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.
Authors: Peng Wang, Hongjian Ni, Ruihe Wang
Proper citation: Peng Wang, Hongjian Ni, Ruihe Wang 2018. Fig 9. Effect of installation distance of shakers on weight on bit and accelerations of the drill-string. A. Change of weight on bit in the bottom hole over time. B. Maximum acceleration along the drill-string. C. Root mean square acceleration along the dr. protocols.io dx.doi.org/10.17504/protocols.io.kfactie Copy
Authors: Jason Kim
Group: Mouse Metabolic Phenotyping Centers
Summary: Summary:
Insulin clearance test measure systemic clearance of insulin following a bolus injection. Liver accounts for the majority of systemic insulin clearance following secretion from pancreatic β- cells into portal circulation. Hepatic clearance of insulin may be affected by obesity and in other mouse models of altered metabolism. Alterations in insulin clearance may also affect glucose and lipid metabolism.
Proper citation: Jason Kim 2019. U Mass - Insulin clearance. protocols.io dx.doi.org/10.17504/protocols.io.x2wfqfe Copy
Authors: Stephen Floor
Group: Stephen Floor Lab
Summary: This protocol is designed for 'around-the-horn' or 'divergent' PCR, where primers go around most or all of a plasmid but are pointed away from each other so they generate a linear product. Note that this protocol is written for Q5 polymerase, but works fine with other polymerases. To switch polymerases, just change the PCR reaction setup.
Proper citation: Stephen Floor 2018. Around-the-horn PCR and cloning. protocols.io dx.doi.org/10.17504/protocols.io.rf2d3qe Copy
Authors: Maria Rubio-Brotons
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Multicellgenomelab
Proper citation: Maria Rubio-Brotons 2017. Transient transfection of unicellular relative to animals Corallochytrium limacisporum with electroporation using Neon SystemVersion 1. protocols.io dx.doi.org/10.17504/protocols.io.hmwb47e Copy
Authors: Catherine J. Baker, Stephanie A. Smith, James H. Morrissey
Summary: Investigation of the biological roles of inorganic polyphosphate has been facilitated by our previous development of a carbodiimide-based method for covalently coupling primary amine-containing molecules to the terminal phosphates of polyphosphate (Choi et al., Biochemistry 49:9935, 2010). We now extend that approach by using readily available “bridging molecules” containing a primary amine and an additional reactive moiety, including another primary amine, a thiol or a click chemistry reagent such as dibenzocyclooctyne. This two-step labeling method is used to covalently attach commercially available derivatives of biotin, peptide epitope tags, and fluorescent dyes to the ends of polyphosphate. This protocol specifically describes the labeling of heterogenous long-chain polyP with cystamine and the subsequent addition of maleimide-biotin.
Proper citation: Catherine J. Baker, Stephanie A. Smith, James H. Morrissey 2020. Derivitization of polyphosphate with cystamine to facilitate secondary labeling with biotin. protocols.io dx.doi.org/10.17504/protocols.io.7z3hp8n Copy
Authors: Anika Wiegard
Group: Axmann Lab
Summary: This protocol can be used for:(i) heterologous expression of GST-tagged proteins from pGEX-6P1 based expression vectors in E. coli.(ii) purification of recombinant proteins via affinity chromatography using glutathione-agarose or glutathione-sepharose (GST tagged protein can be eluted with glutathione. Alternatively, the tag can be cleaved off by prescission protease)(iii) further purification of the eluted protein via anion exchange chromatographyThis protocol was modified fromWiegard A, Dörrich AK, Deinzer HT, Beck C, Wilde A, Holtzendorff J, Axmann IM: Biochemical analysis of three putative KaiC clock proteins from Synechocystis sp. PCC 6803 suggests their functional divergence. Microbiology 2013, 159, 948-958Snijder J, Schuller JM, Wiegard A, Lössel, P, Schmelling NM, Axmann IM, Plitzko JM, Förster F, Heck AJR: Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state. Science 2017, 355(6330):1181-1184
Proper citation: Anika Wiegard 2018. Expression and purification of (GST-tagged) (Kai) proteins. protocols.io dx.doi.org/10.17504/protocols.io.k68czhw Copy
Authors: Bhavesh Patel
Summary: The structure-based material constitutive model typically used for the colon tissue (DOI:10.1016/j.jmbbm.2017.08.031, DOI:10.1016/j.jmbbm.2013.02.016) is not readily available in the Finite Element software Abaqus, which is commonly used for biomechanical simuations. In this protocol, we provide step-by-step guidelines to use such material model in Abaqus using the User Subroutine implemented by the autor.
