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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol provides step by step instructions for shutting down the BD FACS Aria II and cleaning it of potentially hazardous materials.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. BD FACS Aria II Shutdown. protocols.io https://dx.doi.org/10.17504/protocols.io.bdvpi65n Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol provides guidance in the assessment of quality of tissues post perfusion and dissection and applies to all such procedures. Perfusion and dissection quality will be categorized on the following scale: perfect, good, fair, and poor. This SOP also presents written descriptions, and images, of specific category attributes. 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. Tissue Quality Evaluation for Brain Perfusion/Dissection Specimens. protocols.io https://dx.doi.org/10.17504/protocols.io.bd8yi9xw Copy   

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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.beppjdmn Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol is used to operate the Bioanalyzer which is used as a quality control step for IVT products. Peak size, shape, and sample concentration are recorded and used to evaluate samples on a pass/fail level.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number 1U19MH114830-01. 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 2021. Bioanalyzer Operation for IVT Products. protocols.io https://dx.doi.org/10.17504/protocols.io.brt3m6qn Copy   

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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 and BD FACSDiva software in preparation for single-cell sorting.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. BD FACS Aria II Start-up and Calibration. protocols.io https://dx.doi.org/10.17504/protocols.io.bdvqi65w Copy   

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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.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. Patch-Seq Internal Solution with Biocytin. protocols.io https://dx.doi.org/10.17504/protocols.io.besdjea6 Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the QC step that occurs after the week of TissueCyte runs, and prior to analysis.

Proper citation: Allen Institute for Brain Science 2020. TissueCyte Image QC. protocols.io https://dx.doi.org/10.17504/protocols.io.bbybipsn Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.

Proper citation: Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid III (ACSF.III). protocols.io https://dx.doi.org/10.17504/protocols.io.beptjdnn Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the procedure for transcardial perfusion of an adult mouse, followed by brain dissection, embedding, slicing, blockface imaging, ROI microdissection, and tissue dissociation. The output of this protocol is a cell suspension that can be sorted via FACS for single-cell transcriptional profiling.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 2021. Slice Preparation with Tissue Dissociation - Mouse Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bq6wmzfe Copy   

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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.bgpvjvn6 Copy   

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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.

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.bbx3ipqn Copy   

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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.bet4jeqw Copy   

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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.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. TissueCyte Installation And Alignment Guide. protocols.io https://dx.doi.org/10.17504/protocols.io.bdpti5nn Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocols provides detailed instructions for procedures needed for maintenance of the TissueCyte scanning systems.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. Maintenance of TissueCyte System. protocols.io https://dx.doi.org/10.17504/protocols.io.bdpui5nw Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the preparation of a fixed mouse brain specimen bonded to an agarose block for blockface imaging and sectioning using the TissueCyte 1000 system.

Proper citation: Allen Institute for Brain Science 2020. TissueCyte Specimen Embedding Acrylamide Coembedding. protocols.io https://dx.doi.org/10.17504/protocols.io.bbx5ipq6 Copy   

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Authors: Brian Lee, Kristen Hadley, Allen Institute for Brain Science
Group: Allen Institute for Brain Science
Summary: This protocol is a detailed version of the Allen Institute's Patch-Seq Recording and Extraction protocol, which 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.

Proper citation: Brian Lee, Kristen Hadley, Allen Institute for Brain Science 2020. Patch-Seq Recording and Extraction Detailed Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bpbuminw Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the preparation of a fixed mouse brain specimen bonded to an agarose block for blockface imaging and sectioning using the TissueCyte 1000 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. TissueCyte Specimen Embedding Acrylamide Coembedding. protocols.io https://dx.doi.org/10.17504/protocols.io.ber4jd8w Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.

Proper citation: Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid VII (ACSF.VII). protocols.io https://dx.doi.org/10.17504/protocols.io.beznjf5e Copy   

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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.be4djgs6 Copy   

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Authors: ZengU19 BRAIN grant
Group: BICCN, Allen Institute for Brain Science
Summary: Protocol for isolation of nuclei from microdissected mouse brain tissue sections for FPCR and/or RNA-seq analysis.

Proper citation: ZengU19 BRAIN grant 2019. Isolation of Nuclei from Adult Mouse Brain Tissue Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.7dxhi7n Copy   

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