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 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Determination of minimum inhibitory concentration values (MICs) against Sporothrix brasiliensis and Sporothrix schenckii Resource Report Resource Website |
luanaborba | 10.17504/protocols.io.bjfbkjin | L. P. Borba-Santos | Universidade Federal do Rio de Janeiro | 1 | 2020 | luanaborba 2020. Determination of minimum inhibitory concentration values (MICs) against Sporothrix brasiliensis and Sporothrix schenckii. protocols.io dx.doi.org/10.17504/protocols.io.bjfbkjin | 2021-03-29 03:09:56 | ||||
|
LyGo protocol collection Resource Report Resource Website |
Kristoffer Bach Falkenberg, Maja Rennig, Cristina Hernandez Rollan, Andreas Birk Bertelsen, Morten Norholm | 10.17504/protocols.io.9nvh5e6 | Technical University of Denmark, Technical University of Denmark, Technical University of Denmark, Technical University of Denmark, Technical University of Denmark | 1 | 2020 | Kristoffer Bach Falkenberg, Maja Rennig, Cristina Hernandez Rollan, Andreas Birk Bertelsen, Morten Norholm 2020. LyGo protocol collection. protocols.io dx.doi.org/10.17504/protocols.io.9nvh5e6 | 2021-03-29 03:10:00 | |||||
|
Fluorescent Focus Unit Assay using LICOR Imaging System Resource Report Resource Website |
Bernardo Mainou | 10.17504/protocols.io.kqicvue | Indirect immunofluorescence infectivity assay for reovirus using LICOR Imaging System | Berger AK, Yi H, Kearns DB, Mainou BA (2017) Bacteria and bacterial envelope components enhance mammalian reovirus thermostability. PLoS Pathog 13(12): e1006768. doi: 10.1371/journal.ppat.1006768 | Emory University | https://doi.org/10.1371/journal.ppat.1006768 | 1 | 2017 | Bernardo Mainou 2017. Fluorescent Focus Unit Assay using LICOR Imaging System. protocols.io dx.doi.org/10.17504/protocols.io.kqicvue | 2021-03-29 03:10:00 | ||
|
Transcription Factor-Mediated Differentiation of Human iPSCs into Neurons Resource Report Resource Website |
Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | 10.17504/protocols.io.54rg8v6 | Neurodegeneration Method Development Community | Accurate modeling of human neuronal cell biology has been a long-standing challenge. However, methods to differentiate human induced pluripotent stem cells (iPSCs) to neurons have recently provided experimentally tractable cell models. Numerous methods that use small molecules to direct iPSCs into neuronal lineages have arisen in recent years. Unfortunately, these methods entail numerous challenges, including poor efficiency, variable cell type heterogeneity, and lengthy, expensive differentiation procedures. We recently developed a new method to generate stable transgenic lines of human iPSCs with doxycycline-inducible transcription factors at safe-harbor loci. Using a simple two-step protocol, these lines can be inducibly differentiated into either cortical (i3Neurons) or lower motor neurons (i3LMN) in a rapid, efficient, and scalable manner (Wang et al., 2017). In this manuscript, we describe a set of protocols to assist investigators in the culture and genetic engineering of iPSC lines to enable transcription factor-mediated differentiation of iPSCs into i3Neurons or i3LMNs, and we present neuronal culture conditions for various experimental applications. © 2018 by John Wiley & Sons, Inc. | National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, California, Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, California, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland | https://doi.org/10.1002/cpcb.51 | 1 | 2019 | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward 2019. Transcription Factor-Mediated Differentiation of Human iPSCs into Neurons. protocols.io dx.doi.org/10.17504/protocols.io.54rg8v6 | 2021-03-29 03:09:57 | ||
|
Smart-seq3 Protocol Resource Report Resource Website |
Michael Hagemann-Jensen, Christoph Ziegenhain, Ping Chen, Daniel Ramsköld, Gert-Jan Hendriks, Anton J.M Larsson, Omid R. Faridani, Rickard Sandberg | 10.17504/protocols.io.bbpyimpw | Karolinska Institute Stockholm, Karolinska Institute Stockholm, Karolinska Institute Stockholm, Karolinska Institute Stockholm, Karolinska Institute Stockholm, Karolinska Institute Stockholm, Karolinska Institute Stockholm, Karolinska Institute Stockholm | 2 | 2020 | Michael Hagemann-Jensen, Christoph Ziegenhain, Ping Chen, Daniel Ramsköld, Gert-Jan Hendriks, Anton J.M Larsson, Omid R. Faridani, Rickard Sandberg 2020. Smart-seq3 Protocol. protocols.io dx.doi.org/10.17504/protocols.io.bbpyimpw | 2021-03-29 03:09:57 | |||||
|
