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 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MSD 96-well human cytokine assay Resource Report Resource Website |
Sandra L. Ross, Marika Sherman, Patricia L. McElroy, Julie A. Lofgren, Gordon Moody, Patrick A. Baeuerle, Angela Coxon, Tara Arvedson | DOI:10.17504/protocols.io.hwzb7f6 | This protocol describes MesoScale Discovery (MSD) assays for measurement of proinflammatory cytokines in supernatants collected from T cell dependent cytotoxicity (TDCC) cultures after BiTE® treatment. | Ross SL, Sherman M, McElroy PL, Lofgren JA, Moody G, Baeuerle PA, Coxon A, Arvedson T, Bispecific T cell engager (BiTE) antibody constructs can mediate bystander tumor cell killing. PLoS ONE 12(8). doi: 10.1371/journal.pone.0183390 | Department of Oncology Research, Amgen Inc., Department of Oncology Research, Amgen Inc., Department of Oncology Research, Amgen Inc., Department of Oncology Research, Amgen Inc., Department of Oncology Research, Amgen Inc., Department of Oncology Research, Amgen Inc., Department of Oncology Research, Amgen Inc., Department of Oncology Research, Amgen Inc. | https://doi.org/10.1371/journal.pone.0183390 | 1 | 2017 | Sandra L. Ross, Marika Sherman, Patricia L. McElroy, Julie A. Lofgren, Gordon Moody, Patrick A. Baeuerle, Angela Coxon, Tara Arvedson 2017. MSD 96-well human cytokine assay. protocols.io https://dx.doi.org/10.17504/protocols.io.hwzb7f6 | 2021-04-15 09:15:43 | ||
|
Bloodstream-form culture Resource Report Resource Website |
Sam Alsford | DOI:10.17504/protocols.io.qhtdt6n | Protocol obtained from the Alsford Lab at the London School of Hygiene & Tropical Medicine(https://blogs.lshtm.ac.uk/alsfordlab/protocols/bloodstream-form-culture/) | Lab Protocol Owner | 1 | 2018 | Sam Alsford 2018. Bloodstream-form culture. protocols.io https://dx.doi.org/10.17504/protocols.io.qhtdt6n | 2021-04-15 09:15:40 | ||||
|
Systemic AAV vectors for widespread and targeted gene delivery in rodents Resource Report Resource Website |
Rosemary C. Challis, Sripriya Ravindra Kumar, Ken Y. Chan, Collin Challis, Keith Beadle, Min J. Jang, Hyun Min Kim, Pradeep S. Rajendran, John D. Tompkins, Kalyanam Shivkumar, Benjamin E. Deverman, Viviana Gradinaru | DOI:10.17504/protocols.io.84ahyse | Neurodegeneration Method Development Community | We recently developed adeno-associated virus (AAV) capsids to facilitate efficient and noninvasive gene transfer to the central and peripheral nervous systems. However, a detailed protocol for generating and systemically delivering novel AAV variants was not previously available. In this protocol, we describe how to produce and intravenously administer AAVs to adult mice to specifically label and/or genetically manipulate cells in the nervous system and organs, including the heart. The procedure comprises three separate stages: AAV production, intravenous delivery, and evaluation of transgene expression. The protocol spans 8 d, excluding the time required to assess gene expression, and can be readily adopted by researchers with basic molecular biology, cell culture, and animal work experience. We provide guidelines for experimental design and choice of the capsid, cargo, and viral dose appropriate for the experimental aims. The procedures outlined here are adaptable to diverse biomedical applications, from anatomical and functional mapping to gene expression, silencing, and editing. | Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA, Cardiac Arrhythmia Center and Neurocardiology Research Center of Excellence, University of California, Los Angeles, Los Angeles, CA, USA, Cardiac Arrhythmia Center and Neurocardiology Research Center of Excellence, University of California, Los Angeles, Los Angeles, CA, USA, Cardiac Arrhythmia Center and Neurocardiology Research Center of Excellence, University of California, Los Angeles, Los Angeles, CA, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA | https://www.nature.com/articles/s41596-018-0097-3 | 1 | 2019 | Rosemary C. Challis, Sripriya Ravindra Kumar, Ken Y. Chan, Collin Challis, Keith Beadle, Min J. Jang, Hyun Min Kim, Pradeep S. Rajendran, John D. Tompkins, Kalyanam Shivkumar, Benjamin E. Deverman, Viviana Gradinaru 2019. Systemic AAV vectors for widespread and targeted gene delivery in rodents. protocols.io https://dx.doi.org/10.17504/protocols.io.84ahyse | 2021-04-15 09:15:40 | ||
