Journal: Cell

Article Title: Fast-spiking interneurons supply feed-forward control of bursting, calcium, and plasticity for efficient learning

doi: 10.1016/j.cell.2018.01.005

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies chicken anti-YFP Aves Labs Inc. GFP-1020 rabbit anti-parvalbumin Swant Inc. PV 27 donkey anti-chicken 488 Jackson Immunoresearch 703-545-155 donkey anti-rabbit 647 Invitrogen A-31573 Bacterial and Virus Strains AAV5-EF1α-Flex-taCasp3-TEVp UNC Vector Core N/A AAV5-EF1α-DIO-eYFP UPenn Vector Core N/A AAV8-hSyn-eGFP UNC Vector Core N/A AAV5-EF1α-DIO-eNpHR3.0-YFP UNC Vector Core N/A AAV5-EF1α-DIO-eNpHR3.0-mCherry UNC Vector Core N/A AAV5-Syn-GCaMP6f UPenn Vector Core N/A AAV5-EF1α-DIO-mCherry UNC Vector Core N/A AAV5-Syn-Flex-ChrimsonR-tdTomato UNC Vector Core N/A Experimental Models: Organisms/Strains Mouse: PA-2A-cre The Jackson Laboratory Jax stock #012358 Mouse: Drd1a-tdTomato The Jackson Laboratory Jax stock #016204 Mouse: Lhx6-GFP GENSAT MGI #3839374 Software and Algorithms MATLAB The MathWorks https://www.mathworks.com/products/matlab Fiji (ImageJ) NIH http://fiji.sc Constrained Non-negative Matrix Factorization (CNMF) ( Zhou et al., 2016 ) N/A Mosaic version 1.2.0 Inscopix Inc. https://www.inscopix.com Open in a separate window KEY RESOURCES TABLE

Techniques: Plasmid Preparation, Software

Journal: Cell

Article Title: The striatum organizes 3D behavior via moment-to-moment action selection

doi: 10.1016/j.cell.2018.04.019

Figure Lengend Snippet: Key Resources Table

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Chicken Anti-GFAP abcam Cat# ab4674 Alexa Fluor 488, Donkey Anti-Chicken IgY Jackson Laboratory Cat# 703-545-155 Rabbit Anti-NeuN abcam Cat# ab104225 Alex Fluor 555, Donkey Anti-Rabbit IgG Thermo-Fisher Cat# A-31572 Bacterial and Virus Strains AAV9-CBA-do(Fas)-GCaMP6s UNC Vector Core N/A AAV9-CBA-DIO-jRCaMP1b UNC Vector Core N/A AAV1.Syn.Flex.GCaMP6f.WPRE.SV40 Penn Vector Core Cat# AV-1-PV2819 AAV1.EF1α.DIO.GCaMP6s.P2A.NLS.dTomato Addgene Cat# 51082 Chemicals, Peptides, and Recombinant Proteins N-Methyl-D-aspartic acid Sigma-Aldrich Cat# M3262-250MG Experimental Models: Organisms/Strains Mouse: B6.FVB(Cg)-Tg(Drd1-cre)EY262Gsat/Mmucd MMRRC-UCD MMRRC Stock# 030989-UCD Mouse: B6.FVB(Cg)-Tg(Adora2a-cre) KG139Gsat/Mmucd MMRRC-UCD MMRRC Stock# 036158-UCD Mouse: C57BL/6J Jackson Laboratory Jax stock #000664 Mouse: B6;129S-Pdyn tm1.1(cre)Mjkr /LowlJ Jackson Laboratory Jax stock #027958 Recombinant DNA pAAV-CBA-DIO-jRCaMP1b This paper Addgene ID 110134 pAAV-CBA-do(Fas)-GCaMP6s This paper Addgene ID 110135 Software and Algorithms MoSeq ( Wiltschko et al., 2015 ) N/A MATLAB The MathWorks https://www.mathworks.com/products/matlab.html Constrained Non-negative Matrix Factorization for microendoscope data (CNMF-E) ( Zhou et al., 2018 ) N/A Mosaic version 1.2.0 Inscopix https://www.inscopix.com Intan Recording System Software Intan Technologies http://intantech.com/downloads.html Other Kinect for Xbox One (Kinect 2) Microsoft https://www.xbox.com/en-US/xboxone/accessories/kinect Xbox One S Kinect Adapter Microsoft https://www.xbox.com/en-US/xboxone/accessories/kinect/kinect-adapter Shallow tank US Plastic Cat# 14317 Open in a separate window Key Resources Table

Techniques: Plasmid Preparation, Recombinant, Software

Journal: Neuron

Article Title: Neurodevelopmental patterns of early postnatal white matter maturation represent distinct underlying microstructure and histology.

