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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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ORCHARDS Household Substudy Protocol 2017 Resource Report Resource Website |
Mitchell Arnold | 10.17504/protocols.io.bhssj6ee | Arnold MT, Temte JL, Barlow SK, Bell CJ, Goss MD, Temte EG, Checovich MM, Reisdorf E, Scott S, Guenther K, Wedig M, Shult P, Uzicanin A (2020) Comparison of participant-collected nasal and staff-collected oropharyngeal specimens for human ribonuclease P detection with RT-PCR during a community-based study. PLoS ONE 15(10): e0239000. doi: 10.1371/journal.pone.0239000 | University of Wisconsin - Madison | https://doi.org/10.1371/journal.pone.0239000 | 1 | 2020 | Mitchell Arnold 2020. ORCHARDS Household Substudy Protocol 2017. protocols.io dx.doi.org/10.17504/protocols.io.bhssj6ee | 2021-03-29 03:09:47 | |||
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Dengue serotyping by Real-Time Taqman PCR Resource Report Resource Website |
Jeyanthi Suppiah | 10.17504/protocols.io.rabd2an | 1) The primers and probes utilized were obtained from published research article as referenced in the text.2) First, Dengue virus RNA was extracted from patient serum by using Qiagen | Suppiah J, Ching S, Amin-Nordin S, Mat-Nor L, Ahmad-Najimudin N, Low GK, Abdul-Wahid M, Thayan R, Chee H (2018) Clinical manifestations of dengue in relation to dengue serotype and genotype in Malaysia: A retrospective observational study. PLoS Negl Trop Dis 12(9): e0006817. doi: 10.1371/journal.pntd.0006817 | https://doi.org/10.1371/journal.pntd.0006817 | 1 | 2018 | Jeyanthi Suppiah 2018. Dengue serotyping by Real-Time Taqman PCR. protocols.io dx.doi.org/10.17504/protocols.io.rabd2an | 2021-03-29 03:09:47 | |||
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HPC Account Set up and Access Resource Report Resource Website |
Courtney Comrie | 10.17504/protocols.io.7ezhjf6 | This protocol will provide instruction on where to access the HPC lab account, and where our data is stored.Only for internal use. | University of Arizona | 1 | 2019 | Courtney Comrie 2019. HPC Account Set up and Access. protocols.io dx.doi.org/10.17504/protocols.io.7ezhjf6 | 2021-03-29 03:09:42 | ||||
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Isolation of live single cells from intestinal biopsy Resource Report Resource Website |
Tatiana Karakasheva, Kathryn Hamilton | 10.17504/protocols.io.bst7nern | CHOP Gastrointestinal Epithelium Modeling Program | This protocol describes dissociation of a human intestinal biopsy tissue into single cells, followed by depletion of dead cells via annexin V MACS beads. The outcome is a single-cell suspension with viability ≥ 90% that is used for single-cell sequencing or establishemt of enteroid/colonoid culture. | Children's Hospital of Philadelphia, Gastrointestinal Epithelium Modeling Program, Children's Hospital of Philadelphia Division of Gastroenterology | 2 | 2021 | Tatiana Karakasheva, Kathryn Hamilton 2021. Isolation of live single cells from intestinal biopsy. protocols.io dx.doi.org/10.17504/protocols.io.bst7nern | 2021-03-29 03:09:43 | |||
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Deep learning in rare disease. Detection of tubers in tuberous sclerosis complex Resource Report Resource Website |
Ivan Sanchez Fernandez et al | 10.17504/protocols.io.bdt3i6qn | Code and results for the article "Deep learning in rare disease. Detection of tubers in tuberous sclerosis complex". | Fernández IS, Yang E, Calvachi P, Amengual-Gual M, Wu JY, Krueger D, Northrup H, Bebin ME, Sahin M, Yu K, Peters JM, obotTSG (2020) Deep learning in rare disease. Detection of tubers in tuberous sclerosis complex. PLoS ONE 15(4): e0232376. doi: 10.1371/journal.pone.0232376 | Boston Children's Hospital | https://doi.org/10.1371/journal.pone.0232376 | 1 | 2020 | Ivan Sanchez Fernandez et al 2020. Deep learning in rare disease. Detection of tubers in tuberous sclerosis complex. protocols.io dx.doi.org/10.17504/protocols.io.bdt3i6qn | 2021-03-29 03:09:47 | ||
