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 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Marchantia Protoplast Isolation Resource Report Resource Website |
Christian Boehm | 10.17504/protocols.io.gmubu6w | OpenPlant Project, Plantae | Marchantia protoplast preparation (adapted from Bopp and Vicktor 1988) | University of Cambridge | 1 | 2016 | Christian Boehm 2016. Marchantia Protoplast Isolation. protocols.io dx.doi.org/10.17504/protocols.io.gmubu6w | 2021-03-29 03:08:57 | |||
|
Direct nuclear tagmentation and RNA-sequencing (DNTR-seq) Resource Report Resource Website |
Vasilios Zachariadis, Huaitao Cheng, Nathanael Andrews, Martin Enge | 10.17504/protocols.io.bdthi6j6 | Enge lab | Understanding how genetic variation alters gene expression - how genotype affects phenotype - is a central challenge in biology. To address this question in complex cell mixtures, we developed Direct Nuclear Tagmentation and RNA-sequencing (DNTR-seq), which enables whole genome and mRNA sequencing jointly in single cells. | Karolinska Institutet, Karolinska Institutet, Karolinska Institutet, Karolinska Institutet | https://www.biorxiv.org/content/10.1101/2020.03.04.976530v1.full | 1 | 2020 | Vasilios Zachariadis, Huaitao Cheng, Nathanael Andrews, Martin Enge 2020. Direct nuclear tagmentation and RNA-sequencing (DNTR-seq). protocols.io dx.doi.org/10.17504/protocols.io.bdthi6j6 | 2021-03-29 03:08:57 | ||
|
Core Protocol for Serial Imaging of Fluorescently-Labeled Mouse Brain on the TissueCyte 1000 System Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bbx4ipqw | BICCN, Allen Institute for Brain Science | This protocol describes the instructions for setup and scanning of fluorescently-labeled tissue sections mounted in agarose and attached to a slide using the TissueCyte 1000 block face 2-photon system. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Core Protocol for Serial Imaging of Fluorescently-Labeled Mouse Brain on the TissueCyte 1000 System. protocols.io dx.doi.org/10.17504/protocols.io.bbx4ipqw | 2021-03-29 03:08:57 | |||
|
Diatom DNA library preparation for Illumina Miseq Sequencing using the rbcL marker gene Resource Report Resource Website |
Cecile Chardon, Valentin Vasselon, Marine Vautier, Sonia Lacroix, Agnès Bouchez, Frédéric Rimet, Isabelle Domaizon | 10.17504/protocols.io.bd94i98w | EcoALpsWater | This protocol is part of the DNA workflow applied in the Eco-ALpsWater Project, here in particular to characterize the diversity of diatom assemblage in biofilms or plankton samples.Different studies have already revealed the potential of diatom metabarcoding applications for freshwater quality assessment (Kermarrec et al. 2014; Vasselon et al. 2017ab; Visco et al. 2015). The choice of the marker gene and barcode region is key for obtaining relevant inventories of diversity and precise taxonomic assignment. For benthic diatoms, the rbcL gene has proved to be an appropriate taxonomic marker for biomonitoring (Kermarrec et al. 2013, 2014; Vasselon et al. 2017a,b) and a well‐curated barcode reference library is already available to assign species names to rbcL sequences (R‐Syst::diatom, Rimet et al. 2016).For the Eco-AlpsWater project, biolfilms sampled in rivers and lakeshores are collected as described in the dedicated protocols (“Lake plankton sample collection ...” and “Biofilms sample collection ...”) and DNA is extracted as described in the protocol “Biofilms DNA extraction” ; all these protocols are part of the Deliverable D.T1.1.2. We present here the following step in the DNA workflow (i.e. PCR amplification of selected barcodes, and wet lab methods to prepare DNA library for downstream MiSeq Sequencing). This protocol has been used in recent studies (e.g. Keck et al 2018 ; Vasselon et al 2018) where diatoms metabarcoding has been used for ecological assessment of rivers.Several primers were proposed in the literature to characterize Diatom communities through environmental DNA metabarcoding approaches, including the 18S, COI and rbcL barcodes. Following the recommendation provided by Kermarrec et al. 2014, who compared the efficiency of those 3 barcodes to accurately characterize diatom communities from freshwater samples (lakes and rivers), the rbcL barcode will be used within the Eco-AlpsWater project as he provides a good taxonomical resolution. | INRAE, CARRTEL, Pole R&D ECLA, Thonon les bains, France, Office Français pour la Biodiversité, Pole R&D ECLA, Thonon les bains, France, INRAE, CARRTEL, Pole R&D ECLA, Thonon les bains, France, INRAE, CARRTEL, Pole R&D ECLA, Thonon les bains, France, INRAE, CARRTEL, Pole R&D ECLA, Thonon les bains, France, INRAE, CARRTEL, Pole R&D ECLA, Thonon les bains, France, INRAE, CARRTEL, Pole R&D ECLA, Thonon les bains, France | 1 | 2020 | Cecile Chardon, Valentin Vasselon, Marine Vautier, Sonia Lacroix, Agnès Bouchez, Frédéric Rimet, Isabelle Domaizon 2020. Diatom DNA library preparation for Illumina Miseq Sequencing using the rbcL marker gene . protocols.io dx.doi.org/10.17504/protocols.io.bd94i98w | 2021-03-29 03:08:58 | |||
|
Demultiplexing Nanopore reads with LAST Resource Report Resource Website |
David Eccles | 10.17504/protocols.io.xj3fkqn | High molecular weight DNA extraction from all kingdoms | This protocol is for a semi-manual method for read demultiplexing, as used after my presentation Sequencing DNA with Linux Cores and Nanopores to work out the number of reads captured by different barcodes.Input: reads as a FASTQ file, barcode sequences as a FASTA fileOutput: reads split into single FASTQ files per target [barcode]Note: barcode / adapter sequences are not trimmed by this protocol | Malaghan Institute of Medical Research (NZ) | https://doi.org/10.5281/zenodo.2535894 | 1 | 2019 | David Eccles 2019. Demultiplexing Nanopore reads with LAST. protocols.io dx.doi.org/10.17504/protocols.io.xj3fkqn | 2021-03-29 03:08:58 | ||
|
Universal Immunoblot analysis for investigating Protein-AG (SpAG)-binding to avian and mammalian immunoglobulins. Resource Report Resource Website |
Angel Justiz-Vaillant | 10.17504/protocols.io.bjseknbe | A protein that combines the binding capacity of SpA and SpG is not comercially available. It can be easy created in the laboratory by combining these two immunoglobulin-binding proteins to horseradish peroxidase by the periodate method [1]. However, a mixture of SpA and SpG could have the same effect as universal reagent in immunodetection. 1. Vaillant AJ, McFarlane-Andersonv N, Wisdom B, Mohammed W, Vuma S, et al. (2013) Immunoglobulin-binding Bacterial Proteins (IBP) Conjugates and their Reactivity with Immunoglobulin in Enzyme-Linked Immunosorbent Assays (ELISA). J Anal Bioanal Tech 4: 175. doi:10.4172/2155-9872.1000175 | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. Universal Immunoblot analysis for investigating Protein-AG (SpAG)-binding to avian and mammalian immunoglobulins.. protocols.io dx.doi.org/10.17504/protocols.io.bjseknbe | 2021-03-29 03:08:58 | ||||
|
ECOGEO 'Omics Training: 3.1 Amplicon Analysis - Mothur Resource Report Resource Website |
