other:Article Title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NIS Elements AR 5.21.03 64-bit Nikon Instruments Inc. https://www.microscope.healthcare.nikon. com/products/software/nis-elements Bowtie- 0.12.9 Langmead et al.73 https://bowtie-bio.sourceforge.net/ index.shtml MAGeCK-iNC Tian et al.11 https://kampmannlab.ucsf.edu/ mageck-inc MATLAB MATLAB R2022a https://www.mathworks.com/products/ matlab.html Seurat Seurat v4.0 https://satijalab.org/seurat/ Fiji/ImageJ Fiji v2.8 RRID: SCR_002285 MetaXpress MetaXpress 6.7.2.290 RRID: SCR_016654 Custom code used for bulk RNA-seq, scRNA-seq, and calcium imaging data analysis https://github.com/lifan36/ Parra-Bravo-4R-P301S-2024 N/A CRISPRbrain Tian et al.36 https://www.crisprbrain.org/ ll Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015
Enzyme-linked Immunosorbent Assay:Article Title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation.
Article Snippet: HiFi Cas9 Nuclease V3 Integrated DNA Technologies Cat#1081060 Papain, Lyophilized Worthington Biochemical Cat#LS003118 DNase I Worthington Biochemical Cat#LS006333 TransIT-Lenti Transfection Reagent Mirus Bio Cat#MIR6600 Lipofectamine 3000 Thermo Fisher Scientific Cat#L3000015 Lenti-X Concentrator Takara Bio Cat#631232 Lentivirus Precipitation Solution Alstem Cat#VC125 Puromycin Thermo Fisher Scientific Cat#A1113803 Bovine Serum Albumin (BSA) Sigma Aldrich Cat#A7906 Janelia Fluor 549 analog JFX-549 HHMI Janelia Gift Clozapine N-oxide Tocris Cat#4936 NucRed Live 647 ReadyProbes Reagent Thermo Fisher Scientific Cat#R37106 iScript Reverse Transcription Supermix Bio-Rad Cat#1708840 Real-time PCR was performed using SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725270 FD Storage solution FD Neurotechnologies, Inc. Cat#PC101 Reveal Decloaker Biocare Medical Cat#RV1000M Hoescht 33342 Thermo Fisher Scientific Cat#62249 Critical commercial assays P3 Primary Cell 4D-Nucleofector X Kit S Lonza Cat#V4XP-303 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 QuickRNA MicroPrep Kit Zymo Research Cat#R1051 Illumina Stranded mRNA Prep Illumina Cat#20040532 Chromium Single Cell 30 Reagent Kits v3.1 10x Genomics Cat#PN-1000268 (Continued on next page) ll Cell 187, 1–19.e1–e13, May 9, 2024 e2 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Human Tau (Total) ELISA Kit Thermo Fisher Scientific Cat#KHB0042 NucleoBond Xtra Maxi EF Kit Macherey-Nagel Cat#740424.5 Laminin coated coverslips Neuvitro Corporation Cat#GG-12-15-Laminin ToxinSensor Chromogenic LAL Endotoxin Assay Kit GenScript Cat#L00350C VECTASHIELD Antifade Mounting Medium without DAPI Vector Laboratories Cat#H-1000-10 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories Cat#H-1200-10 NucleoSpin Blood L kit Macherey Nagel Cat#740954.20 MOM Immunodetection Kit Vector Laboratories CatBMK-2202 Deposited data Raw bulk RNA-seq data This paper GEO: GSE255902 Raw single-cell RNA-seq data This paper GEO: GSE255904 Experimental models: Cell lines Human: HEK293T line ATCC Cat#CRL-11268 Human: i3N iPSC line Wang et al.15 N/A Experimental models: Organisms/strains Mouse: Human Tau P301S (PS19) transgenic mice Jackson Laboratory Cat#008169 Oligonucleotides Primers for sequencing; see Table S1 This paper N/A Primers for qPCR; see Table S6 This paper N/A Recombinant DNA pCDH-EF1-FLPe Kazuhiro Oka Addgene #72262 psPAX Didier Trono Addgene #12260 pMD2.G Didier Trono Addgene #12259 pMDLg/pRRE Didier Trono Addgene #12251 pRSV-REV Didier Trono Addgene #12253 pC13N-CLYBL-CAG-dCas9-BFP-KRAB Martin Kampmann Addgene #127968 pMK1334 Martin Kampmann Addgene #127965 pFUGW-hSyn-jGCaMP8f This paper N/A PFUGW-hSyn-hM4D(Gi)-mCherry This paper N/A pFUGW-eGFP Manu Sharma Gift pFUGW-GFP-VAMP72-120 (VAMPDN) Manu Sharma Gift Software and algorithms R 4.2.2 The R project https://www.r-project.org/ RStudio 2022.07.2 RStudio: Integrated Development for R. RStudio https://rstudio.com Gene set enrichment analysis (GSEA) Subramanian et al.70 https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp ClueGO Bindea et al.71; Shannon et al.72 https://apps.cytoscape.org/apps/cluego Adobe Illustrator Illustrator v26.5.2 https://www.adobe.com/products/ illustrator.html GraphPad Prism 6 Prism v9.2 https://www.graphpad.com FlowJo FlowJo v10 https://www.flowjo.com/ Cell Ranger- 6.1.2 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/what-is-cell-ranger (Continued on next page) ll e3 Cell 187, 1–19.e1–e13, May 9, 2024 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER NIS Elements AR 5.21.03 64-bit Nikon Instruments Inc. https://www.microscope.healthcare.nikon. com/products/software/nis-elements Bowtie- 0.12.9 Langmead et al.73 https://bowtie-bio.sourceforge.net/ index.shtml MAGeCK-iNC Tian et al.11 https://kampmannlab.ucsf.edu/ mageck-inc MATLAB MATLAB R2022a https://www.mathworks.com/products/ matlab.html Seurat Seurat v4.0 https://satijalab.org/seurat/ Fiji/ImageJ Fiji v2.8 RRID: SCR_002285 MetaXpress MetaXpress 6.7.2.290 RRID: SCR_016654 Custom code used for bulk RNA-seq, scRNA-seq, and calcium imaging data analysis https://github.com/lifan36/ Parra-Bravo-4R-P301S-2024 N/A CRISPRbrain Tian et al.36 https://www.crisprbrain.org/ ll Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015
Endotoxin Assay:Article Title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation.
Article Snippet: HiFi Cas9 Nuclease V3 Integrated DNA Technologies Cat#1081060 Papain, Lyophilized Worthington Biochemical Cat#LS003118 DNase I Worthington Biochemical Cat#LS006333 TransIT-Lenti Transfection Reagent Mirus Bio Cat#MIR6600 Lipofectamine 3000 Thermo Fisher Scientific Cat#L3000015 Lenti-X Concentrator Takara Bio Cat#631232 Lentivirus Precipitation Solution Alstem Cat#VC125 Puromycin Thermo Fisher Scientific Cat#A1113803 Bovine Serum Albumin (BSA) Sigma Aldrich Cat#A7906 Janelia Fluor 549 analog JFX-549 HHMI Janelia Gift Clozapine N-oxide Tocris Cat#4936 NucRed Live 647 ReadyProbes Reagent Thermo Fisher Scientific Cat#R37106 iScript Reverse Transcription Supermix Bio-Rad Cat#1708840 Real-time PCR was performed using SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725270 FD Storage solution FD Neurotechnologies, Inc. Cat#PC101 Reveal Decloaker Biocare Medical Cat#RV1000M Hoescht 33342 Thermo Fisher Scientific Cat#62249 Critical commercial assays P3 Primary Cell 4D-Nucleofector X Kit S Lonza Cat#V4XP-303 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 QuickRNA MicroPrep Kit Zymo Research Cat#R1051 Illumina Stranded mRNA Prep Illumina Cat#20040532 Chromium Single Cell 30 Reagent Kits v3.1 10x Genomics Cat#PN-1000268 (Continued on next page) ll Cell 187, 1–19.e1–e13, May 9, 2024 e2 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Human Tau (Total) ELISA Kit Thermo Fisher Scientific Cat#KHB0042 NucleoBond Xtra Maxi EF Kit Macherey-Nagel Cat#740424.5 Laminin coated coverslips Neuvitro Corporation Cat#GG-12-15-Laminin ToxinSensor Chromogenic LAL Endotoxin Assay Kit GenScript Cat#L00350C VECTASHIELD Antifade Mounting Medium without DAPI Vector Laboratories Cat#H-1000-10 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories Cat#H-1200-10 NucleoSpin Blood L kit Macherey Nagel Cat#740954.20 MOM Immunodetection Kit Vector Laboratories CatBMK-2202 Deposited data Raw bulk RNA-seq data This paper GEO: GSE255902 Raw single-cell RNA-seq data This paper GEO: GSE255904 Experimental models: Cell lines Human: HEK293T line ATCC Cat#CRL-11268 