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Authors: Michela Del Pasqua, Anja Schulze, María Ana Tovar-Hernández, Erica Keppel, Marco Lezzi, Maria Cristina Gambi, Adriana Giangrande
Proper citation: Michela Del Pasqua, Anja Schulze, María Ana Tovar-Hernández, Erica Keppel, Marco Lezzi, Maria Cristina Gambi, Adriana Giangrande 2018. amplification and sequencing of the mitochondrial gene cytochrome c oxidase subunit I (COI) in Sabellidae polychaetes. protocols.io dx.doi.org/10.17504/protocols.io.nx6dfre Copy
Authors: Glen Wheeler, Rowena Stern, Cecilia Balesteri
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Proper citation: Glen Wheeler, Rowena Stern, Cecilia Balesteri 2017. Method for electroporation of Isochrysis galbana CCMP1323. protocols.io dx.doi.org/10.17504/protocols.io.hmab42e Copy
Authors: Luciano Martelotto
Summary: This protocol is the result of the combination of various nuclei isolation protocols for single cell RNA-seq experiments using droplet-based methods, and is an extension of the Frankenstein (S.O.F means Son Of Frankenstein). Developed to prepare nuclei isolates from fresh and frozen material of small-to-large sizes. The good thing is that it does not uses FACS but OptiPrep® discontinuous gradient to remove debris. It is the alternative protocol when FACS is not available.
Proper citation: Luciano Martelotto 2021. S.O.F protocol for nuclei isolation from fresh and frozen tissues using OptiPrep® discontinuous gradient . protocols.io dx.doi.org/10.17504/protocols.io.brdcm22w Copy
Authors: Jorge Carlos Ruiz Ruiz
Summary: Flavonoid content determination using the aluminum chloride method.
Proper citation: Jorge Carlos Ruiz Ruiz 2018. Determination of flavonoid content. protocols.io dx.doi.org/10.17504/protocols.io.sfnebme Copy
Authors: Chika Yokota, Daniel Gyllborg, Mats Nilsson
Group: Molecular Diagnostics - Mats Nilsson Group
Summary: In situ sequencing method for parallel targeted analysis of short RNA fragments in morphologically preserved tissue. This protocol can be used to detect RNA molecules at the single cell level to aid in the identification of cell types according to their gene expression. The technique uses padlock probes to target desired genes of interest and rolling circle amplification to amplify signal for a high throughput methodolgy of spatial transcriptomics. With the use of barcode sequencing, identification of numerous genes is possible through multiplexing.Version 2 Update: Only minor mistakes were corrected for version 2 of this protocol, no major changes to protocol were done. Some references were also updated.
Proper citation: Chika Yokota, Daniel Gyllborg, Mats Nilsson 2020. In situ sequencing for RNA analysis in tissue sections. protocols.io dx.doi.org/10.17504/protocols.io.bb2giqbw Copy
Authors: Hyunsuk Frank Roh, Chang-Guk Kim, Soon-Ho Chon, Jung Mogg Kim
Summary: Purpose:Time-to-event data of hazard ratios were used to generate a forest plot of all-cause mortality on extracorporeal membrane oxygenation (ECMO) in both overall and individual indications of cardiopulmonary disease in adults.Materials and Methods:A systemic search was conducted in PubMed from 1975 to 2018. Among 4,121 articles, a total of 34 clinical reports comprising 20,610patients (1,631 of the patients who underwent ECMO and 18,979 of the patients who did not undergo ECMO) met the inclusion criteria.Results:The pooled hazard ratio of 1.2828 (95% confidence interval: 0.9649, 1.7054) suggests that the ECMO group was not significantly associated with a reduction in mortality compared with the no-ECMO group in the overall ECMO indications. The results of subgroup analyses showed a significantly improved patient survival in respiratory failure with 0.6308 (0.5037, 0.7900), and a worse patient survival after lung transplantation with 2.0600 (1.6987, 2.4981), in bridging to heart transplantation with 1.4212 (1.0309, 1.9592), and after heart transplantation with 5.6365 (1.7569, 18.0827).Conclusions:Most of the included studies are retrospective, which diminishes the significance of the findings due to a higher risk of selection bias, which was exemplified by the allocation of ECMO based on the patients’ severity condition.