Ben Tully | 10.17504/protocols.io.fi4bkgw | ECOGEO | mothur is a bioinformatics tool for analyzing 16S rRNA gene sequences, which can be used to process data generated by Sanger, PacBio, IonTorrent, 454, and Illumina (MiSeq/HiSeq). | EarthCube Oceanography and Geobiology Environmental 'Omics | 2 | 2016 | Ben Tully 2016. ECOGEO 'Omics Training: 3.1 Amplicon Analysis - Mothur. protocols.io dx.doi.org/10.17504/protocols.io.fi4bkgw | 2021-03-29 03:08:57 | |||
|
High quality DNA extraction from very small individual insects Resource Report Resource Website |
Sam Mugford, Roland Wouters, Thomas C Mathers, Saskia Hogenhout | 10.17504/protocols.io.bg6wjzfe | Genomic studies of natural populations frequently benefit by having data from single individuals. This approach has a number of advantages: it avoids the risk of accidently pooling together individuals of closely related species, and it enables better resolution of haplotypes by separating non-identical individuals. However, especially in the case of very small invertebrates, recovering sufficient nucleic acid from individual samples can be challenging. Here we present a method suitable for extraction of DNA from single individual aphids (weighing approximately 0.5mg). We are able to recover 100’s of ng of high-quality DNA suitable for whole-genome sequencing using short-read technologies. DNA extraction using Cetrimonium bromide (CTAB) is a tried and tested method, and the protocol presented here is adapted from that of Marzachì et al. (1998). We present some modifications to optimize this popular method to maximize yield and quality from small single insect samples.We have used this method across a range of aphid species, and also other sap-sucking hemipteran insects. It has enabled sequencing and de-novo assembly of a range of species from single individuals collected from the field, and also resequencing of individuals of the model aphid Myzus persicae. This is compatible with the method of ambient storage of dehydrated filed collected samples we describe in Wouters et al. (2020).Marzachì, C, Veratti, F, & Bosco, D (1998). Direct PCR detection of phytoplasmas in experimentally infected insects. Annals of Applied Biology, 133(1), 45-54.Wouters, R; Mugford S, & Hogenhout, S (2020). Ambient sample storage system of field-collected insect samples for genomics. protocols.io dx.doi.org/10.17504/protocols.io.bgxnjxme | John Innes Centre, Norwich, UK, John Innes Centre, Norwich, UK, John Innes Centre, Norwich, UK, John Innes Centre, Norwich, UK | 1 | 2020 | Sam Mugford, Roland Wouters, Thomas C Mathers, Saskia Hogenhout 2020. High quality DNA extraction from very small individual insects. protocols.io dx.doi.org/10.17504/protocols.io.bg6wjzfe | 2021-03-29 03:08:57 | ||||
|
Transformation of Phaeodactylum tricornutum by electroporation Resource Report Resource Website |
Gina Filloramo | 10.17504/protocols.io.s4cegsw | Protist Research to Optimize Tools in Genetics (PROT-G) | Successful transformation of Phaeodactylum tricornutum (CMP632) by electroporation was achieved based on a modified version of Zhang & Hu (2014). | Dalhousie University | Zhang, C., & Hu, H. (2014). High-efficiency nuclear transformation of the diatom Phaeodactylum tricornutum by electroporation. Marine genomics, 16, 63-66. | 1 | 2018 | Gina Filloramo 2018. Transformation of Phaeodactylum tricornutum by electroporation. protocols.io dx.doi.org/10.17504/protocols.io.s4cegsw | 2021-03-29 03:08:58 | ||
|
Tau Thioflavin T Assay Resource Report Resource Website |
