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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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20% Paraformaldehyde in 5X PBS Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bg4zjyx6 | BICCN, Allen Institute for Brain Science | This protocol is used to prepare 20% Paraformaldehyde (PFA) in 5X Phosphate-buffered saline (PBS). 20% PFA in 5X PBS is utilized to make the 4% PFA in 1X PBS reagent.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. 20% Paraformaldehyde in 5X PBS. protocols.io https://dx.doi.org/10.17504/protocols.io.bg4zjyx6 | 2021-04-15 09:15:15 | |||
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DAB Solutions Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdpdi5i6 | 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.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 Solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.bdpdi5i6 | 2021-04-15 09:15:25 | |||
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Post Patch Clamp Slice Fixation Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bg5tjy6n | 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 | 5 | 2020 | Allen Institute for Brain Science 2020. Post Patch Clamp Slice Fixation. protocols.io https://dx.doi.org/10.17504/protocols.io.bg5tjy6n | 2021-04-15 09:14:57 | |||
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BD FACS Aria II Shutdown Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdvpi65n | BICCN, Allen Institute for Brain Science | 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. | Allen Institute | 2 | 2020 | Allen Institute for Brain Science 2020. BD FACS Aria II Shutdown. protocols.io https://dx.doi.org/10.17504/protocols.io.bdvpi65n | 2021-04-15 09:15:30 | |||
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Tissue Quality Evaluation for Brain Perfusion/Dissection Specimens Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bd8yi9xw | BICCN, Allen Institute for Brain Science | 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. | Allen Institute | 1 | 2020 | 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 | 2021-04-15 09:15:04 | |||
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Artificial Cerebrospinal Fluid IX (ACSF.IX) Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.beppjdmn | 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 | 3 | 2020 | Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid IX (ACSF.IX). protocols.io https://dx.doi.org/10.17504/protocols.io.beppjdmn | 2021-04-15 09:15:04 | |||
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Bioanalyzer Operation for IVT Products Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.brt3m6qn | BICCN, Allen Institute for Brain Science | 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 | Allen Institute | https://community.brain-map.org/ | 1 | 2021 | Allen Institute for Brain Science 2021. Bioanalyzer Operation for IVT Products. protocols.io https://dx.doi.org/10.17504/protocols.io.brt3m6qn | 2021-04-15 09:15:01 | ||
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BD FACS Aria II Start-up and Calibration Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdvqi65w | 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.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. BD FACS Aria II Start-up and Calibration. protocols.io https://dx.doi.org/10.17504/protocols.io.bdvqi65w | 2021-04-15 09:15:31 | |||
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Patch-Seq Internal Solution with Biocytin Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.besdjea6 | 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.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. Patch-Seq Internal Solution with Biocytin. protocols.io https://dx.doi.org/10.17504/protocols.io.besdjea6 | 2021-04-15 09:15:32 | |||
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TissueCyte Image QC Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bbybipsn | BICCN, Allen Institute for Brain Science | This protocol describes the QC step that occurs after the week of TissueCyte runs, and prior to analysis. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. TissueCyte Image QC. protocols.io https://dx.doi.org/10.17504/protocols.io.bbybipsn | 2021-04-15 09:15:34 | |||
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Artificial Cerebrospinal Fluid III (ACSF.III) Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.beptjdnn | 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 | 3 | 2020 | Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid III (ACSF.III). protocols.io https://dx.doi.org/10.17504/protocols.io.beptjdnn | 2021-04-15 09:15:36 | |||
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Slice Preparation with Tissue Dissociation - Mouse Protocol Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bq6wmzfe | BICCN, Allen Institute for Brain Science | 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. | Allen Institute | 2 | 2021 | Allen Institute for Brain Science 2021. Slice Preparation with Tissue Dissociation - Mouse Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bq6wmzfe | 2021-04-15 09:15:09 | |||
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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.bgpvjvn6 | 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 | 3 | 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.bgpvjvn6 | 2021-04-15 09:15:13 | |||
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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.bbx3ipqn | 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. | Allen Institute | 1 | 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.bbx3ipqn | 2021-04-15 09:15:41 | |||
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Human Neurosurgical Tissue Processing Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bet4jeqw | 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 | 5 | 2020 | Allen Institute for Brain Science 2020. Human Neurosurgical Tissue Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.bet4jeqw | 2021-04-15 09:15:38 | |||
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TissueCyte Installation And Alignment Guide Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdpti5nn | 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.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 Installation And Alignment Guide. protocols.io https://dx.doi.org/10.17504/protocols.io.bdpti5nn | 2021-04-15 09:15:13 | |||
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Maintenance of TissueCyte System Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdpui5nw | BICCN, Allen Institute for Brain Science | 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. | Allen Institute | 2 | 2020 | Allen Institute for Brain Science 2020. Maintenance of TissueCyte System. protocols.io https://dx.doi.org/10.17504/protocols.io.bdpui5nw | 2021-04-15 09:15:39 | |||
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TissueCyte Specimen Embedding Acrylamide Coembedding Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bbx5ipq6 | 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. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. TissueCyte Specimen Embedding Acrylamide Coembedding. protocols.io https://dx.doi.org/10.17504/protocols.io.bbx5ipq6 | 2021-04-15 09:15:15 | |||
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TissueCyte Specimen Embedding Acrylamide Coembedding Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.ber4jd8w | 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 | 3 | 2020 | Allen Institute for Brain Science 2020. TissueCyte Specimen Embedding Acrylamide Coembedding. protocols.io https://dx.doi.org/10.17504/protocols.io.ber4jd8w | 2021-04-15 09:15:19 | |||
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STPT protocol Resource Report Resource Website |
Kannan Umadevi Venkataraju, Ramesh Palaniswamy, Pavel Osten | DOI:10.17504/protocols.io.smvec66 | BICCN | Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory | 1 | 2018 | Kannan Umadevi Venkataraju, Ramesh Palaniswamy, Pavel Osten 2018. STPT protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.smvec66 | 2021-04-15 09:15:18 |
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