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 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SPARC C2 Spinal Cord Hemisection Protocol in Rats Resource Report Resource Website |
Elisa Gonzalez-Rothi, Marissa Ciesla, Latoya Allen, Gordon Mitchell | DOI:10.17504/protocols.io.2kngcve | SPARC | This protocol describes the procedure for performing a left lateral C2 spinal cord hemisection in rats | University of Florida, University of Florida, University of Florida, University of Florida | 1 | 2019 | Elisa Gonzalez-Rothi, Marissa Ciesla, Latoya Allen, Gordon Mitchell 2019. SPARC C2 Spinal Cord Hemisection Protocol in Rats. protocols.io https://dx.doi.org/10.17504/protocols.io.2kngcve | 2021-04-15 09:14:37 | |||
|
Human Pancreas Optical Clearing by iDISCO and VISIKOL Resource Report Resource Website |
Martha Campbell Thompson, Malavika Nair | DOI:10.17504/protocols.io.ba4qigvw | Optical Clearing of Tissue, SPARC | Optical clearing of tissues to improve deep tissue microscopy was described over a century ago and methods have improved considerably following publication of the CLARITY method from Karl Deisseroth in 2013. Improvements in organic and inorganic methods are constantly reported for multiple species and organs. Large volume imaging was needed for human pancreas studies due to known heterogeneity in normal islet sizes and proportions of endocrine cells. Lobularity in islet beta-cell loss and islet inflammation is also seen in patients with type 1 diabetes. The iDISCO protocol allows for rapid clearing, easy staining, and high resolution confocal imaging. Human pancreas samples were cleared using iDISCO as originally published. This protocol describes steps to clear 4mm x 6mm x 400um deep sections of 4% paraformaldehyde fixed human pancreas using iDISCO-like reagents purchased from Visikol. | University of Florida, University of Florida | 1 | 2020 | Martha Campbell Thompson, Malavika Nair 2020. Human Pancreas Optical Clearing by iDISCO and VISIKOL . protocols.io https://dx.doi.org/10.17504/protocols.io.ba4qigvw | 2021-04-15 09:14:51 | |||
|
Intracardiac perfusion with fixative for anatomical studies [keast-001-stage02] Resource Report Resource Website |
Janet Keast, Peregrine Osborne | DOI:10.17504/protocols.io.w3ffgjn | SPARC | This protocol is suitable for preserving tissues for anatomical studies of organs, ganglia, spinal cord or brain in adult rats. The protocol is performed under anesthesia and should incorporate all local requirements for standards of animal experimentation. | University of Melbourne, University of Melbourne | 1 | 2019 | Janet Keast, Peregrine Osborne 2019. Intracardiac perfusion with fixative for anatomical studies [keast-001-stage02]. protocols.io https://dx.doi.org/10.17504/protocols.io.w3ffgjn | 2021-04-15 09:14:40 | |||
|
Dissection and immunohistochemistry of mouse vagal ganglia Resource Report Resource Website |
Thomas Taylor-Clark, Seol-Hee Kim | DOI:10.17504/protocols.io.w6cfhaw | SPARC | Mice are euthanized, perfused with fixative and the vagal ganglia extracted. Vagal ganglia are then cyosectioned. Slices are stained for protein expression using immunohistochemistry. Expression of specific proteins and reporter proteins isarevisualized using microscopy. | University of South Florida, University of South Florida | 1 | 2019 | Thomas Taylor-Clark, Seol-Hee Kim 2019. Dissection and immunohistochemistry of mouse vagal ganglia. protocols.io https://dx.doi.org/10.17504/protocols.io.w6cfhaw | 2021-04-15 09:14:41 | |||
|
Sectioning Rat Heart Resource Report Resource Website |
Shaina Robbins, Sean Nieves | DOI:10.17504/protocols.io.w53fg8n | SPARC | This is the straightforward procedure we follow when sectioning rat heart. | Thomas Jefferson University, Thomas Jefferson University | 1 | 2020 | Shaina Robbins, Sean Nieves 2020. Sectioning Rat Heart. protocols.io https://dx.doi.org/10.17504/protocols.io.w53fg8n | 2021-04-15 09:15:13 | |||
|
Light microscopic analysis of synaptic input to neurons in the rat major pelvic ganglion [keast-003] Resource Report Resource Website |