|
Adult human kidney tissue cell dissociation (on ice) Resource Report Resource Website |
Andrew Potter | DOI:10.17504/protocols.io.q6cdzaw | Human Cell Atlas Method Development Community | This protocol can be used to dissociate adult human kidney “on ice” - maintaining authentic gene expression profiles. It was designed using a mix of Collagenases (Type 4, and A) which provide broad proteolytic activity, but preferentially cleave extracellular bonds, largely leaving cells intact. The total incubation time is 1 hour 20 minutes divided into two layers. At the end of the procedure, RBC lysis is performed. The total yield at the end of the procedure is ~1200 (non-RBC) cells released per mg tissue with 87% viability.In the digest mix, there is trypsin inhibitor from soybean which is designed to limit the activity of tryptic proteins in the collagenase mix which can damage the integrity of the cell. There is also 5 mM CaCl2, an activator of collagenase activity, in addition to DNAse - which chews up DNA released from dead cells, reducing cell clumping. The dissociation itself it carried out in two layers. The first layer is 30 minutes and includes trituration and shaking. After this layer, tissue clumps are settled for 1 min, and the supernatant containing released cells is removed and filtered using a 30 µM filter and rinsed with ice-cold PBS-BSA. This helps to preserve the integrity of released cells while continuing the digest clumps of undissociated cells. To the residual clumps, an additional 1 mL of enzyme mix is added and the digestion is continued for 50 additional minutes (1 hr 20 mins total time). | University of Cincinnati | 1 | 2018 | Andrew Potter 2018. Adult human kidney tissue cell dissociation (on ice). protocols.io https://dx.doi.org/10.17504/protocols.io.q6cdzaw | 2021-04-15 09:15:40 | |||
|
MRM-LC-MS/MS Assay for inflammatrory associated proteins in serum Resource Report Resource Website |
DOI:10.17504/protocols.io.bm4vk8w6 | Metabolomics Protocols & Workflows, Translational Mass Spectrometry Research Group | Multiplex targeted proteomic assay to measure human proteins associated with inflammation in serum. A unique peptide is selected to represent a protein and is measured using multiple reaction monitoring (MRM) mass spectrometry. | Doykov I, Hällqvist J, Gilmour KC, Grandjean L, Mills K, Heywood WE, ‘The long tail of Covid-19’ - The detection of a prolonged inflammatory response after a SARS-CoV-2 infection in asymptomatic and mildly affected patients. F1000Research doi: 10.12688/f1000research.27287.1 | University College London, University of London | https://doi.org/10.12688/f1000research.27287.1 | 1 | 2020 | 2020. MRM-LC-MS/MS Assay for inflammatrory associated proteins in serum. protocols.io https://dx.doi.org/10.17504/protocols.io.bm4vk8w6 | 2021-04-15 09:15:43 | ||
|
Efficacy of metformin in patients with breast cancer receiving chemotherapy or endocrine therapy：Systematic review and meta-analysis (protocol) Resource Report Resource Website |
Kayoko Morio, Yasuko Kurata, Nobuko Kawaguchi-Sakita, Akihiro Shiroshita, Yuki Kataoka | DOI:10.17504/protocols.io.bmzak72e | Department of Pharmacy, Kobe University Hospital 7-5-2, Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan, Department of Pharmacy, Okayama University Hospital, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan, Department of Clinical Oncology, Kyoto University Hospital, 54 Shogoin-Kawaracho, Sakyo-ku, Kyoto 606-8507, Japan, Department of respiratory medicine, Ichinomiya-nishi hospital, Japan, Hospital Care Research Unit, Hyogo Prefectural Amagasaki General Medical Center, Higashinaniwa-cho 2-17-77, Amagasaki 660-8550, Japan | 2 | 2020 | Kayoko Morio, Yasuko Kurata, Nobuko Kawaguchi-Sakita, Akihiro Shiroshita, Yuki Kataoka 2020. Efficacy of metformin in patients with breast cancer receiving chemotherapy or endocrine therapy：Systematic review and meta-analysis (protocol). protocols.io https://dx.doi.org/10.17504/protocols.io.bmzak72e | 2021-04-15 09:15:55 | |||||