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DroNc-seq step-by-step Resource Report Resource Website |
Anindita Basu, Inbal Avraham-Davidi, Naomi Habib, Aviv Regev, Feng Zhang, Karthik Shekhar, Matan Hofree, David Weitz, Orit Rozenblatt-Rosen, Tyler Burks, Sourav Choudhury, François Aguet, Ellen Gelfand, Kristin Ardlie | 10.17504/protocols.io.md2c28e | Human Cell Atlas Method Development Community | Currently, most single cell protocols require the preparation of a single cell suspension from fresh tissue, a major roadblock to clinical deployment, to archived materials and to certain tissues such as adult brain. In the adult brain the harsh enzymatic dissociation harms the integrity of the cells and their RNA, and biases toward easily dissociated cell types, and is restricted to young animals.We developed DroNc-seq, a droplet microfluidic and DNA barcoding technique for analysis of RNA profiles of single nuclei from fresh, frozen or lightly fixed tissues at high throughput and low cost. The utility of DroNc-Seq lies in working with hard-to-dissociate, frozen and/or archived tissues. To demonstrate the utility of this technique, we sequenced over 39 thousand nuclei from mouse and human archived brain samples, including post-mortem human brain tissue from GTEx project. | Broad Institute, Harvard University, Broad Institute, Broad Institute, Broad Institute, Broad Institute, Broad Institute, Droplet microfluidics, Broad Institute, Harvard University, Broad Institute, Broad Institute, Broad Institute, Broad Institute, Droplet microfluidics, Broad Institute, Broad Institute | https://www.nature.com/protocolexchange/protocols/6163 | 1 | 2018 | Anindita Basu, Inbal Avraham-Davidi, Naomi Habib, Aviv Regev, Feng Zhang, Karthik Shekhar, Matan Hofree, David Weitz, Orit Rozenblatt-Rosen, Tyler Burks, Sourav Choudhury, François Aguet, Ellen Gelfand, Kristin Ardlie 2018. DroNc-seq step-by-step. protocols.io dx.doi.org/10.17504/protocols.io.md2c28e | 2021-03-29 03:09:46 | ||
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HuBMAP | Formalin Fixation and Paraffin Embedding of Tissue Samples Resource Report Resource Website |
Kelley Knizner, Christopher Simmons | 10.17504/protocols.io.bqp6mvre | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | This method details formalin fixation and paraffin embedding of the HuBMAP tissue specimens.Protocol adopted from Marda Jorgensen, Jerelyn Nick (02/24/2020). HuBMAP: Paraffin Embedding Tissue Samples . https://dx.doi.org/10.17504/protocols.io.bam9ic96 | University of Pittsburgh Medical Center, University of Pittsburgh Medical Center | 1 | 2020 | Kelley Knizner, Christopher Simmons 2020. HuBMAP | Formalin Fixation and Paraffin Embedding of Tissue Samples . protocols.io dx.doi.org/10.17504/protocols.io.bqp6mvre | 2021-03-29 03:09:47 | |||
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Test-mate (Model 400) erythrocyte acetylcholinesterase (AChE) test Resource Report Resource Website |
H.K. Jeevan Dhanarisi, Indika B. Gawarammana, Fahim Mohamed, Michael Eddleston | 10.17504/protocols.io.wpyfdpw | South Asian Clinical Toxicology Research Collaboration, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka, Department of Medicine, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka, Faculty of Allied Health Sciences, University of Peradeniya, Peradeniya, Sri Lanka, Pharmacology, Toxicology, & Therapeutics, University/BHF Centre for Cardiovascular Science, University of Edinburgh, UK | https://doi.org/10.1371/journal.pone.0200133 | 2 | 2019 | H.K. Jeevan Dhanarisi, Indika B. Gawarammana, Fahim Mohamed, Michael Eddleston 2019. Test-mate (Model 400) erythrocyte acetylcholinesterase (AChE) test. protocols.io dx.doi.org/10.17504/protocols.io.wpyfdpw | 2021-03-29 03:09:47 | ||||
