Virus:Article Title: Amygdala-hippocampus somatostatin interneuron beta-synchrony underlies a cross-species biomarker of emotional state.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAV5-EF1a-double floxed-hChR2(H134R)-EYFP Depositing lab: Karl Deisseroth, Stanford Addgene; 20298-AAV5 AAV5-Ef1a-DIO-eNpHR 3.0-EYFP https://doi.org/10.1016/j.cell.2010.02.037 Addgene; #26966-AAV5 AAV5-EF1a-DIO-eYFP Depositing lab: Karl Deisseroth, Stanford Addgene; 27056-AAV5 AAV1-CAG-DIO-Ace2N-4AA-mNeon Virovek (Plasmid provided by Mark J Schnitzer – Stanford) N/A AAV8-nEF-Con/Foff 2.0-ChR2(ET/TC)-EYFP https://doi.org/10.1016/j.neuron.2020.06.003 Addgene; #137140-AAV8 AAV2-Syn-tdTomato SignaGen Laboratories SL100896 AAV1-EF1a-Flpo https://doi.org/10.1038/nmeth.2996 Addgene; #55637-AAV1 Chemicals, peptides, and recombinant proteins Gabazine Tocris #1262 CNQX Tocris #0190 AP5 Tocris #0106 Experimental models: Organisms/strains SST-Cre mice The Jackson Laboratory IMSR_JAX:013044 PV-Cre mice The Jackson Laboratory IMSR_JAX:008069 C57BL/6J mice The Jackson Laboratory IMSR_JAX:000664 Software and algorithms MATLAB Mathworks SCR_001622 GraphPad Prism GraphPad SCR_002798 ImageJ ImageJ SCR_003070 pCLAMP 10 Molecular Devices SCR_011323 Open Ephys GUI Open Ephys SCR_021624 Chronux toolbox Chronux SCR_005547 Bonsai Bonsai SCR_021512 ANY-maze Stoelting Co. SCR_014289 Analysis code This paper https://doi.org/10.5281/ zenodo.10407015 ..
Article Title: Negative feedback control of hypothalamic feeding circuits by the taste of food.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAV1.CAG.Flex.GCaMP6s.WPRE.SV40 Chen et al.80 Addgene Cat#: 100842-AAV1 AAV1.CAG.FLEX.GCaMP8s HHMI Janelia Ref ID: 1-1322-2 AAV8.hSyn.DIO.hM4D(Gi).mCherry Krashes et al.19 Addgene Cat#:44362-AAV8 AAV1.hSyn.DIO.mCherry Bryan Roth Lab Addgene Cat:50459-AAV1 Chemicals, peptides, and recombinant proteins Devazepide R&D Systems Cat#:2304/10 Intralipid Sigma Aldrich; Medline Cat#:I141-100mL; Cat#:BHL2B6064H Silicone Oil Sigma Aldrich Cat#:378348 DAPI Fluoromount-G Southern Biotech Cat#:0100-20 Deschloroclozapine dihydrochloride Hello bio Cat#: HB9126 Clozapine-N-oxide Tocris Cat#: 4936 Experimental models: Organisms/strains B6.129-Leprtm3(cre)Mgmj/J (Common name: LepRCre) The Jackson Laboratory RRID: IMSR_JAX:032457 STOCK Agrptm1(cre)Lowl/J (Common name: Agrp-Ires-Cre) The Jackson Laboratory RRID: IMSR_JAX:012899 B6;129S-Gt(ROSA)26Sortm32(CAGCOP4*H134R/EYFP)Hze/J (Common name: Ai32(RCL-ChR2(H134R)/EYFP)) The Jackson Laboratory RRID: IMSR_JAX:012569 C57BL/6J The Jackson Laboratory RRID: IMSR_JAX:000664 Software and algorithms GraphPad Prism 8 GraphPad Software RRID: SCR_002798 MATLAB 2017b Mathworks RRID: SCR_001622 Inscopix Data Acquisition Software Inscopix https://iqlearning.inscopix.com/ software-downloads/idas Inscopix Mosaic Software 1.2.0 Inscopix https://support.inscopix.com/support/ products/mosaic/mosaic-downloads Inscopix Data Processing Software v.1.3.1 Inscopix https://iqlearning.inscopix.com/ software-downloads/idps-archive CNMFe Zhou et al.81 https://github.com/zhoupc/CNMF_E CellReg Sheintuch et al.82 https://github.com/zivlab/CellReg R Studio version 2023.03.1 Posit RRID: SCR_000432 ImageJ (Fiji) Open source RRID: SCR_002285 Synapse Tucker-Davis Technologies https://www.tdt.com/component/ synapse-software/ Custom code Dr. Zachary Knight’s Lab Github: https://github.com/ zackknightlabucsf/zackknightlabucsf Other Rodent diet PicoLab Cat#:5053 GRIN lens Inscopix Cat#:1050-004610 Metabond Parkwell Cat#:S380 Baseplate Inscopix Cat#:100-000279 Baseplate cover Inscopix Cat#:100-000241 Mono Fiberoptic Cannula Doric Lenses Cat#:MFC_400/430-0.48 Sleeve Bronze 2.5mm Doric Lenses Cat#:SLEEVE_BR_2.5 (Continued on next page) e1 Neuron 112, 1–17.e1–e5, October 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Optical Fiber Thorlabs Cat#:FT200UMT Fiberoptic Cannula Thorlabs Cat#:CFLC230-10 Gastric catheter Instech Labs Cat#:C30PU-RGA1439 Sterile access button Instech Labs Cat#:VABM1B/22 Aluminum cap Instech Labs Cat#:VABM1C Ensure Vanilla Abbott Cat#:00750 nVista 3.0 Inscopix https://www.inscopix.com/nvista nVoke 2.0 Inscopix https://www.inscopix.com/nvoke Patch cable Doric Lenses Cat#:MFP_400/460/900- 0.48_2m_FCM-MF2.5 Four-channel LED Driver Thorlabs Cat#:DC4104 Minicube Thorlabs Cat#:FMC6_AE(400–410)_E1(450–490)_ F1(500–540)_E2(550–580)_ F2(600–680)_S Photoreceiver Newport Cat#:2151 Base Processor Tucker-Davis Technologies Cat#:RZ5P Davis Rig Med Associates Cat#:MED-DAV-160M
Article Title: Higher-order cortical and thalamic pathways shape visual processing streams in the mouse cortex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies chicken anti-eGFP Thermo Fisher Scientific Cat# A10262; RRID:AB_2534023 Alexa 488 donkey anti-chicken Immuno-Jackson Cat# 703-545-155; RRID: AB_2340375 Bacterial and virus strains retroAAV-CAG-tdTomato Addgene Cat# 59462-AAVrg AAV1-CAG-FLEX-jGCaMP8m-WPRE Addgene Cat# 162381-AAV1 AAV1.CAG.GCaMP6f.WPRE.SV40 Addgene Cat# 100836-AAV1 AAV1.Syn.GCaMP6f.WPRE.SV40 Addgene Cat# 100837-AAV1 Chemicals, peptides, and recombinant proteins Donkey serum Invitrogen Cat #116-4101 Fluoroshield with DAPI Merck Cat# F6057-20ML Deposited data Raw and analyzed data This paper https://doi.org/10.6084/m9.figshare.25590528 Codes for analysis This paper https://doi.org/10.6084/m9.figshare.25590528 Experimental models: Organisms/strains Mouse: B6;DBA-Tg(tetO-GCaMP6s)2Niell/J The Jackson Laboratory RRID:IMSR_JAX:024742 Mouse: B6.Cg-Tg(Camk2a-tTA)1Mmay/DboJ The Jackson Laboratory RRID:IMSR_JAX:007004 Mouse: Tg(Rbp4-cre)KL100Gsat Mutant Mouse Resource Research Centers MMRRC:031125-UCD; MGI:4367067 Mouse: C57BL/6J KU Leuven Animal Facility N/A Software and algorithms Napari Ahler et al.45 https://doi.org/10.5281/zenodo.3555620 Stardist plugin for Napari Weigert et al.46 https://github.com/stardist/stardist-napari napari-deeplabcut plugin Mathis et al.47 https://github.com/DeepLabCut/napari- deeplabcut.git ImageJ National Institutes of Health https://imagej.nih.gov/ij/index.html MATLAB The Mathworks http://mathworks.com Two-sample Kolmogorov-Smirnov test Muir48 https://www.mathworks.com/matlabcentral/ fileexchange/38617-kstest_2s_2d-x1-x2-alpha ..
