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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Use of tracer dyes to label neural projections to lower urinary tract organs Resource Report Resource Website |
Janet Keast, Peregrine Osborne | 10.17504/protocols.io.w2xfgfn | SPARC | This protocol is used to visualise sensory and autonomic neurons innervating the bladder body (dome), bladder trigone or proximal urethra in an experimental adult male or female rat. The protocol is performed under anesthesia and should incorporate all local requirements for standards of animal experimentation, including methods of anesthesia, surgical environment, and post-operative monitoring and care. | University of Melbourne, University of Melbourne | 1 | 2020 | Janet Keast, Peregrine Osborne 2020. Use of tracer dyes to label neural projections to lower urinary tract organs. protocols.io dx.doi.org/10.17504/protocols.io.w2xfgfn | 2021-03-29 03:09:27 | |||
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Golden Gate Cloning LVL 0 Resource Report Resource Website |
Daniel Marchal | 10.17504/protocols.io.uvhew36 | iGEM Team Marburg 2018 | 2 | 2018 | Daniel Marchal 2018. Golden Gate Cloning LVL 0. protocols.io dx.doi.org/10.17504/protocols.io.uvhew36 | 2021-03-29 03:09:27 | |||||
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Yale - Blood or Urine Calcium Resource Report Resource Website |
John Stack, Gary Cline | 10.17504/protocols.io.y3nfyme | Mouse Metabolic Phenotyping Centers | Procedure used to determine the concentration of calcium in blood, serum, and plasma. Calcium is measured as the complex with arsenazo III and monitored at 600nm. | Yale University, Yale University | https://mmpc.org/shared/document.aspx?id=216&docType=Protocol | 1 | 2019 | John Stack, Gary Cline 2019. Yale - Blood or Urine Calcium. protocols.io dx.doi.org/10.17504/protocols.io.y3nfyme | 2021-03-29 03:09:27 | ||
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RNA in situ hybridization Resource Report Resource Website |
Nicholas Leigh, Garrett Dunlap, Kimberly Johnson, Rachelle Mariano, Rachel Oshiro, Alan Y. Wong, Donald M. Bryant, Bess Miller, Jessica L. Whited | 10.17504/protocols.io.p33dqqn | This protocol provides details on tissue harvest and fixation, RNA probe generation, and RNA in situ hybridization for use in sectioned axolotl tissue. This protocol was modified from Brent et al, A somitic compartment of tendon progenitors, Cell 2003 | Leigh ND, Dunlap GS, Johnson K, Mariano R, Oshiro R, Wong AY, Bryant DM, Miller BM, Ratner A, Chen A, Ye WW, Haas BJ, Whited JL, Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution. Nature Communications doi: 10.1038/s41467-018-07604-0 | Brigham and Women's Hospital/Harvard Medical School, Brigham and Women's Hospital/Harvard Medical School, Brigham and Women's Hospital/Harvard Medical School, Brigham and Women's Hospital/Harvard Medical School, Brigham and Women's Hospital/Harvard Medical School, Brigham and Women's Hospital/Harvard Medical School, Brigham and Women's Hospital/Harvard Medical School, Brigham and Women's Hospital/Harvard Medical School, Brigham and Women's Hospital/Harvard Medical School | https://doi.org/10.1038/s41467-018-07604-0 | 1 | 2018 | Nicholas Leigh, Garrett Dunlap, Kimberly Johnson, Rachelle Mariano, Rachel Oshiro, Alan Y. Wong, Donald M. Bryant, Bess Miller, Jessica L. Whited 2018. RNA in situ hybridization. protocols.io dx.doi.org/10.17504/protocols.io.p33dqqn | 2021-03-29 03:09:24 | ||
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Artificial Cerebrospinal Fluid IV (ACSF.IV) Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdpbi5in | BICCN, Allen Institute for Brain Science | This protocol describes making Artificial Cerebrospinal Fluid IV (ACSF.IV). ACSF.IV is used for multiple applications including incubation of fresh mouse brain slices prior to electrophysiological recording.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 2 | 2020 | Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid IV (ACSF.IV). protocols.io dx.doi.org/10.17504/protocols.io.bdpbi5in | 2021-03-29 03:09:27 | |||
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Competitive enzyme-linked immunosorbent assay for investigating SpL binding to mammalian and avian immunoglobulins Resource Report Resource Website |
Angel Justiz-Vaillant | 10.17504/protocols.io.bjqckmsw | University of the West Indies, [email protected] | This ELISA was based on the theory that antibodies present in different samples would compete with human IgG for binding to SpL, resulting in inhibition of human IgG-SpL interactions [1].Reference:1. Justiz-Vaillant AA, Akpaka PE, McFarlane-Anderson N, Smikle MF. Comparison of techniques of detecting immunoglobulin-binding protein reactivity to immunoglobulin produced by different avian and mammalian species.West Indian Med J. 2013;62(1):12-20. | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. Competitive enzyme-linked immunosorbent assay for investigating SpL binding to mammalian and avian immunoglobulins. protocols.io dx.doi.org/10.17504/protocols.io.bjqckmsw | 2021-03-29 03:09:24 | |||