Janet Keast, Peregrine Osborne | DOI:10.17504/protocols.io.bakiicue | SPARC | This collection describes the procedures required to visualise and characterize synaptic boutons associated with functionally classified pelvic ganglion autonomic neurons of adult male and female Sprague-Dawley rats. This collection includes protocols for:STAGE 1: Surgery to micro-inject fluorescent retrograde tracer dyes into one or more sites within the lower urinary tractSTAGE 2: Intracardiac perfusion with fixative to preserve neural tissues of interestSTAGE 3: Immunohistochemical labeling of thick cryosections of pelvic gangliaSTAGE 4: Confocal microscopy and image analysis of synaptic boutons associated with ganglion neurons. | University of Melbourne, University of Melbourne | 1 | 2020 | Janet Keast, Peregrine Osborne 2020. Light microscopic analysis of synaptic input to neurons in the rat major pelvic ganglion [keast-003]. protocols.io https://dx.doi.org/10.17504/protocols.io.bakiicue | 2021-04-15 09:15:15 | |||
|
A multi-scale model of cardiac electrophysiology Resource Report Resource Website |
Colleen clancy, Pei-Chi, Parya Aghasafari | DOI:10.17504/protocols.io.5nkg5cw | SPARC | Multi-scale computational modeling is a major branch of computational biology as evidenced by the US federal interagency Multi-Scale Modeling Consortium and major international projects. It invariably involves specific and detailed sequences of data analysis and simulation, often with multiple tools and datasets, and the community recognizes improved modularity, reuse, reproducibility, portability and scalability as critical unmet needs in this area. Scientific workflows are a well-recognized strategy for addressing these needs in scientific computing. While there are good examples if the use of scientific workflows in bioinformatics, medical informatics, biomedical imaging and data analysis, there are fewer examples in multi-scale computational modeling in general and cardiac electrophysiology in particular. Cardiac electrophysiology simulation is a mature area of multi-scale computational biology that serves as an excellent use case for developing and testing new scientific workflows. In this dataset, we develop, describe and test a computational workflow that serves as a proof of concept of a platform for the robust integration and implementation of a reusable and reproducible multi-scale cardiac cell and tissue model that is expandable, modular and portable. The workflow described leverages Python and Kepler-Python actor for plotting and pre/post-processing. During all stages of the workflow design, we rely on freely available open-source tools, to make our workflow freely usable by scientists. | University of California, Davis, University of California, Davis, University of California, Davis | https://github.com/ClancyLabUCD/Workflow_Kepler | 1 | 2019 | Colleen clancy, Pei-Chi, Parya Aghasafari 2019. A multi-scale model of cardiac electrophysiology. protocols.io https://dx.doi.org/10.17504/protocols.io.5nkg5cw | 2021-04-15 09:14:51 | ||
|
Immunofluorescent methods for antibody test in mouse colon Resource Report Resource Website |
Lixin Wang, Pu-Qing Yuan, Honghui Liang, Yvette Tache | DOI:10.17504/protocols.io.bqi2muge | SPARC | A table listed the information of antibodies used in the mouse colon. The protocol described the methods of colon tissues sampling, whole mount preparations, passive clarity technique, and respective fluorescent Immunohistochemistry for the antibody tests in different tissue preparations. | University of California, Los Angeles, University of California, Los Angeles, University of California, Los Angeles, University of California, Los Angeles | 1 | 2021 | Lixin Wang, Pu-Qing Yuan, Honghui Liang, Yvette Tache 2021. Immunofluorescent methods for antibody test in mouse colon. protocols.io https://dx.doi.org/10.17504/protocols.io.bqi2muge | 2021-04-15 09:15:29 | |||
|
Human Pancreas Histopathology Assessment Resource Report Resource Website |
Martha Campbell Thompson | DOI:10.17504/protocols.io.br7tm9nn | Human Cell Atlas Method Development Community, Optical Clearing of Tissue, SPARC | DRAFTPurpose:The purpose of this protocol is to outline proper procedures for fixed specimen processing using an automatic paraffin processor and sectioning and staining for histopathological review of normalcy. Scope:This protocol applies to human pancreas specimens that will be processed to paraffin blocks for HuBMAP Tissue Mapping Centers.Expected Outcome:Pancreas samples are processed properly and efficiently to whole slide images for histopathology review. Nuclei should stain blue. Cytoplasm of acinar cells should stain pink with blue zymogen granules. The large blood vessels should demonstrate clear differentiation of RBCs when present, surrounding collagen, and endothelial nuclei with scant cytoplasm. | University of Florida | 1 | 2021 | Martha Campbell Thompson 2021. Human Pancreas Histopathology Assessment. protocols.io https://dx.doi.org/10.17504/protocols.io.br7tm9nn | 2021-04-15 09:15:11 | |||