Alexandra Netter-Glangeaud | 10.17504/protocols.io.wxgffjw | StressMarq | StressMarq Biosciences Inc | https://www.stressmarq.com/support/technical-support/protocols/tau-protocol/ | 1 | 2019 | Alexandra Netter-Glangeaud 2019. Tau Thioflavin T Assay. protocols.io dx.doi.org/10.17504/protocols.io.wxgffjw | 2021-03-29 03:08:57 | |||
|
Plasmid Modification by Annealed Oligo Cloning Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | 10.17504/protocols.io.47tgznn | This protocol describes plasmid modification by annealed oligo cloning. To see the full abstract and additional resources, please visit the Addgene protocol page. | Addgene | https://www.addgene.org/protocols/annealed-oligo-cloning/ | 1 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. Plasmid Modification by Annealed Oligo Cloning. protocols.io dx.doi.org/10.17504/protocols.io.47tgznn | 2021-03-29 03:08:57 | |||
|
Fixation of marine samples for flow cytometry sorting Resource Report Resource Website |
Daniel Vaulot | 10.17504/protocols.io.d2x8fm | Ecology of Marine Plankton (ECOMAP) team - Roscoff | Protocol to fix marine samples for flow cytometry sorting of phytoplankton. Fix at least 2 samples per depth sampled and at least 6 to 10 depths per vertical profile.Back to the laboratory, pico and nano-plankton populations can be sorted and used for clone library construction or metabarcoding with Next Generation Sequencing (e.g. Illumina). This was successfully tested on samples from a cruise off Brazil (unpublished data)ReferenceRibeiro C., Lopes A., Marie D., Vaulot D. Unpublished data | Station Biologique, Roscoff, France | 1 | 2015 | Daniel Vaulot 2015. Fixation of marine samples for flow cytometry sorting. protocols.io dx.doi.org/10.17504/protocols.io.d2x8fm | 2021-03-29 03:08:57 | |||
|
Modified Qiagen PCR purification (no gel extraction) with MinElute spin column. Resource Report Resource Website |
Daniel Richter | 10.17504/protocols.io.ivece3e | Ecology of Marine Plankton (ECOMAP) team - Roscoff, Protist Research to Optimize Tools in Genetics (PROT-G) |
Richter, Daniel J and Fozouni, Parinaz and Eisen, Michael and King, Nicole. Gene family innovation, conservation and loss on the animal stem lineage. 2018;7:e34226 https://doi.org/10.7554/eLife.34226 |
https://elifesciences.org/articles/34226 | 1 | 2017 | Daniel Richter 2017. Modified Qiagen PCR purification (no gel extraction) with MinElute spin column.. protocols.io dx.doi.org/10.17504/protocols.io.ivece3e | 2021-03-29 03:08:59 | |||
|
Preparation of Chemically Competent Cells Resource Report Resource Website |
Nus Igem | 10.17504/protocols.io.7pnhmme | National University of Singapore | 1 | 2019 | Nus Igem 2019. Preparation of Chemically Competent Cells. protocols.io dx.doi.org/10.17504/protocols.io.7pnhmme | 2021-03-29 03:08:59 | |||||
|
Triterpene extraction protocol from Synechocystis sp. PCC6803 Resource Report Resource Website |
Maximilian Dietsch, Vera Wewer | 10.17504/protocols.io.mspc6dn | Axmann Lab, CyanoWorld | In this protocol, the extraction of naturally occurring as well as heterologously synthesized triterpenes in Synechocystis and R. capsulatus are described | Institute for Synthetic Microbiology, Heinrich-Heine University, Düsseldorf, Biocenter MS platform, University of Cologne | 2 | 2018 | Maximilian Dietsch, Vera Wewer 2018. Triterpene extraction protocol from Synechocystis sp. PCC6803. protocols.io dx.doi.org/10.17504/protocols.io.mspc6dn | 2021-03-29 03:08:59 | |||
|
DNA extraction and Sequencing Resource Report Resource Website |
