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Authors: steve.puts
Group: Coronavirus Method Development Community, Mmolecular, XPRIZE Rapid Covid Testing
Summary: The Direct One-Step RT-qPCR COVID-19 Test Kit is designed for quantitativereal-time analysis of target RNA directly from, swabs without the requirement of any priorRNA purification steps.Shipping: shipped on blue ice Storage Conditions: store at -20 °C Additional Storage Conditions: avoid freeze/thaw cycles stable at 4 °C for up to 4 weeks Shelf Life: 12 monthsForm: liquid / lyophilized
Proper citation: steve.puts 2020. Mmolecular COVID-19 Extraction-Free Direct-One-Step Fast Cycling Protocol. protocols.io dx.doi.org/10.17504/protocols.io.bkjpkumn Copy
Authors: Etienne Laliberté
Group: Plant Functional Ecology Lab, Canadian Airborne Biodiversity Observatory
Summary: Here we describe the standardised protocol used by the Canadian Airborne Biodiversity Observatory (CABO) to measure leaf water content and specific leaf area, using the WinFOLIA™ software (Régent Instruments). These leaf area and water measurements are done on a subset of leaves from the same bulk leaf sample used to measure leaf spectral reflectance and transmittance. Briefly, after removing their petioles, fresh leaves are weighed, rehydrated for 6 h, scanned for total leaf area and weighed again; they are then oven-dried at 65 ºC for 72 h, and weighed one last time. This allows us to measure leaf dry matter content and its complement, leaf water content, as well as leaf relative water content. Leaf area measurements are used to estimate specific leaf area, a key functional trait central to the leaf economics spectrum. Specific leaf area allows us to estimate equivalent water thickness and to convert concentrations of foliar biochemical constitutents from a leaf mass to a leaf area basis.
Proper citation: Etienne Laliberté 2018. Measuring specific leaf area and water content. protocols.io dx.doi.org/10.17504/protocols.io.p3tdqnn Copy
Authors: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
Group: University of the West Indies, [email protected]
Summary: IgD is a monomer with a molecular weight of 184 Kd. IgD is present in a meager amount in the serum (0.03 mg/mL) and has an unknown function against pathogens. It is regarded as a BCR. IgD may play an essential role in antigen-triggered lymphocyte differentiation. [1]
Proper citation: Angel Justiz-Vaillant, Belkis Ferrer-Cosme 2020. ELISA for quantification of human immunoglobulin D (IgD) in serum or plasma.. protocols.io dx.doi.org/10.17504/protocols.io.bj7wkrpe Copy
Authors: Peter J. Skene, Steven Henikoff
Group: Human Cell Atlas Method Development Community
Summary: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an epigenomic profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. As only the targeted fragments enter into solution, and the vast majority of DNA is left behind, CUT&RUN has exceptionally low background levels. CUT&RUN outperforms the most widely used Chromatin Immunoprecipitation (ChIP) protocols in resolution, signal-to-noise, and depth of sequencing required. In contrast to ChIP, CUT&RUN is free of solubility and DNA accessibility artifacts and can be used to profile insoluble chromatin and to detect long-range 3D contacts without cross-linking. Here we present an improved CUT&RUN protocol that does not require isolation of nuclei and provides high-quality data starting with only 100 cells for a histone modification and 1000 cells for a transcription factor. From cells to purified DNA CUT&RUN requires less than a day at the lab bench.In summary, CUT&RUN has several advantages over ChIP-seq: (1) The method is performed in situ in non-crosslinked cells and does not require chromatin fragmentation or solubilization; (2) The intrinsically low background allows low sequence depth and identification of low signal genomic features invisible to ChIP; (3) The simple procedure can be completed within a day and is suitable for robotic automation; (4) The method can be used with low cell numbers compared to existing methodologies; (5) A simple spike-in strategy can be used for accurate quantitation of protein-DNA interactions. As such, CUT&RUN represents an attractive replacement for ChIPseq, which is one of the most popular methods in biological research.
