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Authors: G-Biosciences
Group: G-Biosciences
Summary: This protocol is for the ProteSEEKER™ kit, designed to identify the specific type of proteases present in cell or tissue lysates, and allows determining the minimal number of individual protease inhibitors required for a sample. 

Proper citation: G-Biosciences 2017. ProteSEEKER™. protocols.io https://dx.doi.org/10.17504/protocols.io.e5fbg3n Copy   

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Authors: Sasa T, Matjaž H
Summary: [insert abstract from MACA_Bulk paper]

Proper citation: Sasa T, Matjaž H 2019. SmartSeq2 for HTP Generation of Bulk RNA Libraries- with Pipetting plan . protocols.io https://dx.doi.org/10.17504/protocols.io.7f2hjqe Copy   

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Authors: Eyleen Nabyla Alvarenga Niitsuma, Gabriel da Rocha Fernandes, Francisco Carlos Félix Lana

Proper citation: Eyleen Nabyla Alvarenga Niitsuma, Gabriel da Rocha Fernandes, Francisco Carlos Félix Lana 2018. PCR Protocol for TaqMan® Genotyping Assays. protocols.io https://dx.doi.org/10.17504/protocols.io.sfzebp6 Copy   

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Authors: Ioannis Bellos, Georgia Fitrou, Aakash Pandita
Summary: Preterm birth is often associated with respiratory distress syndrome, which may lead to bronchopulmonary dysplasia and high rates of morbidity and mortality. The current treatment approach is the initial use of nasal continuous positive airway pressure (nCPAP), followed by surfactant administration in neonates with worsening respiratory distress. The aim of the present network meta-analysis is to simultaneously assess the effects of less invasive methods for administering surfactant on clinical outcomes and compare them to the conventional InSurE (Intubation, Surfactant administration and Extubation) method.

Proper citation: Ioannis Bellos, Georgia Fitrou, Aakash Pandita 2020. Less invasive surfactant administration in preterm neonates with respiratory distress syndrome: a network meta-analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.bcbmisk6 Copy   

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Authors: William Brydon, Sricharan Kadimi
Group: UConn iGEM
Summary: LB (Luria-Bertani) media is commonly used for bacterial culture. We use it for overnight cultures after transformations.

Proper citation: William Brydon, Sricharan Kadimi 2019. LB Media. protocols.io https://dx.doi.org/10.17504/protocols.io.3idgka6 Copy   

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Authors: Janet Keast, Peregrine Osborne, Nicole Wiedmann
Group: SPARC
Summary: This protocol is used for immunohistochemical visualisation of immediate early gene expression (c-Fos or Egr-1) in cryosections of rat lumbosacral spinal cord. Free-floating sections are processed in a double labelling protocol to distinguish immediate early gene expression in different neurochemical classes of spinal cord neurons:ChAT [choline acetyltransferase]: preganglionic neuronsTH [tyrosine hydroxyls]: dopaminergic neuronsPax2: inhibitory interneurons

Proper citation: Janet Keast, Peregrine Osborne, Nicole Wiedmann 2020. Immunohistochemical labelling of spinal cord neurons involved in bladder activity. protocols.io https://dx.doi.org/10.17504/protocols.io.bakkicuw Copy   

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Authors: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
Summary: Adrenergic Modulation of Migration, CD11b and CD18 Expression, ROS and interleukin-8 Production by Human Polymorphonuclear Leukocytes.Angela Scanzano, Laura Schembri, Emanuela Rasini, Alessandra Luini, Jessica Dallatorre, Massimiliano Legnaro, Raffaella Bombelli, Terenzio Congiu, Marco Cosentino, Franca Marino. Inflamm Res. 2015 Feb;64(2):127-35. doi: 10.1007/s00011-014-0791-8. Epub 2015 Jan 6.