|
Sandwich ELISA Protocol Resource Report Resource Website |
Sam Li | DOI:10.17504/protocols.io.98xh9xn | BioLegend | BioLegend | https://www.biolegend.com/protocols/sandwich-elisa-protocol/4268/ | 3 | 2019 | Sam Li 2019. Sandwich ELISA Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.98xh9xn | 2021-04-15 09:15:43 | |||
|
Pig ICN recording Resource Report Resource Website |
Jeffrey Ardell | DOI:10.17504/protocols.io.2jugcnw | SPARC | Yorshire pigs are anthesized for ICN/ neuromodulation recodings. Montior hemodynics A1mid-sternotomy | University of California, Los Angeles | 1 | 2019 | Jeffrey Ardell 2019. Pig ICN recording. protocols.io https://dx.doi.org/10.17504/protocols.io.2jugcnw | 2021-04-15 09:15:39 | |||
|
Immunoprecipitation Protocol Resource Report Resource Website |
Kelsey Knight | DOI:10.17504/protocols.io.tkmeku6 | BioLegend | Immunoprecipitation is a procedure by which proteins or peptides that react specifically with an antibody are removed from solution and examined for quantity or physical characteristics. Immunoprecipitation can also be used to “enrich” a protein population prior to Western Blotting. For example, one can perform immunoprecipitation with a pan-specific antibody against a protein of interest followed by Western blotting with a modification-specific antibody (such as a phospho-specific antibody or an acetylation-specific antibody). | BioLegend | https://www.biolegend.com/protocols/immunoprecipitation-protocol/4258/ | 2 | 2018 | Kelsey Knight 2018. Immunoprecipitation Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.tkmeku6 | 2021-04-15 09:15:54 | ||
|
Transcriptomics Resource Report Resource Website |
Andreea S | DOI:10.17504/protocols.io.bme9k3h6 | iGEM Groningen 2020 | The potato root secretes root exudates, a mixture of organic molecules out of which solanine is found in the highest concentration (range of ug/ml). Also, solanine is a molecule specifically found in the root exudate of potato plants, which makes it a good candidate for a dependecy molecule which will ensure that Bacillus mycoides doesn't escape the designated action area. Studies have shown that there are soil bacteria able to metabolize solanine as a carbon source. Unfortunately, we weren't able to find an already described solanine-inducing promoter. Because the natural habitat of B. mycoides is the potato rhizosphere, we have strong reasons to believe that if such a promoter may already be present in its genome. In order to find this promoter, we designed a CHIP-Seq experiment. B. mycoides will be incubated with a different range of solanine concentrations. The DNA will be extracted and the CHIP-Seq technique will be used to detect potential binding sites of solanine operators using monoclonal anti-solanine antibodies. | University of Groningen | 1 | 2020 | Andreea S 2020. Transcriptomics. protocols.io https://dx.doi.org/10.17504/protocols.io.bme9k3h6 | 2021-04-15 09:15:43 | |||
|
Phenol-chloroform DNA purification Resource Report Resource Website |
Tomasz Suchan | DOI:10.17504/protocols.io.re6d3he | Molecular Biogeography Group | Because of the influence of salts on enzymatic reactions, Qiagen extractions can be purified before making RAD tags. First, it is necessary to perform a chloropane extraction (phenol / chloroform 50/50) by adding SDS to the aqueous phase (final conc. 0.1%), this eliminates contaminants introduced by the matrix of the column. Then, perform an ethanol precipitation followed by a wash with 70% ethanol. This is to eliminate the salt that was used to bind the nucleic acids to the column and also to remove EDTA (inhibitor!) which is 0.5 mM in the buffer AE. Eluting with water is nonsense as the pH is not optimal and thus yield is poor and the DNA is not buffered and there is always too much salt. | W. Szafer Institute of Botany, Polish Academy of Sciences | 1 | 2020 | Tomasz Suchan 2020. Phenol-chloroform DNA purification. protocols.io https://dx.doi.org/10.17504/protocols.io.re6d3he | 2021-04-15 09:15:39 | |||