Human: i3N iPSC line Wang et al.15 N/A Experimental models: Organisms/strains Mouse: Human Tau P301S (PS19) transgenic mice Jackson Laboratory Cat#008169 Oligonucleotides Primers for sequencing; see Table S1 This paper N/A Primers for qPCR; see Table S6 This paper N/A Recombinant DNA pCDH-EF1-FLPe Kazuhiro Oka Addgene #72262 psPAX Didier Trono Addgene #12260 pMD2.G Didier Trono Addgene #12259 pMDLg/pRRE Didier Trono Addgene #12251 pRSV-REV Didier Trono Addgene #12253 pC13N-CLYBL-CAG-dCas9-BFP-KRAB Martin Kampmann Addgene #127968 pMK1334 Martin Kampmann Addgene #127965 pFUGW-hSyn-jGCaMP8f This paper N/A PFUGW-hSyn-hM4D(Gi)-mCherry This paper N/A pFUGW-eGFP Manu Sharma Gift pFUGW-GFP-VAMP72-120 (VAMPDN) Manu Sharma Gift Software and algorithms R 4.2.2 The R project https://www.r-project.org/ RStudio 2022.07.2 RStudio: Integrated Development for R. RStudio https://rstudio.com Gene set enrichment analysis (GSEA) Subramanian et al.70 https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp ClueGO Bindea et al.71; Shannon et al.72 https://apps.cytoscape.org/apps/cluego Adobe Illustrator Illustrator v26.5.2 https://www.adobe.com/products/ illustrator.html GraphPad Prism 6 Prism v9.2 https://www.graphpad.com FlowJo FlowJo v10 https://www.flowjo.com/ Cell Ranger- 6.1.2 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/what-is-cell-ranger (Continued on next page) ll e3 Cell 187, 1–19.e1–e13, May 9, 2024 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER NIS Elements AR 5.21.03 64-bit Nikon Instruments Inc. https://www.microscope.healthcare.nikon. com/products/software/nis-elements Bowtie- 0.12.9 Langmead et al.73 https://bowtie-bio.sourceforge.net/ index.shtml MAGeCK-iNC Tian et al.11 https://kampmannlab.ucsf.edu/ mageck-inc MATLAB MATLAB R2022a https://www.mathworks.com/products/ matlab.html Seurat Seurat v4.0 https://satijalab.org/seurat/ Fiji/ImageJ Fiji v2.8 RRID: SCR_002285 MetaXpress MetaXpress 6.7.2.290 RRID: SCR_016654 Custom code used for bulk RNA-seq, scRNA-seq, and calcium imaging data analysis https://github.com/lifan36/ Parra-Bravo-4R-P301S-2024 N/A CRISPRbrain Tian et al.36 https://www.crisprbrain.org/ ll Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015
Immunodetection:Article Title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation.
Article Snippet: HiFi Cas9 Nuclease V3 Integrated DNA Technologies Cat#1081060 Papain, Lyophilized Worthington Biochemical Cat#LS003118 DNase I Worthington Biochemical Cat#LS006333 TransIT-Lenti Transfection Reagent Mirus Bio Cat#MIR6600 Lipofectamine 3000 Thermo Fisher Scientific Cat#L3000015 Lenti-X Concentrator Takara Bio Cat#631232 Lentivirus Precipitation Solution Alstem Cat#VC125 Puromycin Thermo Fisher Scientific Cat#A1113803 Bovine Serum Albumin (BSA) Sigma Aldrich Cat#A7906 Janelia Fluor 549 analog JFX-549 HHMI Janelia Gift Clozapine N-oxide Tocris Cat#4936 NucRed Live 647 ReadyProbes Reagent Thermo Fisher Scientific Cat#R37106 iScript Reverse Transcription Supermix Bio-Rad Cat#1708840 Real-time PCR was performed using SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725270 FD Storage solution FD Neurotechnologies, Inc. Cat#PC101 Reveal Decloaker Biocare Medical Cat#RV1000M Hoescht 33342 Thermo Fisher Scientific Cat#62249 Critical commercial assays P3 Primary Cell 4D-Nucleofector X Kit S Lonza Cat#V4XP-303 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 QuickRNA MicroPrep Kit Zymo Research Cat#R1051 Illumina Stranded mRNA Prep Illumina Cat#20040532 Chromium Single Cell 30 Reagent Kits v3.1 10x Genomics Cat#PN-1000268 (Continued on next page) ll Cell 187, 1–19.e1–e13, May 9, 2024 e2 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Human Tau (Total) ELISA Kit Thermo Fisher Scientific Cat#KHB0042 NucleoBond Xtra Maxi EF Kit Macherey-Nagel Cat#740424.5 Laminin coated coverslips Neuvitro Corporation Cat#GG-12-15-Laminin ToxinSensor Chromogenic LAL Endotoxin Assay Kit GenScript Cat#L00350C VECTASHIELD Antifade Mounting Medium without DAPI Vector Laboratories Cat#H-1000-10 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories Cat#H-1200-10 NucleoSpin Blood L kit Macherey Nagel Cat#740954.20 MOM Immunodetection Kit Vector Laboratories CatBMK-2202 Deposited data Raw bulk RNA-seq data This paper GEO: GSE255902 Raw single-cell RNA-seq data This paper GEO: GSE255904 Experimental models: Cell lines Human: HEK293T line ATCC Cat#CRL-11268 Human: i3N iPSC line Wang et al.15 N/A Experimental models: Organisms/strains Mouse: Human Tau P301S (PS19) transgenic mice Jackson Laboratory Cat#008169 Oligonucleotides Primers for sequencing; see Table S1 This paper N/A Primers for qPCR; see Table S6 This paper N/A Recombinant DNA pCDH-EF1-FLPe Kazuhiro Oka Addgene #72262 psPAX Didier Trono Addgene #12260 pMD2.G Didier Trono Addgene #12259 pMDLg/pRRE Didier Trono Addgene #12251 pRSV-REV Didier Trono Addgene #12253 pC13N-CLYBL-CAG-dCas9-BFP-KRAB Martin Kampmann Addgene #127968 pMK1334 Martin Kampmann Addgene #127965 pFUGW-hSyn-jGCaMP8f This paper N/A PFUGW-hSyn-hM4D(Gi)-mCherry This paper N/A pFUGW-eGFP Manu Sharma Gift pFUGW-GFP-VAMP72-120 (VAMPDN) Manu Sharma Gift Software and algorithms R 4.2.2 The R project https://www.r-project.org/ RStudio 2022.07.2 RStudio: Integrated Development for R. RStudio https://rstudio.com Gene set enrichment analysis (GSEA) Subramanian et al.70 https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp ClueGO Bindea et al.71; Shannon et al.72 https://apps.cytoscape.org/apps/cluego Adobe Illustrator Illustrator v26.5.2 https://www.adobe.com/products/ illustrator.html GraphPad Prism 6 Prism v9.2 https://www.graphpad.com FlowJo FlowJo v10 https://www.flowjo.com/ Cell Ranger- 6.1.2 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/what-is-cell-ranger (Continued on next page) ll e3 Cell 187, 1–19.e1–e13, May 9, 2024 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER NIS Elements AR 5.21.03 64-bit Nikon Instruments Inc. https://www.microscope.healthcare.nikon. com/products/software/nis-elements Bowtie- 0.12.9 Langmead et al.73 https://bowtie-bio.sourceforge.net/ index.shtml MAGeCK-iNC Tian et al.11 https://kampmannlab.ucsf.edu/ mageck-inc MATLAB MATLAB R2022a https://www.mathworks.com/products/ matlab.html Seurat Seurat v4.0 https://satijalab.org/seurat/ Fiji/ImageJ Fiji v2.8 RRID: SCR_002285 MetaXpress MetaXpress 6.7.2.290 RRID: SCR_016654 Custom code used for bulk RNA-seq, scRNA-seq, and calcium imaging data analysis https://github.com/lifan36/ Parra-Bravo-4R-P301S-2024 N/A CRISPRbrain Tian et al.36 https://www.crisprbrain.org/ ll Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015
RNA Sequencing:Article Title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation.
Article Snippet: HiFi Cas9 Nuclease V3 Integrated DNA Technologies Cat#1081060 Papain, Lyophilized Worthington Biochemical Cat#LS003118 DNase I Worthington Biochemical Cat#LS006333 TransIT-Lenti Transfection Reagent Mirus Bio Cat#MIR6600 Lipofectamine 3000 Thermo Fisher Scientific Cat#L3000015 Lenti-X Concentrator Takara Bio Cat#631232 Lentivirus Precipitation Solution Alstem Cat#VC125 Puromycin Thermo Fisher Scientific Cat#A1113803 Bovine Serum Albumin (BSA) Sigma Aldrich Cat#A7906 Janelia Fluor 549 analog JFX-549 HHMI Janelia Gift Clozapine N-oxide Tocris Cat#4936 NucRed Live 647 ReadyProbes Reagent Thermo Fisher Scientific Cat#R37106 iScript Reverse Transcription Supermix Bio-Rad