Article Title: Human assembloids reveal the consequences of CACNA1G gene variants in the thalamocortical pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies TCF7L2 Cell Signaling Technology Cat # 2569S, RRID: AB_2199816 GFP GeneTex Cat # GTX13970, RRID: AB_371416 VGLUT2 Millipore Cat# MAB5504, RRID: AB_2187552 mCherry GeneTex Cat # GTX128508, RRID: AB_2721247 Bacterial and virus strains AAV-DJ-hSYN1::EYFP Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-16 AAV-DJ-hSYN1::mCherry Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-17 AAV-DJ-EF1-DIO-tdTomato Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-169 AAV-DJ-hSYN1::GCaMP6f Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-96 AAV1-hSYN1::Cre James M. Wilson Lab Addgene #105553-AAV1 AAV1-hSYN1::ChrimsonR-tdTomato Klapoetke et al.49 Addgene #59171-AAV1 Chemicals, peptides, and recombinant proteins B-27 Plus Supplement Thermo Fisher Scientific Cat# A3582801 B-27 supplement without vitamin A Thermo Fisher Scientific Cat# 12587010 Human recombinant FGF-2 R&D Systems Cat# 233-FB Human recombinant EGF R&D Systems Cat# 236-EG Human recombinant BDNF Peprotech Cat# 450-02 Human recombinant NT3 Peprotech Cat# 450-03 L-Ascorbic Acid Wako Cat# 321-44823 cAMP Sigma-Aldrich Cat# D0627 Dorsomorphin Sigma-Aldrich Cat# P5499 SB-431542 Tocris Cat# 1614 CHIR 99021 Selleckchem Cat# S1263 SAG Millipore Cat# 566660 BMP7 Peprotech Cat # 120-03P DAPT STEMCELL Technologies Cat# 72082 Y-27632 Selleckchem Cat# S1049 DHA Millipore Sigma Cat # D2534 Tetrodotoxin citrate (TTX) Tocris Cat# 1069 GlutaMAX Supplement Thermo Fisher Scientific Cat # 35050079 Penicillin-Streptomycin Thermo Fisher Scientific Cat # 15070063 Critical commercial assays Chromium Single cell 30 GEM, Library & Gel Bead Kit v3 10x Genomics PN- 1000121 Deposited data Processed single cell RNA-seq data This study GEO: GSE224766 Experimental models: Cell lines Human iPS cell line 2242-1 Khan et al.63 N/A Human iPS cell line 0410-1 Khan et al.63 N/A Human iPS cell line 1208-2 Khan et al.63 N/A (Continued on next page) Neuron 112, 1–12.e1–e7, December 18, 2024 e1 .. Characterization and maintenance of hiPS cells Human induced pluripotent stem (hiPS) cell lines used in this study were validated using methods described in previous studies.45,63,67 Genome-wide SNP genotyping was performed using the Illumina genome-wide GSAMD-24v2-0 SNP microarray at the Children’s Hospital of Philadelphia.
Article Title: Non-reciprocal callosal projections and input gradients underlie interhemispheric communication in binocular visual cortex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAVrg-hSyn-eGFP Penn Vector Core/AddGene AddGene Cat #50465-AAVrg AAVrg-hSyn-hChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat #26973-AAVrg AAV1-hSyn-Cre Penn Vector Core/AddGene AddGene Cat #105553-AAV1 AAV1-hSyn-DIO-mCherry Penn Vector Core/AddGene AddGene Cat #50459-AAV1 AAV1-hSyn-ChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat #26973-AAV1 AAV1-Syn-ChrimsonR-tdTomato Penn Vector Core/AddGene AddGene Cat #59171-AAV1 AAV1-Ef1a-DIO-hChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat 20298-AAV1 Chemicals, peptides, and recombinant proteins Urethane Sigma-Aldrich Cat #U2500 Isoflurane Southern Anesthesia & Surgical Cat #PIR001325-EA Chlorprothixene hydrochloride Sigma-Aldrich Cat #C1671 SR 95531 hydrobromide (Gabazine) HelloBio Cat #HB0901 6,7-Dinitroquinoxaline-2,3-dione (DNQX) HelloBio Cat #HB0261 D-(− )-2-Amino-5-phosphonopentanoic acid (D-APV) HelloBio Cat #HB0225 Tetrodotoxin citrate (TTX) Tocris Cat #1069 4-Aminopyridine (4-AP) Tocris Cat #0940 α-Dendrotoxin Alomone Labs Cat #D-350 Atropine Bausch and Lomb Cat #9775600 Biocytin Sigma-Aldrich Cat #B4261 Paraformaldehyde Sigma-Aldrich Cat #158127 Vectastain Elite ABC Kit Vector laboratories Cat #PK-6100 Actinomycin D Millipore sigma Cat #A1410 BD FACS Pre-Sort buffer BD Biosciences Cat #563503 Fluoromount-G Sigma Cat #00-4958-02 Critical commercial assays SMART-Seq mRNA Single Cell LP kit Takara Bio Cat #634787 Unique Dual Index Kit Takara Bio Cat #634752 High Sensitivity DNA chip Agilent Cat #NC1738319 Deposited data Spike sorting GitHub https://github.com/ Layer 2/3 pyramidal neuron model This paper (ModelDB: 2020504) https://modeldb.science/2020504 RNA-seq data This paper (GEO: GSE310829) https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE310829 Experimental models: Organisms/strains Mouse: C57BL/6J Jackson Laboratory Strain: #00064 Mouse: PV-Cre Jackson Laboratory Strain: #010777 Software and algorithms Axograph X Axograph https://axograph.com/ MATLAB Mathworks https://mathworks.com/ Psychtoolbox NA http://psychtoolbox.org/ Fiji image ImageJ https://imagej.net/software/fiji/ NEURON 7.4 Carnevale and Hines, 2006 http://www.neuron.yale.edu (Continued on next page) 18 Cell Reports 45, 116806, January 27, 2026 ..
