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 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SYBR Gold working solutions Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.c7azid | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Li Deng 2016. SYBR Gold working solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.c7azid | 2021-04-15 09:15:17 | ||||
|
Single molecule FISH Resource Report Resource Website |
Thuc Nguyen, Emma Garren | DOI:10.17504/protocols.io.xb2fiqe | CZI Spatial Transcriptomics Protocol Repository | This protocol describes multiround hybrization of directly-conjugated FISH probes for single molecule RNA detection. Thin tissue sections (10-μm) are placed onto silanized coverslips (24x50) that fit onto an ASI imaging chamber. A SecureSeal chamber is placed around the sections, which act as a reaction chamber and imaging chamber. | Allen Institute for Brain Science, Allen Institute for Brain Science | 1 | 2019 | Thuc Nguyen, Emma Garren 2019. Single molecule FISH. protocols.io https://dx.doi.org/10.17504/protocols.io.xb2fiqe | 2021-04-15 09:15:17 | |||
|
ChroSpin - IMAC Resource Report Resource Website |
Alexandra Ehl, David Frommholz, Nadine Stefanczyk | DOI:10.17504/protocols.io.tv3en8n | Purification Guide for the Isolation of Histidine-tagged Proteins with ChroSpin Columns by DALEX Biotech.ChroSpin-IMAC by DALEX Biotech offers a robust and convenient way to isolate polyhistidine-tagged proteins from bacterial, mammalian, and insect cell cultures.Immobilized metal affinity chromatography (IMAC) is based on the interaction of the imidazole ring of histidine with transition metal ions immobilized on a solid support. Recombinant proteins with a 3 - 10 histidine fusion tag bind to these metal ions while unwanted proteins are removed by washing with excess binding buffer. Elution of the target protein is achieved by the addition of imidazole, EDTA or a low pH. Easy and quick small scale fusion protein purification from various sources.Low metal leaching from column.Tolerates reducing reagents (e.g. DTT up to 10 mM).The proprietary resin does not shrink or swell in aqueous buffers.High pressure stability.pH stability short term 2 - 8, long term 3 - 8.Excellent thermal stability up to 15 minutes at 120 °C in aqueous buffers at neutral pH.Can be dried for long term storage (80 °C for > 2 h). | DALEX Biotech, DALEX Biotech, DALEX Biotech | https://dalex-biotech.com | 1 | 2018 | Alexandra Ehl, David Frommholz, Nadine Stefanczyk 2018. ChroSpin - IMAC. protocols.io https://dx.doi.org/10.17504/protocols.io.tv3en8n | 2021-04-15 09:15:18 | |||
|
Post-Fixation Heavy Metal Staining and Resin Embedding for Electron Microscopy (EM) Resource Report Resource Website |
Jessica Riesterer, Erin Stempinski, Claudia Lopez | DOI:10.17504/protocols.io.36vgre6 | NCIHTAN | Tissues, cell monolayers, organoids and xenografts all image differently depending on the sample preparation method utilized. Moreover, the same tissue type from different species may also need different fixation solution and processing methods to have optimal contrast and charge mitigation when the same microscope is used (Borrett & Hughes, 2016; Kizilyaprak, Longo, Daraspe, & Humbel, 2015; Kopek et al., 2017). For example, brain tissue may be processed successfully using a protocol that yields poor images when applied to cancer tissues (unpublished data). Researchers are therefore encouraged to dive into the literature and test new sample preparation protocols for a specific sample-type. Also, and if available, having the ability to evaluate the use of FIB-SEM versus SBF-SEM will help the researcher to design a data collection strategy. The protocols evaluated during development of this workflow included the Dresden protocol (Paridaen, Wilsch-Bräuninger, & Huttner, 2013), Renovo (Mukherjee et al., 2016) and the Hua method (Hua, Laserstein, & Helmstaedter, 2015). We settled on the the Hua method with some modifications as described below, for human cancer biopsies. The final protocol described is sufficient for large format mapping and 3DEM FIB-SEM and SBF-SEM, eliminating the need for multiple samples processed with different protocols. In the case of biopsy tissue, where sample acquisition is limited and precious, flexibility is an important advantage of this workflow. | Oregon Health and Sciences University, Oregon Health and Sciences University, Oregon Health and Sciences University | 1 | 2019 | Jessica Riesterer, Erin Stempinski, Claudia Lopez 2019. Post-Fixation Heavy Metal Staining and Resin Embedding for Electron Microscopy (EM). protocols.io https://dx.doi.org/10.17504/protocols.io.36vgre6 | 2021-04-15 09:15:17 | |||
|
