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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Artificial Cerebrospinal Fluid IV (ACSF.IV) Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bctpiwmn | 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. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid IV (ACSF.IV). protocols.io https://dx.doi.org/10.17504/protocols.io.bctpiwmn | 2021-04-15 09:15:49 | |||
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Pulling Pipettes using the DMZ-Zeitz Universal Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bctgiwjw | BICCN, Allen Institute for Brain Science | Protocol is used for the manufacture of glass pipettes for patch clamp electrophysiology using the DMZ-Zeitz Universal puller. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Pulling Pipettes using the DMZ-Zeitz Universal. protocols.io https://dx.doi.org/10.17504/protocols.io.bctgiwjw | 2021-04-15 09:15:30 | |||
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Human Neurosurgical Tissue Processing Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bctdiwi6 | BICCN, Allen Institute for Brain Science | This protocol describes the procedure for receiving human surgical tissue, followed by trimming, mounting, embedding, and slicing under sterile conditions in order to produce tissue suitable for both slice culture as well as acute slice electrophysiology recording. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Human Neurosurgical Tissue Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.bctdiwi6 | 2021-04-15 09:15:37 | |||
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TissueCyte Image QC Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bep9jdr6 | BICCN, Allen Institute for Brain Science | This protocol describes the QC step that occurs after the week of TissueCyte runs, and prior to analysis.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 | 3 | 2020 | Allen Institute for Brain Science 2020. TissueCyte Image QC. protocols.io https://dx.doi.org/10.17504/protocols.io.bep9jdr6 | 2021-04-15 09:15:35 | |||
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Post Patch Clamp Slice Fixation Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bctciwiw | BICCN, Allen Institute for Brain Science | This protocol describes the process to fix recorded/filled cells from mouse and human brain slices with 4% PFA/2.5% Glutaraldehyde in PBS for future histochemical processing. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Post Patch Clamp Slice Fixation. protocols.io https://dx.doi.org/10.17504/protocols.io.bctciwiw | 2021-04-15 09:15:36 | |||
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Injection of Viral Tracers by Nanoject Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.besfjebn | BICCN, Allen Institute for Brain Science | This protocol describes the delivery of a neuronal tracer using the Nanoject II. The surgery uses a stereotaxic system to target specific brain coordinates in the mouse. 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. Injection of Viral Tracers by Nanoject. protocols.io https://dx.doi.org/10.17504/protocols.io.besfjebn | 2021-04-15 09:15:38 | |||
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Post Patch Clamp Slice Fixation Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.be2ijgce | BICCN, Allen Institute for Brain Science | This protocol describes the process to fix recorded/filled cells from mouse and human brain slices with 4% PFA/2.5% Glutaraldehyde in PBS for future histochemical processing.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 | 4 | 2020 | Allen Institute for Brain Science 2020. Post Patch Clamp Slice Fixation. protocols.io https://dx.doi.org/10.17504/protocols.io.be2ijgce | 2021-04-15 09:15:43 | |||
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Human Neurosurgical Tissue Processing Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdvki64w | BICCN, Allen Institute for Brain Science | This protocol describes the procedure for receiving human surgical tissue, followed by trimming, mounting, embedding, and slicing under sterile conditions in order to produce tissue suitable for both slice culture as well as acute slice electrophysiology recording. | Allen Institute | 3 | 2020 | Allen Institute for Brain Science 2020. Human Neurosurgical Tissue Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.bdvki64w | 2021-04-15 09:15:42 | |||
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Artificial Cerebrospinal Fluid III (ACSF.III) Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bctniwme | BICCN, Allen Institute for Brain Science | Artificial Cerebrospinal Fluid III (ACSF.III) is used for applications including tissue bath solution during electrophysiological recording. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid III (ACSF.III). protocols.io https://dx.doi.org/10.17504/protocols.io.bctniwme | 2021-04-15 09:15:49 | |||
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DAB Solutions Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bctkiwkw | BICCN, Allen Institute for Brain Science | 3, 3´ Diaminobenzidine (DAB) is a commonly used chromogen for histological staining. In the presence of peroxidase enzyme, DAB produces a brown precipitate that is insoluble in alcohol and xylene. Peroxidase catalyzes hydrogen peroxide oxidation of substrate DAB. This SOP provides instructions to prepare four different formulations of DAB. DAB for Immunohistochemical staining (IHC), DAB for Acetylcholinesterase (AChE) Staining, Nickel Enchanced DAB for Biocytin staining, and DAB for Biocytin staining. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. DAB Solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.bctkiwkw | 2021-04-15 09:15:56 | |||