avinash.kale | 10.17504/protocols.io.bjdxki7n | UM-DAE Centre for Excellence in Basic Sciences | domnic colvin | 1 | 2020 | avinash.kale 2020. DNA extraction and Sequencing. protocols.io dx.doi.org/10.17504/protocols.io.bjdxki7n | 2021-03-29 03:08:59 | ||||
|
Does Perineural Clonidine Prolong the Duration of an Adductor Canal Block When Controlling for Possible Systemic effects? - A Randomized Paired Trial in Healthy Volunteers Resource Report Resource Website |
Jakob H. Andersen | 10.17504/protocols.io.hsnb6de | Andersen JH, Jaeger P, Sonne TL, Dahl JB, Mathiesen O, Grevstad U (2017) Clonidine used as a perineural adjuvant to ropivacaine, does not prolong the duration of sensory block when controlling for systemic effects: A paired, blinded, randomized trial in healthy volunteers. PLoS ONE 12(9): e0181351. doi: 10.1371/journal.pone.0181351 | https://doi.org/10.1371/journal.pone.0181351 | 1 | 2017 | Jakob H. Andersen 2017. Does Perineural Clonidine Prolong the Duration of an Adductor Canal Block When Controlling for Possible Systemic effects? - A Randomized Paired Trial in Healthy Volunteers. protocols.io dx.doi.org/10.17504/protocols.io.hsnb6de | 2021-03-29 03:08:59 | ||||
|
Meta-analysis of scope harvesting radial artery Resource Report Resource Website |
Tzu-yen Huang | 10.17504/protocols.io.bhrdj526 | Huang T, Huang T, Cheng Y, Wang Y, Chen T, Yin S, Yeh C (2020) Radial artery harvesting in coronary artery bypass grafting surgery—Endoscopic or open method? A meta-analysis. PLoS ONE 15(7): e0236499. doi: 10.1371/journal.pone.0236499 | Chang Gung Memorial Hospital, Keelung | https://doi.org/10.1371/journal.pone.0236499 | 1 | 2020 | Tzu-yen Huang 2020. Meta-analysis of scope harvesting radial artery. protocols.io dx.doi.org/10.17504/protocols.io.bhrdj526 | 2021-03-29 03:08:58 | |||
|
Methods from: The influence of agricultural tillage practices on soil biodiversity Resource Report Resource Website |
Jeff Strohm, Robert Hanner, Richard J Heck | 10.17504/protocols.io.efsbbne | This is a collection of methods from [tentative citation]: Jeff Strohm, Robert Hanner, Richard J Heck. (2018) A metabarcoding perspective on soil biodiversity under different tillage treatments. Submitted to Metabarcoding and Metagenomics | University of Guelph, University of Guelph, University of Guelph | 1 | 2018 | Jeff Strohm, Robert Hanner, Richard J Heck 2018. Methods from: The influence of agricultural tillage practices on soil biodiversity. protocols.io dx.doi.org/10.17504/protocols.io.efsbbne | 2021-03-29 03:08:56 | ||||
|
SpinSmart PCR Purification and Gel Purification Procedures Resource Report Resource Website |
Denville Scientific | 10.17504/protocols.io.gr6bv9e | Denville Scientific, Inc. | The SpinSmart PCR purification and gel extraction technologies utilize a lysis buffer containing chaotropic salts that allow DNA to bind to a silica membrane. Binding buffer PCR 1 is added to a PCR reaction or agarose gel slice; the mixture is subsequently loaded directly onto SpinSmart PCR Columns. Salts, enzymes, and other soluble components are washed away with ethanolic PCR 2 Wash buffer. Purified DNA is eluted using PCR 3 Elution buffer (5 mM Tris/HCl, pH 8.5). Please follow one of the protocols below, depending on whether you are doing a DNA gel extraction or PCR purification. | https://www.denvillescientific.com/products/spinsmart%E2%84%A2-pcr-purification-gel-extraction-columns-only--with-collection-tubes--50-per-pack | 1 | 2016 | Denville Scientific 2016. SpinSmart PCR Purification and Gel Purification Procedures. protocols.io dx.doi.org/10.17504/protocols.io.gr6bv9e | 2021-03-29 03:08:56 |
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