|
Setting $PATH on UA HPC Resource Report Resource Website |
Bonnie Hurwitz, Ken Youens-Clark | DOI:10.17504/protocols.io.jh8cj9w | Hurwitz Lab, Metafunc Course 2017 | Set up your Unix PATH so you can find important tools on the HPC for the class. | University of Arizona, University of Arizona | 1 | 2017 | Bonnie Hurwitz, Ken Youens-Clark 2017. Setting $PATH on UA HPC. protocols.io https://dx.doi.org/10.17504/protocols.io.jh8cj9w | 2021-04-15 09:15:54 | |||
|
Basal cortisol Resource Report Resource Website |
Worapaka Manosroi | DOI:10.17504/protocols.io.7iphkdn | Manosroi W, Phimphilai M, Khorana J, Atthakomol P (2019) Diagnostic performance of basal cortisol level at 0900-1300h in adrenal insufficiency. PLoS ONE 14(11): e0225255. doi: 10.1371/journal.pone.0225255 | Faculty of medicine, Chiang Mai University | https://doi.org/10.1371/journal.pone.0225255 | 1 | 2019 | Worapaka Manosroi 2019. Basal cortisol. protocols.io https://dx.doi.org/10.17504/protocols.io.7iphkdn | 2021-04-15 09:15:39 | |||
|
Virus and bacteria counts by epifluorescence microscopy with SYBR Green Resource Report Resource Website |
Anand Patel, Rachel T Noble, Joshua A Steele, Michael S Schwalbach, Ian Hewson, Jed A Fuhrman | DOI:10.17504/protocols.io.r2dd8a6 | VERVE Net, Fuhrman Lab | The protocol provides an inexpensive, rapid (30 min) and reliable technique for obtaining counts of viruses and prokaryotes simultaneously. The method is from:Patel A, Noble RT, Steele JA, Schwalbach MS, Hewson I, Fuhrman JA.Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nat Protoc. 2007;2(2):269-76.Please see the full manuscript for more details. | Fuhrman Lab, Fuhrman Lab, Fuhrman Lab, Fuhrman Lab, Fuhrman Lab, Fuhrman Lab | http://www.nature.com/nprot/journal/v2/n2/full/nprot.2007.6.html | 2 | 2018 | Anand Patel, Rachel T Noble, Joshua A Steele, Michael S Schwalbach, Ian Hewson, Jed A Fuhrman 2018. Virus and bacteria counts by epifluorescence microscopy with SYBR Green. protocols.io https://dx.doi.org/10.17504/protocols.io.r2dd8a6 | 2021-04-15 09:15:40 | ||
|
rev-ChIP Resource Report Resource Website |
Lorane Texari, Carlos Guzman, Sven Heinz | DOI:10.17504/protocols.io.vp5e5q6 | Understanding the precise regulation of transcriptional programs in human health and disease requires the accurate identification and characterization of genomic regulatory networks. Next-generation sequencing (NGS) technologies are powerful, and widely applied tools to map the in vivo genome-wide location of transcription factors (TFs), histone modifications, chromatin accessibility, and nascent transcription that make up these regulatory networks. While chromatin immunoprecipitation followed by sequencing (ChIP-seq) is one of the oldest, and most-utilized experimental techniques to study the location and abundance of TFs, experiments still frequently require optimization to reproducibly yield good data with high signal-to-noise ratios due to the massive variability between possible antibody-antigen combinations and commercial reagents. .justify:after { content: ""; display:inline-block; width: 100%; } To overcome these obstacles, we systematically carried out well over 500 ChIP-seq experiments designed to test every aspect of typical ChIP-seq experiments and developed rev-ChIP, a novel ChIP-seq method that is optimized for scalability, robustness, low-input, speed, cost efficiency and data quality. We find that rev-ChIP can be scaled to work for cell numbers ranging from millions to under a thousand, and from a single sample to 500 samples a week in a non-automated fashion with minimal hands-on time. Additionally, rev-ChIP has been tested on a variety of sample types ranging from cell lines to sorted primary cells and solid tissues. .justify:after { content: ""; display:inline-block; width: 100%; } | University of California, San Diego, University of California, San Diego, University of California, San Diego | 1 | 2018 | Lorane Texari, Carlos Guzman, Sven Heinz 2018. rev-ChIP. protocols.io https://dx.doi.org/10.17504/protocols.io.vp5e5q6 | 2021-04-15 09:15:54 | ||||