Plasmid Preparation:Article Title: Amygdala-hippocampus somatostatin interneuron beta-synchrony underlies a cross-species biomarker of emotional state.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAV5-EF1a-double floxed-hChR2(H134R)-EYFP Depositing lab: Karl Deisseroth, Stanford Addgene; 20298-AAV5 AAV5-Ef1a-DIO-eNpHR 3.0-EYFP https://doi.org/10.1016/j.cell.2010.02.037 Addgene; #26966-AAV5 AAV5-EF1a-DIO-eYFP Depositing lab: Karl Deisseroth, Stanford Addgene; 27056-AAV5 AAV1-CAG-DIO-Ace2N-4AA-mNeon Virovek (Plasmid provided by Mark J Schnitzer – Stanford) N/A AAV8-nEF-Con/Foff 2.0-ChR2(ET/TC)-EYFP https://doi.org/10.1016/j.neuron.2020.06.003 Addgene; #137140-AAV8 AAV2-Syn-tdTomato SignaGen Laboratories SL100896 AAV1-EF1a-Flpo https://doi.org/10.1038/nmeth.2996 Addgene; #55637-AAV1 Chemicals, peptides, and recombinant proteins Gabazine Tocris #1262 CNQX Tocris #0190 AP5 Tocris #0106 Experimental models: Organisms/strains SST-Cre mice The Jackson Laboratory IMSR_JAX:013044 PV-Cre mice The Jackson Laboratory IMSR_JAX:008069 C57BL/6J mice The Jackson Laboratory IMSR_JAX:000664 Software and algorithms MATLAB Mathworks SCR_001622 GraphPad Prism GraphPad SCR_002798 ImageJ ImageJ SCR_003070 pCLAMP 10 Molecular Devices SCR_011323 Open Ephys GUI Open Ephys SCR_021624 Chronux toolbox Chronux SCR_005547 Bonsai Bonsai SCR_021512 ANY-maze Stoelting Co. SCR_014289 Analysis code This paper https://doi.org/10.5281/ zenodo.10407015 ..
Recombinant:Article Title: Amygdala-hippocampus somatostatin interneuron beta-synchrony underlies a cross-species biomarker of emotional state.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAV5-EF1a-double floxed-hChR2(H134R)-EYFP Depositing lab: Karl Deisseroth, Stanford Addgene; 20298-AAV5 AAV5-Ef1a-DIO-eNpHR 3.0-EYFP https://doi.org/10.1016/j.cell.2010.02.037 Addgene; #26966-AAV5 AAV5-EF1a-DIO-eYFP Depositing lab: Karl Deisseroth, Stanford Addgene; 27056-AAV5 AAV1-CAG-DIO-Ace2N-4AA-mNeon Virovek (Plasmid provided by Mark J Schnitzer – Stanford) N/A AAV8-nEF-Con/Foff 2.0-ChR2(ET/TC)-EYFP https://doi.org/10.1016/j.neuron.2020.06.003 Addgene; #137140-AAV8 AAV2-Syn-tdTomato SignaGen Laboratories SL100896 AAV1-EF1a-Flpo https://doi.org/10.1038/nmeth.2996 Addgene; #55637-AAV1 Chemicals, peptides, and recombinant proteins Gabazine Tocris #1262 CNQX Tocris #0190 AP5 Tocris #0106 Experimental models: Organisms/strains SST-Cre mice The Jackson Laboratory IMSR_JAX:013044 PV-Cre mice The Jackson Laboratory IMSR_JAX:008069 C57BL/6J mice The Jackson Laboratory IMSR_JAX:000664 Software and algorithms MATLAB Mathworks SCR_001622 GraphPad Prism GraphPad SCR_002798 ImageJ ImageJ SCR_003070 pCLAMP 10 Molecular Devices SCR_011323 Open Ephys GUI Open Ephys SCR_021624 Chronux toolbox Chronux SCR_005547 Bonsai Bonsai SCR_021512 ANY-maze Stoelting Co. SCR_014289 Analysis code This paper https://doi.org/10.5281/ zenodo.10407015 ..
Article Title: Negative feedback control of hypothalamic feeding circuits by the taste of food.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAV1.CAG.Flex.GCaMP6s.WPRE.SV40 Chen et al.80 Addgene Cat#: 100842-AAV1 AAV1.CAG.FLEX.GCaMP8s HHMI Janelia Ref ID: 1-1322-2 AAV8.hSyn.DIO.hM4D(Gi).mCherry Krashes et al.19 Addgene Cat#:44362-AAV8 AAV1.hSyn.DIO.mCherry Bryan Roth Lab Addgene Cat:50459-AAV1 Chemicals, peptides, and recombinant proteins Devazepide R&D Systems Cat#:2304/10 Intralipid Sigma Aldrich; Medline Cat#:I141-100mL; Cat#:BHL2B6064H Silicone Oil Sigma Aldrich Cat#:378348 DAPI Fluoromount-G Southern Biotech Cat#:0100-20 Deschloroclozapine dihydrochloride Hello bio Cat#: HB9126 Clozapine-N-oxide Tocris Cat#: 4936 Experimental models: Organisms/strains B6.129-Leprtm3(cre)Mgmj/J (Common name: LepRCre) The Jackson Laboratory RRID: IMSR_JAX:032457 STOCK Agrptm1(cre)Lowl/J (Common name: Agrp-Ires-Cre) The Jackson Laboratory RRID: IMSR_JAX:012899 B6;129S-Gt(ROSA)26Sortm32(CAGCOP4*H134R/EYFP)Hze/J (Common name: Ai32(RCL-ChR2(H134R)/EYFP)) The Jackson Laboratory RRID: IMSR_JAX:012569 C57BL/6J The Jackson Laboratory RRID: IMSR_JAX:000664 Software and algorithms GraphPad Prism 8 GraphPad Software RRID: SCR_002798 MATLAB 2017b Mathworks RRID: SCR_001622 Inscopix Data Acquisition Software Inscopix https://iqlearning.inscopix.com/ software-downloads/idas Inscopix Mosaic Software 1.2.0 Inscopix https://support.inscopix.com/support/ products/mosaic/mosaic-downloads Inscopix Data Processing Software v.1.3.1 Inscopix https://iqlearning.inscopix.com/ software-downloads/idps-archive CNMFe Zhou et al.81 https://github.com/zhoupc/CNMF_E CellReg Sheintuch et al.82 https://github.com/zivlab/CellReg R Studio version 2023.03.1 Posit RRID: SCR_000432 ImageJ (Fiji) Open source RRID: SCR_002285 Synapse Tucker-Davis Technologies https://www.tdt.com/component/ synapse-software/ Custom code Dr. Zachary Knight’s Lab Github: https://github.com/ zackknightlabucsf/zackknightlabucsf Other Rodent diet PicoLab Cat#:5053 GRIN lens Inscopix Cat#:1050-004610 Metabond Parkwell Cat#:S380 Baseplate Inscopix Cat#:100-000279 Baseplate cover Inscopix Cat#:100-000241 Mono Fiberoptic Cannula Doric Lenses Cat#:MFC_400/430-0.48 Sleeve Bronze 2.5mm Doric Lenses Cat#:SLEEVE_BR_2.5 (Continued on next page) e1 Neuron 112, 1–17.e1–e5, October 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Optical Fiber Thorlabs Cat#:FT200UMT Fiberoptic Cannula Thorlabs Cat#:CFLC230-10 Gastric catheter Instech Labs Cat#:C30PU-RGA1439 Sterile access button Instech Labs Cat#:VABM1B/22 Aluminum cap Instech Labs Cat#:VABM1C Ensure Vanilla Abbott Cat#:00750 nVista 3.0 Inscopix https://www.inscopix.com/nvista nVoke 2.0 Inscopix https://www.inscopix.com/nvoke Patch cable Doric Lenses Cat#:MFP_400/460/900- 0.48_2m_FCM-MF2.5 Four-channel LED Driver Thorlabs Cat#:DC4104 Minicube Thorlabs Cat#:FMC6_AE(400–410)_E1(450–490)_ F1(500–540)_E2(550–580)_ F2(600–680)_S Photoreceiver Newport Cat#:2151 Base Processor Tucker-Davis Technologies Cat#:RZ5P Davis Rig Med Associates Cat#:MED-DAV-160M
Article Title: Higher-order cortical and thalamic pathways shape visual processing streams in the mouse cortex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies chicken anti-eGFP Thermo Fisher Scientific Cat# A10262; RRID:AB_2534023 Alexa 488 donkey anti-chicken Immuno-Jackson Cat# 703-545-155; RRID: AB_2340375 Bacterial and virus strains retroAAV-CAG-tdTomato Addgene Cat# 59462-AAVrg AAV1-CAG-FLEX-jGCaMP8m-WPRE Addgene Cat# 162381-AAV1 AAV1.CAG.GCaMP6f.WPRE.SV40 Addgene Cat# 100836-AAV1 AAV1.Syn.GCaMP6f.WPRE.SV40 Addgene Cat# 100837-AAV1 Chemicals, peptides, and recombinant proteins Donkey serum Invitrogen Cat #116-4101 Fluoroshield with DAPI Merck Cat# F6057-20ML Deposited data Raw and analyzed data This paper https://doi.org/10.6084/m9.figshare.25590528 Codes for analysis This paper https://doi.org/10.6084/m9.figshare.25590528 Experimental models: Organisms/strains Mouse: B6;DBA-Tg(tetO-GCaMP6s)2Niell/J The Jackson Laboratory RRID:IMSR_JAX:024742 Mouse: B6.Cg-Tg(Camk2a-tTA)1Mmay/DboJ The Jackson Laboratory RRID:IMSR_JAX:007004 Mouse: Tg(Rbp4-cre)KL100Gsat Mutant Mouse Resource Research Centers MMRRC:031125-UCD; MGI:4367067 Mouse: C57BL/6J KU Leuven Animal Facility N/A Software and algorithms Napari Ahler et al.45 https://doi.org/10.5281/zenodo.3555620 Stardist plugin for Napari Weigert et al.46 https://github.com/stardist/stardist-napari napari-deeplabcut plugin Mathis et al.47 https://github.com/DeepLabCut/napari- deeplabcut.git ImageJ National Institutes of Health https://imagej.nih.gov/ij/index.html MATLAB The Mathworks http://mathworks.com Two-sample Kolmogorov-Smirnov test Muir48 https://www.mathworks.com/matlabcentral/ fileexchange/38617-kstest_2s_2d-x1-x2-alpha ..