Proper citation: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino 2020. PMN- 05 Culture of Human PMN - IL-8 production. protocols.io https://dx.doi.org/10.17504/protocols.io.bhdgj23w Copy   

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Authors: Fabia Simona, Huoming Zhang, Christian Voolstra
Group: reefgenomics, Aiptasia-Symbiodiniaceae Model System
Summary: The analysis of gene expression data via RNA sequencing (RNA-Seq) has become a standard method for model and non-model organisms to identify genes of interest associated with a specific stressor of physiological state. More recently, mass spectrometry (MS)-based proteomics started to become a standard method to assay the phenotype of an organism via means of its expressed proteins. MS has also become the method of choice for the study of protein phosphorylation. Phosphoproteomics targets proteins that are subjected to phosphorylation via means of their serine, threonine, and tyrosine residues. Phosphorylation is a reversible modification that plays a key role in controlling the activity of proteins as well as their function and subcellular localization.To bring MS-based phosphoproteomics to the emerging coral model system Aiptasia, we developed a protocol for phosphosphproteins extraction and generation of a phosphoproteome assay (spectral) library, a comprehensive non-redundant collection of Aiptasia phosphoproteins. Based on the assay library, we then performed accurate label-free quantification (by DIA/SWATH-MS) of the Aiptasia phosphoproteome. Our method reproducibly identifies and quantifies a broad fraction of the phosphorylated proteome of Aiptasia and is comparable to methods developed for other model systems

Proper citation: Fabia Simona, Huoming Zhang, Christian Voolstra 2018. Isolation of phosphoproteins from symbiotic and aposymbiotic Aiptasia anemones for elucidation of the phosphoproteome. protocols.io https://dx.doi.org/10.17504/protocols.io.txuepnw Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol provides a method to predict phage community diversity using the algorithm PHACCS. Sequencing of viral communities often results in a high percent of unknown reads, largely due to our incomplete reference databases. To address this unknown factor of viromes, the algorithm PHACCS (PHAge Communities from Contig Spectra) was developed to predict virus community alpha diversity without the use of taxonomic references. Based on the methods from the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.

Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script P5: Diversity. protocols.io https://dx.doi.org/10.17504/protocols.io.efrbbm6 Copy   

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Authors: Adrieli Sachett, Matheus Gallas-Lopes, Radharani , Greicy M M Conterato, Ana Herrmann, Angelo Piato
Group: Fish behavior and physiology
Summary: Zebrafish are increasingly used as a model animal in neuroscience research. Here we describe our protocol to collect and process zebrafish brains so they are well presearved and viable for biochemical assays.

Proper citation: Adrieli Sachett, Matheus Gallas-Lopes, Radharani , Greicy M M Conterato, Ana Herrmann, Angelo Piato 2020. How to prepare zebrafish brain tissue samples for biochemical assays. protocols.io https://dx.doi.org/10.17504/protocols.io.bjkdkks6 Copy   

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Authors: luanaborba
Group: L. P. Borba-Santos

Proper citation: luanaborba 2020. Determination of minimum inhibitory concentration values (MICs) against Sporothrix brasiliensis and Sporothrix schenckii. protocols.io https://dx.doi.org/10.17504/protocols.io.bjgxkjxn Copy   

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Authors: Harley King
Group: USG Fall 2020 BSCI:414

Proper citation: Harley King 2020. BSCI:414--Lab 4 Plate Setup for COVID RT-qPCR. protocols.io https:// Copy   

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Authors: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y.
Group: VERVE Net, Hurwitz Lab
Summary: Contrary to single-genome assemblers (e.g., Velvet and SOAPdenovo), MetaVelvet assumes metagenomics settings. Accordingly, k-mer coverage histogram might be multi-modal rather than uni-modal. Please note that the coverage peak parameters can largely affect MetaVelvet assembling results. Although simple and automatic peak detection algorithm is implemented in meta-velvetg, we strongly recommend manual inspection of k-mer coverage peaks and manual setting of the coverage peak parameters. For manually setting the coverage peak parameters, please execute the following procedures.