Proper citation: Bhavesh Patel 2020. Simulating colonic tissue mechanics using a structure-based material model in Abaqus. protocols.io dx.doi.org/10.17504/protocols.io.wzeff3e Copy
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. Background and Rationale (Part 1 of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io dx.doi.org/10.17504/protocols.io.bj5tkq6n Copy
Authors: Irfan Uddin, Taeeb Ahmad, Furqan Aziz
Summary: This algorithm implements Reversible Data Hiding (RDH) technique by rearranging the columns (or rows) of the image in a way that enhances the smooth regions of an image. Any difference based technique to embed data can then be used in the transformed image.
Proper citation: Irfan Uddin, Taeeb Ahmad, Furqan Aziz 2020. RDH. protocols.io dx.doi.org/10.17504/protocols.io.bdyzi7x6 Copy
Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines the analysis used to generate input files for CoNet for the phage-bacteria network. Based on 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 R15: CoNet Analysis - Formatting Relative Abundance Files. protocols.io dx.doi.org/10.17504/protocols.io.ejpbcmn Copy
Authors: Yang Sun, David Lee, George Hartoularos, Jimmie Ye
Group: Coronavirus Method Development Community
Summary: PurposeTo detail the workflow for scCITE-Seq of 24 PBMC samples with 2 technicians. This is based on internal 10X CITEseq protocol v9.
Proper citation: Yang Sun, David Lee, George Hartoularos, Jimmie Ye 2021. 10X-CITEseq protocol (COVID-19 patient samples +/- tetramer stain). protocols.io dx.doi.org/10.17504/protocols.io.bqnqmvdw Copy
Authors: Elena Yakubovskaya, Tatiana Zaliznyak, Joaquin Martinez Martinez, Gordon Taylor
Group: TaylorLab
Summary: Reliable protocol for virus purification is an essential step for characterization and identification of individual virus particles in order to obtain information on biochemical and physical properties of the virus and for studying interactions between host and virus at the single-cell level. The purified virus should be physically and chemically undamaged by the purification procedure and free from contaminating host-material. To obtain high-quality EhV sample (the virus that infecta coccolithophorid, Emiliania huxleyi) sutable for AFM, Raman and CryoEM analysis, we modified the protocol published by Lawrence and Steward (“Purification of viruses by centrifugation” J. E. Lawrence and G. F. Steward; MAVE Chapter 17, 2010, 166–181 © 2010, by the American Society of Limnology and Oceanography, Inc.).
Proper citation: Elena Yakubovskaya, Tatiana Zaliznyak, Joaquin Martinez Martinez, Gordon Taylor 2020. Virus purification protocol for Ehv-163 and other viruses.. protocols.io dx.doi.org/10.17504/protocols.io.bcpvivn6 Copy
Authors: André M. Comeau and Rachel T. Noble
Group: VERVE Net
Summary: For use in Viral and bacterial isolates, propagation and preparation of stocks.
Proper citation: André M. Comeau and Rachel T. Noble 2016. Pellet resuspension. protocols.io dx.doi.org/10.17504/protocols.io.dzt76m Copy
Authors: Kenneth Schackart, Kattika Kaarj
Group: 481b Laboratory
Summary: How to extract DNA from E. coli K12 using Wizard® Genomic DNA Purification Kit by Promega®.I do not claim any credit for the development of this protocol. It has been adapted from the protocol detailed in: .
