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Authors: Bioline
Group: Bioline
Summary: The steps for preparing the lysate are different depending on the starting material. Please ensure you follow the correct procedure for your starting material (see the section Disrupting and Homogenizing Starting Materials and the different lysate preparation protocols here). The subsequent steps detailed in Genomic DNA removal and total RNA purification are the same in all cases. This protocol is designed for the isolation of all sizes of RNA (including miRNA) from a wide variety of biofluids derived from all human and animal sources collected with nasal or throat swabs. Follow this protocol for isolating RNA from viruses collected with nasal or throat swabs.

Proper citation: Bioline 2016. Lysate Preparation from Biofluids/Viruses Collected with Nasal or Throat Swabs. protocols.io https://dx.doi.org/10.17504/protocols.io.f5cbq2w Copy   

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Authors: Grace Burgin, Noga Rogel, Moshe Biton
Summary: To isolate immune cells from a mouse spleen before sorting 

Proper citation: Grace Burgin, Noga Rogel, Moshe Biton 2019. Immune Cell Isolation from Mouse Spleen. protocols.io https://dx.doi.org/10.17504/protocols.io.nm2dc8e Copy   

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Authors: Mofiz E., Holt, D., Seemann, T., Currie B.J., Fischer K., Papenfuss A.T.
Group: GigaScience Press
Summary: This protocol is from:Mofiz E. et al., Genomic resources and draft reference assemblies of the human and porcine scabies mites, Sarcoptes scabiei var. hominis and var. suis. GigaScience. 2016. DOI: 10.1186/s13742-016-0129-2 http://dx.doi.org/10.1186/s13742-016-0129-2.

Proper citation: Mofiz E., Holt, D., Seemann, T., Currie B.J., Fischer K., Papenfuss A.T. 2016. Draft genome assembly using parasitic mite population NGS DNA sample from mites extracted from host wound environment. protocols.io https://dx.doi.org/10.17504/protocols.io.ez7bf9n Copy   

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Authors: Ning Zhang, Yu Kuang
Group: China Agricultural University

Proper citation: Ning Zhang, Yu Kuang 2019. Copy of Immunohistochemistry. protocols.io https://dx.doi.org/10.17504/protocols.io.zgwf3xe Copy   

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Authors: Hanna Eriksson

Proper citation: Hanna Eriksson 2018. Transformation of E. coli cells of strain DH5?. protocols.io https://dx.doi.org/10.17504/protocols.io.mqqc5vw Copy   

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Authors: Addgene The Nonprofit Plasmid Repository
Summary: This protocol is for general transfection. To see the full abstract and additional resources, visit the Addgene protocol page.Sample Data

Proper citation: Addgene The Nonprofit Plasmid Repository 2019. General Transfection. protocols.io https://dx.doi.org/10.17504/protocols.io.bawuifew Copy   

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Authors: Ben Fair

Proper citation: Ben Fair 2019. MPE-seq. protocols.io https://dx.doi.org/10.17504/protocols.io.zpaf5ie Copy   

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Authors: Hassan Salmanroghani, massoud mirvakili, mahmud baghbanian, roham salmanroghani, golshid sanati, pouria yazdian
Summary: Aim: To evaluate the efficacy and tolerability of replacing tetracycline with high dose of amoxicillin in bismuth-based quadruple therapy for H.pylori eradication.Methods: This randomized, open label clinical trial study was performed on 228 patients with H.pylori infection and duodenal ulcer without the history of previous H.pylori treatment. Patients were randomly divided into two groups. Group one received metronidazole 500mg, bismuth subcitrate 240mg and amoxicillin 1000mg, all three times a day and omeprazole 20 mg twice a day (amoxicillin group)for14 days. The second group received metronidazole 500mg three times a day and bismuth subcitrate240mg and tetracycline HCL 500mg both four times a day and omeprazole 20 mg twice a day (tetracycline group), for 14 days. Evaluation for compliance and drugs side effects were done after two weeks. Eight weeks after treatment, H.pylori eradication rate was assessed by c13-urease breath test.Results: Two hundred twenty-eight patients were enrolled. There was no statistically significant demographic difference between two groups. Amoxicillin containing regimen achieved higher Eradication rate: 105 of 110 ,95.51% (95%CI 91.5% to 99.3%) and 88 of 105, 83.8% (95% CI 76.7% to 90.8%) by per-protocol analysis (p-value=0.005) and 92.9%(95%CI 88.1% to 97.6%) and 76.5% (95% CI 68.7% to 84.2%) by intention-to-treat (p-value=0.001) for amoxicillin and tetracycline groups, respectively. Adverse events were statistically more significant higher in Tetracycline group (65.2%)  amoxicillin group (43.4%) (P value = 0.001).Conclusion: Bismuth based quadruple therapy included high dose of amoxicillin and metronidazole has an acceptable H. pylori infection eradication rate with good tolerance in patients with duodenal ulcer. This can overcome treatment resistance in areas with high prevalence of metronidazole and clarithromycin resistance