Article Title: Human assembloids reveal the consequences of CACNA1G gene variants in the thalamocortical pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies TCF7L2 Cell Signaling Technology Cat # 2569S, RRID: AB_2199816 GFP GeneTex Cat # GTX13970, RRID: AB_371416 VGLUT2 Millipore Cat# MAB5504, RRID: AB_2187552 mCherry GeneTex Cat # GTX128508, RRID: AB_2721247 Bacterial and virus strains AAV-DJ-hSYN1::EYFP Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-16 AAV-DJ-hSYN1::mCherry Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-17 AAV-DJ-EF1-DIO-tdTomato Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-169 AAV-DJ-hSYN1::GCaMP6f Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-96 AAV1-hSYN1::Cre James M. Wilson Lab Addgene #105553-AAV1 AAV1-hSYN1::ChrimsonR-tdTomato Klapoetke et al.49 Addgene #59171-AAV1 Chemicals, peptides, and recombinant proteins B-27 Plus Supplement Thermo Fisher Scientific Cat# A3582801 B-27 supplement without vitamin A Thermo Fisher Scientific Cat# 12587010 Human recombinant FGF-2 R&D Systems Cat# 233-FB Human recombinant EGF R&D Systems Cat# 236-EG Human recombinant BDNF Peprotech Cat# 450-02 Human recombinant NT3 Peprotech Cat# 450-03 L-Ascorbic Acid Wako Cat# 321-44823 cAMP Sigma-Aldrich Cat# D0627 Dorsomorphin Sigma-Aldrich Cat# P5499 SB-431542 Tocris Cat# 1614 CHIR 99021 Selleckchem Cat# S1263 SAG Millipore Cat# 566660 BMP7 Peprotech Cat # 120-03P DAPT STEMCELL Technologies Cat# 72082 Y-27632 Selleckchem Cat# S1049 DHA Millipore Sigma Cat # D2534 Tetrodotoxin citrate (TTX) Tocris Cat# 1069 GlutaMAX Supplement Thermo Fisher Scientific Cat # 35050079 Penicillin-Streptomycin Thermo Fisher Scientific Cat # 15070063 Critical commercial assays Chromium Single cell 30 GEM, Library & Gel Bead Kit v3 10x Genomics PN- 1000121 Deposited data Processed single cell RNA-seq data This study GEO: GSE224766 Experimental models: Cell lines Human iPS cell line 2242-1 Khan et al.63 N/A Human iPS cell line 0410-1 Khan et al.63 N/A Human iPS cell line 1208-2 Khan et al.63 N/A (Continued on next page) Neuron 112, 1–12.e1–e7, December 18, 2024 e1 .. Characterization and maintenance of hiPS cells Human induced pluripotent stem (hiPS) cell lines used in this study were validated using methods described in previous studies.45,63,67 Genome-wide SNP genotyping was performed using the Illumina genome-wide GSAMD-24v2-0 SNP microarray at the Children’s Hospital of Philadelphia.
Article Title: Non-reciprocal callosal projections and input gradients underlie interhemispheric communication in binocular visual cortex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAVrg-hSyn-eGFP Penn Vector Core/AddGene AddGene Cat #50465-AAVrg AAVrg-hSyn-hChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat #26973-AAVrg AAV1-hSyn-Cre Penn Vector Core/AddGene AddGene Cat #105553-AAV1 AAV1-hSyn-DIO-mCherry Penn Vector Core/AddGene AddGene Cat #50459-AAV1 AAV1-hSyn-ChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat #26973-AAV1 AAV1-Syn-ChrimsonR-tdTomato Penn Vector Core/AddGene AddGene Cat #59171-AAV1 AAV1-Ef1a-DIO-hChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat 20298-AAV1 Chemicals, peptides, and recombinant proteins Urethane Sigma-Aldrich Cat #U2500 Isoflurane Southern Anesthesia & Surgical Cat #PIR001325-EA Chlorprothixene hydrochloride Sigma-Aldrich Cat #C1671 SR 95531 hydrobromide (Gabazine) HelloBio Cat #HB0901 6,7-Dinitroquinoxaline-2,3-dione (DNQX) HelloBio Cat #HB0261 D-(− )-2-Amino-5-phosphonopentanoic acid (D-APV) HelloBio Cat #HB0225 Tetrodotoxin citrate (TTX) Tocris Cat #1069 4-Aminopyridine (4-AP) Tocris Cat #0940 α-Dendrotoxin Alomone Labs Cat #D-350 Atropine Bausch and Lomb Cat #9775600 Biocytin Sigma-Aldrich Cat #B4261 Paraformaldehyde Sigma-Aldrich Cat #158127 Vectastain Elite ABC Kit Vector laboratories Cat #PK-6100 Actinomycin D Millipore sigma Cat #A1410 BD FACS Pre-Sort buffer BD Biosciences Cat #563503 Fluoromount-G Sigma Cat #00-4958-02 Critical commercial assays SMART-Seq mRNA Single Cell LP kit Takara Bio Cat #634787 Unique Dual Index Kit Takara Bio Cat #634752 High Sensitivity DNA chip Agilent Cat #NC1738319 Deposited data Spike sorting GitHub https://github.com/ Layer 2/3 pyramidal neuron model This paper (ModelDB: 2020504) https://modeldb.science/2020504 RNA-seq data This paper (GEO: GSE310829) https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE310829 Experimental models: Organisms/strains Mouse: C57BL/6J Jackson Laboratory Strain: #00064 Mouse: PV-Cre Jackson Laboratory Strain: #010777 Software and algorithms Axograph X Axograph https://axograph.com/ MATLAB Mathworks https://mathworks.com/ Psychtoolbox NA http://psychtoolbox.org/ Fiji image ImageJ https://imagej.net/software/fiji/ NEURON 7.4 Carnevale and Hines, 2006 http://www.neuron.yale.edu (Continued on next page) 18 Cell Reports 45, 116806, January 27, 2026 ..