Proper citation: Kenneth Schackart, Kattika Kaarj 2019. E. coli K12 DNA Extraction. protocols.io dx.doi.org/10.17504/protocols.io.yujfwun Copy
Authors: Tim Mercer
Summary: Metagenome sequins are a set of synthetic DNA controls that reflect the sequence complexity, GC content, phylogenetic diversity and abundance of a natural microbial community. The sequins are ‘spiked-in’ to your DNA sample, which together undergo to library preparation, sequencing and analysis. The sequins can then be distinguished from you sample DNA in the output library by their synthetic sequence, and analyzed as internal controls. Sequins are compatible with all standards library preparation and sequencing methods. This protocol describes the laboratory steps required to re-suspend and spike the sequins into your DNA sample, as well as the bioinformatic steps required to analyze sequins in your output library. For further details on the design, validation and use of sequins, we refer users to ‘Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis’ by Hardwick et. al., (2018) Nature Communications.
Proper citation: Tim Mercer 2020. Using sequins in metagenome experiments.. protocols.io dx.doi.org/10.17504/protocols.io.bic3kayn Copy
Authors: Ashley Jones, Cynthia Torkel, David Stanley, Jamila Nasim, Justin Borevitz, Benjamin Schwessinger
Group: High molecular weight DNA extraction from all kingdoms
Summary: Rapid advancements in long-read sequencing technologies have transformed sequencing read lengths from bps to Mbps, which has enabled chromosome-scale genome assemblies. However, read lengths are now becoming limited by the extraction of pure high-molecular weight DNA suitable for long-read sequencing, which is particularly challenging in plants and fungi. To overcome this, we present a protocol collection; high-molecular weight DNA extraction, clean-up and size selection for long-read sequencing. We optimised a gentle magnetic bead based high-molecular weight DNA extraction, which is presented here in detail. The protocol circumvents spin columns and high-centrifugation, to limit DNA fragmentation. The protocol is scalable based on tissue input, which can be used on many species of plants, fungi, reptiles, insects and bacteria. It is also cost effective compared to kit-based protocols and hence applicable at scale at low resource settings. An optional sorbitol wash is listed and is highly recommended for plant and fungal tissues. To further remove any remaining contaminants such as phenols and polysaccharides, optional DNA clean-up and size selection strategies are given. This protocol collection is suitable for all common long-read sequencing platforms, such as technologies offered by PacBio and Nanopore. Using these protocols, sequencing on the Oxford Nanopore MinION can achieve read length N50 values of 30-50 kb, with reads exceeding 200 kb and outputs ranging from 15-30 Gbp. This has been routinely achieved with eucalypts, acacias, rice, themeda, wheat, wheat rusts, various other fungi, geckos, skinks, ticks, ladybird beetles, caterpillars and E. coli.
Proper citation: Ashley Jones, Cynthia Torkel, David Stanley, Jamila Nasim, Justin Borevitz, Benjamin Schwessinger 2021. High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing. protocols.io dx.doi.org/10.17504/protocols.io.bss7nehn Copy
Authors: Ethan Lippmann, Hannah Wilson, Emma Neal
Group: Neurodegeneration Method Development Community
Proper citation: Ethan Lippmann, Hannah Wilson, Emma Neal 2020. Protocol for Subculture of Differentiated Blood-Brain Barrier Endothelial Cells onto Plates and Filters. protocols.io dx.doi.org/10.17504/protocols.io.8g5hty6 Copy
Authors: Sarah Reiling, Marie-Michelle Simon, Anne-Marie Roy, Shu-Huang Chen, Josh Quick, Ioannis Ragoussis
Group: Coronavirus Method Development Community, McGill Genome Centre