Proper citation: Hassan Salmanroghani, massoud mirvakili, mahmud baghbanian, roham salmanroghani, golshid sanati, pouria yazdian 2018. A Randomized Clinical Trial Comparing the Efficacy and Tolerability of Two Quadruple Regimens: Bismuth, Omeprazole, Metronidazole with Amoxicillin or Tetracycline as First-Line Treatment for Eradication of Helicobacter Pylori in Patients with Duodenal Ulce. protocols.io https://dx.doi.org/10.17504/protocols.io.mdjc24n Copy   

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Authors: Nicole A. Pelot, J. Ashley Ezzell, Kara A. Clissold, Warren M. Grill
Group: SPARC
Summary: Protocol for collection, histological processing, and imaging of human vagus nerves.

Proper citation: Nicole A. Pelot, J. Ashley Ezzell, Kara A. Clissold, Warren M. Grill 2020. SPARC_Duke_Grill_OT2-OD025340_HumanVagusNerve_Collection_Histology_Microscopy. protocols.io https://dx.doi.org/10.17504/protocols.io.xcyfixw Copy   

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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 https://dx.doi.org/10.17504/protocols.io.zrrf556 Copy   

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Authors: Eleftheria Orfanou, Marie Himmel, Franziska Aron, Wolfgang Haak
Group: WarinnerGroup, MPI-SHH Archaeogenetics
Summary: This protocol describes how to obtain bone powder from the pars petrosa of disarticulated ossis temporalis, specifically from the dense parts around the cochlea, in a minimally-invasive way by drilling from the outside. The pars petrosa has been shown to consistently yield high amounts of aDNA (Pinhasi et al. 2015 PLoS One, doi: 10.1371/journal.pone.0129102).

Proper citation: Eleftheria Orfanou, Marie Himmel, Franziska Aron, Wolfgang Haak 2020. Minimally-invasive sampling of pars petrosa (os temporale) for ancient DNA extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.bqd8ms9w Copy   

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Authors: Josh Quick, Sam Nicholls, Nick Loman, Shuiquan Tang
Group: Long Read Club
Summary: Background: Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition.Methods: We sequenced two commercially-available mock communities containing ten microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the ten individual species isolates were also sequenced with Illumina technology. Data: We generated 14 and 16 Gbp from GridION owcells and 150 and 153 Gbp from PromethION owcells for theevenly-distributed and log-distributed communities respectively. Read length N50 was 5.3 Kbp and 5.2 Kbp for the evenand log community, respectively. Basecalls and corresponding signal data are made available (4.2 TB in total).Results: Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning.Conclusions: We present ultra-deep, long-read nanopore datasets from a well-dened mock community. These datasetswill be useful for those developing bioinformatics methods for long-read metagenomics and for the validation andcomparison of current laboratory and software pipelines.

Proper citation: Josh Quick, Sam Nicholls, Nick Loman, Shuiquan Tang 2019. Ultra-deep, long-read nanopore sequencing of mock microbial community standards. protocols.io https://dx.doi.org/10.17504/protocols.io.x9tfr6n Copy   

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Authors: Philip D. Weyman
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: A protocol to create a genomic library (2-5 kb insert size) to screen for genomic regions functioning as centromeres. Uses the NEBNext Illumina library prep kit from NEB to add adapters to fragments and then the fragments can be efficiently assembled into a vector containing homology to the adapter sequences using Gibson Assembly.