Software:Article Title: Negative feedback control of hypothalamic feeding circuits by the taste of food.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAV1.CAG.Flex.GCaMP6s.WPRE.SV40 Chen et al.80 Addgene Cat#: 100842-AAV1 AAV1.CAG.FLEX.GCaMP8s HHMI Janelia Ref ID: 1-1322-2 AAV8.hSyn.DIO.hM4D(Gi).mCherry Krashes et al.19 Addgene Cat#:44362-AAV8 AAV1.hSyn.DIO.mCherry Bryan Roth Lab Addgene Cat:50459-AAV1 Chemicals, peptides, and recombinant proteins Devazepide R&D Systems Cat#:2304/10 Intralipid Sigma Aldrich; Medline Cat#:I141-100mL; Cat#:BHL2B6064H Silicone Oil Sigma Aldrich Cat#:378348 DAPI Fluoromount-G Southern Biotech Cat#:0100-20 Deschloroclozapine dihydrochloride Hello bio Cat#: HB9126 Clozapine-N-oxide Tocris Cat#: 4936 Experimental models: Organisms/strains B6.129-Leprtm3(cre)Mgmj/J (Common name: LepRCre) The Jackson Laboratory RRID: IMSR_JAX:032457 STOCK Agrptm1(cre)Lowl/J (Common name: Agrp-Ires-Cre) The Jackson Laboratory RRID: IMSR_JAX:012899 B6;129S-Gt(ROSA)26Sortm32(CAGCOP4*H134R/EYFP)Hze/J (Common name: Ai32(RCL-ChR2(H134R)/EYFP)) The Jackson Laboratory RRID: IMSR_JAX:012569 C57BL/6J The Jackson Laboratory RRID: IMSR_JAX:000664 Software and algorithms GraphPad Prism 8 GraphPad Software RRID: SCR_002798 MATLAB 2017b Mathworks RRID: SCR_001622 Inscopix Data Acquisition Software Inscopix https://iqlearning.inscopix.com/ software-downloads/idas Inscopix Mosaic Software 1.2.0 Inscopix https://support.inscopix.com/support/ products/mosaic/mosaic-downloads Inscopix Data Processing Software v.1.3.1 Inscopix https://iqlearning.inscopix.com/ software-downloads/idps-archive CNMFe Zhou et al.81 https://github.com/zhoupc/CNMF_E CellReg Sheintuch et al.82 https://github.com/zivlab/CellReg R Studio version 2023.03.1 Posit RRID: SCR_000432 ImageJ (Fiji) Open source RRID: SCR_002285 Synapse Tucker-Davis Technologies https://www.tdt.com/component/ synapse-software/ Custom code Dr. Zachary Knight’s Lab Github: https://github.com/ zackknightlabucsf/zackknightlabucsf Other Rodent diet PicoLab Cat#:5053 GRIN lens Inscopix Cat#:1050-004610 Metabond Parkwell Cat#:S380 Baseplate Inscopix Cat#:100-000279 Baseplate cover Inscopix Cat#:100-000241 Mono Fiberoptic Cannula Doric Lenses Cat#:MFC_400/430-0.48 Sleeve Bronze 2.5mm Doric Lenses Cat#:SLEEVE_BR_2.5 (Continued on next page) e1 Neuron 112, 1–17.e1–e5, October 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Optical Fiber Thorlabs Cat#:FT200UMT Fiberoptic Cannula Thorlabs Cat#:CFLC230-10 Gastric catheter Instech Labs Cat#:C30PU-RGA1439 Sterile access button Instech Labs Cat#:VABM1B/22 Aluminum cap Instech Labs Cat#:VABM1C Ensure Vanilla Abbott Cat#:00750 nVista 3.0 Inscopix https://www.inscopix.com/nvista nVoke 2.0 Inscopix https://www.inscopix.com/nvoke Patch cable Doric Lenses Cat#:MFP_400/460/900- 0.48_2m_FCM-MF2.5 Four-channel LED Driver Thorlabs Cat#:DC4104 Minicube Thorlabs Cat#:FMC6_AE(400–410)_E1(450–490)_ F1(500–540)_E2(550–580)_ F2(600–680)_S Photoreceiver Newport Cat#:2151 Base Processor Tucker-Davis Technologies Cat#:RZ5P Davis Rig Med Associates Cat#:MED-DAV-160M
Article Title: Higher-order cortical and thalamic pathways shape visual processing streams in the mouse cortex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies chicken anti-eGFP Thermo Fisher Scientific Cat# A10262; RRID:AB_2534023 Alexa 488 donkey anti-chicken Immuno-Jackson Cat# 703-545-155; RRID: AB_2340375 Bacterial and virus strains retroAAV-CAG-tdTomato Addgene Cat# 59462-AAVrg AAV1-CAG-FLEX-jGCaMP8m-WPRE Addgene Cat# 162381-AAV1 AAV1.CAG.GCaMP6f.WPRE.SV40 Addgene Cat# 100836-AAV1 AAV1.Syn.GCaMP6f.WPRE.SV40 Addgene Cat# 100837-AAV1 Chemicals, peptides, and recombinant proteins Donkey serum Invitrogen Cat #116-4101 Fluoroshield with DAPI Merck Cat# F6057-20ML Deposited data Raw and analyzed data This paper https://doi.org/10.6084/m9.figshare.25590528 Codes for analysis This paper https://doi.org/10.6084/m9.figshare.25590528 Experimental models: Organisms/strains Mouse: B6;DBA-Tg(tetO-GCaMP6s)2Niell/J The Jackson Laboratory RRID:IMSR_JAX:024742 Mouse: B6.Cg-Tg(Camk2a-tTA)1Mmay/DboJ The Jackson Laboratory RRID:IMSR_JAX:007004 Mouse: Tg(Rbp4-cre)KL100Gsat Mutant Mouse Resource Research Centers MMRRC:031125-UCD; MGI:4367067 Mouse: C57BL/6J KU Leuven Animal Facility N/A Software and algorithms Napari Ahler et al.45 https://doi.org/10.5281/zenodo.3555620 Stardist plugin for Napari Weigert et al.46 https://github.com/stardist/stardist-napari napari-deeplabcut plugin Mathis et al.47 https://github.com/DeepLabCut/napari- deeplabcut.git ImageJ National Institutes of Health https://imagej.nih.gov/ij/index.html MATLAB The Mathworks http://mathworks.com Two-sample Kolmogorov-Smirnov test Muir48 https://www.mathworks.com/matlabcentral/ fileexchange/38617-kstest_2s_2d-x1-x2-alpha ..
