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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. DAB Detection of Biocytin Labeled Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.bdpji5kn Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. 0.9% Saline Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.bg44jyyw Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol is used to produce crude preps of AAV of any serotype.
Proper citation: Allen Institute for Brain Science 2019. Production of Crude AAV Virus Extract. protocols.io https://dx.doi.org/10.17504/protocols.io.8djhs4n Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This SOP provides instruction to prepare Internal Solution which is used for patch clamp electrophysiology, modified for cleanliness and mRNA capture and sustainability.
Proper citation: Allen Institute for Brain Science 2019. Patch-Seq Internal Solution with Biocytin. protocols.io https://dx.doi.org/10.17504/protocols.io.9gih3ue Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol is used to produce AAV of any serotype with high purity and high titer.
Proper citation: 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 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: 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 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: 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 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: 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 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid IV (ACSF.IV). protocols.io https://dx.doi.org/10.17504/protocols.io.bdpbi5in Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: 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 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. TissueCyte Installation And Alignment Guide. protocols.io https://dx.doi.org/10.17504/protocols.io.bbx9ipr6 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid IX (ACSF.IX). protocols.io https://dx.doi.org/10.17504/protocols.io.bdn9i5h6 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. Human Neurosurgical Tissue Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.bf66jrhe Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid VIII (ACSF.VIII). protocols.io https://dx.doi.org/10.17504/protocols.io.bctqiwmw Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. cDNA Synthesis. protocols.io https://dx.doi.org/10.17504/protocols.io.bdvui66w Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. Production of Recombinant EnvA Rabies Virus. protocols.io https://dx.doi.org/10.17504/protocols.io.bdvvi666 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. Post Patch Clamp Slice Fixation. protocols.io https://dx.doi.org/10.17504/protocols.io.bep3jdqn Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. FACS Single Cell Sorting. protocols.io https://dx.doi.org/10.17504/protocols.io.bdvsi66e Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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
Proper citation: Allen Institute for Brain Science 2020. Human Post Mortem Brain Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.bezcjf2w Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: 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 Copy
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