Islet Culture and Preparation for Cold Shipping Resource Report Resource Website |
Integrated Islet Distribution Program | 10.17504/protocols.io.bfsfjnbn | Integrated Islet Distribution Program, Integrated Islet Distribution Program and Human Islet Phenotyping Program | This SOP defines a standardized method for packaging and cold shipping of research quality islets to approved investigators of human isolated islet preparations, for use in the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) sponsored research in the Integrated Islet Distribution Program (IIDP). This protocol is written to assist the participating islet isolation centers and investigators who are part of this program.Note: This SOP was developed based on the Prodo Labs, Inc. shipping protocol and results from preliminary studies conducted by the IIDP and commissioned by the original IIDP Project Officer, and External Evaluation Committee (EEC).It was commissioned due to problems with acquiring the supplies that were used in IIDP SOP: SHP-001 and with the hope that this method is a better means for transportation of IIDP islets. Preliminary studies proved the islets by the Prodo Labs’ method were statistically as good as the original IIDP method, it was preferred by the test researchers, and was much more cost effective for the IIDP. This new method may be modified as future methods are tested and approved by the IIDP Team, Project Scientist (PS), the Program Official (PO), and EEC. | [Integrated Islet Distribution Program, City of Hope, Duarte, CA] | https://iidp.coh.org/Investigators/Policies-Standard-Operating-Procedures | 1 | 2020 | Integrated Islet Distribution Program 2020. Islet Culture and Preparation for Cold Shipping. protocols.io dx.doi.org/10.17504/protocols.io.bfsfjnbn | 2021-03-29 03:09:57 | ||
|
Hepatitis A MGB TaqMan Resource Report Resource Website |
Ian Mackay, Mitchell Finger, Michael Lyon, Judy Northill | 10.17504/protocols.io.rk3d4yn | Public Health Virology, Forensic and Scientific Services | This protocol was developed at this laboratory but had not been previously published. The protocol aims explicitly to amplify hepatitis A virus (HAV) strains and not other virus species. The assay targets the 5' untranslated region and is designed as a qualitative test for investigating suspected human cases of HAV infection. | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 1 | 2018 | Ian Mackay, Mitchell Finger, Michael Lyon, Judy Northill 2018. Hepatitis A MGB TaqMan. protocols.io dx.doi.org/10.17504/protocols.io.rk3d4yn | 2021-03-29 03:09:57 | |||
|
Mammalian Cell Staining Resource Report Resource Website |
Kenneth Schackart, Kattika Kaarj | 10.17504/protocols.io.xs7fnhn | 481b Laboratory | This protocol details how to stain mammalian cells cultured on a 96-well plate. Actin filaments, focal adhesion sites (as indicated by the presence vinculin), and nuclei will be stained. | University of Arizona, University of Arizona | 2 | 2019 | Kenneth Schackart, Kattika Kaarj 2019. Mammalian Cell Staining. protocols.io dx.doi.org/10.17504/protocols.io.xs7fnhn | 2021-03-29 03:09:57 | |||
|
MojoSort™ Human NK Cell Isolation Kit Protocol Resource Report Resource Website |
Sam Li | 10.17504/protocols.io.7bihike | BioLegend | BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple protocol consists of following the MojoSort™ protocol to label the cells with pre-diluted MojoSort™ reagents and using the columns as indicated by the manufacturer.Note: Due to the properties of our beads, it may be possible to use far fewer beads and less antibody cocktail that with other commercial suppliers. We recommend a titration to find the best dilution factor. However, as a general rule, dilutions ranging from 1:2 to 1:10 for the antibody cocktail can be used. Dilutions ranging from 1:5 to 1:20 for the Streptavidin Nanobeads can be used. Please contact BioLegend Technical Service ([email protected]) if further assistance is needed. | BioLegend | https://www.biolegend.com/protocols/mojosort-human-nk-cell-isolation-kit-column-protocol/4622/ | 1 | 2019 | Sam Li 2019. MojoSort™ Human NK Cell Isolation Kit Protocol. protocols.io dx.doi.org/10.17504/protocols.io.7bihike | 2021-03-29 03:10:00 | ||
|
RNA extraction from Synechocystis sp. PCC 6803 with Trizol reagent Resource Report Resource Website |
Dennis Dienst | 10.17504/protocols.io.j3scqne | CyanoWorld | Department of Chemistry - Microbial Chemistry, Ångström and Science for Life Laboratory, Uppsala University, Sweden | 1 | 2017 | Dennis Dienst 2017. RNA extraction from Synechocystis sp. PCC 6803 with Trizol reagent. protocols.io dx.doi.org/10.17504/protocols.io.j3scqne | 2021-03-29 03:10:00 | ||||
