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Authors: ZengU19 BICCN Grant
Group: BICCN, Allen Institute for Brain Science
Summary: Allows for rapid generation of 3’ transcriptomic-NGS-ready- single-cell-libraries from pools of cells.
Proper citation: ZengU19 BICCN Grant 2019. 10Xv2 RNASeq Sample Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.ynxfvfn Copy
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 dissection, embedding, slicing, and blockface imaging of the mouse brain using either a Leica vibratome or a compresstome. The output tissue is suitable for use in electrophysiological recordings and/or live cell filling applications.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. Slice Preparation and Blockface Imaging for Electrophysiology - Mouse. protocols.io https://dx.doi.org/10.17504/protocols.io.bep8jdrw Copy
Authors: ZengU19 BRAIN grant
Group: BICCN, Allen Institute for Brain Science
Summary: Protocol to generate full-length cDNA from single cells, or nuclei, using Takara SMARTer V4.
Proper citation: ZengU19 BRAIN grant 2019. SMARTerV4 (0.5x) Amplification for single-cell or single-nuclei RNASeq Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.7d5hi86 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the preparation of Slice Prep Media used for human or mouse slice culture.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. Slice Culture Media. protocols.io https://dx.doi.org/10.17504/protocols.io.bfzzjp76 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.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.ber2jd8e Copy
Authors: ZengU19 BRAIN grant
Group: BICCN, Allen Institute for Brain Science
Summary: Protocol to generate full-length cDNA from single cells, or nuclei, using Takara SMARTer V4.
Proper citation: ZengU19 BRAIN grant 2019. SMARTerV4 (1x) Amplification for single-cell or single-nuclei RNASeq Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.7d6hi9e Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the process to obtain multiple electrophysiological recordings from 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: Allen Institute for Brain Science 2020. Multi-Patch Clamp Recording. protocols.io https://dx.doi.org/10.17504/protocols.io.bep2jdqe Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol is used to prepare Phosphate Buffered Saline (PBS). PBS (-) and PBS (+) which includes Tween are used as biologically neutral wash solutions in many processes including In Situ Hybridization (ISH), Immunohistochemistry (IHC) and Fixation.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. Phosphate Buffered Saline (PBS). protocols.io https://dx.doi.org/10.17504/protocols.io.be2hjgb6 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. PCR Prep from cDNA for IVT Reactions. protocols.io https://dx.doi.org/10.17504/protocols.io.bdpni5me Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes how to prepare Artificial Cerebrospinal Fluid (V). Artificial Cerebrospinal Fluid (V) is used during surgical procedures to maintain tissue hydration and minimize tissue damage, adhesion formation and infection.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 V (ACSF.V). protocols.io https://dx.doi.org/10.17504/protocols.io.bd8xi9xn 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.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 VIII (ACSF.VIII). protocols.io https://dx.doi.org/10.17504/protocols.io.beprjdm6 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 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.besajeae 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.bepxjdpn Copy
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 dissection, embedding, slicing, and blockface imaging of the mouse brain using either a Leica vibratome or a compresstome. The output tissue is suitable for use in electrophysiological recordings and/or live cell filling applications.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. Slice Preparation and Blockface Imaging for Electrophysiology - Mouse. protocols.io https://dx.doi.org/10.17504/protocols.io.be2gjgbw Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. Mouse Cardiac Perfusion Fixation and Brain Collection. protocols.io https://dx.doi.org/10.17504/protocols.io.bg5vjy66 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol is used to prepare 4% Paraformaldehyde (PFA) + 2.5% Glutaraldehyde Fixative. This is utilized to fix the tissue after electrophysiology recordings. 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. 4% PFA + 2.5% Glutaraldehyde Fixative. protocols.io https://dx.doi.org/10.17504/protocols.io.bg5sjy6e 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.bdpii5ke Copy
Authors: Hui Gong, Xiangning Li, Can Zhou
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the steps to prepare and embed biological tissue into Lowicryl HM20® resin and subsequent whole brain imaging via fluorescence micro-optical sectioning tomography (fMOST).
Proper citation: Hui Gong, Xiangning Li, Can Zhou 2018. Resin/HM20 Embedding and fMOST Imaging Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.ssgeebw Copy
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.
Proper citation: Allen Institute for Brain Science 2020. Maintenance of TissueCyte System. protocols.io https://dx.doi.org/10.17504/protocols.io.bbx6ipre Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol is used to prepare 0.1M Phosphate Buffer. 0.1M Phosphate Buffer is used in the preparation of Sucrose solutions for cryoprotection.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. 0.1M Phosphate Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.bg43jyyn Copy
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