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NEPA electroporation of Emiliania huxleyi cells Resource Report Resource Website |
Inbal nussbaum, Daniella Schatz | 10.17504/protocols.io.p4zdqx6 | Protist Research to Optimize Tools in Genetics (PROT-G) | We used the NEPA electroportor to transform Emiliania huxleyi cells. We were able to establish that this method can be used to introduce proteins into the cells. | Weizmann Institute of Science, Weizmann Institute of Science | 1 | 2018 | Inbal nussbaum, Daniella Schatz 2018. NEPA electroporation of Emiliania huxleyi cells. protocols.io dx.doi.org/10.17504/protocols.io.p4zdqx6 | 2021-03-29 03:09:26 | |||
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Copy of Fluorescence analysis using CF imager-v2 Resource Report Resource Website |
Steven Burgess | 10.17504/protocols.io.4t9gwr6 | University of Illinois at Urbana-Champaign | 1 | 2019 | Steven Burgess 2019. Copy of Fluorescence analysis using CF imager-v2. protocols.io dx.doi.org/10.17504/protocols.io.4t9gwr6 | 2021-03-29 03:09:26 | |||||
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Glutamate measurement Resource Report Resource Website |
Karen Maciel de Oliveira | 10.17504/protocols.io.rufd6tn | Glutamate is enzymatically measured in the cerebrospinal fluid by monitoring the fluorescence increase due to NADPH+ production in the presence of glutamate dehydrogenase and NADP+ on a spectrofluorimeter (Shimadzu RF-5301PC, Japan). | Oliveira KM, Binda NS, Lavor MSL, Silva CMO, Rosado IR, Gabellini ELA, Silva JFD, Oliveira CM, Melo MM, Gomez MV, Melo EG (2018) Conotoxin MVIIA improves cell viability and antioxidant system after spinal cord injury in rats. PLoS ONE 13(10): e0204948. doi: 10.1371/journal.pone.0204948 | Universidade Federal de Minas Gerais | https://doi.org/10.1371/journal.pone.0204948 | 1 | 2018 | Karen Maciel de Oliveira 2018. Glutamate measurement. protocols.io dx.doi.org/10.17504/protocols.io.rufd6tn | 2021-03-29 03:09:23 | ||
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SOLUTION- 10 - TEFF/TREG isolation buffer Resource Report Resource Website |
Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | 10.17504/protocols.io.bjadkia6 | Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy) | 1 | 2020 | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino 2020. SOLUTION- 10 - TEFF/TREG isolation buffer. protocols.io dx.doi.org/10.17504/protocols.io.bjadkia6 | 2021-03-29 03:09:27 | |||||
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FCMPASS - Cataloguing fluorescence reference materials Resource Report Resource Website |
Joshua Welsh, Sean Cook, Jennifer Jones | 10.17504/protocols.io.bnimmcc6 | Translational Nanobiology Section | This protocol outlines the steps required to catalogue fluorescence reference materials using the FCMPASS software. This is one of a number of protocols in the pipeline for performing small particle calibration using the fcmpass software package. | Translataional Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Translataional Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Translataional Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health | 2 | 2021 | Joshua Welsh, Sean Cook, Jennifer Jones 2021. FCMPASS - Cataloguing fluorescence reference materials. protocols.io dx.doi.org/10.17504/protocols.io.bnimmcc6 | 2021-03-29 03:09:23 | |||
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Option 2: Bead Cleanup – Alternatively a 2X AMPure XP bead clean up for NEXTflex™ mtDNA-Seq Kit Resource Report Resource Website |
Nina Orellana | 10.17504/protocols.io.dnq5dv | 1 | 2015 | Nina Orellana 2015. Option 2: Bead Cleanup – Alternatively a 2X AMPure XP bead clean up for NEXTflex™ mtDNA-Seq Kit. protocols.io dx.doi.org/10.17504/protocols.io.dnq5dv | 2021-03-29 03:09:27 | ||||||
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Gibson Assembly Cloning Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | 10.17504/protocols.io.43sgyne | This protocol describes Gibson Assembly cloning (Nat Methods 2009;6(5):343-5). To see the full abstract and additional resources, please visit the Addgene protocol page. | Addgene | https://www.addgene.org/protocols/gibson-assembly/ | 1 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. Gibson Assembly Cloning. protocols.io dx.doi.org/10.17504/protocols.io.43sgyne | 2021-03-29 03:09:23 | |||
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Oil Red O Staining Resource Report Resource Website |