|
SPARC bilateral terminal phrenic neurophysiology preparation with moderate acute intermittent hypoxia Resource Report Resource Website |
Elisa Gonzalez-Rothi, Arash Tadjalli, Raphael Perim, Gordon Mitchell | DOI:10.17504/protocols.io.2jpgcmn | SPARC | Protocol for conducting bilateral phrenic neurograms in anesthetized, paralyzed, vagotomized and mechanically ventilated rats - moderate acute intermittent hypoxia-induced phrenic long-term facilitation protocol | University of Florida, University of Florida, University of Florida, University of Florida | 1 | 2019 | Elisa Gonzalez-Rothi, Arash Tadjalli, Raphael Perim, Gordon Mitchell 2019. SPARC bilateral terminal phrenic neurophysiology preparation with moderate acute intermittent hypoxia. protocols.io https://dx.doi.org/10.17504/protocols.io.2jpgcmn | 2021-04-15 09:15:14 | |||
|
Neurolucida 360: Detecting muscle fiber orientation Resource Report Resource Website |
Maci Heal | SPARC | MBF Bioscience | 1 | 2021 | Maci Heal 2021. Neurolucida 360: Detecting muscle fiber orientation . protocols.io https:// | 2021-04-15 09:15:40 | |||||
|
SPARC Serotonin 2B Receptor (5-HT2BR) Immunohistochemistry Protocol in Rat Tissues Labeled with Cholera Toxin B-fragment Resource Report Resource Website |
Elisa Gonzalez-Rothi, Yasin Seven, Latoya Allen, Marissa Ciesla, Gordon Mitchell | DOI:10.17504/protocols.io.2kigcue | SPARC | This protocol describes the immunofluorescent labeling technique used to identify serotonin 2B receptor expression in CtB-labelled phrenic motor neurons and within a defined region of interest surrounding phrenic motor neurons. | University of Florida, University of Florida, University of Florida, University of Florida, University of Florida | 1 | 2019 | Elisa Gonzalez-Rothi, Yasin Seven, Latoya Allen, Marissa Ciesla, Gordon Mitchell 2019. SPARC Serotonin 2B Receptor (5-HT2BR) Immunohistochemistry Protocol in Rat Tissues Labeled with Cholera Toxin B-fragment. protocols.io https://dx.doi.org/10.17504/protocols.io.2kigcue | 2021-04-15 09:15:46 | |||
|
Single-Cell ICN Neuron Mapping and 3D Heart Reconstruction with Tissue Mapper Resource Report Resource Website |
Clara Leung, Maci Heal, Shaina Robbins, Alison Moss, Corey Monteith, Susan Tappan | DOI:10.17504/protocols.io.bdz5i786 | SPARC | This protocol describes the process of using the Tissue Mapper software to map single neurons of the intrinsic cardiac nervous system, annotate or "trace" key cardiac anatomy on select histological sections of an image volume, and to visualize the mapped neurons and traced anatomy in a 3D reconstructed heart. | RRID:SCR_017321 | University of Central Florida, MBF Bioscience, Thomas Jefferson University, Thomas Jefferson University, Strateos, MBF Bioscience | 1 | 2020 | Clara Leung, Maci Heal, Shaina Robbins, Alison Moss, Corey Monteith, Susan Tappan 2020. Single-Cell ICN Neuron Mapping and 3D Heart Reconstruction with Tissue Mapper. protocols.io https://dx.doi.org/10.17504/protocols.io.bdz5i786 | 2021-04-15 09:15:22 | ||
|
Processing Human Colon "Myenteric Plexus" for Single Nuclei RNA-seq Resource Report Resource Website |
Christina M Wright, Robert O Heuckeroth | DOI:10.17504/protocols.io.w26fghe | SPARC | INTRODUCTION: The human enteric nervous system (ENS) is a complex network of neurons and glia that extends throughout the length of the bowel. There are many neuron and glia types, but very little is known about the human ENS compared to other species. There are two main ENS layers. The myenteric plexus neurons are clustered into ganglia with thick nerve fiber bundles running between ganglia. Submucosal neuron ganglia are scattered throughout the region between circular muscle and the epithelial lining of the bowel. One key problem with studying human ENS is that these cells are a very minor component of the bowel wall (OBJECTIVES: To obtain a suspension of single nuclei from human colon myenteric plexus that could be used for RNA-seq.METHODS: 1) Human colon "myenteric plexus" is dissected from the bowel wall after labeling with a live cell dye and then frozen in OCT. 2) Frozen "myenteric plexus" is sectioned on a cryostat to generate small fragments and disrupt muscle and connective tissue. 