Proper citation: Hyunsuk Frank Roh, Chang-Guk Kim, Soon-Ho Chon, Jung Mogg Kim 2020. Extracorporeal membrane oxygenation meta-analysis of time-to-event data in cardiopulmonary disease in adults. protocols.io dx.doi.org/10.17504/protocols.io.bb3tiqnn Copy
Authors: Mengchen Shi
Proper citation: Mengchen Shi 2017. Isolation of cell fractionation. protocols.io dx.doi.org/10.17504/protocols.io.kcfcstn Copy
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 dx.doi.org/10.17504/protocols.io.9vmh646 Copy
Authors: Anibal Arce Medina, Fernan Federici
Group: Laboratorio de Tecnologias Libres
Proper citation: Anibal Arce Medina, Fernan Federici 2017. Step 2: Preparing amino acid, polyphosphates, and maltodextrin-based energy solutions for cell-free reactions. protocols.io dx.doi.org/10.17504/protocols.io.j2ncqde Copy
Authors: Mattia Bottacini, Annalisa Scollo, Sandra A. Edwards, Barbara Contiero, Martina Veloci, Vincenzo Pace, Flaviana Gottardo
Summary: On a high speed slaughter line for pigs, skin scratches were separately scored in the posterior region (defined as the area including the hind legs and the tail) and the anterior one (as the remaining area), while the whole carcass was examined for external hematomas. Chronic ear and tail lesions referable to the rearing phase, and bursitis were recorded as retrospective welfare indicators.
Proper citation: Mattia Bottacini, Annalisa Scollo, Sandra A. Edwards, Barbara Contiero, Martina Veloci, Vincenzo Pace, Flaviana Gottardo 2018. Skin lesions monitoring on slaughtered pigs. protocols.io dx.doi.org/10.17504/protocols.io.ugketuw Copy
Authors: Wen Aw
Group: Cage Studies
Proper citation: Wen Aw 2018. Dietary rotenone and paraquat on larval development. protocols.io dx.doi.org/10.17504/protocols.io.rs8d6hw Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 3, 3´ Diaminobenzidine (DAB) is a commonly used chromogen for histological staining. In the presence of peroxidase enzyme, DAB produces a brown precipitate that is insoluble in alcohol and xylene. Peroxidase catalyzes hydrogen peroxide oxidation of substrate DAB. This SOP provides instructions to prepare four different formulations of DAB. DAB for Immunohistochemical staining (IHC), DAB for Acetylcholinesterase (AChE) Staining, Nickel Enchanced DAB for Biocytin staining, and DAB for Biocytin staining.
Proper citation: Allen Institute for Brain Science 2020. DAB Solutions. protocols.io dx.doi.org/10.17504/protocols.io.bctkiwkw Copy
Authors: april woods
Group: Environmental Biotechnology Lab
Summary: A description of how samples are collected and processed as part of MLML Smith Lab's weekly HAB monitoring efforts in Monterey, CA.Sampling Location: Monterey Commercial Wharf, Monterey, CA. 36° 36.3' N 121° 53.3' WOceanographic and meteorological observations for the time of sampling are referenced from the Monterey, CA NOAA station ID: 9413450
Proper citation: april woods 2016. Monterey Wharf II Weekly Phytoplankton Monitoring Sample Collection and Processing Notes. protocols.io dx.doi.org/10.17504/protocols.io.f2pbqdn Copy
Authors: Jakub Nedbal
Summary: The cooled LED illuminator is a large heatsink with self-adhesive LED strips, four axial fans, and the LED controller attached to it.This document is part of the Illuminated Orbital Shaker for Microalgae Culture project:Procuring Parts for Algal ShakerAssembling LED Controller Electronics3D Printing Case for LED ControllerAssembling Cooled LED Illuminator (this document)Cutting and Drilling Clear Acrylic SheetAssembling Algal Shaker
Proper citation: Jakub Nedbal 2020. Assembling Cooled LED Illuminator. protocols.io dx.doi.org/10.17504/protocols.io.bcrniv5e Copy
Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. They play essential roles in the activation and differentiation of immune cells, as well as proliferation, maturation, migration, and adhesion. They also have pro-inflammatory and anti-inflammatory properties. The primary function of interleukins is, therefore, to modulate growth, differentiation, and activation during inflammatory and immune responses. Interleukins consist of a large group of proteins that can elicit many reactions in cells and tissues by binding to high-affinity receptors in cell surfaces. IL-29 is a type-3 interferon and produced by virus-infected cells, dendritic cells, and regulatory T-cells. It upregulates viral protective responses. Virus-infected cells may regulate IL-29 genome. [1]Reference1. Justiz Vaillant AA, Qurie A. Interleukin. In:StatPearls. Treasure Island (FL): StatPearls Publishing; June 12, 2019.
