UPitt Cell DIVE collaboration for the Human BioMolecular Atlas Program (HuBMAP). It includes links to each of the individual protocols that make up this project workflow.

Proper citation: Liz McDonough 2021. HuBMAP | GE/UPitt Cell DIVE™ Modality Overview. protocols.io https://dx.doi.org/10.17504/protocols.io.bqjimuke Copy   

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