Script R11: Replication Cycle Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.ejfbcjn | VERVE Net, Club Grice | This section outlines the analyses we used in our replication cycle section of our report. We first predict how many contigs are potentially of the temperate replication cycle and display this information using a Euler diagram. We then use a relative abundance approach by visualizing the percent of temperate phages present at each site. We end by visualizing the relative abundances of bacteria annotations of the phage contigs. 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. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script R11: Replication Cycle. protocols.io https://dx.doi.org/10.17504/protocols.io.ejfbcjn | 2021-04-15 09:15:46 | |
|
Dissection and immunohistochemistry of mouse vagal ganglia Resource Report Resource Website |
Thomas Taylor-Clark, Seol-Hee Kim | DOI:10.17504/protocols.io.baumieu6 | SPARC | Mice are euthanized, perfused with fixative and the vagal ganglia extracted. Vagal ganglia are then cyosectioned. Slices are stained for protein expression using immunohistochemistry. Expression of specific proteins and reporter proteins isarevisualized using microscopy. | University of South Florida, University of South Florida | 3 | 2019 | Thomas Taylor-Clark, Seol-Hee Kim 2019. Dissection and immunohistochemistry of mouse vagal ganglia. protocols.io https://dx.doi.org/10.17504/protocols.io.baumieu6 | 2021-04-15 09:15:17 | |||
|
Transformation of supercompetent cells Resource Report Resource Website |
Dave Lunt | DOI:10.17504/protocols.io.etubenw | EvoHull | Protocol to prepare E. coli supercompetent cells to transform with plasmid/ligation. This protocol is originally derived from Hanahan, D. (1983) J. Mol. Biol. 166:557-580 with some changes. This version works exceptionally well for cloning PCR products where the number of colonies is not expected to be as high as from some ligations. These cells outperform commercially purchased supercompetent cells in my hands. | University of Hull, UK | 2 | 2016 | Dave Lunt 2016. Transformation of supercompetent cells. protocols.io https://dx.doi.org/10.17504/protocols.io.etubenw | 2021-04-15 09:15:17 | |||
|
Rqtl_code Resource Report Resource Website |
Anna Miller | DOI:10.17504/protocols.io.bmwtk7en | Miller AK, Chen A, Bartlett J, Wang L, Williams SM, Buchner DA, A Novel Mapping Strategy Utilizing Mouse Chromosome Substitution Strains Identifies Multiple Epistatic Interactions That Regulate Complex Traits. G3: Genes|Genomes|Genetics 10(12). doi: 10.1534/g3.120.401824 | Case Western Reserve University | https://doi.org/10.1534/g3.120.401824 | 3 | 2020 | Anna Miller 2020. Rqtl_code. protocols.io https://dx.doi.org/10.17504/protocols.io.bmwtk7en | 2021-04-15 09:15:18 | |||
|
Protocol Temephos Bioassay Resource Report Resource Website |
Lara Ferrero Gomez | DOI:10.17504/protocols.io.bbstinen | Performing bioassays to assess the larval susceptibility to Temephos | Pires S, Alves J, Dia I, Gómez LF (2020) Susceptibility of mosquito vectors of the city of Praia, Cabo Verde, to Temephos and Bacillus thuringiensis var israelensis. PLoS ONE 15(6): e0234242. doi: 10.1371/journal.pone.0234242 | [Universidade Jean Piaget de Cabo Verde] | https://doi.org/10.1371/journal.pone.0234242 | 1 | 2020 | Lara Ferrero Gomez 2020. Protocol Temephos Bioassay. protocols.io https://dx.doi.org/10.17504/protocols.io.bbstinen | 2021-04-15 09:15:18 | ||
|
Cell Surface Flow Cytometry Staining Protocol Resource Report Resource Website |
Sam Li | DOI:10.17504/protocols.io.baa9iah6 | BioLegend | BioLegend | https://www.biolegend.com/protocols/cell-surface-flow-cytometry-staining-protocol/4283/ | 4 | 2019 | Sam Li 2019. Cell Surface Flow Cytometry Staining Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.baa9iah6 | 2021-04-15 09:15:18 | |||
|
Quick Protocol for Monarch® PCR & DNA Cleanup Kit (5 ?g) (NEB #T1030) Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.ejxbcpn | New England Biolabs (NEB) | This is the "quick" version of Monarch® PCR & DNA Cleanup Kit (5 μg) Protocol (NEB #T1030). For the full protocol, please click here. | New England Biolabs | https://www.neb.com/protocols/2015/12/08/quick-protocol-for-monarch-pcr-dna-cleanup-kit-5-g-t1030 | 1 | 2016 | New England Biolabs 2016. Quick Protocol for Monarch® PCR & DNA Cleanup Kit (5 ?g) (NEB #T1030). protocols.io https://dx.doi.org/10.17504/protocols.io.ejxbcpn | 2021-04-15 09:15:18 | ||
|
Cell lysis, detergent-free Resource Report Resource Website |
Teesha Luehr | DOI:10.17504/protocols.io.y4ffytn | Leonard Foster's Lab | Detergents are generally not compatible with mass spectrometers, so this is a detergent-free method of cell lysis that is compatible with mass spectrometry. Since this protocol does not have a precipitation step, it saves time and minimizes sample loss as well. | University of British Columbia | 1 | 2019 | Teesha Luehr 2019. Cell lysis, detergent-free. protocols.io https://dx.doi.org/10.17504/protocols.io.y4ffytn | 2021-04-15 09:15:18 | |||
