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Authors: He Zou
Summary: The six-minute walk test (6MWT) is a safe, simple, inexpensive tool for evaluating the functional exercise capacity of patients with chronic respiratory disease. However, there is a lack of standard reference equations for the six-minute walk distance (6MWD) in the healthy Chinese population aged 18-59 years.

Proper citation: He Zou 2017. Reference Equations for the Six-Minute Walk Distance in the Healthy Chinese Population Aged 18?59 Years. protocols.io https://dx.doi.org/10.17504/protocols.io.i9sch6e Copy   

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Authors: Michael J. Allen, Bela Tiwari, Matthias E. Futschik, and Debbie Lindell
Group: VERVE Net
Summary: In this virus-focused chapter, we deal primarily with the use of microarrays for expression analysis (the most popular usage) of host and virus systems during infection. We examine aspects related to array platform choice (spotted and oligonucleotide arrays), probe and array design considerations, experimental procedures and data analysis, normalization, processing, and curation. We also provide in-depth examples for the study of viral transcriptome analysis for both spotted long oligonucleotide (coccolithoviruses) and Affymetrix GeneChip (cyanophage) arrays.

Proper citation: Michael J. Allen, Bela Tiwari, Matthias E. Futschik, and Debbie Lindell 2015. Construction of microarrays and their application to virus analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.d3e8jd Copy   

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Authors: Teodor Emilov Mentov
Group: XPRIZE Rapid Covid Testing

Proper citation: Teodor Emilov Mentov 2020. Colorimetric RT-LAMP Research group SARS-COV-2 detection protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bk59ky96 Copy   

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Authors: Rine Lab
Group: Re-Entering Labs Post COVID-19 Shutdown

Proper citation: Rine Lab 2020. Rine Lab Reopening SOP. protocols.io https:// Copy   

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Authors: Anna Behle
Group: Axmann Lab
Summary: This protocol can be used for mapping transcriptional start site(s) (TSS) of a specific gene of interest in bacteria.By slightly modifying this protocol, whole transcriptome TSS could also potentially be mapped.

Proper citation: Anna Behle 2017. 5'RACE (Rapid Amplification of cDNA ends). protocols.io https://dx.doi.org/10.17504/protocols.io.jk7ckzn Copy   

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Authors: Kiyoshi Minoura, Miho Yamada

Proper citation: Kiyoshi Minoura, Miho Yamada 2018. The method to evaluate antibacterial effects of nanoimprinted moth-eye film in practical settings. protocols.io https://dx.doi.org/10.17504/protocols.io.n54dg8w Copy   

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Authors: Marijn Ceelen
Group: iGEM Wageningen 2019
Summary: A variant of the plaque assay in which entire phage dilution ranges can be tested on a single plate.

Proper citation: Marijn Ceelen 2019. Spot assay. protocols.io https://dx.doi.org/10.17504/protocols.io.7i9hkh6 Copy   

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Authors: Guerrino Macori, Seamus Fanning
Group: Coronavirus Method Development Community

Proper citation: Guerrino Macori, Seamus Fanning 2020. SARS-CoV-2 Whole Genome Sequencing on Illumina - Tiling PCR. protocols.io https:// Copy   

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

Proper citation: New England Biolabs 2020. NEB Monarch® RNA Cleanup Kit. protocols.io https:// Copy   

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Authors: Masatoshi Okamatsu

Proper citation: Masatoshi Okamatsu 2017. Rapid and Broad Detection of H5 Hemagglutinin by an Immunochromatographic Kit Using Novel Monoclonal Antibody against Highly Pathogenic Avian Influenza Virus Belonging to the Genetic Clade 2.3.4.4. protocols.io https://dx.doi.org/10.17504/protocols.io.icmcau6 Copy   

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Authors: Paul Brouwer, Henriette Schluepmann
Summary: Method extracted from https://doi.org/10.1111/nph.12708Brouwer P, Bräutigam A, Külahoglu C, Tazelaar AO, Kurz S, Nierop KG, van der Werf A, Weber AP, Schluepmann H. A zolla domestication towards a biobased economy?. New Phytologist. 2014 May;202(3):1069-82.