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Artificial Cerebrospinal Fluid IX (ACSF.IX) Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bctriwm6 | BICCN, Allen Institute for Brain Science | Artificial Cerebrospinal Fluid IX (ACSF.IX) is used for applications including tissue bath solution during electrophysiological recording for probing synaptic connections under physiological conditions. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid IX (ACSF.IX). protocols.io https://dx.doi.org/10.17504/protocols.io.bctriwm6 | 2021-04-15 09:15:58 | |||
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DAB Detection of Biocytin Labeled Tissue Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdpji5kn | BICCN, Allen Institute for Brain Science | This protocol describes the process for diaminobenzidine (DAB) detection of biocytin filled cells. This protocol is optimized for use with brain slices cut at 350 µm thick, in which cells are first filled with biocytin (i.e., post-electrophysiological recording), fixed in 4% PFA/2.5% glutaraldehyde, and transferred to PBS until ready to stain.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. DAB Detection of Biocytin Labeled Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.bdpji5kn | 2021-04-15 09:16:01 | |||
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0.9% Saline Solution Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bg44jyyw | BICCN, Allen Institute for Brain Science | This protocol is used to prepare 0.9% Saline Solution. 0.9% Sterile Saline solution is used as an initial rinse for the brains of mice prior to perfusion. 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 | 1 | 2020 | Allen Institute for Brain Science 2020. 0.9% Saline Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.bg44jyyw | 2021-04-15 09:16:02 | |||
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Production of Crude AAV Virus Extract Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.8djhs4n | BICCN, Allen Institute for Brain Science | This protocol is used to produce crude preps of AAV of any serotype. | Allen Institute | 2 | 2019 | Allen Institute for Brain Science 2019. Production of Crude AAV Virus Extract. protocols.io https://dx.doi.org/10.17504/protocols.io.8djhs4n | 2021-04-15 09:16:04 | |||
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Patch-Seq Internal Solution with Biocytin Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.9gih3ue | BICCN, Allen Institute for Brain Science | This SOP provides instruction to prepare Internal Solution which is used for patch clamp electrophysiology, modified for cleanliness and mRNA capture and sustainability. | Allen Institute | 1 | 2019 | Allen Institute for Brain Science 2019. Patch-Seq Internal Solution with Biocytin. protocols.io https://dx.doi.org/10.17504/protocols.io.9gih3ue | 2021-04-15 09:16:07 | |||
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Production of AAV Virus by Iodixanol Gradient Ultracentrifugation Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.8dmhs46 | BICCN, Allen Institute for Brain Science | This protocol is used to produce AAV of any serotype with high purity and high titer. | Allen Institute | 2 | 2019 | Allen Institute for Brain Science 2019. Production of AAV Virus by Iodixanol Gradient Ultracentrifugation. protocols.io https://dx.doi.org/10.17504/protocols.io.8dmhs46 | 2021-04-15 09:16:01 | |||
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Core Protocol for Serial Imaging of Fluorescently-Labeled Mouse Brain on the TissueCyte 1000 System Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bbx4ipqw | BICCN, Allen Institute for Brain Science | This protocol describes the instructions for setup and scanning of fluorescently-labeled tissue sections mounted in agarose and attached to a slide using the TissueCyte 1000 block face 2-photon system. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Core Protocol for Serial Imaging of Fluorescently-Labeled Mouse Brain on the TissueCyte 1000 System. protocols.io https://dx.doi.org/10.17504/protocols.io.bbx4ipqw | 2021-04-15 09:16:04 | |||
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Mouse Whole Cell Tissue Processing for 10x Genomics Platform Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdn7i5hn | BICCN, Allen Institute for Brain Science | This protocol describes how to isolate tissue from various ROI’s of the mouse brain followed by preparation of a highly concentrated single cell suspension for transcriptomic profiling on 10x Genomics platform.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 | 4 | 2020 | Allen Institute for Brain Science 2020. Mouse Whole Cell Tissue Processing for 10x Genomics Platform. protocols.io https://dx.doi.org/10.17504/protocols.io.bdn7i5hn | 2021-04-15 09:16:09 | |||
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Core Protocol for Serial Imaging of Fluorescently-Labeled Mouse Brain on the TissueCyte 1000 System Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.ber7jd9n | BICCN, Allen Institute for Brain Science | This protocol describes the instructions for setup and scanning of fluorescently-labeled tissue sections mounted in agarose and attached to a slide using the TissueCyte 1000 block face 2-photon system.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 | 3 | 2020 | Allen Institute for Brain Science 2020. Core Protocol for Serial Imaging of Fluorescently-Labeled Mouse Brain on the TissueCyte 1000 System. protocols.io https://dx.doi.org/10.17504/protocols.io.ber7jd9n | 2021-04-15 09:16:11 | |||
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Artificial Cerebrospinal Fluid IV (ACSF.IV) Resource Report Resource Website |
Allen Institute for Brain Science | DOI: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 https://dx.doi.org/10.17504/protocols.io.bdpbi5in | 2021-04-15 09:16:12 |
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