Summary: How the Nextera DNA Flex Assay Works The Nextera DNA Flex library prep kit uses a bead-based transposome complex to tagment genomic DNA, which is a process that fragments DNA and then tags the DNA with adapter sequences in one step. After it is saturated with input DNA, the bead-based transposome complex fragments a set number of DNA molecules. This fragmentation provides flexibility to use a wide DNA input range to generate normalized libraries of consistent tight fragment size distribution. Following tagmentation, a limited-cycle PCR adds Nextera DNA Flex-specific index adapter sequences to the ends of a DNA fragment. This step enables capability across all Illumina sequencing platforms. A subsequent Sample Purification Beads (SPB) cleanup step then purifies libraries for use on an Illumina sequencer. The double-stranded DNA library is denatured before hybridization of the biotin probe oligonucleotide pool. PCR Amplicons for Nextera FlexWhen starting with PCR amplicons, the PCR amplicon must be > 150 bp. The standard clean up protocol depletes libraries Therefore, Illumina recommends that amplicons Shorter amplicons can otherwise be lost during the library cleanup step. Tagmentation cannot add an adapter directly to the distal end of a fragment, so a drop in sequencing coverage of ~50 bp from each distal end is expected. To ensure sufficient coverage of the amplicon target region, design primers to extend beyond the target region by 50 bp per end. More information can be found here: https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera_dna_flex/nextera-dna-flex-library-prep-reference-guide-1000000025416-07.pdf
Proper citation: Sarah Reiling, Marie-Michelle Simon, Anne-Marie Roy, Shu-Huang Chen, Josh Quick, Ioannis Ragoussis 2020. SARS-CoV-2 McGill Nextera Flex sequencing protocol_SS_V3_LA1_5uLRT. protocols.io dx.doi.org/10.17504/protocols.io.bisbkean Copy
Authors: Ian Mackay, Judy Northill
Group: Public Health Virology, Forensic and Scientific Services
Summary: This protocol was designed and developed at this laboratory.
The protocol specifically aims to amplify strains of Influenza B YAMAGATA virus lineage and not strains of the VICTORIA virus lineage or other virus species. The assay targets the haemagglutinin (HA) region and is designed as a qualitative lineage-typing test for human cases of seasonal influenza virus type B infections.
FluB-YAMA-TM2018 is ideally used alongside its companion protocol, "Influenza B virus VICTORIA lineage TaqMan 2018" (FluB-VICT-TM2018), which aims to target influenza B virus VICTORIA lineage strains exclusively. The two assays perform best as UNIPLEX protocols; a drop in sensitivity was observed when combined in a DUPLEX format.
Proper citation: Ian Mackay, Judy Northill 2018. Influenza B virus YAMAGATA lineage TaqMan 2018 / FluB-YAMA-TM2018. protocols.io dx.doi.org/10.17504/protocols.io.rdid24e Copy
Authors: Jon Arizti-Sanz, Catherine A. Freije, Chloe K. Boehm, Sameed M. Siddiqui, Allen M. Goodman, Tinna-Solveig F. Kosoko-Thoroddsen, A'Doriann Y. Bradley, Jeremy Johnson, Pardis C. Sabeti, Cameron Myhrvold
Group: XPRIZE Rapid Covid Testing
Summary: This protocol describes how to perform a SHINE paper-based assay to detect SARS-CoV-2 RNA from a self-collected saliva sample. This protocol is intended for in-home use. All enzymatic components are provided as a single-test freeze-dried pellet for shelf-stable storage, and all steps of the protocol are performed at ambient temperature. The protocol presented here is an improved version of the method presented in Arizti-Sanz J*, Freije CA*, et al. Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2. bioRxiv (2020).
Proper citation: Jon Arizti-Sanz, Catherine A. Freije, Chloe K. Boehm, Sameed M. Siddiqui, Allen M. Goodman, Tinna-Solveig F. Kosoko-Thoroddsen, A'Doriann Y. Bradley, Jeremy Johnson, Pardis C. Sabeti, Cameron Myhrvold 2020. XPRIZE SHINE - Paper-based SARS-CoV-2 Saliva Test. protocols.io dx.doi.org/10.17504/protocols.io.bk2fkybn Copy
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:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
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 sources that were queried against in your search that you can investigate further.
Here are the categories present within dkNET that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
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