Article Title: Non-reciprocal callosal projections and input gradients underlie interhemispheric communication in binocular visual cortex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAVrg-hSyn-eGFP Penn Vector Core/AddGene AddGene Cat #50465-AAVrg AAVrg-hSyn-hChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat #26973-AAVrg AAV1-hSyn-Cre Penn Vector Core/AddGene AddGene Cat #105553-AAV1 AAV1-hSyn-DIO-mCherry Penn Vector Core/AddGene AddGene Cat #50459-AAV1 AAV1-hSyn-ChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat #26973-AAV1 AAV1-Syn-ChrimsonR-tdTomato Penn Vector Core/AddGene AddGene Cat #59171-AAV1 AAV1-Ef1a-DIO-hChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat 20298-AAV1 Chemicals, peptides, and recombinant proteins Urethane Sigma-Aldrich Cat #U2500 Isoflurane Southern Anesthesia & Surgical Cat #PIR001325-EA Chlorprothixene hydrochloride Sigma-Aldrich Cat #C1671 SR 95531 hydrobromide (Gabazine) HelloBio Cat #HB0901 6,7-Dinitroquinoxaline-2,3-dione (DNQX) HelloBio Cat #HB0261 D-(− )-2-Amino-5-phosphonopentanoic acid (D-APV) HelloBio Cat #HB0225 Tetrodotoxin citrate (TTX) Tocris Cat #1069 4-Aminopyridine (4-AP) Tocris Cat #0940 α-Dendrotoxin Alomone Labs Cat #D-350 Atropine Bausch and Lomb Cat #9775600 Biocytin Sigma-Aldrich Cat #B4261 Paraformaldehyde Sigma-Aldrich Cat #158127 Vectastain Elite ABC Kit Vector laboratories Cat #PK-6100 Actinomycin D Millipore sigma Cat #A1410 BD FACS Pre-Sort buffer BD Biosciences Cat #563503 Fluoromount-G Sigma Cat #00-4958-02 Critical commercial assays SMART-Seq mRNA Single Cell LP kit Takara Bio Cat #634787 Unique Dual Index Kit Takara Bio Cat #634752 High Sensitivity DNA chip Agilent Cat #NC1738319 Deposited data Spike sorting GitHub https://github.com/ Layer 2/3 pyramidal neuron model This paper (ModelDB: 2020504) https://modeldb.science/2020504 RNA-seq data This paper (GEO: GSE310829) https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE310829 Experimental models: Organisms/strains Mouse: C57BL/6J Jackson Laboratory Strain: #00064 Mouse: PV-Cre Jackson Laboratory Strain: #010777 Software and algorithms Axograph X Axograph https://axograph.com/ MATLAB Mathworks https://mathworks.com/ Psychtoolbox NA http://psychtoolbox.org/ Fiji image ImageJ https://imagej.net/software/fiji/ NEURON 7.4 Carnevale and Hines, 2006 http://www.neuron.yale.edu (Continued on next page) 18 Cell Reports 45, 116806, January 27, 2026 ..
Mutagenesis:Article Title: Higher-order cortical and thalamic pathways shape visual processing streams in the mouse cortex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies chicken anti-eGFP Thermo Fisher Scientific Cat# A10262; RRID:AB_2534023 Alexa 488 donkey anti-chicken Immuno-Jackson Cat# 703-545-155; RRID: AB_2340375 Bacterial and virus strains retroAAV-CAG-tdTomato Addgene Cat# 59462-AAVrg AAV1-CAG-FLEX-jGCaMP8m-WPRE Addgene Cat# 162381-AAV1 AAV1.CAG.GCaMP6f.WPRE.SV40 Addgene Cat# 100836-AAV1 AAV1.Syn.GCaMP6f.WPRE.SV40 Addgene Cat# 100837-AAV1 Chemicals, peptides, and recombinant proteins Donkey serum Invitrogen Cat #116-4101 Fluoroshield with DAPI Merck Cat# F6057-20ML Deposited data Raw and analyzed data This paper https://doi.org/10.6084/m9.figshare.25590528 Codes for analysis This paper https://doi.org/10.6084/m9.figshare.25590528 Experimental models: Organisms/strains Mouse: B6;DBA-Tg(tetO-GCaMP6s)2Niell/J The Jackson Laboratory RRID:IMSR_JAX:024742 Mouse: B6.Cg-Tg(Camk2a-tTA)1Mmay/DboJ The Jackson Laboratory RRID:IMSR_JAX:007004 Mouse: Tg(Rbp4-cre)KL100Gsat Mutant Mouse Resource Research Centers MMRRC:031125-UCD; MGI:4367067 Mouse: C57BL/6J KU Leuven Animal Facility N/A Software and algorithms Napari Ahler et al.45 https://doi.org/10.5281/zenodo.3555620 Stardist plugin for Napari Weigert et al.46 https://github.com/stardist/stardist-napari napari-deeplabcut plugin Mathis et al.47 https://github.com/DeepLabCut/napari- deeplabcut.git ImageJ National Institutes of Health https://imagej.nih.gov/ij/index.html MATLAB The Mathworks http://mathworks.com Two-sample Kolmogorov-Smirnov test Muir48 https://www.mathworks.com/matlabcentral/ fileexchange/38617-kstest_2s_2d-x1-x2-alpha ..
other:Article Title: PV-dependent reorganization of prelimbic cortex sub-engrams during systems consolidation.
Article Snippet: Article PV-dependent reorganization of prelimbic cortex sub-engrams during systems consolidation Highlights • Prelimbic cortex ‘‘sub-engrams’’ contribute differentially to recent and remote memory • Sub-engram involvement reflects their projection profile • Sub-engram reorganization depends on parvalbuminexpressing interneurons Authors Ali Golbabaei, Sheena A. Josselyn, Paul W. Frankland Correspondence paul.frankland@sickkids.ca In brief Golbabaei et al. explore how the contributions of projection-defined prelimbic cortex ‘‘sub-engrams’’ to contextual fear memory recall change with time.. Sub-engrams projecting to the basal amygdala and lateral entorhinal cortex support recent memory recall, whereas sub-engrams projecting to the nucleus reuniens and nucleus accumbens are additionally recruited at remote delays.. Golbabaei et al., 2026, Neuron 114, 1–17 January 7, 2026 © 2025 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies. https://doi.org/10.1016/j.neuron.2025.09.033 ll
Chocolate:
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Bioprocessing:Article Title: Human assembloids reveal the consequences of CACNA1G gene variants in the thalamocortical pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies TCF7L2 Cell Signaling Technology Cat # 2569S, RRID: AB_2199816 GFP GeneTex Cat # GTX13970, RRID: AB_371416 VGLUT2 Millipore Cat# MAB5504, RRID: AB_2187552 mCherry GeneTex Cat # GTX128508, RRID: AB_2721247 Bacterial and virus strains AAV-DJ-hSYN1::EYFP Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-16 AAV-DJ-hSYN1::mCherry Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-17 AAV-DJ-EF1-DIO-tdTomato Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-169 AAV-DJ-hSYN1::GCaMP6f Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-96 AAV1-hSYN1::Cre James M. Wilson Lab Addgene #105553-AAV1 AAV1-hSYN1::ChrimsonR-tdTomato Klapoetke et al.49 Addgene #59171-AAV1 Chemicals, peptides, and recombinant proteins B-27 Plus Supplement Thermo Fisher Scientific Cat# A3582801 B-27 supplement without vitamin A Thermo Fisher Scientific Cat# 12587010 Human recombinant FGF-2 R&D Systems Cat# 233-FB Human recombinant EGF R&D Systems Cat# 236-EG Human recombinant BDNF Peprotech Cat# 450-02 Human recombinant NT3 Peprotech Cat# 450-03 L-Ascorbic Acid Wako Cat# 321-44823 cAMP Sigma-Aldrich Cat# D0627 Dorsomorphin Sigma-Aldrich Cat# P5499 SB-431542 Tocris Cat# 1614 CHIR 99021 Selleckchem Cat# S1263 SAG Millipore Cat# 566660 BMP7 Peprotech Cat # 120-03P DAPT STEMCELL Technologies Cat# 72082 Y-27632 Selleckchem Cat# S1049 DHA Millipore Sigma Cat # D2534 Tetrodotoxin citrate (TTX) Tocris Cat# 1069 GlutaMAX Supplement Thermo Fisher Scientific Cat # 35050079 Penicillin-Streptomycin Thermo Fisher Scientific Cat # 15070063 Critical commercial assays Chromium Single cell 30 GEM, Library & Gel Bead Kit v3 10x Genomics PN- 1000121 Deposited data Processed single cell RNA-seq data This study GEO: GSE224766 Experimental models: Cell lines Human iPS cell line 2242-1 Khan et al.63 N/A Human iPS cell line 0410-1 Khan et al.63 N/A Human iPS cell line 1208-2 Khan et al.63 N/A (Continued on next page) Neuron 112, 1–12.e1–e7, December 18, 2024 e1 .. Characterization and maintenance of hiPS cells Human induced pluripotent stem (hiPS) cell lines used in this study were validated using methods described in previous studies.45,63,67 Genome-wide SNP genotyping was performed using the Illumina genome-wide GSAMD-24v2-0 SNP microarray at the Children’s Hospital of Philadelphia.
