RNA Sequencing:Article Title: Generating human neural diversity with a multiplexed morphogen screen in organoids.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Neurobasal A Life Technologies 10888 B-27 supplement without Vit A Life Technologies 12587 Glutamax Thermo Fisher Scientific 35050079 Penicillin and streptomycin Thermo Fisher Scientific 15140122 Accutase Innovate Cell Technologies AT-104 Activin A PeproTech 120-14P SR11237 Tocris 3411 Critical commercial assays Chromium Single cell 30 GEM, Library & Gel Bead Kit v3 10x Genomics PN: 1000075 Evercode Whole Transcriptome Kit Parse Biosciences ECW02030 Parse Biosciences Cell Fixation Parse Biosciences ECF2001 Deposited data Spatial transcriptomics data This paper Zenodo: https://doi.org/10.5281/ zenodo.13835782 Single cell RNA sequencing data This paper GEO: GSE233574; https://cells-test.gi. ucsc.edu/?ds=morphogen-screen Human fetal brain scRNA-seq dataset Braun et al.37 https://github.com/linnarsson-lab/ developing-human-brain Human fetal cerebellum scRNA-seq dataset Aldinger et al.52 https://cells.ucsc.edu/?ds=cbl-dev Primate TAC3-IN scRNA-seq dataset Schmitz et al.28 https://dev-inhibitory-neurons.cells.ucsc.edu/ Human fetal striatum scRNA-seq dataset Bhaduri et al.65 https://data.nemoarchive.org/biccn/ grant/u01_devhu/kriegstein/ transcriptome/scell/10x_v2/ human/processed/counts/ Experimental models: Cell lines Human iPSC line 2242-1 Pasca Lab N/A Human iPSC line Q-0306-1 Pasca Lab N/A Human iPSC line Q-0294-2 Pasca Lab N/A Human iPSC line NIH2788 Pasca Lab N/A Experimental models: Organisms/strains FOXN1-/- rats Charles River Laboratories Crl:NIH-Foxn1rnu Software and algorithms ImageJ (Fiji) Schindelin et al.66 https://imagej.net/Fiji Cell Ranger v6.1.0, v7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/pipelines/latest/ what-is-cell-ranger Seurat v4.3.0 Satija Lab, Hao et al.67 https://satijalab.org/seurat/ MERlin spatial transcriptomics processing pipeline Emanuel et al.68 https://github.com/emanuega/merlin Cellpose segmentation algorithm Stringer et al.69 https://www.cellpose.org/ Other 10 cm ultra-low attachment plates Corning 3262 6-well ultra-low attachment plates Corning 3471 White PLA filament Prusa PRM-PLA-175-WHT Original Prusa i3 MK3S+ 3D Printer Prusa PRI-MK3S-COM-ORG-PEI FLOWMI Cell Strainer (40, 70uM) SP Bel Art 136800070 MERSCOPE Vizgen https://vizgen.com/ AggreWell 800 plates STEMCELL Technologies 34815 e2 Cell Stem Cell 31, 1831–1846.e1–e9, December 5, 2024
Software:Article Title: Generating human neural diversity with a multiplexed morphogen screen in organoids.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Neurobasal A Life Technologies 10888 B-27 supplement without Vit A Life Technologies 12587 Glutamax Thermo Fisher Scientific 35050079 Penicillin and streptomycin Thermo Fisher Scientific 15140122 Accutase Innovate Cell Technologies AT-104 Activin A PeproTech 120-14P SR11237 Tocris 3411 Critical commercial assays Chromium Single cell 30 GEM, Library & Gel Bead Kit v3 10x Genomics PN: 1000075 Evercode Whole Transcriptome Kit Parse Biosciences ECW02030 Parse Biosciences Cell Fixation Parse Biosciences ECF2001 Deposited data Spatial transcriptomics data This paper Zenodo: https://doi.org/10.5281/ zenodo.13835782 Single cell RNA sequencing data This paper GEO: GSE233574; https://cells-test.gi. ucsc.edu/?ds=morphogen-screen Human fetal brain scRNA-seq dataset Braun et al.37 https://github.com/linnarsson-lab/ developing-human-brain Human fetal cerebellum scRNA-seq dataset Aldinger et al.52 https://cells.ucsc.edu/?ds=cbl-dev Primate TAC3-IN scRNA-seq dataset Schmitz et al.28 https://dev-inhibitory-neurons.cells.ucsc.edu/ Human fetal striatum scRNA-seq dataset Bhaduri et al.65 https://data.nemoarchive.org/biccn/ grant/u01_devhu/kriegstein/ transcriptome/scell/10x_v2/ human/processed/counts/ Experimental models: Cell lines Human iPSC line 2242-1 Pasca Lab N/A Human iPSC line Q-0306-1 Pasca Lab N/A Human iPSC line Q-0294-2 Pasca Lab N/A Human iPSC line NIH2788 Pasca Lab N/A Experimental models: Organisms/strains FOXN1-/- rats Charles River Laboratories Crl:NIH-Foxn1rnu Software and algorithms ImageJ (Fiji) Schindelin et al.66 https://imagej.net/Fiji Cell Ranger v6.1.0, v7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/pipelines/latest/ what-is-cell-ranger Seurat v4.3.0 Satija Lab, Hao et al.67 https://satijalab.org/seurat/ MERlin spatial transcriptomics processing pipeline Emanuel et al.68 https://github.com/emanuega/merlin Cellpose segmentation algorithm Stringer et al.69 https://www.cellpose.org/ Other 10 cm ultra-low attachment plates Corning 3262 6-well ultra-low attachment plates Corning 3471 White PLA filament Prusa PRM-PLA-175-WHT Original Prusa i3 MK3S+ 3D Printer Prusa PRI-MK3S-COM-ORG-PEI FLOWMI Cell Strainer (40, 70uM) SP Bel Art 136800070 MERSCOPE Vizgen https://vizgen.com/ AggreWell 800 plates STEMCELL Technologies 34815 e2 Cell Stem Cell 31, 1831–1846.e1–e9, December 5, 2024
Proximity Ligation Assay:Article Title: Generating human neural diversity with a multiplexed morphogen screen in organoids.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Neurobasal A Life Technologies 10888 B-27 supplement without Vit A Life Technologies 12587 Glutamax Thermo Fisher Scientific 35050079 Penicillin and streptomycin Thermo Fisher Scientific 15140122 Accutase Innovate Cell Technologies AT-104 Activin A PeproTech 120-14P SR11237 Tocris 3411 Critical commercial assays Chromium Single cell 30 GEM, Library & Gel Bead Kit v3 10x Genomics PN: 1000075 Evercode Whole Transcriptome Kit Parse Biosciences ECW02030 Parse Biosciences Cell Fixation Parse Biosciences ECF2001 Deposited data Spatial transcriptomics data This paper Zenodo: https://doi.org/10.5281/ zenodo.13835782 Single cell RNA sequencing data This paper GEO: GSE233574; https://cells-test.gi. ucsc.edu/?ds=morphogen-screen Human fetal brain scRNA-seq dataset Braun et al.37 https://github.com/linnarsson-lab/ developing-human-brain Human fetal cerebellum scRNA-seq dataset Aldinger et al.52 https://cells.ucsc.edu/?ds=cbl-dev Primate TAC3-IN scRNA-seq dataset Schmitz et al.28 https://dev-inhibitory-neurons.cells.ucsc.edu/ Human fetal striatum scRNA-seq dataset Bhaduri et al.65 https://data.nemoarchive.org/biccn/ grant/u01_devhu/kriegstein/ transcriptome/scell/10x_v2/ human/processed/counts/ Experimental models: Cell lines Human iPSC line 2242-1 Pasca Lab N/A Human iPSC line Q-0306-1 Pasca Lab N/A Human iPSC line Q-0294-2 Pasca Lab N/A Human iPSC line NIH2788 Pasca Lab N/A Experimental models: Organisms/strains FOXN1-/- rats Charles River Laboratories Crl:NIH-Foxn1rnu Software and algorithms ImageJ (Fiji) Schindelin et al.66 