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Carrageenan air pouch (mice) Resource Report Resource Website |
Laura Ruiz Remolina | 10.17504/protocols.io.j8dcrs6 | Ruiz-Remolina L, Ollauri-Ibáñez C, Pérez-Roque L, Núñez-Gómez E, Pérez-Barriocanal F, López-Novoa JM, Pericacho M, Rodríguez-Barbero A (2017) Circulating soluble endoglin modifies the inflammatory response in mice. PLoS ONE 12(11): e0188204. doi: 10.1371/journal.pone.0188204 | University of Salamanca (USAL), Spain | https://doi.org/10.1371/journal.pone.0188204 | 1 | 2017 | Laura Ruiz Remolina 2017. Carrageenan air pouch (mice). protocols.io dx.doi.org/10.17504/protocols.io.j8dcrs6 | 2021-03-29 03:09:47 | |||
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5x SDS (10 mL) Resource Report Resource Website |
Haven Himmighoefer, Rachel Ancar | 10.17504/protocols.io.kuycwxw | Often used in Western Blots. Kept on the bottom shelf of the fridge. | Hesselberth Lab, Hesselberth Lab | 1 | 2017 | Haven Himmighoefer, Rachel Ancar 2017. 5x SDS (10 mL). protocols.io dx.doi.org/10.17504/protocols.io.kuycwxw | 2021-03-29 03:09:43 | ||||
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Propidium Iodide (PI) Staining Method Resource Report Resource Website |
Dr. Steven Wilhelm | 10.17504/protocols.io.ibxcapn | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.Modified from J Mol Biol 13,269 (1965) | 1 | 2017 | Dr. Steven Wilhelm 2017. Propidium Iodide (PI) Staining Method. protocols.io dx.doi.org/10.17504/protocols.io.ibxcapn | 2021-03-29 03:09:44 | ||||
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Basic protocol for elimination of bacteria from microalgal culture using antibiotics Resource Report Resource Website |
Adriana Lopes Dos Santos, Claude Lemieux, Monique Turmel | 10.17504/protocols.io.be9wjh7e | Method used to eliminate bacterial contamination of a marine micro-algal culture. Note, this method is not guaranteed to be 100% successful either due to the fact that the antibiotic combination is not lethal to the bacteria present or it is possible that the strain may not be capable of prolonged growth without the presence of bacteria. This method is based on that of Droop, adapted according to Andersen but using a modern antibiotic mix suggested by S. Slocombe (SAMS - Scottish Association for Marine Science). The method described here have been successfully used by Christian Jeanthon (ECOMAP) to produce axenic cultures of diatoms and E. huxleyi.1. Droop, M. R. A procedure for routine purification of algal cultures with antibiotics. Br. Phycol. Bull. 3, 295–297 (1967).2. Andersen, R. Algal Cultering Techniques. (Academic Press, 2005). | Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore, Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada., Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada. | 1 | 2020 | Adriana Lopes Dos Santos, Claude Lemieux, Monique Turmel 2020. Basic protocol for elimination of bacteria from microalgal culture using antibiotics. protocols.io dx.doi.org/10.17504/protocols.io.be9wjh7e | 2021-03-29 03:09:44 | ||||
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Gel PCR Product Purification Resource Report Resource Website |
Izabela Rezende, Lívia Sacchetto | 10.17504/protocols.io.pxbdpin | MRCA | For isolate the desired product or reoptimize the PCR to obtain a single product. | Federal University of Minas Gerais - Laboratório de Vírus, Federal University of Minas Gerais - Laboratório de Vírus | 1 | 2018 | Izabela Rezende, Lívia Sacchetto 2018. Gel PCR Product Purification. protocols.io dx.doi.org/10.17504/protocols.io.pxbdpin | 2021-03-29 03:09:44 | |||
