Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Lysate Preparation from Biofluids/Viruses Collected with Nasal or Throat Swabs Resource Report Resource Website |
Bioline | DOI:10.17504/protocols.io.f5cbq2w | Bioline | 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. | http://www.bioline.com/us/downloads/dl/file/id/3789/isolate_ii_biofluids_rna_kit_product_manual.pdf | 1 | 2016 | Bioline 2016. Lysate Preparation from Biofluids/Viruses Collected with Nasal or Throat Swabs. protocols.io https://dx.doi.org/10.17504/protocols.io.f5cbq2w | 2021-04-15 09:14:35 | |||
|
Immune Cell Isolation from Mouse Spleen Resource Report Resource Website |
Grace Burgin, Noga Rogel, Moshe Biton | DOI:10.17504/protocols.io.nm2dc8e | To isolate immune cells from a mouse spleen before sorting | Regev Lab, Broad Institute, Regev Lab, Broad Institute, Regev Lab, Broad Institute | 1 | 2019 | Grace Burgin, Noga Rogel, Moshe Biton 2019. Immune Cell Isolation from Mouse Spleen. protocols.io https://dx.doi.org/10.17504/protocols.io.nm2dc8e | 2021-04-15 09:14:35 | ||||
|
Draft genome assembly using parasitic mite population NGS DNA sample from mites extracted from host wound environment Resource Report Resource Website |
Mofiz E., Holt, D., Seemann, T., Currie B.J., Fischer K., Papenfuss A.T. | DOI:10.17504/protocols.io.ez7bf9n | GigaScience Press | 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. | , , , , , , , | http://dx.doi.org/10.1186/s13742-016-0129-2 | 2 | 2016 | 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 | 2021-04-15 09:14:48 | ||
|
Copy of Immunohistochemistry Resource Report Resource Website |
Ning Zhang, Yu Kuang | DOI:10.17504/protocols.io.zgwf3xe | China Agricultural University | Zhang N, Gao P, Yin B, Li J, Wu T, Kuang Y, Wu W, Li J (2019) Cathepsin L promotes secretory IgA response by participating in antigen presentation pathways during Mycoplasma Hyopneumoniae infection. PLoS ONE 14(4): e0215408. doi: 10.1371/journal.pone.0215408 | [China Agricultural University], China Agriculturall University | https://doi.org/10.1371/journal.pone.0215408 | 1 | 2019 | Ning Zhang, Yu Kuang 2019. Copy of Immunohistochemistry. protocols.io https://dx.doi.org/10.17504/protocols.io.zgwf3xe | 2021-04-15 09:14:35 | ||
|
Transformation of E. coli cells of strain DH5? Resource Report Resource Website |
Hanna Eriksson | DOI:10.17504/protocols.io.mqqc5vw | Microbial Chemistry Ångström Laboratory Uppsala University | 1 | 2018 | Hanna Eriksson 2018. Transformation of E. coli cells of strain DH5?. protocols.io https://dx.doi.org/10.17504/protocols.io.mqqc5vw | 2021-04-15 09:14:35 | |||||
|
General Transfection Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.bawuifew | This protocol is for general transfection. To see the full abstract and additional resources, visit the Addgene protocol page.Sample Data | Addgene | https://www.addgene.org/protocols/transfection/ | 2 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. General Transfection. protocols.io https://dx.doi.org/10.17504/protocols.io.bawuifew | 2021-04-15 09:14:35 | |||
|
MPE-seq Resource Report Resource Website |
Ben Fair | DOI:10.17504/protocols.io.zpaf5ie | University of Chicago | 1 | 2019 | Ben Fair 2019. MPE-seq. protocols.io https://dx.doi.org/10.17504/protocols.io.zpaf5ie | 2021-04-15 09:14:35 | |||||
|
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 Resource Report Resource Website |
Hassan Salmanroghani, massoud mirvakili, mahmud baghbanian, roham salmanroghani, golshid sanati, pouria yazdian | DOI:10.17504/protocols.io.mdjc24n | 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 | Salmanroghani H, Mirvakili M, Baghbanian M, Salmanroghani R, Sanati G, Yazdian P (2018) 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 Ulcer: A Randomized Clinical Trial. PLoS ONE 13(6): e0197096. doi: 10.1371/journal.pone.0197096 | Yazd Medical University, Yazd Medical University, Yazd Medical University, Yazd Medical University, Tehran University of Medical Sciences, Yazd Medical University | https://doi.org/10.1371/journal.pone.0197096 | 1 | 2018 | 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 | 2021-04-15 09:14:48 | ||
|
SPARC_Duke_Grill_OT2-OD025340_HumanVagusNerve_Collection_Histology_Microscopy Resource Report Resource Website |
Nicole A. Pelot, J. Ashley Ezzell, Kara A. Clissold, Warren M. Grill | DOI:10.17504/protocols.io.xcyfixw | SPARC | Protocol for collection, histological processing, and imaging of human vagus nerves. | Duke University, University of North Carolina, University of North Carolina, Duke University | 1 | 2020 | 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 | 2021-04-15 09:14:35 | |||
|
Protocol for a reproducible circRNA analysis using Docker4Circ Resource Report Resource Website |
Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Raffaele Adolfo Calogero, Francesca Cordero, Marco Beccuti, Michele De Bortoli | DOI:10.17504/protocols.io.zrrf556 | Q-Bio Turin | 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. | University of Turin, University of Turin, University of Turin, University of Turin, University of Turin, University of Turin, University of Turin, University of Turin, University of Turin | 3 | 2019 | 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 | 2021-04-15 09:14:48 | |||
|
Minimally-invasive sampling of pars petrosa (os temporale) for ancient DNA extraction Resource Report Resource Website |
