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Authors: David Eccles
Summary: This protocol demonstrates how to assemble reads from plasmid DNA, and generate a circularised and non-repetitive consensus sequenceAt the moment, this protocol uses Canu to de-novo assemble high-quality single-cut reads.Input(s): demultiplexed fastq files (see protocol Demultiplexing Nanopore reads with LAST). I've noticed that the default demultiplexing carried out by Guppy (at least up to v4.2.2, as used in the first version of this protocol) has issues with chimeric reads, which can affect assembly.Output(s):Consensus sequence per barcode as a fasta fileOutput(s):
Proper citation: David Eccles 2020. Plasmid Sequence Analysis from Long Reads. protocols.io dx.doi.org/10.17504/protocols.io.bqu3mwyn Copy
Authors: Samantha Coy
Group: Samantha R Coy's Protocols
Summary: This is a protocol for estimating Symbiodiniaceae biomass and growth based on fluorescence (chlorphyll-a). This is not directly comparable to cell counts, as fluorescence might vary depending on culturing conditions.
Proper citation: Samantha Coy 2020. Using the Tecan Infinite M200 Pro plate reader for Symbiodiniaceae Biomass/Growth Estimates. protocols.io dx.doi.org/10.17504/protocols.io.bkpqkvmw Copy
Authors: Bonnie Hurwitz, Ken Youens-Clark
Group: VERVE Net, Hurwitz Lab
Summary: Hurwitz, Bonnie L., and Matthew B. Sullivan. "The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology." PLoS One 8.2 (2013): e57355.
Proper citation: Bonnie Hurwitz, Ken Youens-Clark 2016. Running PCPipe (protein clustering) in iPlant. protocols.io dx.doi.org/10.17504/protocols.io.ef8bbrw Copy
Authors: Jeremy Kamil
Summary: I learned this Colloidal Coomassie Blue staining recipe and protocol when I was a postdoc at Harvard Medical School.. Rumor has it, a postdoc reverse engineered a “safe stain” from a leading commercial supplier. It’s a really great recipe: much more sensitive, faster, and easier to use than traditional methanol based coomassie staining protocols you see in Cold Spring Harbor books, like by Maniatis etc.. Saves a ton of money compared to buying this stuff from commercial vendors. It is downstream compatible with mass spec and most other things you'd want to do with gel slices.
Proper citation: Jeremy Kamil 2020. Colloidal Coomassie Blue Stain: Recipe and Protocol. protocols.io dx.doi.org/10.17504/protocols.io.bmmtk46n Copy
Authors: Neilier Junior
Summary: A buffer solution has the function of resisting changes in pH even when adding powerful acids or bases. However, in the physiological environment the buffered system also provides cofactors for enzymatic reactions, critical salts and even essential nutrients for cells and tissues. Therefore, when trying to reproduce biological conditions in vitro, we must make the appropriate choice of the buffer. After all, it will provide the appropriate medium in which reactions will occur.
Proper citation: Neilier Junior 2020. Hydrochloric Acid-Potassium Chloride Buffer (HCl-KCl). protocols.io dx.doi.org/10.17504/protocols.io.bfycjpsw Copy
Authors: luanaborba
Group: L. P. Borba-Santos
Proper citation: luanaborba 2020. Screening of compounds for inhibition of Sporothix spp. growth. protocols.io dx.doi.org/10.17504/protocols.io.bje9kjh6 Copy
Authors: Ashley Humphrey
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Proper citation: Ashley Humphrey 2016. ESAW Media for Marine Phytoplankton. protocols.io dx.doi.org/10.17504/protocols.io.f36bqre Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol is used to produce AAV of any serotype with high purity and high titer.
Proper citation: Allen Institute for Brain Science 2019. Production of AAV Virus by Iodixanol Gradient Ultracentrifugation. protocols.io dx.doi.org/10.17504/protocols.io.8dmhs46 Copy
Authors: Lukas Beule
Proper citation: Lukas Beule 2020. Protocol for DNA extraction from clay-rich subsoils. protocols.io dx.doi.org/10.17504/protocols.io.bhmjj44n Copy
Authors: William H. Wilson and Declan Schroeder
Group: VERVE Net
Summary: Generation of DNA fragments by DNase digestion involves digesting DNA for a range of times, then picking the time that gives optimal-sized DNA fragments (typically 1000–4000 bp).
Proper citation: William H. Wilson and Declan Schroeder 2016. Generation of DNA fragments by DNase digestion. protocols.io dx.doi.org/10.17504/protocols.io.dy47yv Copy
Authors: Yuri Feito, Lyndsey M. Hornbuckle, Lauren A. Reid, Scott E. Crouter
Summary: This study examined the effects of the ActiGraph’s (AG) low-frequency extension (LFE) filter on steps and physical activity classification in the free-living environment. Thirty-four African-American women (age, 24.5±5.2 years; BMI, 24.9±4.5 kg/m2) had daily activity measured simultaneously with an AG-GT3X+ accelerometer and a New Lifestyles NL-800 pedometer for seven days. Steps per day (steps/d) and time (minutes/day) spent in sedentary, light, and moderate-to-vigorous physical activity (MVPA) were examined with and without the LFE filter (AG-LFE and AG-N, respectively). The AG-LFE recorded more total steps (13,723±4,983 steps/d) compared to AG-N and NL-800 (6,172±2,838 and 5,817±3,037 steps/d, respectively; pppp
Proper citation: Yuri Feito, Lyndsey M. Hornbuckle, Lauren A. Reid, Scott E. Crouter 2017. Effect of ActiGraph’s LFE for estimating steps and physical activity intensity. protocols.io dx.doi.org/10.17504/protocols.io.jfacjie Copy
Authors: Addgene The Nonprofit Plasmid Repository
Summary: This protocol describes plasmid cloning by Polymerase Chain Reaction (PCR). To see the full abstract and additional resources, please visit the Addgene protocol page.