Cat#1708840 Real-time PCR was performed using SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725270 FD Storage solution FD Neurotechnologies, Inc. Cat#PC101 Reveal Decloaker Biocare Medical Cat#RV1000M Hoescht 33342 Thermo Fisher Scientific Cat#62249 Critical commercial assays P3 Primary Cell 4D-Nucleofector X Kit S Lonza Cat#V4XP-303 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 QuickRNA MicroPrep Kit Zymo Research Cat#R1051 Illumina Stranded mRNA Prep Illumina Cat#20040532 Chromium Single Cell 30 Reagent Kits v3.1 10x Genomics Cat#PN-1000268 (Continued on next page) ll Cell 187, 1–19.e1–e13, May 9, 2024 e2 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Human Tau (Total) ELISA Kit Thermo Fisher Scientific Cat#KHB0042 NucleoBond Xtra Maxi EF Kit Macherey-Nagel Cat#740424.5 Laminin coated coverslips Neuvitro Corporation Cat#GG-12-15-Laminin ToxinSensor Chromogenic LAL Endotoxin Assay Kit GenScript Cat#L00350C VECTASHIELD Antifade Mounting Medium without DAPI Vector Laboratories Cat#H-1000-10 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories Cat#H-1200-10 NucleoSpin Blood L kit Macherey Nagel Cat#740954.20 MOM Immunodetection Kit Vector Laboratories CatBMK-2202 Deposited data Raw bulk RNA-seq data This paper GEO: GSE255902 Raw single-cell RNA-seq data This paper GEO: GSE255904 Experimental models: Cell lines Human: HEK293T line ATCC Cat#CRL-11268 Human: i3N iPSC line Wang et al.15 N/A Experimental models: Organisms/strains Mouse: Human Tau P301S (PS19) transgenic mice Jackson Laboratory Cat#008169 Oligonucleotides Primers for sequencing; see Table S1 This paper N/A Primers for qPCR; see Table S6 This paper N/A Recombinant DNA pCDH-EF1-FLPe Kazuhiro Oka Addgene #72262 psPAX Didier Trono Addgene #12260 pMD2.G Didier Trono Addgene #12259 pMDLg/pRRE Didier Trono Addgene #12251 pRSV-REV Didier Trono Addgene #12253 pC13N-CLYBL-CAG-dCas9-BFP-KRAB Martin Kampmann Addgene #127968 pMK1334 Martin Kampmann Addgene #127965 pFUGW-hSyn-jGCaMP8f This paper N/A PFUGW-hSyn-hM4D(Gi)-mCherry This paper N/A pFUGW-eGFP Manu Sharma Gift pFUGW-GFP-VAMP72-120 (VAMPDN) Manu Sharma Gift Software and algorithms R 4.2.2 The R project https://www.r-project.org/ RStudio 2022.07.2 RStudio: Integrated Development for R. RStudio https://rstudio.com Gene set enrichment analysis (GSEA) Subramanian et al.70 https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp ClueGO Bindea et al.71; Shannon et al.72 https://apps.cytoscape.org/apps/cluego Adobe Illustrator Illustrator v26.5.2 https://www.adobe.com/products/ illustrator.html GraphPad Prism 6 Prism v9.2 https://www.graphpad.com FlowJo FlowJo v10 https://www.flowjo.com/ Cell Ranger- 6.1.2 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/what-is-cell-ranger (Continued on next page) ll e3 Cell 187, 1–19.e1–e13, May 9, 2024 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER NIS Elements AR 5.21.03 64-bit Nikon Instruments Inc. https://www.microscope.healthcare.nikon. com/products/software/nis-elements Bowtie- 0.12.9 Langmead et al.73 https://bowtie-bio.sourceforge.net/ index.shtml MAGeCK-iNC Tian et al.11 https://kampmannlab.ucsf.edu/ mageck-inc MATLAB MATLAB R2022a https://www.mathworks.com/products/ matlab.html Seurat Seurat v4.0 https://satijalab.org/seurat/ Fiji/ImageJ Fiji v2.8 RRID: SCR_002285 MetaXpress MetaXpress 6.7.2.290 RRID: SCR_016654 Custom code used for bulk RNA-seq, scRNA-seq, and calcium imaging data analysis https://github.com/lifan36/ Parra-Bravo-4R-P301S-2024 N/A CRISPRbrain Tian et al.36 https://www.crisprbrain.org/ ll Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015
Single Cell:Article Title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation.
