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Authors: Janet Keast, Peregrine Osborne
Group: SPARC
Summary: 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.
Proper citation: 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 Copy
Authors: Daniel Marchal
Proper citation: Daniel Marchal 2018. Golden Gate Cloning LVL 0. protocols.io dx.doi.org/10.17504/protocols.io.uvhew36 Copy
Authors: John Stack, Gary Cline
Group: Mouse Metabolic Phenotyping Centers
Summary: 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.
Proper citation: John Stack, Gary Cline 2019. Yale - Blood or Urine Calcium. protocols.io dx.doi.org/10.17504/protocols.io.y3nfyme Copy
Authors: Nicholas Leigh, Garrett Dunlap, Kimberly Johnson, Rachelle Mariano, Rachel Oshiro, Alan Y. Wong, Donald M. Bryant, Bess Miller, Jessica L. Whited
Summary: 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
Proper citation: 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 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid IV (ACSF.IV). protocols.io dx.doi.org/10.17504/protocols.io.bdpbi5in Copy
Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: 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.
Proper citation: 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 Copy
Authors: Inbal nussbaum, Daniella Schatz
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: 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.
Proper citation: Inbal nussbaum, Daniella Schatz 2018. NEPA electroporation of Emiliania huxleyi cells. protocols.io dx.doi.org/10.17504/protocols.io.p4zdqx6 Copy
Authors: Steven Burgess
Proper citation: Steven Burgess 2019. Copy of Fluorescence analysis using CF imager-v2. protocols.io dx.doi.org/10.17504/protocols.io.4t9gwr6 Copy
Authors: Karen Maciel de Oliveira
Summary: 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).
Proper citation: Karen Maciel de Oliveira 2018. Glutamate measurement. protocols.io dx.doi.org/10.17504/protocols.io.rufd6tn Copy
Authors: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
Proper citation: 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 Copy
Authors: Joshua Welsh, Sean Cook, Jennifer Jones
Group: Translational Nanobiology Section
Summary: 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.
Proper citation: Joshua Welsh, Sean Cook, Jennifer Jones 2021. FCMPASS - Cataloguing fluorescence reference materials. protocols.io dx.doi.org/10.17504/protocols.io.bnimmcc6 Copy
Authors: Nina Orellana
Proper citation: 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 Copy
Authors: Addgene The Nonprofit Plasmid Repository
Summary: 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.
Proper citation: Addgene The Nonprofit Plasmid Repository 2019. Gibson Assembly Cloning. protocols.io dx.doi.org/10.17504/protocols.io.43sgyne Copy
Authors: Yuejun Wang
Summary: 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.
Proper citation: Yuejun Wang 2017. Oil Red O Staining . protocols.io dx.doi.org/10.17504/protocols.io.iemcbc6 Copy
Authors: Rosa Leon
Group: Leon Zayas Lab
Summary: This protocol series will guide students through the experience of analyzing metagenomic data.
Proper citation: Rosa Leon 2018. BIOL 354W - Research Methods in Advance Microbiology. protocols.io dx.doi.org/10.17504/protocols.io.mvec63e Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. DNA Gels. protocols.io dx.doi.org/10.17504/protocols.io.erubd6w Copy
Authors: Neilier Junior
Summary: 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.
Proper citation: Neilier Junior 2020. Carbonate-Bicarbonate Buffer. protocols.io dx.doi.org/10.17504/protocols.io.bfyijpue Copy
Authors: Andrew Potter
Group: Human Cell Atlas Method Development Community
Summary: Protocol for adult (8-10 week) mouse kidney dissociation.
Proper citation: Andrew Potter 2018. Adult mouse kidney dissociation. protocols.io dx.doi.org/10.17504/protocols.io.nf9dbr6 Copy
Authors: Michael Ginda, Katy Borner, Michael Richey, Mark Cousino
Summary: 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.
Proper citation: 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 Copy
Authors: Roscoff Culture Collection
Group: Roscoff Culture Collection
Summary: 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.
Proper citation: Roscoff Culture Collection 2019. K and K+Si medium. protocols.io dx.doi.org/10.17504/protocols.io.s34egqw Copy
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