|
Bicinchoninic acid Acid Protein Concentration measurement Resource Report Resource Website |
JCPrice | Chemistry 586 Advanced Biochemical Methods | BYU | 1 | 2020 | JCPrice 2020. Bicinchoninic acid Acid Protein Concentration measurement . protocols.io https:// | 2021-04-15 09:15:17 | |||||
|
Field Genomics Protocols Resource Report Resource Website |
Mrinalini Watsa, Gideon Erkenswick, Stefan Prost, Aaron Pomerantz | DOI:10.17504/protocols.io.9dnh25e | This collection of protocols are examples of protocols used for education in high throughput sequencing with Oxford Nanopore Technology's MinION sequencer. | Watsa M, Erkenswick GA, Pomerantz A, Prost S (2020) Portable sequencing as a teaching tool in conservation and biodiversity research. PLoS Biol 18(4): e3000667. doi: 10.1371/journal.pbio.3000667 | Washington University, Saint Louis, University of Missouri - Saint Louis, Field Projects International, University of Missouri - Saint Louis, Washington University, Saint Louis, Field Projects International, Senckenberg Museum, University of California, Berkeley | https://doi.org/10.1371/journal.pbio.3000667 | 1 | 2019 | Mrinalini Watsa, Gideon Erkenswick, Stefan Prost, Aaron Pomerantz 2019. Field Genomics Protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.9dnh25e | 2021-04-15 09:15:18 | ||
|
Gamma-diversity partitioning of gobiid fishes (Teleostei: Gobiidae) ensemble along of Eastern Tropical Pacific: biological inventory, latitudinal variation and species turnover Resource Report Resource Website |
Omar Valencia | DOI:10.17504/protocols.io.sbfeajn | Evaluation of β-diversity partitioning in its spatial species turnover (BJTU) and nestedness (BJNE) components along a latitudinal gradient across. | Valencia-Méndez O, Rodríguez-Zaragoza FA, Calderon-Aguilera LE, Domínguez-Domínguez O, López-Pérez A (2018) Gamma-diversity partitioning of gobiid fishes (Teleostei: Gobiidae) ensemble along of Eastern Tropical Pacific: Biological inventory, latitudinal variation and species turnover. PLoS ONE 13(8): e0202863. doi: 10.1371/journal.pone.0202863 | Universidad Autónoma Metropolitana - Iztapalapa | https://doi.org/10.1371/journal.pone.0202863 | 2 | 2018 | Omar Valencia 2018. Gamma-diversity partitioning of gobiid fishes (Teleostei: Gobiidae) ensemble along of Eastern Tropical Pacific: biological inventory, latitudinal variation and species turnover. protocols.io https://dx.doi.org/10.17504/protocols.io.sbfeajn | 2021-04-15 09:15:18 | ||
|
Q5 Polymerase PCR Cloning Resource Report Resource Website |
Nus Igem | DOI:10.17504/protocols.io.7pqhmmw | National University of Singapore | 1 | 2019 | Nus Igem 2019. Q5 Polymerase PCR Cloning. protocols.io https://dx.doi.org/10.17504/protocols.io.7pqhmmw | 2021-04-15 09:15:17 | |||||
|
Orthopoxvirus real-time PCR Resource Report Resource Website |
Judy Northill, David Warrilow, Ian Mackay | DOI:10.17504/protocols.io.n43dgyn | Public Health Virology, Forensic and Scientific Services | A real-time PCR targeting the DNA-dependent RNA polymerase of Orthopoxviruses.This protocol was designed and developed at this laboratory. | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 3 | 2018 | Judy Northill, David Warrilow, Ian Mackay 2018. Orthopoxvirus real-time PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.n43dgyn | 2021-04-15 09:15:46 | |||
|
PCL:PEG Electrospinning Resource Report Resource Website |
Kenneth Schackart, Kattika Kaarj | DOI:10.17504/protocols.io.yaffsbn | 481b Laboratory | This protocol details how to electrospin a PCL:PEG copolymer onto glass cover slip. | University of Arizona, University of Arizona | 1 | 2019 | Kenneth Schackart, Kattika Kaarj 2019. PCL:PEG Electrospinning. protocols.io https://dx.doi.org/10.17504/protocols.io.yaffsbn | 2021-04-15 09:15:17 | |||
|
Neuro2a cell DNA plasmid transfection (PolyJet) Resource Report Resource Website |
Christopher Bartley | DOI:10.17504/protocols.io.cqmvu5 | Transfection of Neuro2a cells with PolyJet | UCSF | 1 | 2015 | Christopher Bartley 2015. Neuro2a cell DNA plasmid transfection (PolyJet). protocols.io https://dx.doi.org/10.17504/protocols.io.cqmvu5 | 2021-04-15 09:15:45 | ||||
|
OD and GFP Plate Reader Assay (72 h Measurement) Resource Report Resource Website |
Alba Balletbó | DOI:10.17504/protocols.io.8aihsce | iGEM Wageningen 2019 | Fluorescence measurements of Optical Density (OD) and Green fluorescent protein (GFP) in Escherichia coli. | Wageningen University | 1 | 2019 | Alba Balletbó 2019. OD and GFP Plate Reader Assay (72 h Measurement). protocols.io https://dx.doi.org/10.17504/protocols.io.8aihsce | 2021-04-15 09:15:17 |
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