Proper citation: Peter J. Skene, Steven Henikoff 2018. CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers. protocols.io dx.doi.org/10.17504/protocols.io.mgjc3un Copy
Authors: Franchesca Farris, Marda Jorgensen, Jerelyn Nick, Jesus Peñaloza
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: Multiplex imaging of lymph node, thymus and spleen is accomplished using the Akoya Biosciences CODEX system at the HubMAP Tissue Mapping Center at the University of Florida, TMC-UF.This protocol is an overview of the CODEX raw data acquisition process guided by the CODEX Instrument Manager (CIM) , which is part of the CODEX Software Suite. The CODEX Instrument Manager is necessary to perform CODEX experiments. It controls the fluidics of the CODEX instrument the integration and synchronization with the Keyence microscope, image data formatting and facilitates transfer of data to the analysis computer.For more information, consult the Akoya Biosciences CODEX User Manual - A.0.
Proper citation: Franchesca Farris, Marda Jorgensen, Jerelyn Nick, Jesus Peñaloza 2020. CODEX Acquisition Protocol. protocols.io dx.doi.org/10.17504/protocols.io.bdifi4bn Copy
Authors: Manuela De Las Casas
Group: AEGIS - Madrid iGEM 2019
Summary: The aim of this protocol is to obtain the purified streptavidin with cellulose binding domains on both sides from the transformed bacteria E. coli. Later on, this protein will be attached to a membrane as part of the detection system. The obtention of the proteins starts at this point with transformed bacteria (E. coli).The previous steps to obtain the transformed bacteria and further steps to use the purified protein do not correspond to this protocol.
Proper citation: Manuela De Las Casas 2019. Streptavidin-CBD purification. protocols.io dx.doi.org/10.17504/protocols.io.6e8hbhw Copy
Authors: Noreen Wauford
Proper citation: Noreen Wauford 2016. Hemolysis Assay. protocols.io dx.doi.org/10.17504/protocols.io.fxkbpkw Copy
Authors: Firuoz Danashgeri
Group: Diabetic Complications Consortium
Summary: This protocol describes the proper procedure for harvesting bladders from rats or mice for use by the DiaComp Uropathy group.Diabetic Complication:
Proper citation: Firuoz Danashgeri 2019. Removal and Preservation of the Urinary Bladder. protocols.io dx.doi.org/10.17504/protocols.io.8fahtie Copy
Authors: Ruiyun Bi
Proper citation: Ruiyun Bi 2017. Real-time PCR. protocols.io dx.doi.org/10.17504/protocols.io.hu2b6ye Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: Artificial Cerebrospinal Fluid IX (ACSF.IX) is used for applications including tissue bath solution during electrophysiological recording for probing synaptic connections under physiological conditions.
Proper citation: Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid IX (ACSF.IX). protocols.io dx.doi.org/10.17504/protocols.io.bctriwm6 Copy
Authors: Adolfo Maria TAMBELLA, Evelina SERRI, Anna Rita ATTILI
Summary: This protocol describes a step-by-step procedure for the production of autologous platelet-rich plasma for topical application in dogs.This protocol was used in the following publication:Tambella AM, Attili AR, Dini F, Palumbo Piccionello A, Vullo C, Serri E, Scrollavezza P, Dupré G. Autologous platelet gel to treat chronic decubital ulcers: a randomized, blind controlled clinical trial in dogs. Veterinary Surgery, 43(6), 2014: 726-733. (ISSN: 0161-3499) (DOI: 10.1111/j.1532-950X.2014.12148.x).http://onlinelibrary.wiley.com/doi/10.1111/j.1532-950X.2014.12148.x/full
Proper citation: Adolfo Maria TAMBELLA, Evelina SERRI, Anna Rita ATTILI 2018. Autologous platelet-rich plasma for topical application as regenerative therapy in dogs. protocols.io dx.doi.org/10.17504/protocols.io.nb6dare Copy
Authors: Jernej Turnsek, Chris Dupont
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: Here we present an efficient way to grow Tp colonies inside a 0.25% superclean agar matrix. This protocol could possibly be applicable to other marine microeukaryotes that are problematic to grow on fully solid support.