|
Recombinant expression and purification of codon-optimized M-MLV and Mashup Resource Report Resource Website |
Maira Rivera, Javiera Reyes, Paula Blazquez-Sanchez, Cesar A Ramirez-Sarmiento | Reclone.org (The Reagent Collaboration Network) | Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile | 1 | 2020 | Maira Rivera, Javiera Reyes, Paula Blazquez-Sanchez, Cesar A Ramirez-Sarmiento 2020. Recombinant expression and purification of codon-optimized M-MLV and Mashup. protocols.io https:// | 2021-04-15 09:15:40 | |||||
|
DISCOVER-Seq: MRE11 ChIP Seq Resource Report Resource Website |
Beeke Wienert | DOI:10.17504/protocols.io.uvuew6w | CornLab | Genome editing using nucleases such as CRISPR-Cas induces programmable DNA damage at a target genomic site, but can also affect off-target sites. We develop a powerful assay for the unbiased identification of off-target sites that we term DISCOVER-seq. This approach takes advantage of the recruitment of endogenous DNA repair factors for genome-wide identification of Cas-induced double strand breaks. One such factor, MRE11, is recruited so precisely to a double stranded break that nuclease cut sites can be determined with single-base resolution. DISCOVER-seq is applicable to multiple types of Cas nucleases and provides an unprecedented molecular picture of events that precede repair of the affected sites. DISCOVER-seq furthermore detects off-targets in cellular models and tissues. | University of California, Berkeley | 1 | 2018 | Beeke Wienert 2018. DISCOVER-Seq: MRE11 ChIP Seq. protocols.io https://dx.doi.org/10.17504/protocols.io.uvuew6w | 2021-04-15 09:15:40 | |||
|
Drawing ROIs in ITK-Snap Resource Report Resource Website |
Courtney Comrie | DOI:10.17504/protocols.io.8nvhve6 | University of Arizona | 1 | 2020 | Courtney Comrie 2020. Drawing ROIs in ITK-Snap. protocols.io https://dx.doi.org/10.17504/protocols.io.8nvhve6 | 2021-04-15 09:15:39 | |||||
|
In vitro transcription, capping, and 2'-O methylation of long RNAs Resource Report Resource Website |
Stephen Floor | DOI:10.17504/protocols.io.4pwgvpe | Stephen Floor Lab | This protocol is for in vitro transcription of long RNAs off plasmid or PCR product templates. It is assumed that the template has been gel purified, is the right size, has a T7 promoter and a 3' polyA tail (typically A60). Following this protocol the RNA will be ready for transfection into mammalian cells or in vitro translation. Significant amounts of template are necessary: at least 1ug of template per 100ul reaction; ideally closer to 5ug of template, especially for very long templates. Use RNase sensitive protocols and reagents for all steps of this procedure. The basic protocol is: - PCR amplification of the template- in vitro transcription- capping and 2'-O-Methylation - quality control and optional purification Based on protocols from Kaihong Zhou (Doudna lab) and RNA: A Laboratory Manual (Rio, Ares, Hannon, Nilsen). | University of California, San Francisco | 1 | 2019 | Stephen Floor 2019. In vitro transcription, capping, and 2'-O methylation of long RNAs. protocols.io https://dx.doi.org/10.17504/protocols.io.4pwgvpe | 2021-04-15 09:15:39 | |||
|
Confocal microscopy and characterization of synaptic boutons associated with ganglion neurons Resource Report Resource Website |
Janet Keast, Peregrine Osborne | DOI:10.17504/protocols.io.bakdics6 | SPARC | This protocol describes confocal microscopy and image analysis procedures for characterizing neuronal cell bodies and their associated synaptic boutons in thick (50 µm) cryosections. The protocol has been applied to rat pelvic ganglia, where neuronal cell bodies have been identified using immunohistochemical markers of specific neuron populations and/or fluorescent retrograde tracer. | University of Melbourne, University of Melbourne | 1 | 2020 | Janet Keast, Peregrine Osborne 2020. Confocal microscopy and characterization of synaptic boutons associated with ganglion neurons. protocols.io https://dx.doi.org/10.17504/protocols.io.bakdics6 | 2021-04-15 09:15:39 |
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