Proper citation: Paul Brouwer, Henriette Schluepmann 2019. Azolla filiculoides sporocarp cryo-preservation. protocols.io https://dx.doi.org/10.17504/protocols.io.9bdh2i6 Copy   

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Authors: Daniel Gyllborg, Mats Nilsson
Group: Human Cell Atlas Method Development Community, Molecular Diagnostics - Mats Nilsson Group, Neurodegeneration Method Development Community
Summary: Protocol for multiplexed in situ sequencing in tissue sections as an image-based spatial transcriptomic method. This is the second iteration of In Situ Sequencing (HybISS: Hybridization based In Situ Sequencing) based on the principles published in Ke et al. Nature Methods, 2013 and more recently Qian et al. Nature Methods, 2019. Here we present a modified method in detection chemistry using sequencing by hybridization approach for combinatorial decoding. This results in a more robust method for detecting larger probe panels for a more high-throughput in situ sequencing method.

Proper citation: Daniel Gyllborg, Mats Nilsson 2020. HybISS: Hybridization-based In Situ Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.xy4fpyw Copy   

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Authors: Bianca Hemmeryckx, Dries Bauters, H. Roger Lijnen
Summary: Increasing energy expenditure by stimulating thermogenesis through activation of brown adipose tissue (BAT) and/or induction of browning of white adipose tissue (WAT) is considered a promising strategy to treat/prevent obesity and related metabolic diseases. Whereas WAT is adapted to store energy as triglycerides, BAT produces heat (non-shivering thermogenesis). In brown adipocytes, the uncoupling protein-1 (UCP-1) regulates conversion of energy into heat by uncoupling ATP production from mitochondrial respiration. Also in WAT adaptive UCP-1 positive adipocytes (brown in white: brite or beige) can arise, predominantly in subcutaneous (s) WAT. This browning of WAT is enhanced by exposure to cold.

Proper citation: Bianca Hemmeryckx, Dries Bauters, H. Roger Lijnen 2018. Cold exposure murine models. protocols.io https://dx.doi.org/10.17504/protocols.io.kbbcsin Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the slicing and microdissection procedure on frozen post-mortem human brain tissue to be used to isolate nuclei for subsequent transcriptional profiling.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U01MH114812. 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 2021. Human Tissue Slicing and Dissections for Nuclear Isolations. protocols.io https://dx.doi.org/10.17504/protocols.io.bq6ymzfw Copy   

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Authors: Modified by Sabrina Geraci-Yee FROM: RAGHUKUMAR S, SCHAUMANN K. 1993. AN EPIFLUORESCENCE MICROSCOPY METHOD FOR DIRECT DETECTION AND ENUMERATION OF THE, THE THRAUSTOCHYTRIDS. LIMNOL. OCEANOGR.
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab

Proper citation: Modified by Sabrina Geraci-Yee FROM: RAGHUKUMAR S, SCHAUMANN K. 1993. AN EPIFLUORESCENCE MICROSCOPY METHOD FOR DIRECT DETECTION AND ENUMERATION OF THE, THE THRAUSTOCHYTRIDS. LIMNOL. OCEANOGR. 2017. Acriflavine Centrifuge Stain for Labyrinthulomycetes. protocols.io https://dx.doi.org/10.17504/protocols.io.hgib3ue Copy   