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Chimeric Protein-LAG and Streptococcal protein G sandwich ELISA Resource Report Resource Website |
Angel Justiz-Vaillant | 10.17504/protocols.io.btbcniiw | Carbon | This ELISA was used to study the interactions between protein-LAG (PLAG) and streptococcal protein-G (SpG) with different immunoglobulin preparations of mammalian and avian species. | University of the West Indies St. Augustine | 1 | 2021 | Angel Justiz-Vaillant 2021. Chimeric Protein-LAG and Streptococcal protein G sandwich ELISA. protocols.io dx.doi.org/10.17504/protocols.io.btbcniiw | 2021-03-29 03:09:44 | |||
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Tissue collection and extractions for RNA-seq Resource Report Resource Website |
David Lowry | 10.17504/protocols.io.basiiece | Mimulus | Michigan State University | 1 | 2019 | David Lowry 2019. Tissue collection and extractions for RNA-seq. protocols.io dx.doi.org/10.17504/protocols.io.basiiece | 2021-03-29 03:09:44 | ||||
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0.5M NH4Cl Resource Report Resource Website |
Matthew Sullivan Lab | 10.17504/protocols.io.c77zrm | VERVE Net, Sullivan Lab | Supplement to seawater for growth of cyanobacteria. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. 0.5M NH4Cl. protocols.io dx.doi.org/10.17504/protocols.io.c77zrm | 2021-03-29 03:09:44 | |||
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During data acquisition Resource Report Resource Website |
Lukas Snoek, Tinka Beemsterboer | 10.17504/protocols.io.w8ffhtn | Spinoza Centre, REC-L | This protocol lists all the steps necessary to run your MRI experiment/data acquisition safely and in a way that yields high-quality data. Moreover, if you use the centre's QC/preprocessing service, it lists the steps necessary to make sure we can convert the data into BIDS and run them through the QC/preprocessing pipelines. | Spinoza Centre, REC-L, Spinoza Centre, REC-L | 9 | 2019 | Lukas Snoek, Tinka Beemsterboer 2019. During data acquisition. protocols.io dx.doi.org/10.17504/protocols.io.w8ffhtn | 2021-03-29 03:09:47 | |||
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C_HW10: Sample read count to functional categories for Anvi'o bar chart Resource Report Resource Website |
Bonnie Hurwitz | 10.17504/protocols.io.gkibuue | Hurwitz Lab, MetaFunc Course | Create a script to add functional information about the samples into Anvi'o. | University of Arizona | 1 | 2016 | Bonnie Hurwitz 2016. C_HW10: Sample read count to functional categories for Anvi'o bar chart. protocols.io dx.doi.org/10.17504/protocols.io.gkibuue | 2021-03-29 03:09:48 | |||
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One-Step Transformation of Yeast Resource Report Resource Website |
Alan Cone | 10.17504/protocols.io.ddv265 | Ju Lab | Quick and easy method to transform a free plasmid into either budding or fission yeast. | Wright State University | 1 | 2015 | Alan Cone 2015. One-Step Transformation of Yeast. protocols.io dx.doi.org/10.17504/protocols.io.ddv265 | 2021-03-29 03:09:43 | |||
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Image analysis of immediate early gene expression in spinal cord sections Resource Report Resource Website |
Janet Keast, Peregrine Osborne, Nicole Wiedmann | 10.17504/protocols.io.bakmicu6 | SPARC | This protocol is used for analysing expression pattens of immediate early gene products (e.g., c-Fos) in immunostained transverse sections of spinal cord. | University of Melbourne, University of Melbourne, University of Melbourne | 1 | 2020 | Janet Keast, Peregrine Osborne, Nicole Wiedmann 2020. Image analysis of immediate early gene expression in spinal cord sections. protocols.io dx.doi.org/10.17504/protocols.io.bakmicu6 | 2021-03-29 03:09:43 |
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