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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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DAB Detection of Biocytin Labeled Tissue Resource Report Resource Website |
Allen Institute for Brain Science | 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 dx.doi.org/10.17504/protocols.io.bdpji5kn | 2021-03-29 03:08:48 | |||
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Production of AAV Virus by Iodixanol Gradient Ultracentrifugation Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdvxi67n | BICCN, Allen Institute for Brain Science | This protocol is used to produce AAV of any serotype with high purity and high titer.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. Production of AAV Virus by Iodixanol Gradient Ultracentrifugation. protocols.io dx.doi.org/10.17504/protocols.io.bdvxi67n | 2021-03-29 03:08:50 | |||
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Production of Crude AAV Virus Extract Resource Report Resource Website |
Allen Institute for Brain Science | 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 dx.doi.org/10.17504/protocols.io.8djhs4n | 2021-03-29 03:08:50 | |||
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Production of AAV Virus by Iodixanol Gradient Ultracentrifugation Resource Report Resource Website |
Allen Institute for Brain Science | 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 dx.doi.org/10.17504/protocols.io.8dmhs46 | 2021-03-29 03:08:53 | |||
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Patch-Seq Internal Solution with Biocytin Resource Report Resource Website |
Allen Institute for Brain Science | 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 dx.doi.org/10.17504/protocols.io.9gih3ue | 2021-03-29 03:08:53 | |||
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Digoxigenin Labeled In Vitro Transcription and Ribogreen Quantification Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bg4vjyw6 | BICCN, Allen Institute for Brain Science | This protocol is used for in vitro transcription (IVT) reaction generating DIG-labeled anti-sense (AS) RNA from polymerase chain reaction (PCR) product for in situ hybridization (ISH), as well as fluorescent quantification of products using Ribogreen immediately following. This protocol is written for 96 reactions but can also be used for single reactions or in multiples of 96 by adjusting the amount of materials and equipment appropriately.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. Digoxigenin Labeled In Vitro Transcription and Ribogreen Quantification. protocols.io dx.doi.org/10.17504/protocols.io.bg4vjyw6 | 2021-03-29 03:08:56 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.bbx4ipqw | 2021-03-29 03:08:57 | |||
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DAB Solutions Resource Report Resource Website |
Allen Institute for Brain Science | 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 dx.doi.org/10.17504/protocols.io.bctkiwkw | 2021-03-29 03:08:34 | |||
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Mouse Cardiac Perfusion Fixation and Brain Collection Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.beudjes6 | BICCN, Allen Institute for Brain Science | This protocol describes the procedures for intracardiac perfusion fixation of postnatal mice, including anesthesia, exsanguination, fixation, brain removal and post-fixation storage. 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. Mouse Cardiac Perfusion Fixation and Brain Collection. protocols.io dx.doi.org/10.17504/protocols.io.beudjes6 | 2021-03-29 03:08:36 | |||
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Artificial Cerebrospinal Fluid III (ACSF.III) Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdpci5iw | BICCN, Allen Institute for Brain Science | Artificial Cerebrospinal Fluid III (ACSF.III) is used for applications including tissue bath solution during 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 III (ACSF.III). protocols.io dx.doi.org/10.17504/protocols.io.bdpci5iw | 2021-03-29 03:08:39 | |||
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Slide Preparation for Mounting Samples for TissueCyte 1000 Sectioning and Imaging Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdvni65e | BICCN, Allen Institute for Brain Science | This protocol describes the preparation of 1x3 glass slides for mounting embedded mouse brain samples for subsequent imaging and sectioning on TissueCyte 1000. 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. Slide Preparation for Mounting Samples for TissueCyte 1000 Sectioning and Imaging. protocols.io dx.doi.org/10.17504/protocols.io.bdvni65e | 2021-03-29 03:08:57 | |||
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Phosphate Buffered Saline (PBS) Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bezgjf3w | BICCN, Allen Institute for Brain Science | This protocol is used to prepare Phosphate Buffered Saline (PBS). PBS (-) and PBS (+) which includes Tween are used as biologically neutral wash solutions in many processes including In Situ Hybridization (ISH), Immunohistochemistry (IHC) and Fixation.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. Phosphate Buffered Saline (PBS). protocols.io dx.doi.org/10.17504/protocols.io.bezgjf3w | 2021-03-29 03:09:03 | |||
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PCR Prep from cDNA for IVT Reactions Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bcsfiwbn | BICCN, Allen Institute for Brain Science | This protocol describes PCR1 and PCR2 reactions beginning with cDNA to generate transcript templates ready for IVT reaction. This protocol is written for 192 (2x96) reactions but can also be used for fewer or more reactions by adjusting the amount of materials and equipment appropriately. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. PCR Prep from cDNA for IVT Reactions. protocols.io dx.doi.org/10.17504/protocols.io.bcsfiwbn | 2021-03-29 03:09:09 | |||
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Artificial Cerebrospinal Fluid IV (ACSF.IV) Resource Report Resource Website |
Allen Institute for Brain Science | 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 dx.doi.org/10.17504/protocols.io.bdpbi5in | 2021-03-29 03:09:27 | |||
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TissueCyte Troubleshooting Guide Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdpsi5ne | BICCN, Allen Institute for Brain Science | This protocol outlines strategies to solve common problems that occur when setting up the TissueCyte 1000 system for normal operation.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. TissueCyte Troubleshooting Guide. protocols.io dx.doi.org/10.17504/protocols.io.bdpsi5ne | 2021-03-29 03:11:59 | |||
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PCR Prep from cDNA for IVT Reactions Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdpni5me | BICCN, Allen Institute for Brain Science | This protocol describes PCR1 and PCR2 reactions beginning with cDNA to generate transcript templates ready for IVT reaction. This protocol is written for 192 (2x96) reactions but can also be used for fewer or more reactions by adjusting the amount of materials and equipment appropriately.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. PCR Prep from cDNA for IVT Reactions. protocols.io dx.doi.org/10.17504/protocols.io.bdpni5me | 2021-03-29 03:12:03 | |||
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Patch-Seq Recording and Extraction Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdpei5je | BICCN, Allen Institute for Brain Science | This protocol describes the process to obtain electrophysiological recordings and cellular contents from neurons in postnatal mouse and/or human brain slices.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. Patch-Seq Recording and Extraction. protocols.io dx.doi.org/10.17504/protocols.io.bdpei5je | 2021-03-29 03:07:46 | |||
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Intramuscular Injection Adult Mouse Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bfzfjp3n | BICCN, Allen Institute for Brain Science | This protocol describes the general procedures used for intramuscular injection in adult mice. 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. Intramuscular Injection Adult Mouse. protocols.io dx.doi.org/10.17504/protocols.io.bfzfjp3n | 2021-03-29 03:08:07 | |||
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Zeiss AxioImager Multi Channel 20X Image Capture Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdpki5kw | BICCN, Allen Institute for Brain Science | This protocol describes the capture of 20X multi-channel images using human and mouse tissue.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. Zeiss AxioImager Multi Channel 20X Image Capture. protocols.io dx.doi.org/10.17504/protocols.io.bdpki5kw | 2021-03-29 03:08:14 | |||
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Leica SP8 Confocal Imaging Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bd8wi9xe | BICCN, Allen Institute for Brain Science | This protocol describes the basic setup and scanning using the Leica SP8 confocal microscope of fluorescently-labeled mouse brain tissue sections mounted on positively charged 1” x 3” microscope slides.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. Leica SP8 Confocal Imaging. protocols.io dx.doi.org/10.17504/protocols.io.bd8wi9xe | 2021-03-29 03:08:15 |
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