Proper citation: Philip D. Weyman 2017. Cloned Genomic Library using Illumina Adapters. protocols.io https://dx.doi.org/10.17504/protocols.io.hfbb3in Copy   

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Authors: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
Group: University of the West Indies, [email protected]
Summary: IFN-γ is a key player in driving cellular immunity. It is capable of orchestrating numerous and vital protective functions to enhance immune responses in cancers and infectious diseases. It exhibits its immunomodulatory effects by enhancing antigen processing and presentation,, inducing an anti-viral state, increasing leukocyte trafficking, boosting the anti-microbial properties of immune cells and by affecting cellular proliferation and apoptosis. [1]ReferenceKak G, Raza M, Tiwari BK. Interferon-gamma (IFN-γ): Exploring its implications in infectious diseases.Biomol Concepts. 2018;9(1):64-79. Published 2018 May 30. doi:10.1515/bmc-2018-0007

Proper citation: Angel Justiz-Vaillant, Belkis Ferrer-Cosme 2020. ELISA for quantification of human immunoglobulin M (IgM) in serum or plasma.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj7rkrm6 Copy   

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Authors: Tinka Beemsterboer, Lukas Snoek
Group: Spinoza Centre, REC-L
Summary: Dear researcher,This protocol gives you the steps to start an MRI project at the Spinoza Centre Roeterseiland. If you haven't had contact with Steven Scholte or Tinka Beemsterboer, make sure to contact them before completing this protocol. You can reach us by email:Steven Scholte: [email protected] Beemsterboer: [email protected] you have any suggestions for improving the workflow, don't hesitate to add comments to the steps in the protocol.Hope to see you soon!The Spinoza REC team,Steven Scholte, Tinka Beemsterboer, and Lukas Snoek 

Proper citation: Tinka Beemsterboer, Lukas Snoek 2018. Before data acquisition -- Start MRI Project Spinoza REC. protocols.io https://dx.doi.org/10.17504/protocols.io.n4mdgu6 Copy   

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Authors: Jocelyne Ayotte, Etienne Laliberté
Group: Plant Functional Ecology Lab, Canadian Airborne Biodiversity Observatory
Summary: Here we describe the standardized protocol used by the Canadian Airborne Biodiversity Observatory (CABO) to measure carbon fractions in leaf samples, using the ANKOM2000 Fiber Analyzer. Prior to the analysis, leaf samples are oven-dried, and then ground with a cyclone mill (2-mm screen). Then, carbon fractions are measured using a sequential digestion procedure to measure neutral detergent fiber (NDF, acid detergent fiber (ADF), acid detergent lignin (ADL). Finally, the residues are ashed in a muffle furnace to determine inorganic recalcitrant materials. This protocol is based on the manufacturer's protocols.

Proper citation: Jocelyne Ayotte, Etienne Laliberté 2019. Measuring leaf carbon fractions with the ANKOM2000 Fiber Analyzer. protocols.io https://dx.doi.org/10.17504/protocols.io.yinfude Copy   

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Authors: Yu-Hua Fang
Summary: This protocol describes how to calculate the hyperemic myocardial blood flow, a clinically critical parameter, with CZT-based SPECT and a single-scan rest/stress protocol that is proposed in our manuscript.

Proper citation: Yu-Hua Fang 2017. Hyperemic myocardial blood flow quantification with CZT-based SPECT cameras and a rapid, single-scan rest/stress scan. protocols.io https://dx.doi.org/10.17504/protocols.io.iqjcdun Copy   

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Authors: Harold Bien
Summary: This is a modified protocol from the original NEB splitting the 50uL aliquot into two separate tubes for dual reactions from a single tube.

Proper citation: Harold Bien 2015. High Efficiency Transformation Protocol (modified). protocols.io https://dx.doi.org/10.17504/protocols.io.dq45yv Copy   

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Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]

Proper citation: Angel Justiz-Vaillant 2020. Binding properties of immunoglobulin-binding protein by double immunodiffusion (Ouchterlony) technique.. protocols.io https://dx.doi.org/10.17504/protocols.io.bjsjkncn Copy   

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Authors: Jakub Nedbal
Summary: Counting culture cell density offers a reliable way of consistend seeding density for freshly inoculated cultures and allows tracking the growth of the cultures. Cell densiry counting, as described in this protocol, is performed manually under the microscope in a Neubauer hemocytometer..

Proper citation: Jakub Nedbal 2020. Counting Microalgae Culture Density. protocols.io https://dx.doi.org/10.17504/protocols.io.bd8ni9ve Copy   

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