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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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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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Slide Preparation for Mounting Samples for TissueCyte 1000 Sectioning and Imaging Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.ber8jd9w | 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 | 3 | 2020 | Allen Institute for Brain Science 2020. Slide Preparation for Mounting Samples for TissueCyte 1000 Sectioning and Imaging. protocols.io https://dx.doi.org/10.17504/protocols.io.ber8jd9w | 2021-04-15 09:16:13 | |||
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TissueCyte Installation And Alignment Guide Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bbx9ipr6 | BICCN, Allen Institute for Brain Science | This protocol outlines some of the steps that are required to align a TissueCyte 1000 serial two-photon imaging system and install commonly replaced parts. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. TissueCyte Installation And Alignment Guide. protocols.io https://dx.doi.org/10.17504/protocols.io.bbx9ipr6 | 2021-04-15 09:16:24 | |||
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Artificial Cerebrospinal Fluid IX (ACSF.IX) Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdn9i5h6 | 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.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 IX (ACSF.IX). protocols.io https://dx.doi.org/10.17504/protocols.io.bdn9i5h6 | 2021-04-15 09:16:15 | |||
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Human Neurosurgical Tissue Processing Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bf66jrhe | 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 | 7 | 2020 | Allen Institute for Brain Science 2020. Human Neurosurgical Tissue Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.bf66jrhe | 2021-04-15 09:16:14 | |||
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Artificial Cerebrospinal Fluid VIII (ACSF.VIII) Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bctqiwmw | 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. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid VIII (ACSF.VIII). protocols.io https://dx.doi.org/10.17504/protocols.io.bctqiwmw | 2021-04-15 09:16:22 | |||
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cDNA Synthesis Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdvui66w | BICCN, Allen Institute for Brain Science | This protocol describes the synthesis of first-strand cDNA from total RNA using the Invitrogen SuperScript III Reverse Transcriptase 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. cDNA Synthesis. protocols.io https://dx.doi.org/10.17504/protocols.io.bdvui66w | 2021-04-15 09:16:28 | |||
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10xV3 Genomics Sample Processing Protocol Resource Report Resource Website |
ZengU19 | DOI:10.17504/protocols.io.7d4hi8w | BICCN, Allen Institute for Brain Science | Protocol allows for rapid generation of 3’ transcriptomic-NGS-ready- single-cell-libraries from pools of cells. | Allen Institute | 1 | 2019 | ZengU19 2019. 10xV3 Genomics Sample Processing Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.7d4hi8w | 2021-04-15 09:16:17 | |||
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Nuclei Isolation for SNARE-seq2 Resource Report Resource Website |
Carter Palmer, Christine Liu, Jerold Chun | DOI:10.17504/protocols.io.8tvhwn6 | BICCN | This protocol is intended to be used for the isolation of nuclei from fresh-frozen brain tissue in preparation for analysis by Single-Nucleus Chromatin Accessibility and mRNA Expression sequencing (SNARE-seq). It has been applied to tissues from mouse, marmoset, and human. | University of California, San Diego, and Sanford Burnham Prebys Medical Discovery Institute, University of California, San Diego, and Sanford Burnham Prebys Medical Discovery Institute, Sanford Burnham Prebys Medical Discovery Institute | 1 | 2020 | Carter Palmer, Christine Liu, Jerold Chun 2020. Nuclei Isolation for SNARE-seq2 . protocols.io https://dx.doi.org/10.17504/protocols.io.8tvhwn6 | 2021-04-15 09:16:31 | |||
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Production of Recombinant EnvA Rabies Virus Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdvvi666 | BICCN, Allen Institute for Brain Science | This protocol is used for the large-scale production of EnvA-pseudotyped recombinant rabies virus.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 Recombinant EnvA Rabies Virus. protocols.io https://dx.doi.org/10.17504/protocols.io.bdvvi666 | 2021-04-15 09:16:36 | |||
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Post Patch Clamp Slice Fixation Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bep3jdqn | 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 | 3 | 2020 | Allen Institute for Brain Science 2020. Post Patch Clamp Slice Fixation. protocols.io https://dx.doi.org/10.17504/protocols.io.bep3jdqn | 2021-04-15 09:16:26 | |||
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FACS Single Cell Sorting Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdvsi66e | 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 | 2 | 2020 | Allen Institute for Brain Science 2020. FACS Single Cell Sorting. protocols.io https://dx.doi.org/10.17504/protocols.io.bdvsi66e | 2021-04-15 09:16:53 | |||
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Isolation of Nuclei from Adult Human Brain Tissue for 10x Genomics Platform Resource Report Resource Website |
LeinU01 BRAIN grant | DOI:10.17504/protocols.io.y6rfzd6 | BICCN, Allen Institute for Brain Science | Isolation of nuclei from frozen adult human brain tissue or thawed and microdissected brain tissue sections for RNA-seq analysis. | Allen Institute | 1 | 2019 | LeinU01 BRAIN grant 2019. Isolation of Nuclei from Adult Human Brain Tissue for 10x Genomics Platform. protocols.io https://dx.doi.org/10.17504/protocols.io.y6rfzd6 | 2021-04-15 09:16:55 | |||
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Human Post Mortem Brain Processing Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bezcjf2w | BICCN, Allen Institute for Brain Science | This protocol describes the steps for processing post-mortem human brain, starting from whole brain or a single hemisphere.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. Human Post Mortem Brain Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.bezcjf2w | 2021-04-15 09:16:56 | |||
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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.besgjebw | 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 | 2 | 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.besgjebw | 2021-04-15 09:16:54 |
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