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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Human Tissue Slicing and Dissections for Nuclear Isolations Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bq6ymzfw | BICCN, Allen Institute for Brain Science | This protocol describes the slicing and microdissection procedure on frozen post-mortem human brain tissue to be used to isolate nuclei for subsequent 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 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 | 3 | 2021 | Allen Institute for Brain Science 2021. Human Tissue Slicing and Dissections for Nuclear Isolations. protocols.io https://dx.doi.org/10.17504/protocols.io.bq6ymzfw | 2021-04-15 09:14:22 | |||
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10% Triton X-100 Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bezhjf36 | BICCN, Allen Institute for Brain Science | This protocol is used to attain 10% Triton X-100 which is utilized in several Immunohistochemistry (IHC) reagents to reduce the surface tension of the reagents and to make the cell membranes of the tissue more permeable.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. 10% Triton X-100. protocols.io https://dx.doi.org/10.17504/protocols.io.bezhjf36 | 2021-04-15 09:14:22 | |||
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Tris Buffered Saline (TNT) Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bgncjvaw | 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 | 2 | 2020 | Allen Institute for Brain Science 2020. Tris Buffered Saline (TNT). protocols.io https://dx.doi.org/10.17504/protocols.io.bgncjvaw | 2021-04-15 09:14:30 | |||
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Fresh 4% Paraformaldehyde in PBS Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bezijf4e | BICCN, Allen Institute for Brain Science | Freshly prepared 4% Paraformaldehyde in PBS is used to fix adult and developing mouse brains during the transcardial perfusion process, as well as for immersion fixation. This solution can be used for no more than one week post-preparation date.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. Fresh 4% Paraformaldehyde in PBS. protocols.io https://dx.doi.org/10.17504/protocols.io.bezijf4e | 2021-04-15 09:14:28 | |||
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DAB Detection of Biocytin Labeled Tissue Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bep5jdq6 | 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.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. DAB Detection of Biocytin Labeled Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.bep5jdq6 | 2021-04-15 09:14:36 | |||
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cDNA Synthesis Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bgnbjvan | 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 | 4 | 2020 | Allen Institute for Brain Science 2020. cDNA Synthesis. protocols.io https://dx.doi.org/10.17504/protocols.io.bgnbjvan | 2021-04-15 09:14:28 | |||
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cDNA Synthesis Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.besejebe | 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 | 3 | 2020 | Allen Institute for Brain Science 2020. cDNA Synthesis. protocols.io https://dx.doi.org/10.17504/protocols.io.besejebe | 2021-04-15 09:14:40 | |||
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DAB Detection of Biocytin Labeled Tissue Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bg5yjy7w | 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.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. DAB Detection of Biocytin Labeled Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.bg5yjy7w | 2021-04-15 09:14:36 | |||
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Electrode Internal Solution with Biocytin II Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdn8i5hw | BICCN, Allen Institute for Brain Science | This SOP provides instructions to prepare Internal Solution II used for simultaneous patch clamp electrophysiology experiments to probe circuit connectivity.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. Electrode Internal Solution with Biocytin II. protocols.io https://dx.doi.org/10.17504/protocols.io.bdn8i5hw | 2021-04-15 09:14:48 | |||
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10Xv3.1 Genomics Sample Processing Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.brt5m6q6 | BICCN, Allen Institute for Brain Science | This protocol is used for the rapid generation of 3’ transcriptomic-NGS-ready- single-cell-libraries from pools of cells.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number's 1U01MH114812-01 and 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. 10Xv3.1 Genomics Sample Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.brt5m6q6 | 2021-04-15 09:14:47 | ||
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2100 Bioanalyzer Operation for PCR, GTP and IVT Products Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bfzjjp4n | BICCN, Allen Institute for Brain Science | This protocol describes bioanalyzer operation. The Agilent Bioanalyzer is used as a quality control step for PCR and 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 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. 2100 Bioanalyzer Operation for PCR, GTP and IVT Products. protocols.io https://dx.doi.org/10.17504/protocols.io.bfzjjp4n | 2021-04-15 09:14:51 | |||
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DAB Solutions Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bew7jfhn | 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 | 5 | 2020 | Allen Institute for Brain Science 2020. DAB Solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.bew7jfhn | 2021-04-15 09:14:49 | |||
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Patch-Seq Internal Solution with Biocytin Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bdvti66n | 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 | 2 | 2020 | Allen Institute for Brain Science 2020. Patch-Seq Internal Solution with Biocytin. protocols.io https://dx.doi.org/10.17504/protocols.io.bdvti66n | 2021-04-15 09:15:03 | |||
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FACS Single Cell Sorting Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bambic2n | 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. | Allen Institute | 1 | 2019 | Allen Institute for Brain Science 2019. FACS Single Cell Sorting. protocols.io https://dx.doi.org/10.17504/protocols.io.bambic2n | 2021-04-15 09:15:04 | |||
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Brain Dissection of Post-natal Mice Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bd93i98n | BICCN, Allen Institute for Brain Science | This protocol describes the procedure for removal and embedding of the post-natal mouse brain.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. Brain Dissection of Post-natal Mice. protocols.io https://dx.doi.org/10.17504/protocols.io.bd93i98n | 2021-04-15 09:14:41 | |||
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PCR Prep from cDNA for IVT Reactions Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bep7jdrn | BICCN, Allen Institute for Brain Science | This protocol describes PCR1 and PCR2 reactions beginning with cDNA to generate transcript templates ready for IVT reaction. This protocol is written for 192 (2x96) reactions but can also be used for fewer or more reactions by adjusting the amount of materials and equipment appropriately.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. PCR Prep from cDNA for IVT Reactions. protocols.io https://dx.doi.org/10.17504/protocols.io.bep7jdrn | 2021-04-15 09:15:05 | |||
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Isolation of Nuclei from Adult_Human_Brain_Tissue Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bq7dmzi6 | BICCN, Allen Institute for Brain Science | Isolation of nuclei from frozen adult human brain tissue or thawed and microdissected brain tissue sections for FPCR and/or RNA-seq analysis. 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 | 2021 | Allen Institute for Brain Science 2021. Isolation of Nuclei from Adult_Human_Brain_Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.bq7dmzi6 | 2021-04-15 09:14:45 | |||
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PCR Prep from cDNA for IVT Reactions Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bgm9ju96 | BICCN, Allen Institute for Brain Science | This protocol describes PCR1 and PCR2 reactions beginning with cDNA to generate transcript templates ready for IVT reaction. This protocol is written for 192 (2x96) reactions but can also be used for fewer or more reactions by adjusting the amount of materials and equipment appropriately.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. PCR Prep from cDNA for IVT Reactions. protocols.io https://dx.doi.org/10.17504/protocols.io.bgm9ju96 | 2021-04-15 09:15:16 | |||
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Intraperitoneal Injection in an Adult Mouse Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bfzgjp3w | BICCN, Allen Institute for Brain Science | This protocol describes the general procedure used for intraperitoneal injection in adult mice.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. Intraperitoneal Injection in an Adult Mouse. protocols.io https://dx.doi.org/10.17504/protocols.io.bfzgjp3w | 2021-04-15 09:15:18 | |||
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DAB Solutions Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.betzjep6 | 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 | 4 | 2020 | Allen Institute for Brain Science 2020. DAB Solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.betzjep6 | 2021-04-15 09:15:23 |
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