Article Snippet: HiFi Cas9 Nuclease V3 Integrated DNA Technologies Cat#1081060 Papain, Lyophilized Worthington Biochemical Cat#LS003118 DNase I Worthington Biochemical Cat#LS006333 TransIT-Lenti Transfection Reagent Mirus Bio Cat#MIR6600 Lipofectamine 3000 Thermo Fisher Scientific Cat#L3000015 Lenti-X Concentrator Takara Bio Cat#631232 Lentivirus Precipitation Solution Alstem Cat#VC125 Puromycin Thermo Fisher Scientific Cat#A1113803 Bovine Serum Albumin (BSA) Sigma Aldrich Cat#A7906 Janelia Fluor 549 analog JFX-549 HHMI Janelia Gift Clozapine N-oxide Tocris Cat#4936 NucRed Live 647 ReadyProbes Reagent Thermo Fisher Scientific Cat#R37106 iScript Reverse Transcription Supermix Bio-Rad Cat#1708840 Real-time PCR was performed using SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725270 FD Storage solution FD Neurotechnologies, Inc. Cat#PC101 Reveal Decloaker Biocare Medical Cat#RV1000M Hoescht 33342 Thermo Fisher Scientific Cat#62249 Critical commercial assays P3 Primary Cell 4D-Nucleofector X Kit S Lonza Cat#V4XP-303 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 QuickRNA MicroPrep Kit Zymo Research Cat#R1051 Illumina Stranded mRNA Prep Illumina Cat#20040532 Chromium Single Cell 30 Reagent Kits v3.1 10x Genomics Cat#PN-1000268 (Continued on next page) ll Cell 187, 1–19.e1–e13, May 9, 2024 e2 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Human Tau (Total) ELISA Kit Thermo Fisher Scientific Cat#KHB0042 NucleoBond Xtra Maxi EF Kit Macherey-Nagel Cat#740424.5 Laminin coated coverslips Neuvitro Corporation Cat#GG-12-15-Laminin ToxinSensor Chromogenic LAL Endotoxin Assay Kit GenScript Cat#L00350C VECTASHIELD Antifade Mounting Medium without DAPI Vector Laboratories Cat#H-1000-10 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories Cat#H-1200-10 NucleoSpin Blood L kit Macherey Nagel Cat#740954.20 MOM Immunodetection Kit Vector Laboratories CatBMK-2202 Deposited data Raw bulk RNA-seq data This paper GEO: GSE255902 Raw single-cell RNA-seq data This paper GEO: GSE255904 Experimental models: Cell lines Human: HEK293T line ATCC Cat#CRL-11268 Human: i3N iPSC line Wang et al.15 N/A Experimental models: Organisms/strains Mouse: Human Tau P301S (PS19) transgenic mice Jackson Laboratory Cat#008169 Oligonucleotides Primers for sequencing; see Table S1 This paper N/A Primers for qPCR; see Table S6 This paper N/A Recombinant DNA pCDH-EF1-FLPe Kazuhiro Oka Addgene #72262 psPAX Didier Trono Addgene #12260 pMD2.G Didier Trono Addgene #12259 pMDLg/pRRE Didier Trono Addgene #12251 pRSV-REV Didier Trono Addgene #12253 pC13N-CLYBL-CAG-dCas9-BFP-KRAB Martin Kampmann Addgene #127968 pMK1334 Martin Kampmann Addgene #127965 pFUGW-hSyn-jGCaMP8f This paper N/A PFUGW-hSyn-hM4D(Gi)-mCherry This paper N/A pFUGW-eGFP Manu Sharma Gift pFUGW-GFP-VAMP72-120 (VAMPDN) Manu Sharma Gift Software and algorithms R 4.2.2 The R project https://www.r-project.org/ RStudio 2022.07.2 RStudio: Integrated Development for R. RStudio https://rstudio.com Gene set enrichment analysis (GSEA) Subramanian et al.70 https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp ClueGO Bindea et al.71; Shannon et al.72 https://apps.cytoscape.org/apps/cluego Adobe Illustrator Illustrator v26.5.2 https://www.adobe.com/products/ illustrator.html GraphPad Prism 6 Prism v9.2 https://www.graphpad.com FlowJo FlowJo v10 https://www.flowjo.com/ Cell Ranger- 6.1.2 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/what-is-cell-ranger (Continued on next page) ll e3 Cell 187, 1–19.e1–e13, May 9, 2024 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER NIS Elements AR 5.21.03 64-bit Nikon Instruments Inc. https://www.microscope.healthcare.nikon. com/products/software/nis-elements Bowtie- 0.12.9 Langmead et al.73 https://bowtie-bio.sourceforge.net/ index.shtml MAGeCK-iNC Tian et al.11 https://kampmannlab.ucsf.edu/ mageck-inc MATLAB MATLAB R2022a https://www.mathworks.com/products/ matlab.html Seurat Seurat v4.0 https://satijalab.org/seurat/ Fiji/ImageJ Fiji v2.8 RRID: SCR_002285 MetaXpress MetaXpress 6.7.2.290 RRID: SCR_016654 Custom code used for bulk RNA-seq, scRNA-seq, and calcium imaging data analysis https://github.com/lifan36/ Parra-Bravo-4R-P301S-2024 N/A CRISPRbrain Tian et al.36 https://www.crisprbrain.org/ ll Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015
Transgenic Assay:Article Title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation.