Yuejun Wang | 10.17504/protocols.io.iemcbc6 | Adipogenic differentiation was induced by using the StemPro adipogenesis differentiation kit (Invitrogen, Carlsbad, CA, USA). WJCMSCs were grown in the adipose-inducing medium for 3 weeks. For Oil Red O staining, after induction, cells were fixed with 10% formalin for at least 1 h at room temperature. Next, cells were stained with the 60% Oil Red O in isopropanol as working solution for 10 min. The proportion of Oil Red O-positive cells was determined by counting stained cells under a light microscope. The final OD value in each group was normalized with the total protein concentrations prepared from a duplicate plate. | Wang Y, Liu Y, Fan Z, Liu D, Wang F, Zhou Y (2017) IGFBP2 enhances adipogenic differentiation potentials of mesenchymal stem cells from Wharton's jelly of the umbilical cord via JNK and Akt signaling pathways. PLoS ONE 12(8): e0184182. doi: 10.1371/journal.pone.0184182 | Department of Prosthodontics, Peking University School and Hospital of Stomatology | https://doi.org/10.1371/journal.pone.0184182 | 1 | 2017 | Yuejun Wang 2017. Oil Red O Staining . protocols.io dx.doi.org/10.17504/protocols.io.iemcbc6 | 2021-03-29 03:09:23 | ||
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BIOL 354W - Research Methods in Advance Microbiology Resource Report Resource Website |
Rosa Leon | 10.17504/protocols.io.mvec63e | Leon Zayas Lab | This protocol series will guide students through the experience of analyzing metagenomic data. | Willamette University | 3 | 2018 | Rosa Leon 2018. BIOL 354W - Research Methods in Advance Microbiology. protocols.io dx.doi.org/10.17504/protocols.io.mvec63e | 2021-03-29 03:09:23 | |||
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DNA Gels Resource Report Resource Website |
David Dunigan and Irina Agarkova | 10.17504/protocols.io.erubd6w | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. DNA Gels. protocols.io dx.doi.org/10.17504/protocols.io.erubd6w | 2021-03-29 03:09:27 | ||||
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Carbonate-Bicarbonate Buffer Resource Report Resource Website |
Neilier Junior | 10.17504/protocols.io.bfyijpue | A buffer solution has the function of resisting changes in pH even when adding powerful acids or bases. However, in the physiological environment the buffered system also provides cofactors for enzymatic reactions, critical salts and even essential nutrients for cells and tissues. Therefore, when trying to reproduce biological conditions in vitro, we must make the appropriate choice of the buffer. After all, it will provide the appropriate medium in which reactions will occur. | Universidade Federal de Viçosa | 1 | 2020 | Neilier Junior 2020. Carbonate-Bicarbonate Buffer. protocols.io dx.doi.org/10.17504/protocols.io.bfyijpue | 2021-03-29 03:09:27 | ||||
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Adult mouse kidney dissociation Resource Report Resource Website |
Andrew Potter | 10.17504/protocols.io.nf9dbr6 | Human Cell Atlas Method Development Community | Protocol for adult (8-10 week) mouse kidney dissociation. | Cincinnati Children's Hospital Medical Center | 1 | 2018 | Andrew Potter 2018. Adult mouse kidney dissociation. protocols.io dx.doi.org/10.17504/protocols.io.nf9dbr6 | 2021-03-29 03:09:25 | |||
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edX Learner and Course Analytics and Visualization Pipeline Resource Report Resource Website |
Michael Ginda, Katy Borner, Michael Richey, Mark Cousino | 10.17504/protocols.io.be9ijh4e | The edX Student and Course Analytics and Visualization Pipeline is analytics and visualization pipeline using edX course database and user logs, written in R to 1) to extract and process student users and performance data, course structures and event logs; 2) create learner trajectory networks of use and pathways through course content and activity modules; 3) analyze the students use of course content modules; and 4) aggregate student performance and interaction measurements for a given course. | Indiana University at Bloomington, Indiana University at Bloomington, The Boeing Corportation, The Boeing Corporation | https://github.com/cns-iu/edx-learnertrajectorynetpipeline | 5 | 2020 | Michael Ginda, Katy Borner, Michael Richey, Mark Cousino 2020. edX Learner and Course Analytics and Visualization Pipeline. protocols.io dx.doi.org/10.17504/protocols.io.be9ijh4e | 2021-03-29 03:09:24 | |||
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K and K+Si medium Resource Report Resource Website |
Roscoff Culture Collection | 10.17504/protocols.io.s34egqw | Roscoff Culture Collection | Medium to grow most phytoplankton species in small eukaryotes (Mamiellophyceae, Pelagophyceae etc...).When using for diatoms and coccolithophorids add silica (Si).ReferenceKeller, M.D., Selvin, R.C., Claus, W. & Guillard, R.R.L. 1987. Media for the culture of oceanic ultraphytoplankton. J. Phycol. 23:633–8. | CNRS-Sorbonne Université, Station Biologique, Place G. Tessier 29680 Roscoff FRANCE | 1 | 2019 | Roscoff Culture Collection 2019. K and K+Si medium. protocols.io dx.doi.org/10.17504/protocols.io.s34egqw | 2021-03-29 03:09:24 |
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