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Authors: David Eccles
Group: Coronavirus Method Development Community
Summary: This is a fast "gunk to graph" protocol for analysing viral RNA from nasopharyngeal swabs. The approach involves swab lysis and inactivation at the point of sampling, uses a cellulose binding / wash protocol to reduce extraction cost, incorporates sample-specific barcodes during first-strand synthesis, nanopore rapid-attachment primers during PCR amplification, and nanopore sequencing with parallel RAMPART analysis for fast assembly and phylogenetics.Note: this is a one-step RT-PCR reaction protocol. For an alternative method that allows more multiplexing flexibility, see the protocol that this has been forked from:https://dx.doi.org/10.17504/protocols.io.bd3yi8pw

Proper citation: David Eccles 2020. Viral Sequencing, from Gunk to Graph (One-Step four-primer PCR alternative). protocols.io https://dx.doi.org/10.17504/protocols.io.bd5ni85e Copy   

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Authors: Marine Vautier, Valentin Vasselon, Cecile Chardon, Frédéric Rimet, Agnès Bouchez, Isabelle Domaizon
Group: EcoALpsWater
Summary: This protocol is part of the DNA workflow applied in the Eco-AlpsWater Project.The methodological step described here is the extraction of DNA, this is a critical step for obtaining relevant results since molecular inventories might be influenced by the DNA extraction method used.The choice of the methodology for biofilms DNA extraction is based on previous studies and in particular on the work done by Vasselon et al. (2017) where the authors have tested 5 DNA extraction methods combining various types of cell lysis and DNA purification to extract DNA (from pure diatom cultures and biofilms samples from streams and lakes).For the Eco-AlpsWater project, after being sampled in lakes or rivers, biofilms are stored in 50 mL tubes in ethanol at 4°C, and for a maximum of 3 months before DNA extraction (the extraction should preferably be done in the month following the sampling).The DNA extraction protocol presented below has been used in several recent studies (e.g. Vasselon et al 2017ab, 2018) focussed on the application of diatoms metabarcoding; this extraction is based on a protocol adapted from the NucleoSpin® Soil kit (MACHEREY-NAGEL) with specific modifications for biofilm DNA extraction.

Proper citation: Marine Vautier, Valentin Vasselon, Cecile Chardon, Frédéric Rimet, Agnès Bouchez, Isabelle Domaizon 2020. DNA extraction from environmental biofilm using the NucleoSpin® Soil kit (MACHEREY-NAGEL) . protocols.io https://dx.doi.org/10.17504/protocols.io.bd52i88e Copy   

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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. They have both paracrine and autocrine function. Interleukins are also used in animal studies to investigate aspect related to clinical medicine.T cells and stem cells make IL-3. It functions as a multilineage colony-stimulating factor [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-3 in human serum.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj23kqgn Copy   

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Authors: Shin Lin, Yiing Lin
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community

Proper citation: Shin Lin, Yiing Lin 2020. Protocol for Freezing in OCT. protocols.io https://dx.doi.org/10.17504/protocols.io.bpx7mprn Copy   

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Authors: Kameran Lashkari, Gianna Teague, Ursula Beattie, Joanna Betts, Megan M McLaughlin, Francisco J Lopez

Proper citation: Kameran Lashkari, Gianna Teague, Ursula Beattie, Joanna Betts, Megan M McLaughlin, Francisco J Lopez 2020. PONE-S-20-05322-2 DATA SETS, BOX PLOTS and GRAPHS. protocols.io https://dx.doi.org/10.17504/protocols.io.bhwuj7ew Copy   

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Authors: Pei-Chun Lin
Group: Innovative Genomics Institute, CornLab
Summary: Re-amplification of CRISPRa and CRISPRi Libraries

Proper citation: Pei-Chun Lin 2015. Re-amplification of CRISPRa and CRISPRi libraries. protocols.io https://dx.doi.org/10.17504/protocols.io.dkv4w5 Copy   

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Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: This protocols is to be performed with the Quick Ligation Reaction Buffer. Please see the NEB website for more information.

Proper citation: New England Biolabs 2014. Quick Ligation Protocol (M2200). protocols.io https://dx.doi.org/10.17504/protocols.io.cdgs3v Copy   

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Authors: Martin Thomas Jahn
Group: hostmicrobeprotocols
Summary: Fixative for FISH and other applications

Proper citation: Martin Thomas Jahn 2019. 4% PFA for fixation. protocols.io https://dx.doi.org/10.17504/protocols.io.jtwcnpe Copy   

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Authors: Rachele Cesaroni, Angela Piersanti
Group: Protist Research to Optimize Tools in Genetics (PROT-G)

Proper citation: Rachele Cesaroni, Angela Piersanti 2019. Euplotes crassus micronuclear enrichment by PFGE. protocols.io https://dx.doi.org/10.17504/protocols.io.zk7f4zn Copy   

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Authors: Kelsey Miller
Group: BioLegend
Summary: The cells targeted by the Streptavidin Nanobeads are either selected or depleted by incubating your sample with the magnetic particles after incubating with a biotin-conjugated antibody or antibody cocktail. The magnetically labeled fraction is retained by the use of a magnetic separator. After collection of the targeted cells, downstream applications include functional assays, gene expression, phenotypic characterization, etc.