Article Snippet: HiFi Cas9 Nuclease V3 Integrated DNA Technologies Cat#1081060 Papain, Lyophilized Worthington Biochemical Cat#LS003118 DNase I Worthington Biochemical Cat#LS006333 TransIT-Lenti Transfection Reagent Mirus Bio Cat#MIR6600 Lipofectamine 3000 Thermo Fisher Scientific Cat#L3000015 Lenti-X Concentrator Takara Bio Cat#631232 Lentivirus Precipitation Solution Alstem Cat#VC125 Puromycin Thermo Fisher Scientific Cat#A1113803 Bovine Serum Albumin (BSA) Sigma Aldrich Cat#A7906 Janelia Fluor 549 analog JFX-549 HHMI Janelia Gift Clozapine N-oxide Tocris Cat#4936 NucRed Live 647 ReadyProbes Reagent Thermo Fisher Scientific Cat#R37106 iScript Reverse Transcription Supermix Bio-Rad Cat#1708840 Real-time PCR was performed using SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725270 FD Storage solution FD Neurotechnologies, Inc. Cat#PC101 Reveal Decloaker Biocare Medical Cat#RV1000M Hoescht 33342 Thermo Fisher Scientific Cat#62249 Critical commercial assays P3 Primary Cell 4D-Nucleofector X Kit S Lonza Cat#V4XP-303 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 QuickRNA MicroPrep Kit Zymo Research Cat#R1051 Illumina Stranded mRNA Prep Illumina Cat#20040532 Chromium Single Cell 30 Reagent Kits v3.1 10x Genomics Cat#PN-1000268 (Continued on next page) ll Cell 187, 1–19.e1–e13, May 9, 2024 e2 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Human Tau (Total) ELISA Kit Thermo Fisher Scientific Cat#KHB0042 NucleoBond Xtra Maxi EF Kit Macherey-Nagel Cat#740424.5 Laminin coated coverslips Neuvitro Corporation Cat#GG-12-15-Laminin ToxinSensor Chromogenic LAL Endotoxin Assay Kit GenScript Cat#L00350C VECTASHIELD Antifade Mounting Medium without DAPI Vector Laboratories Cat#H-1000-10 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories Cat#H-1200-10 NucleoSpin Blood L kit Macherey Nagel Cat#740954.20 MOM Immunodetection Kit Vector Laboratories CatBMK-2202 Deposited data Raw bulk RNA-seq data This paper GEO: GSE255902 Raw single-cell RNA-seq data This paper GEO: GSE255904 Experimental models: Cell lines Human: HEK293T line ATCC Cat#CRL-11268 Human: i3N iPSC line Wang et al.15 N/A Experimental models: Organisms/strains Mouse: Human Tau P301S (PS19) transgenic mice Jackson Laboratory Cat#008169 Oligonucleotides Primers for sequencing; see Table S1 This paper N/A Primers for qPCR; see Table S6 This paper N/A Recombinant DNA pCDH-EF1-FLPe Kazuhiro Oka Addgene #72262 psPAX Didier Trono Addgene #12260 pMD2.G Didier Trono Addgene #12259 pMDLg/pRRE Didier Trono Addgene #12251 pRSV-REV Didier Trono Addgene #12253 pC13N-CLYBL-CAG-dCas9-BFP-KRAB Martin Kampmann Addgene #127968 pMK1334 Martin Kampmann Addgene #127965 pFUGW-hSyn-jGCaMP8f This paper N/A PFUGW-hSyn-hM4D(Gi)-mCherry This paper N/A pFUGW-eGFP Manu Sharma Gift pFUGW-GFP-VAMP72-120 (VAMPDN) Manu Sharma Gift Software and algorithms R 4.2.2 The R project https://www.r-project.org/ RStudio 2022.07.2 RStudio: Integrated Development for R. RStudio https://rstudio.com Gene set enrichment analysis (GSEA) Subramanian et al.70 https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp ClueGO Bindea et al.71; Shannon et al.72 https://apps.cytoscape.org/apps/cluego Adobe Illustrator Illustrator v26.5.2 https://www.adobe.com/products/ illustrator.html GraphPad Prism 6 Prism v9.2 https://www.graphpad.com FlowJo FlowJo v10 https://www.flowjo.com/ Cell Ranger- 6.1.2 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/what-is-cell-ranger (Continued on next page) ll e3 Cell 187, 1–19.e1–e13, May 9, 2024 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER NIS Elements AR 5.21.03 64-bit Nikon Instruments Inc. https://www.microscope.healthcare.nikon. com/products/software/nis-elements Bowtie- 0.12.9 Langmead et al.73 https://bowtie-bio.sourceforge.net/ index.shtml MAGeCK-iNC Tian et al.11 https://kampmannlab.ucsf.edu/ mageck-inc MATLAB MATLAB R2022a https://www.mathworks.com/products/ matlab.html Seurat Seurat v4.0 https://satijalab.org/seurat/ Fiji/ImageJ Fiji v2.8 RRID: SCR_002285 MetaXpress MetaXpress 6.7.2.290 RRID: SCR_016654 Custom code used for bulk RNA-seq, scRNA-seq, and calcium imaging data analysis https://github.com/lifan36/ Parra-Bravo-4R-P301S-2024 N/A CRISPRbrain Tian et al.36 https://www.crisprbrain.org/ ll Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015
Sequencing:Article Title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation.
