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| Name | Authors | DOI | Group |
Summary |
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RRIDs used | ||||||
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DAB Solutions Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.betzjep6 | 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.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. DAB Solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.betzjep6 | 2021-04-15 09:15:23 | |||
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Multi-Patch Clamp Recording Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bcteiwje | BICCN, Allen Institute for Brain Science | This protocol describes the process to obtain multiple electrophysiological recordings from postnatal mouse and/or human brain slices. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Multi-Patch Clamp Recording. protocols.io https://dx.doi.org/10.17504/protocols.io.bcteiwje | 2021-04-15 09:15:20 | |||
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Zeiss AxioImager Multi Channel 20X Image Capture Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bcskiwcw | BICCN, Allen Institute for Brain Science | This protocol describes the capture of 20X multi-channel images using human and mouse tissue. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Zeiss AxioImager Multi Channel 20X Image Capture. protocols.io https://dx.doi.org/10.17504/protocols.io.bcskiwcw | 2021-04-15 09:14:56 | |||
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Stereotaxic Surgery for Delivery of Tracers by Iontophoresis Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bd8ti9wn | BICCN, Allen Institute for Brain Science | This protocol describes the delivery of a neuronal tracer using the iontophoretic method. 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 | 1 | 2020 | Allen Institute for Brain Science 2020. Stereotaxic Surgery for Delivery of Tracers by Iontophoresis. protocols.io https://dx.doi.org/10.17504/protocols.io.bd8ti9wn | 2021-04-15 09:14:57 | |||
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BD FACS Aria II Shutdown Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bameic3e | BICCN, Allen Institute for Brain Science | This protocol provides step by step instructions for shutting down the BD FACS Aria II and cleaning it of potentially hazardous materials. | Allen Institute | 1 | 2019 | Allen Institute for Brain Science 2019. BD FACS Aria II Shutdown. protocols.io https://dx.doi.org/10.17504/protocols.io.bameic3e | 2021-04-15 09:14:55 | |||
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20X Anatomic and Layer Identification for Biocytin Filled Cells Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bey9jfz6 | BICCN, Allen Institute for Brain Science | To characterize the orientation, laminar position, and anatomical location of in vitro single cells reconstructed in mouse and human brain slices, a 3-step process is used. Briefly, 20X brightfield and/or fluorescent images of DAPI (4',6-diamidino-2-phenylindole) are annotated to determine layer position and brain region, of biocytin-filled cells.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. 20X Anatomic and Layer Identification for Biocytin Filled Cells. protocols.io https://dx.doi.org/10.17504/protocols.io.bey9jfz6 | 2021-04-15 09:15:26 | |||
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FACS Single Cell Sorting Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.be4cjgsw | BICCN, Allen Institute for Brain Science | This protocol provides step by step instructions for performing single-cell sorting by using BD FACSAria II machine or BD FACSAria Fusion machine and BD FACSDiva software.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. FACS Single Cell Sorting. protocols.io https://dx.doi.org/10.17504/protocols.io.be4cjgsw | 2021-04-15 09:15:31 | |||
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Production of Recombinant EnvA Rabies Virus Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.8dnhs5e | BICCN, Allen Institute for Brain Science | This protocol is used for the large-scale production of EnvA-pseudotyped recombinant rabies virus. | Allen Institute | 2 | 2019 | Allen Institute for Brain Science 2019. Production of Recombinant EnvA Rabies Virus. protocols.io https://dx.doi.org/10.17504/protocols.io.8dnhs5e | 2021-04-15 09:15:32 | |||
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Artificial Cerebrospinal Fluid V (ACSF.V) Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.besjjecn | BICCN, Allen Institute for Brain Science | This protocol describes how to prepare Artificial Cerebrospinal Fluid (V). Artificial Cerebrospinal Fluid (V) is used during surgical procedures to maintain tissue hydration and minimize tissue damage, adhesion formation and infection.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 V (ACSF.V). protocols.io https://dx.doi.org/10.17504/protocols.io.besjjecn | 2021-04-15 09:15:31 | |||
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5 uM DAPI cell staining solution Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bg47jyzn | BICCN, Allen Institute for Brain Science | This protocol is used for preparation of 5 µM DAPI cell staining solution that is applicable for staining adult mouse brain sections.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. 5 uM DAPI cell staining solution. protocols.io https://dx.doi.org/10.17504/protocols.io.bg47jyzn | 2021-04-15 09:15:30 | |||
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Slice Preparation and Blockface Imaging for Electrophysiology - Mouse Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdpqi5mw | BICCN, Allen Institute for Brain Science | This protocol describes the procedure for transcardial perfusion of an adult mouse, followed by dissection, embedding, slicing, and blockface imaging of the mouse brain using either a Leica vibratome or a compresstome. The output tissue is suitable for use in electrophysiological recordings and/or live cell filling applications.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. Slice Preparation and Blockface Imaging for Electrophysiology - Mouse. protocols.io https://dx.doi.org/10.17504/protocols.io.bdpqi5mw | 2021-04-15 09:15:34 | |||