Proper citation: Angel Justiz-Vaillant 2020. ELISA for quantification of IL-29 in human serum.. protocols.io dx.doi.org/10.17504/protocols.io.bj3ykqpw Copy
Authors: James R. Collins, Krista Longnecker, Helen F. Fredricks, Benjamin A. S. Van Mooy
Group: Van Mooy Lab @ WHOI
Summary: This protocol (like its companion protocol for liposome suspension and extrusion) was original created by Krista Longnecker and Jamie Collins for creating lipsomes to be used in lipid photo-oxidation experiments. The results of these experiments are detailed in Chapter 4 of:Collins, J. R. 2017. The remineralization of marine organic matter by diverse biological and abiotic processes. Ph.D. thesis. Cambridge, Massachusetts: Massachusetts Institute of Technology, 300 pp; doi:10.1575/1912/8721A manuscript of the chapter is forthcoming.
Proper citation: James R. Collins, Krista Longnecker, Helen F. Fredricks, Benjamin A. S. Van Mooy 2017. Part 1: Preparation of lipid films for phospholipid liposomes. protocols.io dx.doi.org/10.17504/protocols.io.hasb2ee Copy
Authors: Lei Lei1, Lijun Ding, Jing Su, Mengyuan Liu, Qingqing Shi, Jianjun Zhou, Haixiang Sun, Guijun Yan
Proper citation: Lei Lei1, Lijun Ding, Jing Su, Mengyuan Liu, Qingqing Shi, Jianjun Zhou, Haixiang Sun, Guijun Yan 2017. Attenuated expression of MTR in both prenatally androgenized mice and women with the hyperandrogenic phenotype of PCOS. protocols.io dx.doi.org/10.17504/protocols.io.jiuckew Copy
Authors: Jake Willows, Kristy Townsend, Magdalena Blaszkiewicz
Group: Townsend Lab Neurobiology & Energy Balance
Summary: AbstractLittle is known about the diversity and function of adipose tissue nerves due, in part, to the inability to effectively visualize the various nerve subtypes residing within these tissues. The tools currently available for researchers to image and quantify adipose tissue innervation are limited and dependent on optical clearing techniques and light sheet microscopy. Here we present a method of tissue processing that uses a method of mechanically compressing tissue to decrease tissue thickness in the z-axis by expanding it in the x and y-axes whilst leaving cells intact. This has been combined with autofluorescence quenching techniques to permit imaging of intact whole tissues on both widefield and confocal microscopes and a complementary means to perform whole tissue neurite density quantification. We have included examples of how this technique can be used to further our current knowledge of adipose-nerve communication by characterizing the nerves, nerve-subtypes, and neurovascular interactions within the inguinal subcutaneous white adipose tissue in mice.
Proper citation: Jake Willows, Kristy Townsend, Magdalena Blaszkiewicz 2021. Adipose depot innervation: whole mount staining, imaging, quantification. protocols.io dx.doi.org/10.17504/protocols.io.brs2m6ge Copy
Authors: Jing-Zhe (Ginger) Jiang, Hong-Ying Wei
Group: Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: This protocol is a continuation of the previous protocol (dx.doi.org/10.17504/protocols.io.m4yc8xw) for viral metagenomic researches with the tissues of Molluscs, such as abalone, oyster, clam, scallop and so on. This maybe also applicable for other animals, such as shrimp and fish, based on the principle of the protocol. But we havn't verified this idea yet.
Proper citation: Jing-Zhe (Ginger) Jiang, Hong-Ying Wei 2018. Nucleic Acid Extraction, Amplification and Library Construction for Viral Metagenomic Sequencing.. protocols.io dx.doi.org/10.17504/protocols.io.m5vc866 Copy
Authors: Florence Blanchard, Alexis Carteron, Xavier Guilbeault-Mayers, Etienne Laliberté
Group: Plant Functional Ecology Lab
Proper citation: Florence Blanchard, Alexis Carteron, Xavier Guilbeault-Mayers, Etienne Laliberté 2019. Semi-quantitative measure of roots colonization by arbuscular mycorrhizal fungi using standard light microscopy. protocols.io dx.doi.org/10.17504/protocols.io.zbgf2jw Copy
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