Proper citation: Jernej Turnsek, Chris Dupont 2017. Pour plating of Thalassiosira pseudonana (Tp). protocols.io dx.doi.org/10.17504/protocols.io.i6qchdw Copy
Authors: Mariana Rius, Jackie Collier
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab
Summary: Electroporation strategy used in the transformation of Aurantiochytrium limacinum (ATCC MYA-1381; Stramenopile/ Heterokont, Thraustochytrid). This protocol is following the guidance of Ono et al. 2011. US Patent # 7,888,123 B2.
Proper citation: Mariana Rius, Jackie Collier 2018. Electroporation of Aurantiochytrium limacinum (ATCC MYA-1381). protocols.io dx.doi.org/10.17504/protocols.io.qjcduiw Copy
Authors: Hendrik F Van Essen
Proper citation: Hendrik F Van Essen 2019. aCGH results extraction from TIFF file. protocols.io dx.doi.org/10.17504/protocols.io.zj7f4rn Copy
Authors: Marine Phage Lab, Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Version 1b17 October 2012This protocol decribes the extraction of DNA from viral particles using Wizard Prep Resin and Columns from Promega.
Proper citation: Marine Phage Lab, Matthew Sullivan Lab 2016. DNA Extraction of Cesium Chloride-Purified Viruses using Wizard Prep Columns. protocols.io dx.doi.org/10.17504/protocols.io.c26yhd Copy
Authors: Anibal Arce Medina, Isaac Núñez, Tamara Matute, Fernan Federici
Group: Laboratorio de Tecnologias Libres, Reclone.org (The Reagent Collaboration Network)
Summary: This protocol explains how to prepare dsDNA and ssRNA target positive control for LAMP and RT-LAMP reactions. Particularly it describes the pipeline for SARS-Cov-2 Nucleocapsid (N) gene positive control which is included in the ReClone collection. The general procedure involves amplifying the gene of interest with primers which add T7 promoter and T7 terminator to its sequence followed by T7 in vitro transcription to obtain the ssRNA. Sequence elaboration:Sequence OrfN_5 was designed and synthesized based on IDT SARS-CoV-2 positive control plasmid (CAT#10006625_2019).
Proper citation: Anibal Arce Medina, Isaac Núñez, Tamara Matute, Fernan Federici 2021. LAMP/RT-LAMP COVID positive control. protocols.io dx.doi.org/10.17504/protocols.io.bsknncve Copy
Authors: Claudio Slamovits, Pia Elustondo, Ronie Haro, Susana [email protected]
Group: Slamovits Lab
Summary: Map and sequence of the construct used to transform Oxyrrhis marina using electroporation.
Proper citation: Claudio Slamovits, Pia Elustondo, Ronie Haro, Susana [email protected] 2019. Om-mCherry-hsp90. protocols.io dx.doi.org/10.17504/protocols.io.74hhqt6 Copy
Authors: Igem Dusseldorf
Proper citation: Igem Dusseldorf 2019. Pichia pastoris strain and growth condition. protocols.io dx.doi.org/10.17504/protocols.io.8hcht2w Copy
Authors: Sarah Piccirillo, Melissa G. White, Jeffrey C. Murphy, Douglas J. Law, and Saul M. Honigberg
Group: Genetics
Summary: The following is a modification of a Scherz R., 2001 method for colony embedding. The protocol described here is from:Sarah Piccirillo, et. al. The Rim101p/PacC Pathway and Alkaline pH Regulate Pattern Formation in Yeast Colonies(2010)Genetics184:707-716; doi:10.1534/genetics.109.113480Please see the full manuscript for additional details.
Proper citation: Sarah Piccirillo, Melissa G. White, Jeffrey C. Murphy, Douglas J. Law, and Saul M. Honigberg 2015. Embedding yeast colonies for light and electron microscopy. protocols.io dx.doi.org/10.17504/protocols.io.dw97h5 Copy
Authors: Angel Justiz-Vaillant
Group: Carbon
Summary: This ELISA was used to study the interactions between protein-LAG (PLAG) and protein-LA (SpLA) with different immunoglobulin preparations from mammalian and avian species.
Proper citation: Angel Justiz-Vaillant 2021. Chimeric Protein-LAG and Protein LA sandwich ELISA . protocols.io dx.doi.org/10.17504/protocols.io.btbenije Copy
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