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Brain Dissection of Post-natal Mice Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.besnjede | BICCN, Allen Institute for Brain Science | This protocol describes the procedure for removal and embedding of the post-natal mouse brain.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. Brain Dissection of Post-natal Mice. protocols.io https://dx.doi.org/10.17504/protocols.io.besnjede | 2021-04-15 09:15:33 | |||
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Artificial Cerebrospinal Fluid I (ACSF.I) Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bezkjf4w | BICCN, Allen Institute for Brain Science | This protocol is used to prepare Artificial Cerebrospinal Fluid I (ACSF.I). ACSF.I is used for applications including transcardial perfusion prior to fresh mouse brain slicing and as a bathing solution during fresh mouse 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 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. Artificial Cerebrospinal Fluid I (ACSF.I). protocols.io https://dx.doi.org/10.17504/protocols.io.bezkjf4w | 2021-04-15 09:15:08 | |||
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Bright Field Image Capture with Zeiss AxioImager Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdpmi5k6 | BICCN, Allen Institute for Brain Science | This protocol describes the system that is used to capture Z stack images which are reassembled post-processing into 3D reconstructions.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. Bright Field Image Capture with Zeiss AxioImager. protocols.io https://dx.doi.org/10.17504/protocols.io.bdpmi5k6 | 2021-04-15 09:15:06 | |||
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3D Reconstruction of Neurons in Vaa3D Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdppi5mn | BICCN, Allen Institute for Brain Science | This protocol is used to generate accurate digital representations of neuron morphologies from a variety of brain regions and species. Each reconstruction captures the positions and thicknesses of the soma, dendrites and axon of a biocytin-filled cell within a slice of brain tissue. To generate the reconstruction we use an image stack containing ~200-700 serial 2D images that captures the full extent of the cell within the slice. We use the Vaa3D (Terafly) program with a Kazom’s Mozak user interface (Mozak for short) to visualize the 2D images in 3D. Once the stack is loaded in Mozak, our reconstruction is generated by placing nodes in 3D space. The placement of these nodes is dependent on the signal in the images. Our final output, an SWC text file (.swc format), contains many thousand rows. Each row contains a node ID, an x, y, z coordinate, radius value, neurite type, and parent node ID. After tracing is complete, we preform post processing to provide radius values, check for errors and consistency then the SWCs are uploaded into our Laboratory Information Management 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 | 2 | 2020 | Allen Institute for Brain Science 2020. 3D Reconstruction of Neurons in Vaa3D. protocols.io https://dx.doi.org/10.17504/protocols.io.bdppi5mn | 2021-04-15 09:15:37 | |||
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Isolation of Nuclei from Adult Mouse Brain Tissue Protocol Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bq7emzje | BICCN, Allen Institute for Brain Science | Protocol for isolation of nuclei from microdissected mouse brain tissue sections for FPCR and/or RNA-seq 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 | 2 | 2021 | Allen Institute for Brain Science 2021. Isolation of Nuclei from Adult Mouse Brain Tissue Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bq7emzje | 2021-04-15 09:15:40 | |||
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10% Tween 20 Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bfzmjp46 | BICCN, Allen Institute for Brain Science | This protocol is used to prepare 10% Tween 20. Tween 20, when added to aqueous solutions acts as a surfactant, decreasing the surface tension of the solution. It also punches holes in membranes, allowing easier penetration of macromolecules into cells and organelles, and reduces non-specific binding of antisera in immunohistochemistry.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. 10% Tween 20. protocols.io https://dx.doi.org/10.17504/protocols.io.bfzmjp46 | 2021-04-15 09:15:16 | |||
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Injection of Viral Tracers by Nanoject Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bgpujvnw | 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 | 3 | 2020 | Allen Institute for Brain Science 2020. Injection of Viral Tracers by Nanoject. protocols.io https://dx.doi.org/10.17504/protocols.io.bgpujvnw | 2021-04-15 09:15:19 | |||
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10Xv2 RNASeq Sample Processing Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bq68mzhw | BICCN, Allen Institute for Brain Science | Allows for rapid generation of 3’ transcriptomic-NGS-ready- single-cell-libraries from pools of cells.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 | 2021 | Allen Institute for Brain Science 2021. 10Xv2 RNASeq Sample Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.bq68mzhw | 2021-04-15 09:15:45 | |||
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Artificial Cerebrospinal Fluid VIII (ACSF.VIII) Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdpai5ie | BICCN, Allen Institute for Brain Science | This protocol describes how to make Artificial Cerebrospinal Fluid VIII (ACSF.VIII). ACSF.VIII is used for multiple applications including incubation of fresh human 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 VIII (ACSF.VIII). protocols.io https://dx.doi.org/10.17504/protocols.io.bdpai5ie | 2021-04-15 09:15:20 |
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