Proper citation: Addgene The Nonprofit Plasmid Repository 2019. Plasmid Cloning by PCR. protocols.io dx.doi.org/10.17504/protocols.io.43rgym6 Copy
Authors: Elis Sales Muniz Lima, Ana Cesarina Silva Gomes, Hyara Brena Oliveira Rufino, Jamile Xavier de Oliveira
Proper citation: Elis Sales Muniz Lima, Ana Cesarina Silva Gomes, Hyara Brena Oliveira Rufino, Jamile Xavier de Oliveira 2020. Mulheres na praça, saúde de graça: relato de experiência da equipe multiprofissional do grupo de mulheres do bairro Tamarindo. protocols.io dx.doi.org/10.17504/protocols.io.bay4ifyw Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This SOP provides instruction to prepare Internal Solution which is used for patch clamp electrophysiology, modified for cleanliness and mRNA capture and sustainability.
Proper citation: Allen Institute for Brain Science 2019. Patch-Seq Internal Solution with Biocytin. protocols.io dx.doi.org/10.17504/protocols.io.9gih3ue Copy
Authors: Saurabh Mehta, Bryan Gannon, Camille E. Jones, Laura S. Hackl, Shoba A. Udipi, Varsha Thakker, Aparna Thorat, Wesley Bonam, Jere D. Haas, Julia Finkelstein
Group: Mehta Research Group @ Cornell
Proper citation: Saurabh Mehta, Bryan Gannon, Camille E. Jones, Laura S. Hackl, Shoba A. Udipi, Varsha Thakker, Aparna Thorat, Wesley Bonam, Jere D. Haas, Julia Finkelstein 2020. Effect of Multiple Biofortified Food Crops-based Meals on Micronutrient Status and Immune Function in The First 1000 Days of Life in India: Study Protocol for a Randomized Controlled Feeding Trial. protocols.io dx.doi.org/10.17504/protocols.io.bqcmmsu6 Copy
Authors: Ian Mackay
Summary: This version is based on a recipe (see forked version) my team and I used this assay between 2008-2015; we dubbed it the 'Nix assay'. It targets the 5'UTR and employs quite degenerate oligos.In silico sequence alignments indicated the olignucleotides could theoretically detect aft least HPeV 1-7, 17 and 18. Further validation of this recipe is ongoing.However during a period of assay comparison, another assay (see link below), the 'Benschop assay' (J.Clin.Virol. 2008. 41(2):69-74), was found to produce more sigmoidal and higher curves and 1-5 cycle improvements to CT values when compared among the sample sampe extract set.
Proper citation: Ian Mackay 2017. Human Parechovirus A real-time RT-PCR ["Nix assay"; 2017-]. protocols.io dx.doi.org/10.17504/protocols.io.k2kcycw Copy
Authors: Chang-Ming Bai
Summary: This protocol is used to outline the process of Nanopore library preparation for Scapharca broughtonii genome.
Proper citation: Chang-Ming Bai 2019. The Nanopore libraries preparation for the Scapharca broughtonii. protocols.io dx.doi.org/10.17504/protocols.io.z8bf9sn Copy
Authors: Tanya Puccio, Todd Kitten
Summary: Streptococcus sanguinis is a lactic acid-forming bacterium that can be cultured in both aerobic and anaerobic conditions. It is a primary colonizer of the oral cavity but can also cause a heart disease called infective endocarditis. Our main objective for this protocol was to grow large, controlled cultures before and after manganese depletion for various analyses. In order to obtain large scale, reproducible growth of S. sanguinis, a biostat was used to maintain controlled conditions. After optimization, it was determined that traditional chemostat conditions (Burne and Chen, 1998) were not appropriate for these experiments. Thus, we decided on this modified protocol. Using this method, we were able to identify a concentration of the non-specific metal chelator, EDTA, that would lead to a decreased growth rate in a manganese transporter mutant but not in the wild-type strain.
Proper citation: Tanya Puccio, Todd Kitten 2020. Fermentor Growth of Streptococcus sanguinis. protocols.io dx.doi.org/10.17504/protocols.io.bkayksfw Copy
Authors: Josh Quick
Group: Diaz-Munoz Lab, Coronavirus Method Development Community, Szentagothai Research Centre Virology
Proper citation: Josh Quick 2019. Priming and loading a MinION flowcell. protocols.io dx.doi.org/10.17504/protocols.io.7q5hmy6 Copy
Authors: Izabela Rezende, Lívia Sacchetto
Group: MRCA
Summary: For investigate the presence of YFV genome by quantitative PCR assays in the hydrolysis probe detection format. The target is the 5’-noncoding region (5’-NC) of the YFV genome (Domingo et al., 2012).
Proper citation: Izabela Rezende, Lívia Sacchetto 2018. Real-time Reverse Transcription Polymerase Chain Reaction (RT- qPCR). protocols.io dx.doi.org/10.17504/protocols.io.pw8dphw Copy
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