https://imagej.net/Fiji Cell Ranger v6.1.0, v7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/pipelines/latest/ what-is-cell-ranger Seurat v4.3.0 Satija Lab, Hao et al.67 https://satijalab.org/seurat/ MERlin spatial transcriptomics processing pipeline Emanuel et al.68 https://github.com/emanuega/merlin Cellpose segmentation algorithm Stringer et al.69 https://www.cellpose.org/ Other 10 cm ultra-low attachment plates Corning 3262 6-well ultra-low attachment plates Corning 3471 White PLA filament Prusa PRM-PLA-175-WHT Original Prusa i3 MK3S+ 3D Printer Prusa PRI-MK3S-COM-ORG-PEI FLOWMI Cell Strainer (40, 70uM) SP Bel Art 136800070 MERSCOPE Vizgen https://vizgen.com/ AggreWell 800 plates STEMCELL Technologies 34815 e2 Cell Stem Cell 31, 1831–1846.e1–e9, December 5, 2024
Targeted Proteomics:Article Title: Generating human neural diversity with a multiplexed morphogen screen in organoids.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Neurobasal A Life Technologies 10888 B-27 supplement without Vit A Life Technologies 12587 Glutamax Thermo Fisher Scientific 35050079 Penicillin and streptomycin Thermo Fisher Scientific 15140122 Accutase Innovate Cell Technologies AT-104 Activin A PeproTech 120-14P SR11237 Tocris 3411 Critical commercial assays Chromium Single cell 30 GEM, Library & Gel Bead Kit v3 10x Genomics PN: 1000075 Evercode Whole Transcriptome Kit Parse Biosciences ECW02030 Parse Biosciences Cell Fixation Parse Biosciences ECF2001 Deposited data Spatial transcriptomics data This paper Zenodo: https://doi.org/10.5281/ zenodo.13835782 Single cell RNA sequencing data This paper GEO: GSE233574; https://cells-test.gi. ucsc.edu/?ds=morphogen-screen Human fetal brain scRNA-seq dataset Braun et al.37 https://github.com/linnarsson-lab/ developing-human-brain Human fetal cerebellum scRNA-seq dataset Aldinger et al.52 https://cells.ucsc.edu/?ds=cbl-dev Primate TAC3-IN scRNA-seq dataset Schmitz et al.28 https://dev-inhibitory-neurons.cells.ucsc.edu/ Human fetal striatum scRNA-seq dataset Bhaduri et al.65 https://data.nemoarchive.org/biccn/ grant/u01_devhu/kriegstein/ transcriptome/scell/10x_v2/ human/processed/counts/ Experimental models: Cell lines Human iPSC line 2242-1 Pasca Lab N/A Human iPSC line Q-0306-1 Pasca Lab N/A Human iPSC line Q-0294-2 Pasca Lab N/A Human iPSC line NIH2788 Pasca Lab N/A Experimental models: Organisms/strains FOXN1-/- rats Charles River Laboratories Crl:NIH-Foxn1rnu Software and algorithms ImageJ (Fiji) Schindelin et al.66 https://imagej.net/Fiji Cell Ranger v6.1.0, v7.1.0 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/ software/pipelines/latest/ what-is-cell-ranger Seurat v4.3.0 Satija Lab, Hao et al.67 https://satijalab.org/seurat/ MERlin spatial transcriptomics processing pipeline Emanuel et al.68 https://github.com/emanuega/merlin Cellpose segmentation algorithm Stringer et al.69 https://www.cellpose.org/ Other 10 cm ultra-low attachment plates Corning 3262 6-well ultra-low attachment plates Corning 3471 White PLA filament Prusa PRM-PLA-175-WHT Original Prusa i3 MK3S+ 3D Printer Prusa PRI-MK3S-COM-ORG-PEI FLOWMI Cell Strainer (40, 70uM) SP Bel Art 136800070 MERSCOPE Vizgen https://vizgen.com/ AggreWell 800 plates STEMCELL Technologies 34815 e2 Cell Stem Cell 31, 1831–1846.e1–e9, December 5, 2024
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