Single Cell:Article Title: Human assembloids reveal the consequences of CACNA1G gene variants in the thalamocortical pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies TCF7L2 Cell Signaling Technology Cat # 2569S, RRID: AB_2199816 GFP GeneTex Cat # GTX13970, RRID: AB_371416 VGLUT2 Millipore Cat# MAB5504, RRID: AB_2187552 mCherry GeneTex Cat # GTX128508, RRID: AB_2721247 Bacterial and virus strains AAV-DJ-hSYN1::EYFP Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-16 AAV-DJ-hSYN1::mCherry Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-17 AAV-DJ-EF1-DIO-tdTomato Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-169 AAV-DJ-hSYN1::GCaMP6f Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-96 AAV1-hSYN1::Cre James M. Wilson Lab Addgene #105553-AAV1 AAV1-hSYN1::ChrimsonR-tdTomato Klapoetke et al.49 Addgene #59171-AAV1 Chemicals, peptides, and recombinant proteins B-27 Plus Supplement Thermo Fisher Scientific Cat# A3582801 B-27 supplement without vitamin A Thermo Fisher Scientific Cat# 12587010 Human recombinant FGF-2 R&D Systems Cat# 233-FB Human recombinant EGF R&D Systems Cat# 236-EG Human recombinant BDNF Peprotech Cat# 450-02 Human recombinant NT3 Peprotech Cat# 450-03 L-Ascorbic Acid Wako Cat# 321-44823 cAMP Sigma-Aldrich Cat# D0627 Dorsomorphin Sigma-Aldrich Cat# P5499 SB-431542 Tocris Cat# 1614 CHIR 99021 Selleckchem Cat# S1263 SAG Millipore Cat# 566660 BMP7 Peprotech Cat # 120-03P DAPT STEMCELL Technologies Cat# 72082 Y-27632 Selleckchem Cat# S1049 DHA Millipore Sigma Cat # D2534 Tetrodotoxin citrate (TTX) Tocris Cat# 1069 GlutaMAX Supplement Thermo Fisher Scientific Cat # 35050079 Penicillin-Streptomycin Thermo Fisher Scientific Cat # 15070063 Critical commercial assays Chromium Single cell 30 GEM, Library & Gel Bead Kit v3 10x Genomics PN- 1000121 Deposited data Processed single cell RNA-seq data This study GEO: GSE224766 Experimental models: Cell lines Human iPS cell line 2242-1 Khan et al.63 N/A Human iPS cell line 0410-1 Khan et al.63 N/A Human iPS cell line 1208-2 Khan et al.63 N/A (Continued on next page) Neuron 112, 1–12.e1–e7, December 18, 2024 e1 .. Characterization and maintenance of hiPS cells Human induced pluripotent stem (hiPS) cell lines used in this study were validated using methods described in previous studies.45,63,67 Genome-wide SNP genotyping was performed using the Illumina genome-wide GSAMD-24v2-0 SNP microarray at the Children’s Hospital of Philadelphia.
Article Title: Non-reciprocal callosal projections and input gradients underlie interhemispheric communication in binocular visual cortex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAVrg-hSyn-eGFP Penn Vector Core/AddGene AddGene Cat #50465-AAVrg AAVrg-hSyn-hChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat #26973-AAVrg AAV1-hSyn-Cre Penn Vector Core/AddGene AddGene Cat #105553-AAV1 AAV1-hSyn-DIO-mCherry Penn Vector Core/AddGene AddGene Cat #50459-AAV1 AAV1-hSyn-ChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat #26973-AAV1 AAV1-Syn-ChrimsonR-tdTomato Penn Vector Core/AddGene AddGene Cat #59171-AAV1 AAV1-Ef1a-DIO-hChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat 20298-AAV1 Chemicals, peptides, and recombinant proteins Urethane Sigma-Aldrich Cat #U2500 Isoflurane Southern Anesthesia & Surgical Cat #PIR001325-EA Chlorprothixene hydrochloride Sigma-Aldrich Cat #C1671 SR 95531 hydrobromide (Gabazine) HelloBio Cat #HB0901 6,7-Dinitroquinoxaline-2,3-dione (DNQX) HelloBio Cat #HB0261 D-(− )-2-Amino-5-phosphonopentanoic acid (D-APV) HelloBio Cat #HB0225 Tetrodotoxin citrate (TTX) Tocris Cat #1069 4-Aminopyridine (4-AP) Tocris Cat #0940 α-Dendrotoxin Alomone Labs Cat #D-350 Atropine Bausch and Lomb Cat #9775600 Biocytin Sigma-Aldrich Cat #B4261 Paraformaldehyde Sigma-Aldrich Cat #158127 Vectastain Elite ABC Kit Vector laboratories Cat #PK-6100 Actinomycin D Millipore sigma Cat #A1410 BD FACS Pre-Sort buffer BD Biosciences Cat #563503 Fluoromount-G Sigma Cat #00-4958-02 Critical commercial assays SMART-Seq mRNA Single Cell LP kit Takara Bio Cat #634787 Unique Dual Index Kit Takara Bio Cat #634752 High Sensitivity DNA chip Agilent Cat #NC1738319 Deposited data Spike sorting GitHub https://github.com/ Layer 2/3 pyramidal neuron model This paper (ModelDB: 2020504) https://modeldb.science/2020504 RNA-seq data This paper (GEO: GSE310829) https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE310829 Experimental models: Organisms/strains Mouse: C57BL/6J Jackson Laboratory Strain: #00064 Mouse: PV-Cre Jackson Laboratory Strain: #010777 Software and algorithms Axograph X Axograph https://axograph.com/ MATLAB Mathworks https://mathworks.com/ Psychtoolbox NA http://psychtoolbox.org/ Fiji image ImageJ https://imagej.net/software/fiji/ NEURON 7.4 Carnevale and Hines, 2006 http://www.neuron.yale.edu (Continued on next page) 18 Cell Reports 45, 116806, January 27, 2026 ..