3) RNA quality is assessed from a few sections using an Agilent Bioanalyzer. 4) Nuclei are obtained from frozen sections using Dounce homogenization and labeled with Hoechst 33342 dye. 5). Nuclei are separated from other cell debris by FACS. 6) RNA-seq data were obtained using the 10X Genomic single cell sequencing platform.RESULTS: Live dye labeling works well on living tissue to visualize the ENS in human colon. Careful dissection is required to micro-dissect "myenteric plexus" from from within bowel wall muscle layers. A suspension of single nuclei is efficiently isolated by freezing isolated tissue in OCT, frozen sectioning, Dounce homogenizing, and FACS sorting Hoechst 33342 stained nuclei. The isolated nuclei are suitable for sequencing on the 10X Genomics single cell sequencing platform. This procedure dramatically enriched for cells in the region of the myenteric plexus, but unfortunately only a small percentage of the cells isolated are myenteric neurons. In addition to myenteric neurons, we obtained data from enteric glia, smooth muscle, muscularis macrophage, interstitial cells of Cajal, and PDGFRalpha+ cells that are known to be closely associated with myenteric plexus.CONCLUSION: We tried many approaches to optimize this procedure including additional steps to enrich for myenteric neuron nuclei. These additional procedures invariably reduced total cell yield without enriching significantly for neuronal nuclei. We do not know yet why neuronal nuclei remain a small component of our total nuclei population, but suspect that neuronal nuclei are more fragile than other nuclei isolated. This approach generated valuable data at a single nucleus RNA-seq level for all cell types within the muscle wall known to control bowel motility. | Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania | 1 | 2021 | Christina M Wright, Robert O Heuckeroth 2021. Processing Human Colon "Myenteric Plexus" for Single Nuclei RNA-seq. protocols.io https://dx.doi.org/10.17504/protocols.io.w26fghe | 2021-04-15 09:15:22 | |||
|
Tache_Yuan_OT2OD024899_CLARITYAnd3DImagingOfColonicENSintheMouseAndPig_1_2019-Pig_Protocol Resource Report Resource Website |
Pu-Qing Yuan, Yvette Taché | DOI:10.17504/protocols.io.4r9gv96 | SPARC | University of California, Los Angeles, University of California, Los Angeles | 1 | 2019 | Pu-Qing Yuan, Yvette Taché 2019. Tache_Yuan_OT2OD024899_CLARITYAnd3DImagingOfColonicENSintheMouseAndPig_1_2019-Pig_Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.4r9gv96 | 2021-04-15 09:15:30 | ||||
|
Tache_Yuan_OT2OD024899_CLARITYAnd3DImagingOfColonicENSintheMouseAndPig_1_2019-Mouse_Protocol (Annotation Copy) Resource Report Resource Website |
Pu-Qing Yuan, Lixin Wang, Yvette Taché | DOI:10.17504/protocols.io.4sagwae | SPARC | University of California, Los Angeles, University of California, Los Angeles, University of California, Los Angeles | 1 | 2019 | Pu-Qing Yuan, Lixin Wang, Yvette Taché 2019. Tache_Yuan_OT2OD024899_CLARITYAnd3DImagingOfColonicENSintheMouseAndPig_1_2019-Mouse_Protocol (Annotation Copy). protocols.io https://dx.doi.org/10.17504/protocols.io.4sagwae | 2021-04-15 09:15:52 | ||||
|
Processing Human Colon muscle layers for Single Nuclei RNA-seq using PHOX2B antibody immunoselection Resource Report Resource Website |
Christina M Wright, Robert O Heuckeroth | DOI:10.17504/protocols.io.w3afgie | SPARC | ABSTRACTINTRODUCTION: The human enteric nervous system (ENS) is a complex network of neurons and glia that extends throughout the length of the bowel. There are many neuron and glia types, but very little is known about the human ENS compared to other species. There are two main ENS layers. The myenteric plexus neurons are clustered into ganglia with thick nerve fiber bundles running between ganglia. Submucosal neuron ganglia are scattered throughout the region between circular muscle and the epithelial lining of the bowel. One key problem with studying human ENS is that these cells are a very minor component of the bowel wall (< 1: 10,000 cells) and they are surrounded by other tissue. The bowel wall is not easily dissociated making it challenging to isolate cells of the human ENS for any type of analsysis. OBJECTIVES: To enrich for neurons from human colon myenteric plexus using PHOX2B antibody and FACS METHODS: 1) Human colon muscle was dissected from the bowel wall and then frozen in OCT. 2) Frozen muscle was sectioned on a cryostat to generate small fragments and disrupt muscle and connective tissue. 