|
Calculating number of Co-Migrated DNA Fragments across Pulsed Field gel electrophoresis (PFGE) profiles: Image analysis algorithm Resource Report Resource Website |
Ibrahim El-khalil Adam | 10.17504/protocols.io.bthtnj6n | The author describes a new image analysis algorithm that enables identification of how many DNA fragments co-migrate during PFGE. The method is named factor of co-migration based on exponential correlation between single-fragment bands and their pixel densities "FCM-ECSB". | department of zoology, faculty of Science, University of Khartoum | https://www.researchgate.net/publication/348389960_Novel_Algorithms_for_PFGE_Bacterial_Typing_Number_of_Co-Migrated_DNA_Fragments_Linking_PFGE_to_WGS_Results_and_Computer_simulations_for_Evaluation_of_PulseNet_International_Typing_Protocols | 2 | 2021 | Ibrahim El-khalil Adam 2021. Calculating number of Co-Migrated DNA Fragments across Pulsed Field gel electrophoresis (PFGE) profiles: Image analysis algorithm. protocols.io dx.doi.org/10.17504/protocols.io.bthtnj6n | 2021-03-29 03:09:59 | |||
|
Using De-MetaST-BLAST Resource Report Resource Website |
Dr. Steven Wilhelm, Samantha Coy | 10.17504/protocols.io.ii2ccge | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Samantha R Coy's Protocols | Please contact Dr. Steven Wilhelm ([email protected]) or Samantha Coy ([email protected]) for additional information regarding this protocol. De-MetaST-BLAST, written in C++, is a script that can validate degenerate primers by performing in silico PCR amplification of the primers against metagenomic and metatranscriptomic databases (e.g. CAMERA; MG-RAST). The output is a list of in-silco PCR amplicons that are then blasted against GenBank to determine the most homologous sequence to the amplicon. Modified from Gulvik, C. A., Effler, T. C., Wilhelm, S. W., & Buchan, A. (2012). De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes. PLoS ONE,7(11). doi:10.1371/journal.pone.0050362 | , | 1 | 2017 | Dr. Steven Wilhelm, Samantha Coy 2017. Using De-MetaST-BLAST. protocols.io dx.doi.org/10.17504/protocols.io.ii2ccge | 2021-03-29 03:09:59 | |||
|
Steps to Create FASTQ of CCS Overlapping Genomic SSR - CCS ROI Resource Report Resource Website |
Gregory Harhay | 10.17504/protocols.io.9i7h4hn | The virulence and pathogenicity of bacterial pathogens are related to their adaptability to changing environments. One process enabling adaptation is based on minor changes in genome sequence, as small as a few base pairs, within segments of genome called simple sequence repeats (SSRs) that consist of multiple copies of a short sequence (from one to several nucleotides), repeated in series. SSRs are found in eukaryotes as well as prokaryotes, and variation in them occurs at frequencies up to a million-fold higher than the average bacterial mutation rate through a process of slipped stranded mispairing (SSM) by DNA polymerase during replication. The characterization of SSR length by standard sequencing methods is complicated by the appearance of length variation introduced during the sequencing process that does not accurately quantify lower-abundance repeat number variants in a population. Here we report a computational approach to correct for process-induced artifacts, validated for tetranucleotide repeats by use of synthetic constructs of fixed, known length. We apply this method to a laboratory culture ofHistophilus somni, prepared from a single colony, and demonstrate that the culture consists of populations of distinct sequence phase and read length variants at individual tetranucleotide SSR loci.Input requirements: Closed Genome - It is recommended that only organisms with closed genomes be the subject of the analyses described here. Mapping repetitive reads to to contigs of non-closed genomes may map to multiple locations, complicating tha analysis. Mapping CCS (circular consensus sequence) wiith repetitve sequence to closed genomes are guaranted to map to a single locus if sufficent unique flanking sequence is used to confim the unique mapping. Consequently, long CCS with high base quality are the most desirable input into this workflow. | United States Department of Agriculture | 5 | 2019 | Gregory Harhay 2019. Steps to Create FASTQ of CCS Overlapping Genomic SSR - CCS ROI . protocols.io dx.doi.org/10.17504/protocols.io.9i7h4hn | 2021-03-29 03:09:59 | ||||
|
PCR Cloning with Blue/White Selection--CHEM 584 Resource Report Resource Website |
