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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Tris Buffered Saline (TNT) Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.brdkm24w | BICCN, Allen Institute for Brain Science | This protocol is used to prepare Tris Buffered Saline (TNT). 10X TNT is the stock solution used to prepare 1X TNT, which equilibrates tissue and maintains pH in physiological range.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 | 2021 | Allen Institute for Brain Science 2021. Tris Buffered Saline (TNT). protocols.io dx.doi.org/10.17504/protocols.io.brdkm24w | 2021-03-29 03:10:45 | |||
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Nextera XT at 0.2X On the Mantis Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.brdjm24n | BICCN, Allen Institute for Brain Science | Protocol to generate Nextera libraries using 0.2x reagents in a 96-well PCR plate using the Formulatrix Mantis instrument.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. Nextera XT at 0.2X On the Mantis. protocols.io dx.doi.org/10.17504/protocols.io.brdjm24n | 2021-03-29 03:10:51 | |||
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Isolation of Nuclei from Adult Human Brain Tissue for 10x Genomics Platform Resource Report Resource Website |
LeinU01 BRAIN grant | 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 dx.doi.org/10.17504/protocols.io.y6rfzd6 | 2021-03-29 03:10:51 | |||
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Stereotaxic Surgery for Delivery of Tracers by Iontophoresis Resource Report Resource Website |
Allen Institute for Brain Science | 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 dx.doi.org/10.17504/protocols.io.besgjebw | 2021-03-29 03:10:46 | |||
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Human Post Mortem Brain Processing Resource Report Resource Website |
Allen Institute for Brain Science | 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 dx.doi.org/10.17504/protocols.io.bezcjf2w | 2021-03-29 03:10:56 | |||
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TissueCyte Specimen Embedding Acrylamide Coembedding Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bf65jrg6 | BICCN, Allen Institute for Brain Science | 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. | Allen Institute | 4 | 2020 | Allen Institute for Brain Science 2020. TissueCyte Specimen Embedding Acrylamide Coembedding. protocols.io dx.doi.org/10.17504/protocols.io.bf65jrg6 | 2021-03-29 03:10:57 | |||
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30% Sucrose for Cryoprotection of brains after Perfusions Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bg5ujy6w | BICCN, Allen Institute for Brain Science | This protocol is used to prepare 30% Sucrose Solution in 0.1M phosphate buffer. 30% Sucrose in 0.1M phosphate buffer is used for the cryoprotection of mice brains post 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. | Allen Institute | 2 | 2020 | Allen Institute for Brain Science 2020. 30% Sucrose for Cryoprotection of brains after Perfusions. protocols.io dx.doi.org/10.17504/protocols.io.bg5ujy6w | 2021-03-29 03:11:06 | |||
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50 mM Phosphate Buffer (with 0.02% sodium azide option) Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bg52jy8e | BICCN, Allen Institute for Brain Science | 50 mM Phosphate Buffer can be used as a general buffer solution for multiple applications. It is suitable for use as a buffer for specimen embedding, as part of brain preparation associated with TissueCyte 2P Serial Imaging, described in PF0315 TissueCyte Specimen Embedding Acrylamide Coembedding.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. 50 mM Phosphate Buffer (with 0.02% sodium azide option). protocols.io dx.doi.org/10.17504/protocols.io.bg52jy8e | 2021-03-29 03:11:05 | |||
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BD FACS Aria II Start-up and Calibration Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bamdic26 | BICCN, Allen Institute for Brain Science | 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. | Allen Institute | 1 | 2019 | Allen Institute for Brain Science 2019. BD FACS Aria II Start-up and Calibration. protocols.io dx.doi.org/10.17504/protocols.io.bamdic26 | 2021-03-29 03:11:09 | |||
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Nextera XT at 0.2X On the Mantis Resource Report Resource Website |
ZengU19 BRAIN Grant | 10.17504/protocols.io.63rhgm6 | BICCN, Allen Institute for Brain Science | Protocol to generate Nextera libraries using 0.2x reagents in a 96-well PCR plate using the Formulatrix Mantis instrument. | Allen Institute | 1 | 2019 | ZengU19 BRAIN Grant 2019. Nextera XT at 0.2X On the Mantis. protocols.io dx.doi.org/10.17504/protocols.io.63rhgm6 | 2021-03-29 03:09:28 | |||
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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.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 dx.doi.org/10.17504/protocols.io.ber8jd9w | 2021-03-29 03:09:28 | |||
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Human Neurosurgical Tissue Processing Resource Report Resource Website |
Allen Institute for Brain Science | 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 dx.doi.org/10.17504/protocols.io.bf66jrhe | 2021-03-29 03:09:35 | |||
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Artificial Cerebrospinal Fluid IX (ACSF.IX) Resource Report Resource Website |
Allen Institute for Brain Science | 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 dx.doi.org/10.17504/protocols.io.bdn9i5h6 | 2021-03-29 03:09:41 | |||
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TissueCyte Installation And Alignment Guide Resource Report Resource Website |
Allen Institute for Brain Science | 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 dx.doi.org/10.17504/protocols.io.bbx9ipr6 | 2021-03-29 03:09:40 | |||
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Production of Crude AAV Virus Extract Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdvwi67e | BICCN, Allen Institute for Brain Science | This protocol is used to produce crude preps of AAV of any serotype.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 Crude AAV Virus Extract. protocols.io dx.doi.org/10.17504/protocols.io.bdvwi67e | 2021-03-29 03:09:37 | |||
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Nuclei Isolation for SNARE-seq2 Resource Report Resource Website |
Carter Palmer, Christine Liu, Jerold Chun | 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 dx.doi.org/10.17504/protocols.io.8tvhwn6 | 2021-03-29 03:09:55 | |||
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Mouse Cardiac Perfusion Fixation and Brain Collection Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bd8vi9w6 | 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 | 1 | 2020 | Allen Institute for Brain Science 2020. Mouse Cardiac Perfusion Fixation and Brain Collection. protocols.io dx.doi.org/10.17504/protocols.io.bd8vi9w6 | 2021-03-29 03:09:59 | |||
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Production of Recombinant EnvA Rabies Virus Resource Report Resource Website |
Allen Institute for Brain Science | 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 dx.doi.org/10.17504/protocols.io.bdvvi666 | 2021-03-29 03:10:06 | |||
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TissueCyte Specimen Embedding Acrylamide Coembedding Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdpvi5n6 | BICCN, Allen Institute for Brain Science | 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. | Allen Institute | 2 | 2020 | Allen Institute for Brain Science 2020. TissueCyte Specimen Embedding Acrylamide Coembedding. protocols.io dx.doi.org/10.17504/protocols.io.bdpvi5n6 | 2021-03-29 03:10:13 | |||
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DAB Detection of Biocytin Labeled Tissue Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bctbiwin | 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. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. DAB Detection of Biocytin Labeled Tissue. protocols.io dx.doi.org/10.17504/protocols.io.bctbiwin | 2021-03-29 03:10:27 |
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