Proper citation: Kelsey Miller 2016. MojoSort™ Streptavidin Nanobeads Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.e2rbgd6 Copy   

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Authors: Lenny Teytelman, Hannah Gershik, JUST
Summary: This recipe is a traditional Eastern-European Jewish latkes (potato pancakes).

Proper citation: Lenny Teytelman, Hannah Gershik, JUST 2019. Vegan Latkes with JUST Egg. protocols.io https://dx.doi.org/10.17504/protocols.io.bas3iegn Copy   

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Authors: Ran Zhou, Oni Basu
Group: Human Cell Atlas Method Development Community, Helmsley project_Basu lab
Summary: The protocol is adapted from Fujii's and Smillies's reports for single cell transcriptome analysis from human intestines. It provides details on acquirement of single cell suspension from epithelium and lamina propria. This methods is modified to generate appropriate meterials from patient's intestinal biopsies for sinlge-cell transcriptome and genomic applications.

Proper citation: Ran Zhou, Oni Basu 2020. Preparation of single cell suspensions from human intestinal biopsies for single cell genomics applications. protocols.io https://dx.doi.org/10.17504/protocols.io.bkp6kvre Copy   

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Authors: Jason Kim
Group: Mouse Metabolic Phenotyping Centers
Summary: Summary:In-cage free running wheel is used to voluntarily induce exercise in awake mice. Exercise affects insulin sensitivity and glucose metabolism.

Proper citation: Jason Kim 2019. U Mass - Exercise model. protocols.io https://dx.doi.org/10.17504/protocols.io.xwyfpfw Copy   

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Authors: Alyssa Ayala
Group: UCSC BME 22L

Proper citation: Alyssa Ayala 2020. Introduction to Materials. protocols.io https:// Copy   

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Authors: Szymon T Calus, Umer Zeeshan Ijaz, Ameet Pinto
Group: Pinto Lab

Proper citation: Szymon T Calus, Umer Zeeshan Ijaz, Ameet Pinto 2018. NanoAmpli-Seq - Sample processing and sequencing library preparation workflow. protocols.io https://dx.doi.org/10.17504/protocols.io.u26eyhe Copy   

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Authors: Verity Goodwin, Emily Souster, Mathew Garnett, Fiona Behan, Charlotte Beaver, Rizwan Ansari, Adam Jackson
Group: Cellular Generation and Phenotyping
Summary: This protocol is designed to outline the process of fixing cell pellets in 1.5ml tubes. It has been developed within the Cellular Generation and Phenotyping Group at the Wellcome Sanger Institute.Process diagram:

Proper citation: Verity Goodwin, Emily Souster, Mathew Garnett, Fiona Behan, Charlotte Beaver, Rizwan Ansari, Adam Jackson 2020. Fixing Cell Pellets for Flow Cytometry. protocols.io https://dx.doi.org/10.17504/protocols.io.bixakfie Copy   

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Authors: Diego Bonatto
Group: Grupo de Estudos de Leveduras Cervejeiras
Summary: Malt extract - yeast extract - peptone - glucose rich medium for yeast growth and maintenance.

Proper citation: Diego Bonatto 2018. MYPG liquid medium. protocols.io https://dx.doi.org/10.17504/protocols.io.pnbdman Copy   

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Authors: Kirstyn Brunker
Summary: This protocol details the steps involved to perform RNA extraction on rabies virus brain tissue samples collected by the WHO recommended "straw method" in the field (Meslin F-X, Kaplan MM, Koprowski H. Laboratory techniques in rabies. World Health Organization; 1996.[10]). The protocol is field-friendly and can be performed using portable, battery powered equipment.

Proper citation: Kirstyn Brunker 2020. RNA extraction from field-collected brain tissue samples from suspect rabid animals. protocols.io https://dx.doi.org/10.17504/protocols.io.bdcei2te Copy   

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Authors: Hansheng Zhao
Summary: We performed a considerate prediction of intact protein-coding gene models using three independent approaches, i.e.,de novoprediction, homology-based method, and RNA-Seq approach.

Proper citation: Hansheng Zhao 2018. Gene modeling and prediction. protocols.io https://dx.doi.org/10.17504/protocols.io.rf7d3rn Copy   

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Authors: Alejandro Morales Suarez, Susan Rutherford
Summary: This extraction protocol follows the DArT DNA Extraction protocol but contains modifications (including increasing the concentration of PVP to 4 %

Proper citation: Alejandro Morales Suarez, Susan Rutherford 2018. gDNA Extraction of Eucalypts pauciflora for full genome sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.j7ecrje Copy   

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