3) RNA quality was assessed from a few sections using an Agilent Bioanalyzer. 4) Nuclei were obtained from frozen sections using Dounce homogenization and stained with antibody to PHOX2B. 5). Nuclei were separated from other cell debris by FACS. 6) RNA-seq data were obtained using the 10X Genomic single cell sequencing platform. RESULTS: This procedure worked well to isolate nuclei from human colon muscle. PHOX2B antibody labeling led to a small population of nuclei that appeared to be antibody stained under the microscope and have attached antibody by FACS. Unfortunately, single nucleus RNA-seq demonstrated that we had not enriched for myenteric neurons with this approach. RNA-seq data were obtained from many other cell types within the muscle layers of the bowel wall. CONCLUSION: This approach generated valuable data at a single nucleus RNA-seq level for many cell types within the muscle wall known to control bowel motility, but did not enrich for neuronal nuclei, even though PHOX2B antibody selectively stains myenteric plexus nuclei within the human bowel myenteric plexus | Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania | 1 | 2021 | Christina M Wright, Robert O Heuckeroth 2021. Processing Human Colon muscle layers for Single Nuclei RNA-seq using PHOX2B antibody immunoselection. protocols.io https://dx.doi.org/10.17504/protocols.io.w3afgie | 2021-04-15 09:15:54 | |||
|
High-Density Penetrating Microelectrode Recordings from Anesthetized Feline Dorsal Root Ganglia Resource Report Resource Website |
Zachariah Sperry, Kyounghwan Na, Mihaly Vöröslakos, Saman Parizi, James Jun, Tim M. Bruns, Euisik Yoon, John P. Seymour | DOI:10.17504/protocols.io.w5nfg5e | SPARC | Dorsal root ganglia (DRG) are components of spinal roots containing sensory cell bodies, and hold significant promise as neural recording sites for sensory neuroprostheses.This protocol details the fabrication and use of a high-density flexible polyimide electrode array into the sacral DRG of an anesthetized feline for neural recordings. | University of Michigan - Ann Arbor, University of Michigan - Ann Arbor, University of Szeged, University of Michigan - Ann Arbor, Flatiron Institute, University of Michigan - Ann Arbor, University of Michigan - Ann Arbor, University of Michigan - Ann Arbor | https://doi.org/10.1101/435800 | 1 | 2021 | Zachariah Sperry, Kyounghwan Na, Mihaly Vöröslakos, Saman Parizi, James Jun, Tim M. Bruns, Euisik Yoon, John P. Seymour 2021. High-Density Penetrating Microelectrode Recordings from Anesthetized Feline Dorsal Root Ganglia. protocols.io https://dx.doi.org/10.17504/protocols.io.w5nfg5e | 2021-04-15 09:15:55 | ||
|
Immunohistochemistry and high resolution microscopy of pig gastric enteroendocrine cells Resource Report Resource Website |
Linda J. Fothergill, Martin Stebbing, Billie Hunne, Giorgia Galiazzo, Josiane Fahkry, Frank Weissenborn, Therese Fazio Coles, John B. Furness | SPARC | University of Melbourne, University of Melbourne, University of Melbourne, University of Melbourne, University of Melbourne, The Florey Institute of Neuroscience and Mental Health, University of Melbourne, University of Melbourne | 1 | 2021 | Linda J. Fothergill, Martin Stebbing, Billie Hunne, Giorgia Galiazzo, Josiane Fahkry, Frank Weissenborn, Therese Fazio Coles, John B. Furness 2021. Immunohistochemistry and high resolution microscopy of pig gastric enteroendocrine cells. protocols.io https:// | 2021-04-15 09:16:01 | |||||
|
Use of tracer dyes to label neural projections to lower urinary tract organs [keast-001-stage01] Resource Report Resource Website |
Janet Keast, Peregrine Osborne | DOI:10.17504/protocols.io.w3dfgi6 | 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 | 2019 | Janet Keast, Peregrine Osborne 2019. Use of tracer dyes to label neural projections to lower urinary tract organs [keast-001-stage01]. protocols.io https://dx.doi.org/10.17504/protocols.io.w3dfgi6 | 2021-04-15 09:15:59 |
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