doi: 10.1016/j.neuron.2022.09.020

Figure Lengend Snippet: Figure 6. Distinct cellular elements in the periventricular and intermediate NeWMaPs (A–D) Glial fibrillary acidic protein (GFAP) immu- nohistochemistry of the glial cells. Coronal sections through the frontoparietal junction (A), mid-parietal lobe (B), and posterior frontal lobe (C). (A–C) The dorsal frontoparietal periventricular NeWMaP-2 is demarcated from the surrounding parietal and periroladic intermediate white matter NeWMaPs (NeWMaP-6 and NeWMaP-9) and rostral frontal periventricular NeWMaP-8 by its intense GFAP immunoreactivity (marked by asterisk). (D) A distinct feature of the intermediate white matter compartment areas corresponding to NeWMaP-6 and NeWMaP-9 was the presence of radially oriented GFAP-reactive fibers, which likely represent remnants of the radial glial cells. (E) NeWMaP-8 is distinguished from the sur- rounding frontal white matter (e.g., NeWMaP-2) by Nissl staining (dashed arrow). A fine band of faint Nissl staining in the deep white matter was also represented by NeWMaP-8 (arrowheads). (F) Stain vector decomposition demonstrated doublecortin (DCX, a marker of young migrating neurons) expression in frontal periventricular white matter NeWMaP-8 (dashed arrow). See also Figure S6.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies GFAP Dako RRID:AB_10013382; Cat# z0334 DCX (Doublecortin) Santa Cruz Biotechnology RRID:AB_10610966; Cat# sc-271390 MBP (SMI-99) Biolegend RRID:AB_2564741; Cat# 808401 Neurofilament Marker (pan axonal, SMI-312) Biolegend RRID:AB_2566782; Cat# 837904 Deposited data The Developing Human Connectome Project (dHCP) Makropoulos et al. (2018) http://www.developingconnectome.org/ Early Life Adversity, Biological Embedding (eLABE) and Risk for Developmental Precursors of Mental Disorders Sylvester et al. (2021) https://eedp.wustl.edu/research/ elabe-study/ The Zagreb Collection of Human Brains Hraba c et al. (2018) http://www.zagrebbraincollection.hr/ index.php Newborn White Matter Maturation Patterns (NeWMaPs) This paper. https://doi.org/10.5281/zenodo.6782004 Unbiased Morphological Atlas of Neonatal Brain Development (part of dHCP) Schuh et al. (2018) https://gin.g-node.org/BioMedIA/dhcp- volumetric-atlas-groupwise Software and Algorithms Non-negative Matrix Factorization (NMF) Sotiras et al. (2015); Yang and Oja (2010) [https://doi.org/10.5281/zenodo.7076560] https://github.com/asotiras/brainparts R Project for Statistical Computing The R Foundation RRID:SCR_001905; https://www.r-project.org/ Advanced Normalization Tools (ANTs) Avants et al. (2011) RRID:SCR_004757; http://stnava.github. io/ANTs/ FMRIB Software Library (FSL) Jenkinson et al. (2012) RRID:SCR_002823; https://fsl.fmrib.ox.ac. uk/fsl/ Analysis of Functional NeuroImages (AFNI) Cox (2012) RRID:SCR_005927; http://afni.nimh.nih. gov/afni/ Microstructure Diffusion Toolbox (MDT) Harms and Roebroeck (2018) https://github.com/robbert-harms/MDT 4dfp Suite https://4dfp.readthedocs.io/ M-CRIB-S Adamson et al. (2020) https://github.com/ DevelopmentalImagingMCRI/MCRIBS QuPath Bankhead et al. (2017) RRID:SCR_018257; https://qupath.github.io/ MATLAB MathWorks RRID:SCR_001622; https://www. mathworks.com/

Techniques: Staining, Plasmid Preparation, Marker, Expressing

Journal: Cell

Article Title: The striatum organizes 3D behavior via moment-to-moment action selection

doi: 10.1016/j.cell.2018.04.019

Figure Lengend Snippet: A. AAVs expressing Cre-On jRCaMP1b and Cre-Off GCaMP6s were injected into the DLS to assess direct (dSPN, red) and indirect (iSPN, green) pathway activity via multicolor photometry (see Methods). Top, sagittal schematic of injection site. Middle and bottom, histological verification of jRCaMP1b (dSPN, red) and GCaMP6s (iSPN, green) expression (sagittal sections, SNr = substantia nigra pars reticulata, GP = globus pallidus). Scale bar, 1 mm.