Ken Christensen, Promega, Trevor Wagner | 10.17504/protocols.io.bmtzk6p6 | Protocol for PCR Cloning with Blue/White Selection and Easy Insert Excision using pGEM®-T Easy Vector Systems.(For use with A3600, A3610, A1360, or A1380.) | Brigham Young University, Promega Corporation, Promega Corporation | https://www.promega.com/-/media/files/resources/protocols/technical-manuals/0/pgem-t-and-pgem-t-easy-vector-systems-protocol.pdf?la=en | 1 | 2020 | Ken Christensen, Promega, Trevor Wagner 2020. PCR Cloning with Blue/White Selection--CHEM 584. protocols.io dx.doi.org/10.17504/protocols.io.bmtzk6p6 | 2021-03-29 03:10:04 | |||
|
EVALUATION OF TEST ITEMS EFFICACY IN PROMOTING STROKE REHABILITATION IN THE RAT STROKE MODEL (t-MCAO). Resource Report Resource Website |
Aharon Levy, Michael Krakovsky | 10.17504/protocols.io.bf69jrh6 | The objective of this protocol is to present the details of the procedures for evaluating test items’ (such as small molecules, biologics, and others) efficacy in promoting stroke rehabilitation, in the rat transient Middle Cerebral Carotid Occlusion (t-MCAO) model. | Alam JJ, Krakovsky M, Germann U, Levy A (2020) Continuous administration of a p38α inhibitor during the subacute phase after transient ischemia-induced stroke in the rat promotes dose-dependent functional recovery accompanied by increase in brain BDNF protein level. PLoS ONE 15(12): e0233073. doi: 10.1371/journal.pone.0233073 | Pharmaseed Ltd., Pharmaseed Ltd. | https://doi.org/10.1371/journal.pone.0233073 | 1 | 2020 | Aharon Levy, Michael Krakovsky 2020. EVALUATION OF TEST ITEMS EFFICACY IN PROMOTING STROKE REHABILITATION IN THE RAT STROKE MODEL (t-MCAO).. protocols.io dx.doi.org/10.17504/protocols.io.bf69jrh6 | 2021-03-29 03:10:04 | ||
|
DH5α bacteria transformation protocol Resource Report Resource Website |
Yoan Coudert | 10.17504/protocols.io.bghijt4e | CoudertLab | Ecole Normale Supérieure de Lyon | 1 | 2020 | Yoan Coudert 2020. DH5α bacteria transformation protocol. protocols.io dx.doi.org/10.17504/protocols.io.bghijt4e | 2021-03-29 03:10:03 | ||||
|
Naegleria gruberi plasmids Resource Report Resource Website |
Anastasios Tsaousis, Eleana Kazana, Tobias von der Haar | 10.17504/protocols.io.7w4hpgw | Maps and nucleotide sequences of the Naegleria gruberi transfection plasmids (pNaeg-HYG and pNaeg-NEO) reported in Faktorová D. et al. | Faktorová D, Nisbet RER, Robledo JAF, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget F, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano J, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Vanclová AMGN, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Smith GJ, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, Dassow Pv, Haar Tvd, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J, Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods 17(5). doi: 10.1038/s41592-020-0796-x | University of Kent, University of Kent, University of Kent | https://dx.doi.org/10.17504/protocols.io.4nrgvd6 | 1 | 2019 | Anastasios Tsaousis, Eleana Kazana, Tobias von der Haar 2019. Naegleria gruberi plasmids. protocols.io dx.doi.org/10.17504/protocols.io.7w4hpgw | 2021-03-29 03:10:03 | ||
|
Western Blotting Protocol Resource Report Resource Website |
BioLegend, Inc. | 10.17504/protocols.io.e2abgae | BioLegend | , | http://www.biolegend.com/media_assets/support_protocol/WB_Analysis_BetaAmyloid_12-04-14.pdf | 1 | 2016 | BioLegend, Inc. 2016. Western Blotting Protocol. protocols.io dx.doi.org/10.17504/protocols.io.e2abgae | 2021-03-29 03:10:02 | |||
|
Action Spectra protocol for Opentrons OT-1 liquid handling robot Resource Report Resource Website |
andrei.herdean | 10.17504/protocols.io.br6vm9e6 | Climate Change Cluster | University of Technology Sydney | 1 | 2021 | andrei.herdean 2021. Action Spectra protocol for Opentrons OT-1 liquid handling robot . protocols.io dx.doi.org/10.17504/protocols.io.br6vm9e6 | 2021-03-29 03:10:02 | ||||
|
Fluorescence-based Thermal Shift Assay (TSA) Resource Report Resource Website |
Paloma Varela | 10.17504/protocols.io.vg2e3ye | Varela PF, Velours C, Aumont-Niçaise M, Pineau B, Legrand P, Poquet I (2019) Biophysical and structural characterization of a zinc-responsive repressor of the MarR superfamily. PLoS ONE 14(2): e0210123. doi: 10.1371/journal.pone.0210123 | Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France | https://doi.org/10.1371/journal.pone.0210123 | 1 | 2019 | Paloma Varela 2019. Fluorescence-based Thermal Shift Assay (TSA). protocols.io dx.doi.org/10.17504/protocols.io.vg2e3ye | 2021-03-29 03:10:02 |
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