Eleftheria Orfanou, Marie Himmel, Franziska Aron, Wolfgang Haak | DOI:10.17504/protocols.io.bqd8ms9w | WarinnerGroup, MPI-SHH Archaeogenetics | 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). | Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Max Planck Institute for the Science of Human History | 2 | 2020 | 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 | 2021-04-15 09:14:35 | |||
|
Ultra-deep, long-read nanopore sequencing of mock microbial community standards Resource Report Resource Website |
Josh Quick, Sam Nicholls, Nick Loman, Shuiquan Tang | DOI:10.17504/protocols.io.x9tfr6n | Long Read Club | 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-de ned 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. | University of Birmingham, University of Birmingham, University of Birmingham, Zymo Research Corporation | https://www.biorxiv.org/content/biorxiv/early/2018/12/04/487033.full.pdf | 1 | 2019 | 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 | 2021-04-15 09:14:35 | ||
|
Cloned Genomic Library using Illumina Adapters Resource Report Resource Website |
Philip D. Weyman | DOI:10.17504/protocols.io.hfbb3in | Protist Research to Optimize Tools in Genetics (PROT-G) | 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. | J. Craig Venter Institute | 1 | 2017 | Philip D. Weyman 2017. Cloned Genomic Library using Illumina Adapters. protocols.io https://dx.doi.org/10.17504/protocols.io.hfbb3in | 2021-04-15 09:14:48 | |||
|
ELISA for quantification of human immunoglobulin M (IgM) in serum or plasma. Resource Report Resource Website |
Angel Justiz-Vaillant, Belkis Ferrer-Cosme | DOI:10.17504/protocols.io.bj7rkrm6 | University of the West Indies, [email protected] | 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 | University of the West Indies St. Augustine, "Saturnino Lora Torres' Provincial Teaching Clinical Surgical Hospital. Cuba | 1 | 2020 | 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 | 2021-04-15 09:14:37 | |||
|
Before data acquisition -- Start MRI Project Spinoza REC Resource Report Resource Website |
Tinka Beemsterboer, Lukas Snoek | DOI:10.17504/protocols.io.n4mdgu6 | Spinoza Centre, REC-L | 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 | Spinoza Centre, REC-L, Spinoza Centre, REC-L | 5 | 2018 | Tinka Beemsterboer, Lukas Snoek 2018. Before data acquisition -- Start MRI Project Spinoza REC. protocols.io https://dx.doi.org/10.17504/protocols.io.n4mdgu6 | 2021-04-15 09:14:54 | |||
|
Measuring leaf carbon fractions with the ANKOM2000 Fiber Analyzer Resource Report Resource Website |
Jocelyne Ayotte, Etienne Laliberté | DOI:10.17504/protocols.io.yinfude | Plant Functional Ecology Lab, Canadian Airborne Biodiversity Observatory | 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. | Université de Montréal, Université de Montréal | 1 | 2019 | 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 | 2021-04-15 09:14:38 | |||
|
Hyperemic myocardial blood flow quantification with CZT-based SPECT cameras and a rapid, single-scan rest/stress scan Resource Report Resource Website |
Yu-Hua Fang | DOI:10.17504/protocols.io.iqjcdun | 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. | Fang YD, Liu Y, Ho K, Kuo F, Yang C, Yen T, Hsieh I (2017) Single-scan rest/stress imaging with 99mTc-Sestamibi and cadmium zinc telluride-based SPECT for hyperemic flow quantification: A feasibility study evaluated with cardiac magnetic resonance imaging. PLoS ONE 12(8): e0183402. doi: 10.1371/journal.pone.0183402 | Department of Biomedical Engineering, National Cheng Kung University, Taiwan | https://doi.org/10.1371/journal.pone.0183402 | 1 | 2017 | 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 | 2021-04-15 09:14:57 | ||
|
High Efficiency Transformation Protocol (modified) Resource Report Resource Website |
Harold Bien | DOI:10.17504/protocols.io.dq45yv | This is a modified protocol from the original NEB splitting the 50uL aliquot into two separate tubes for dual reactions from a single tube. | Stony Brook University | https://www.neb.com/protocols/1/01/01/high-efficiency-transformation-protocol-c2987 | 1 | 2015 | Harold Bien 2015. High Efficiency Transformation Protocol (modified). protocols.io https://dx.doi.org/10.17504/protocols.io.dq45yv | 2021-04-15 09:14:57 | |||
|
Binding properties of immunoglobulin-binding protein by double immunodiffusion (Ouchterlony) technique. Resource Report Resource Website |
Angel Justiz-Vaillant | DOI:10.17504/protocols.io.bjsjkncn | University of the West Indies, [email protected] | University of the West Indies St. Augustine | 1 | 2020 | 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 | 2021-04-15 09:14:54 | ||||
|
Counting Microalgae Culture Density Resource Report Resource Website |
Jakub Nedbal | DOI:10.17504/protocols.io.bd8ni9ve | 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.. | King's College London | https://app.labstep.com/sharelink/1bfe1dae-317f-460d-a934-6d23c1696ac2 | 2 | 2020 | Jakub Nedbal 2020. Counting Microalgae Culture Density. protocols.io https://dx.doi.org/10.17504/protocols.io.bd8ni9ve | 2021-04-15 09:14:40 |
Can't find your Protocol?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. If you want to find a specific protocol and you know the DOI of the protocol already, it's easier to enter a DOI to search. You can refine the search results using Facets on the left side of the search results page. If you are on the table view, you can also search in a specific column by clicking the column title and enter the keywords.
If you still could not find your protocol in the search results, please help us by adding it into the system — it's easy. Create and publish your protocols at Protocols.io.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