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Chicken Anti-GFAP abcam Cat# ab4674 Alexa Fluor 488, Donkey Anti-Chicken IgY Jackson Laboratory Cat# 703-545-155 Rabbit Anti-NeuN abcam Cat# ab104225 Alex Fluor 555, Donkey Anti-Rabbit IgG Thermo-Fisher Cat# A-31572 Bacterial and Virus Strains AAV9-CBA-do(Fas)-GCaMP6s UNC Vector Core N/A AAV9-CBA-DIO-jRCaMP1b UNC Vector Core N/A AAV1.Syn.Flex.GCaMP6f.WPRE.SV40 Penn Vector Core Cat# AV-1-PV2819 AAV1.EF1α.DIO.GCaMP6s.P2A.NLS.dTomato Addgene Cat# 51082 Chemicals, Peptides, and Recombinant Proteins N-Methyl-D-aspartic acid Sigma-Aldrich Cat# M3262-250MG Experimental Models: Organisms/Strains Mouse: B6.FVB(Cg)-Tg(Drd1-cre)EY262Gsat/Mmucd MMRRC-UCD MMRRC Stock# 030989-UCD Mouse: B6.FVB(Cg)-Tg(Adora2a-cre) KG139Gsat/Mmucd MMRRC-UCD MMRRC Stock# 036158-UCD Mouse: C57BL/6J Jackson Laboratory Jax stock #000664 Mouse: B6;129S-Pdyn tm1.1(cre)Mjkr /LowlJ Jackson Laboratory Jax stock #027958 Recombinant DNA pAAV-CBA-DIO-jRCaMP1b This paper Addgene ID 110134 pAAV-CBA-do(Fas)-GCaMP6s This paper Addgene ID 110135 Software and Algorithms MoSeq ( Wiltschko et al., 2015 ) N/A MATLAB The MathWorks https://www.mathworks.com/products/matlab.html Constrained Non-negative Matrix Factorization for microendoscope data (CNMF-E) ( Zhou et al., 2018 ) N/A Mosaic version 1.2.0 Inscopix https://www.inscopix.com Intan Recording System Software Intan Technologies http://intantech.com/downloads.html Other Kinect for Xbox One (Kinect 2) Microsoft https://www.xbox.com/en-US/xboxone/accessories/kinect Xbox One S Kinect Adapter Microsoft https://www.xbox.com/en-US/xboxone/accessories/kinect/kinect-adapter Shallow tank US Plastic Cat# 14317 Open in a separate window Key Resources Table

Techniques: Expressing, Injection, Activity Assay

Journal: Cell

Article Title: The striatum organizes 3D behavior via moment-to-moment action selection

doi: 10.1016/j.cell.2018.04.019

Figure Lengend Snippet: Key Resources Table

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Chicken Anti-GFAP abcam Cat# ab4674 Alexa Fluor 488, Donkey Anti-Chicken IgY Jackson Laboratory Cat# 703-545-155 Rabbit Anti-NeuN abcam Cat# ab104225 Alex Fluor 555, Donkey Anti-Rabbit IgG Thermo-Fisher Cat# A-31572 Bacterial and Virus Strains AAV9-CBA-do(Fas)-GCaMP6s UNC Vector Core N/A AAV9-CBA-DIO-jRCaMP1b UNC Vector Core N/A AAV1.Syn.Flex.GCaMP6f.WPRE.SV40 Penn Vector Core Cat# AV-1-PV2819 AAV1.EF1α.DIO.GCaMP6s.P2A.NLS.dTomato Addgene Cat# 51082 Chemicals, Peptides, and Recombinant Proteins N-Methyl-D-aspartic acid Sigma-Aldrich Cat# M3262-250MG Experimental Models: Organisms/Strains Mouse: B6.FVB(Cg)-Tg(Drd1-cre)EY262Gsat/Mmucd MMRRC-UCD MMRRC Stock# 030989-UCD Mouse: B6.FVB(Cg)-Tg(Adora2a-cre) KG139Gsat/Mmucd MMRRC-UCD MMRRC Stock# 036158-UCD Mouse: C57BL/6J Jackson Laboratory Jax stock #000664 Mouse: B6;129S-Pdyn tm1.1(cre)Mjkr /LowlJ Jackson Laboratory Jax stock #027958 Recombinant DNA pAAV-CBA-DIO-jRCaMP1b This paper Addgene ID 110134 pAAV-CBA-do(Fas)-GCaMP6s This paper Addgene ID 110135 Software and Algorithms MoSeq ( Wiltschko et al., 2015 ) N/A MATLAB The MathWorks https://www.mathworks.com/products/matlab.html Constrained Non-negative Matrix Factorization for microendoscope data (CNMF-E) ( Zhou et al., 2018 ) N/A Mosaic version 1.2.0 Inscopix https://www.inscopix.com Intan Recording System Software Intan Technologies http://intantech.com/downloads.html Other Kinect for Xbox One (Kinect 2) Microsoft https://www.xbox.com/en-US/xboxone/accessories/kinect Xbox One S Kinect Adapter Microsoft https://www.xbox.com/en-US/xboxone/accessories/kinect/kinect-adapter Shallow tank US Plastic Cat# 14317 Open in a separate window Key Resources Table

Techniques: Plasmid Preparation, Recombinant, Software