Single Cell RNA-Seq:Article Title: Human assembloids reveal the consequences of CACNA1G gene variants in the thalamocortical pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies TCF7L2 Cell Signaling Technology Cat # 2569S, RRID: AB_2199816 GFP GeneTex Cat # GTX13970, RRID: AB_371416 VGLUT2 Millipore Cat# MAB5504, RRID: AB_2187552 mCherry GeneTex Cat # GTX128508, RRID: AB_2721247 Bacterial and virus strains AAV-DJ-hSYN1::EYFP Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-16 AAV-DJ-hSYN1::mCherry Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-17 AAV-DJ-EF1-DIO-tdTomato Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-169 AAV-DJ-hSYN1::GCaMP6f Stanford University Neuroscience Gene Vector and Virus Core GVVC-AAV-96 AAV1-hSYN1::Cre James M. Wilson Lab Addgene #105553-AAV1 AAV1-hSYN1::ChrimsonR-tdTomato Klapoetke et al.49 Addgene #59171-AAV1 Chemicals, peptides, and recombinant proteins B-27 Plus Supplement Thermo Fisher Scientific Cat# A3582801 B-27 supplement without vitamin A Thermo Fisher Scientific Cat# 12587010 Human recombinant FGF-2 R&D Systems Cat# 233-FB Human recombinant EGF R&D Systems Cat# 236-EG Human recombinant BDNF Peprotech Cat# 450-02 Human recombinant NT3 Peprotech Cat# 450-03 L-Ascorbic Acid Wako Cat# 321-44823 cAMP Sigma-Aldrich Cat# D0627 Dorsomorphin Sigma-Aldrich Cat# P5499 SB-431542 Tocris Cat# 1614 CHIR 99021 Selleckchem Cat# S1263 SAG Millipore Cat# 566660 BMP7 Peprotech Cat # 120-03P DAPT STEMCELL Technologies Cat# 72082 Y-27632 Selleckchem Cat# S1049 DHA Millipore Sigma Cat # D2534 Tetrodotoxin citrate (TTX) Tocris Cat# 1069 GlutaMAX Supplement Thermo Fisher Scientific Cat # 35050079 Penicillin-Streptomycin Thermo Fisher Scientific Cat # 15070063 Critical commercial assays Chromium Single cell 30 GEM, Library & Gel Bead Kit v3 10x Genomics PN- 1000121 Deposited data Processed single cell RNA-seq data This study GEO: GSE224766 Experimental models: Cell lines Human iPS cell line 2242-1 Khan et al.63 N/A Human iPS cell line 0410-1 Khan et al.63 N/A Human iPS cell line 1208-2 Khan et al.63 N/A (Continued on next page) Neuron 112, 1–12.e1–e7, December 18, 2024 e1 .. Characterization and maintenance of hiPS cells Human induced pluripotent stem (hiPS) cell lines used in this study were validated using methods described in previous studies.45,63,67 Genome-wide SNP genotyping was performed using the Illumina genome-wide GSAMD-24v2-0 SNP microarray at the Children’s Hospital of Philadelphia.
FACS:Article Title: Non-reciprocal callosal projections and input gradients underlie interhemispheric communication in binocular visual cortex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAVrg-hSyn-eGFP Penn Vector Core/AddGene AddGene Cat #50465-AAVrg AAVrg-hSyn-hChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat #26973-AAVrg AAV1-hSyn-Cre Penn Vector Core/AddGene AddGene Cat #105553-AAV1 AAV1-hSyn-DIO-mCherry Penn Vector Core/AddGene AddGene Cat #50459-AAV1 AAV1-hSyn-ChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat #26973-AAV1 AAV1-Syn-ChrimsonR-tdTomato Penn Vector Core/AddGene AddGene Cat #59171-AAV1 AAV1-Ef1a-DIO-hChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat 20298-AAV1 Chemicals, peptides, and recombinant proteins Urethane Sigma-Aldrich Cat #U2500 Isoflurane Southern Anesthesia & Surgical Cat #PIR001325-EA Chlorprothixene hydrochloride Sigma-Aldrich Cat #C1671 SR 95531 hydrobromide (Gabazine) HelloBio Cat #HB0901 6,7-Dinitroquinoxaline-2,3-dione (DNQX) HelloBio Cat #HB0261 D-(− )-2-Amino-5-phosphonopentanoic acid (D-APV) HelloBio Cat #HB0225 Tetrodotoxin citrate (TTX) Tocris Cat #1069 4-Aminopyridine (4-AP) Tocris Cat #0940 α-Dendrotoxin Alomone Labs Cat #D-350 Atropine Bausch and Lomb Cat #9775600 Biocytin Sigma-Aldrich Cat #B4261 Paraformaldehyde Sigma-Aldrich Cat #158127 Vectastain Elite ABC Kit Vector laboratories Cat #PK-6100 Actinomycin D Millipore sigma Cat #A1410 BD FACS Pre-Sort buffer BD Biosciences Cat #563503 Fluoromount-G Sigma Cat #00-4958-02 Critical commercial assays SMART-Seq mRNA Single Cell LP kit Takara Bio Cat #634787 Unique Dual Index Kit Takara Bio Cat #634752 High Sensitivity DNA chip Agilent Cat #NC1738319 Deposited data Spike sorting GitHub https://github.com/ Layer 2/3 pyramidal neuron model This paper (ModelDB: 2020504) https://modeldb.science/2020504 RNA-seq data This paper (GEO: GSE310829) https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE310829 Experimental models: Organisms/strains Mouse: C57BL/6J Jackson Laboratory Strain: #00064 Mouse: PV-Cre Jackson Laboratory Strain: #010777 Software and algorithms Axograph X Axograph https://axograph.com/ MATLAB Mathworks https://mathworks.com/ Psychtoolbox NA http://psychtoolbox.org/ Fiji image ImageJ https://imagej.net/software/fiji/ NEURON 7.4 Carnevale and Hines, 2006 http://www.neuron.yale.edu (Continued on next page) 18 Cell Reports 45, 116806, January 27, 2026 ..
RNA Sequencing:Article Title: Non-reciprocal callosal projections and input gradients underlie interhemispheric communication in binocular visual cortex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAVrg-hSyn-eGFP Penn Vector Core/AddGene AddGene Cat #50465-AAVrg AAVrg-hSyn-hChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat #26973-AAVrg AAV1-hSyn-Cre Penn Vector Core/AddGene AddGene Cat #105553-AAV1 AAV1-hSyn-DIO-mCherry Penn Vector Core/AddGene AddGene Cat #50459-AAV1 AAV1-hSyn-ChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat #26973-AAV1 AAV1-Syn-ChrimsonR-tdTomato Penn Vector Core/AddGene AddGene Cat #59171-AAV1 AAV1-Ef1a-DIO-hChR2(H134R)-eYFP Penn Vector Core/AddGene AddGene Cat 20298-AAV1 Chemicals, peptides, and recombinant proteins Urethane Sigma-Aldrich Cat #U2500 Isoflurane Southern Anesthesia & Surgical Cat #PIR001325-EA Chlorprothixene hydrochloride Sigma-Aldrich Cat #C1671 SR 95531 hydrobromide (Gabazine) HelloBio Cat #HB0901 6,7-Dinitroquinoxaline-2,3-dione (DNQX) HelloBio Cat #HB0261 D-(− )-2-Amino-5-phosphonopentanoic acid (D-APV) HelloBio Cat #HB0225 Tetrodotoxin citrate (TTX) Tocris Cat #1069 4-Aminopyridine (4-AP) Tocris Cat #0940 α-Dendrotoxin Alomone Labs Cat #D-350 Atropine Bausch and Lomb Cat #9775600 Biocytin Sigma-Aldrich Cat #B4261 Paraformaldehyde Sigma-Aldrich Cat #158127 Vectastain Elite ABC Kit Vector laboratories Cat #PK-6100 Actinomycin D Millipore sigma Cat #A1410 BD FACS Pre-Sort buffer BD Biosciences Cat #563503 Fluoromount-G Sigma Cat #00-4958-02 Critical commercial assays SMART-Seq mRNA Single Cell LP kit Takara Bio Cat #634787 Unique Dual Index Kit Takara Bio Cat #634752 High Sensitivity DNA chip Agilent Cat #NC1738319 Deposited data Spike sorting GitHub https://github.com/ Layer 2/3 pyramidal neuron model This paper (ModelDB: 2020504) https://modeldb.science/2020504 RNA-seq data This paper (GEO: GSE310829) https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE310829 Experimental models: Organisms/strains Mouse: C57BL/6J Jackson Laboratory Strain: #00064 Mouse: PV-Cre Jackson Laboratory Strain: #010777 Software and algorithms Axograph X Axograph https://axograph.com/ MATLAB Mathworks https://mathworks.com/ Psychtoolbox NA http://psychtoolbox.org/ Fiji image ImageJ https://imagej.net/software/fiji/ NEURON 7.4 Carnevale and Hines, 2006 http://www.neuron.yale.edu (Continued on next page) 18 Cell Reports 45, 116806, January 27, 2026 ..
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