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Authors: Tamara Matute, Isaac Núñez, Fernan Federici
Group: Laboratorio de Tecnologias Libres, Reclone.org (The Reagent Collaboration Network)
Summary: This protocol describes how to perform LAMP / RT-LAMP reactions with home-made reagents, which means home-made buffers and positive controls, together with home-brewed BstLF and MMLV enzymes.Home-brewed enzymes information:BstLF polymerase:expression and purification protocol. expression plasmid sequence.M-MLV reverse transcriptase:expression and purification protocol. expression plasmid sequence. Positive control informationSample preparation protocol here.TestingWe test this protocol in LAMP or RT-LAMP reactions with SARS-CoV-2 synthetic dsDNA or ssRNA respectively. As shown in Figure 1, the general performance of reactions with homemade reagents seems appropriate compared with the commercial standard option. No amplification was observed in non-template controls (NTC).[1] Zhang, Y. et al. Enhancing colorimetric loop-mediated isothermal amplification speed and sensitivity with guanidine chloride. Biotechniques69, (2020).

Proper citation: Tamara Matute, Isaac Núñez, Fernan Federici 2021. LAMP/RT-LAMP Reaction protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bsefnbbn Copy   

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Authors: Courtney Comrie
Summary: This protocol will provide a basic guide to utilizing the DIFFPREP tool in TORTIOSE.Note: Steps may vary based upon image.

Proper citation: Courtney Comrie 2020. DIFFPREP for DTI Processing and Corrections. protocols.io https://dx.doi.org/10.17504/protocols.io.89rhz56 Copy   

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Authors: Cristina Dutra Vieira, Andreza Nayla de Assis Aguiar, Camila Aparecida Silva de Oliveira Lima, Zilma Reis
Summary: Background: Spontaneous preterm birth is a worldwide concern due to the impact on infant mortality. Good quality of antenatal care pregnancy has the potential to reduce the rate of prematurity and improve neonatal outcome. Periodontal disease suppose to affect preterm labor. The impact of interventions to promote the oral health of pregnant women in the prevention of preterm birth is still controverse.Objective: To assess evidence on the impact of oral health interventions during prenatal care in preventing spontaneous preterm birth.Methods: A comprehensive integrative literature review to respond to the primary research question: Which the interventions to promote oral health during antenatal care associated with higher duration of gestation? First version, March-09-2019.Stage of review: Ongoin

Proper citation: Cristina Dutra Vieira, Andreza Nayla de Assis Aguiar, Camila Aparecida Silva de Oliveira Lima, Zilma Reis 2019. Impact of preventive oral health interventions during the prenatal care on preterm delivery, an integrative review protocol.. protocols.io https://dx.doi.org/10.17504/protocols.io.yyzfxx6 Copy   

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Authors: Kenneth Schackart
Group: Yoon Lab
Summary: This describes how to make differentiation medium for SH-SY5Y using all-trans-retinoic acid.

Proper citation: Kenneth Schackart 2019. Making Differentiation Media for SH-SY5Y. protocols.io https://dx.doi.org/10.17504/protocols.io.xuufnww Copy   

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Authors: Steven J. Burgess
Summary: Protocol for DNase I digestion of nuclei for 'double hit' DNase-SEQ analysis adapted from doi:10.1038/nmeth.2762As a general guide DNA should show moderate to light smearing after completing the protocol as seen the gel image in Figure 1.Figure 1: A representative 2% (w/v) LMP agarose gel of DNAse I treated nuclei (~2x108) from Sorghum bicolor. To each sample the following amounts of DNase I were added: none, 7.5U, 12.5U.Over-digested samples will result in a high background signal from unspecific cutting of DNA and should be avoided. An example of an over-digested sample is provided in lane 5 of Figure 2.Figure 2: A representative 2% (w/v) LMP agarose gel of DNAse I treated nuclei (~2x108) from Sorghum bicolor. To each sample the following amounts of DNase I were added: none, 5,U 7.5U,10U, 12.5U.Gel fragments from ~50-600bp should be excised and DNA purified. From experience taking only smaller fragments (50-200 bp) caused difficulties in library preparation.

Proper citation: Steven J. Burgess 2017. DNA Digestion with DNase I. protocols.io https://dx.doi.org/10.17504/protocols.io.hdfb23n Copy   

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