Proper citation: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2016. Manual setting of k-mer coverage peaks. protocols.io https://dx.doi.org/10.17504/protocols.io.d7k9kv Copy   

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Authors: Anita Broellochs, protocols.io Ambassadors
Group: protocols.io Ambassadors
Summary: Communicate and collaborate effectively with protocols.io. Research data and protocols will never leave the team, even if a person does. With protocols.io it is fast and easy to find the information that you want— a central place for all of your scientific data.If your team is planning to start using protocols.io, a protocol hackathon is a great way to get everyone on board. Protocol hackathons are fun as the entire team works on getting their protocols up on protocols.io at the same time rather than every team member trying to enter protocols one at the time by themselves.A protocol hackathon can take place remotely or in person. This protocol gives you a great overview of how you can go about setting up a protocol entry session (hackathon) for your team.

Proper citation: Anita Broellochs, protocols.io Ambassadors 2020. How to set up a protocol hackathon for your team. protocols.io https://dx.doi.org/10.17504/protocols.io.bgf8jtrw Copy   

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Authors: Tomasz Suchan

Proper citation: Tomasz Suchan 2020. SIngle-strand library protocol adapter barcodes. protocols.io https:// Copy   

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Authors: Julie Huber, Caroline Fortunato
Group: Center for Dark Energy Biosphere Investigations, Huber Lab, Chemistry Method Development Community
Summary: This protocol is following RNA-SIP experiments and RNA extraction to fractionate the RNA according to density. The protocol is based on Leuders et al. 2010.

Proper citation: Julie Huber, Caroline Fortunato 2017. Density Gradient Fractionation of RNA from RNA-SIP Experiments. protocols.io https://dx.doi.org/10.17504/protocols.io.iu2ceye Copy   

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Authors: Eftychis Frangedakis, Susana Sauret-Gueto, Anthony West, Marta Tomaselli, Nicola Patron, Marius Rebmann, Jim Haseloff
Group: OpenPlant Project
Summary: Protocol based onPollak B, Cerda A, Delmans M, et al (2019) Loop assembly: a simple and open system for recursive fabrication of DNA circuits. New Phytol 222:628–640https://doi.org/10.1111/nph.15625

Proper citation: Eftychis Frangedakis, Susana Sauret-Gueto, Anthony West, Marta Tomaselli, Nicola Patron, Marius Rebmann, Jim Haseloff 2019. Loop L2 (even level) type IIS cloning - pCs-ye vectors. protocols.io https://dx.doi.org/10.17504/protocols.io.4wcgxaw Copy   

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Authors: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
Group: Coronavirus Method Development Community
Summary: This is a collection of protocols for: "Phase 3 randomized, double-blinded, placebo-controlled trial to evaluate the safety, immunogenicity, and efficacy of Vaccine Candidate against COVID-19 in adults > 18 years of age"This generic Phase 3 protocol was developed by the PATH team with support of the Bill and Melinda Gates Foundation. The aim of the collection is to share recommended best practices in designing and implementing a Phase 3 study of a COVID-19 vaccine candidate. As Phase 3 trials of different Vaccine Candidates proceed around the world, following the same protocols will ensure consistency and comparability of the Phase 3 trial results.Please note that this is an evolving document, to be versioned and updated, based on community feedback and new data.

Proper citation: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores 2020. Collection of Protocols and Guidelines for Phase 3 study of Vaccine Candidate for COVID-19. protocols.io https://dx.doi.org/10.17504/protocols.io.bj5pkq5n Copy   

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Authors: Sparky Jr.
Group: PDI Test

Proper citation: Sparky Jr. 2021. Sample run SOP for ECD/FID/TCD. protocols.io https:// Copy   

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Authors: Lutz Berwanger
Group: Axmann Lab, CyanoWorld
Summary: In vitro transcriptions assay for cyanobacterial RNA polymerase. This protocol can be used either to do an in vitro transcription with small DNA fragments with desired promoter region or to use it with a promoter region integrated in a plasmid.

Proper citation: Lutz Berwanger 2018. In vitro Transcription assay for cyanobacterial DNA-dependent RNA Polymerase. protocols.io https://dx.doi.org/10.17504/protocols.io.mpvc5n6 Copy   

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