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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Artificial Cerebrospinal Fluid VII (ACSF.VII) Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.beznjf5e | BICCN, Allen Institute for Brain Science | This protocol is used to prepare Artificial Cerebrospinal Fluid VII (ACSF.VII). ACSF.VII is used for applications including fresh human brain tissue transportation and as a bathing solution during fresh human brain slicing.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U01MH114812. 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. Artificial Cerebrospinal Fluid VII (ACSF.VII). protocols.io https://dx.doi.org/10.17504/protocols.io.beznjf5e | 2021-04-15 09:15:20 | |||
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Human Neurosurgical Tissue Processing Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.be4djgs6 | 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.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U01MH114812. 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 | 6 | 2020 | Allen Institute for Brain Science 2020. Human Neurosurgical Tissue Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.be4djgs6 | 2021-04-15 09:15:47 | |||
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OLST protocol Resource Report Resource Website |
Arun Narasimhan, Kannan Umadevi Venkataraju, Judith Mizrachi, Dinu F. Albeanu, Pavel Osten | DOI:10.17504/protocols.io.smwec7e | BICCN | Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory | 1 | 2018 | Arun Narasimhan, Kannan Umadevi Venkataraju, Judith Mizrachi, Dinu F. Albeanu, Pavel Osten 2018. OLST protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.smwec7e | 2021-04-15 09:15:23 | ||||
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Isolation of Nuclei from Adult Mouse Brain Tissue Protocol Resource Report Resource Website |
ZengU19 BRAIN grant | DOI:10.17504/protocols.io.7dxhi7n | BICCN, Allen Institute for Brain Science | Protocol for isolation of nuclei from microdissected mouse brain tissue sections for FPCR and/or RNA-seq analysis. | Allen Institute | 1 | 2019 | ZengU19 BRAIN grant 2019. Isolation of Nuclei from Adult Mouse Brain Tissue Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.7dxhi7n | 2021-04-15 09:15:28 | |||
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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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Preparation of frozen nuclei for single-nucleus RNA seq Resource Report Resource Website |
Kimberly Siletti, Sten Linnarsson | DOI:10.17504/protocols.io.nx3dfqn | Human Cell Atlas Method Development Community, BICCN | This protocol describes our preparation of nuclei for single-nucleus RNA sequencing on the 10X Genomics Chromium system, starting from FAC-sorted frozen nuclei. | Karolinska Institutet, Karolinska Institutet | 1 | 2019 | Kimberly Siletti, Sten Linnarsson 2019. Preparation of frozen nuclei for single-nucleus RNA seq. protocols.io https://dx.doi.org/10.17504/protocols.io.nx3dfqn | 2021-04-15 09:15:40 | |||
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Methyl-C sequencing of single cell nuclei: snmC-seq2 Resource Report Resource Website |
Chongyuan Luo, Joseph Ecker | DOI:10.17504/protocols.io.pjvdkn6 | BICCN | Protocol to apply bisulfite conversion of methyl cytosine to the analysis of the epigenome of single cell nuclei isolated from brain tissue, as performed within the Center for Epigenomics of the Mouse Bain Atlas (CEMBA) and in coordination with the BRAIN Initiative Cell Census Network (BICCN). | Genomic Analysis Laboratory, Salk Institute for Biological Studies, HHMI and Genomic Analysis Laboratory, Salk Institute for Biological Studies | 1 | 2018 | Chongyuan Luo, Joseph Ecker 2018. Methyl-C sequencing of single cell nuclei: snmC-seq2. protocols.io https://dx.doi.org/10.17504/protocols.io.pjvdkn6 | 2021-04-15 09:15:43 | |||
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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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