Article Snippet: HiFi Cas9 Nuclease V3 Integrated DNA Technologies Cat#1081060 Papain, Lyophilized Worthington Biochemical Cat#LS003118 DNase I Worthington Biochemical Cat#LS006333 TransIT-Lenti Transfection Reagent Mirus Bio Cat#MIR6600 Lipofectamine 3000 Thermo Fisher Scientific Cat#L3000015 Lenti-X Concentrator Takara Bio Cat#631232 Lentivirus Precipitation Solution Alstem Cat#VC125 Puromycin Thermo Fisher Scientific Cat#A1113803 Bovine Serum Albumin (BSA) Sigma Aldrich Cat#A7906 Janelia Fluor 549 analog JFX-549 HHMI Janelia Gift Clozapine N-oxide Tocris Cat#4936 NucRed Live 647 ReadyProbes Reagent Thermo Fisher Scientific Cat#R37106 iScript Reverse Transcription Supermix Bio-Rad Cat#1708840 Real-time PCR was performed using SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725270 FD Storage solution FD Neurotechnologies, Inc. Cat#PC101 Reveal Decloaker Biocare Medical Cat#RV1000M Hoescht 33342 Thermo Fisher Scientific Cat#62249 Critical commercial assays P3 Primary Cell 4D-Nucleofector X Kit S Lonza Cat#V4XP-303 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 QuickRNA MicroPrep Kit Zymo Research Cat#R1051 Illumina Stranded mRNA Prep Illumina Cat#20040532 Chromium Single Cell 30 Reagent Kits v3.1 10x Genomics Cat#PN-1000268 (Continued on next page) ll Cell 187, 1–19.e1–e13, May 9, 2024 e2 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Human Tau (Total) ELISA Kit Thermo Fisher Scientific Cat#KHB0042 NucleoBond Xtra Maxi EF Kit Macherey-Nagel Cat#740424.5 Laminin coated coverslips Neuvitro Corporation Cat#GG-12-15-Laminin ToxinSensor Chromogenic LAL Endotoxin Assay Kit GenScript Cat#L00350C VECTASHIELD Antifade Mounting Medium without DAPI Vector Laboratories Cat#H-1000-10 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories Cat#H-1200-10 NucleoSpin Blood L kit Macherey Nagel Cat#740954.20 MOM Immunodetection Kit Vector Laboratories CatBMK-2202 Deposited data Raw bulk RNA-seq data This paper GEO: GSE255902 Raw single-cell RNA-seq data This paper GEO: GSE255904 Experimental models: Cell lines Human: HEK293T line ATCC Cat#CRL-11268 Human: i3N iPSC line Wang et al.15 N/A Experimental models: Organisms/strains Mouse: Human Tau P301S (PS19) transgenic mice Jackson Laboratory Cat#008169 Oligonucleotides Primers for sequencing; see Table S1 This paper N/A Primers for qPCR; see Table S6 This paper N/A Recombinant DNA pCDH-EF1-FLPe Kazuhiro Oka Addgene #72262 psPAX Didier Trono Addgene #12260 pMD2.G Didier Trono Addgene #12259 pMDLg/pRRE Didier Trono Addgene #12251 pRSV-REV Didier Trono Addgene #12253 pC13N-CLYBL-CAG-dCas9-BFP-KRAB Martin Kampmann Addgene #127968 pMK1334 Martin Kampmann Addgene #127965 pFUGW-hSyn-jGCaMP8f This paper N/A PFUGW-hSyn-hM4D(Gi)-mCherry This paper N/A pFUGW-eGFP Manu Sharma Gift pFUGW-GFP-VAMP72-120 (VAMPDN) Manu Sharma Gift Software and algorithms R 4.2.2 The R project https://www.r-project.org/ RStudio 2022.07.2 RStudio: Integrated Development for R. RStudio https://rstudio.com Gene set enrichment analysis (GSEA) Subramanian et al.70 https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp ClueGO Bindea et al.71; Shannon et al.72 https://apps.cytoscape.org/apps/cluego Adobe Illustrator Illustrator v26.5.2 https://www.adobe.com/products/ illustrator.html GraphPad Prism 6 Prism v9.2 https://www.graphpad.com FlowJo FlowJo v10 https://www.flowjo.com/ Cell Ranger- 6.1.2 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/what-is-cell-ranger (Continued on next page) ll e3 Cell 187, 1–19.e1–e13, May 9, 2024 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER NIS Elements AR 5.21.03 64-bit Nikon Instruments Inc. https://www.microscope.healthcare.nikon. com/products/software/nis-elements Bowtie- 0.12.9 Langmead et al.73 https://bowtie-bio.sourceforge.net/ index.shtml MAGeCK-iNC Tian et al.11 https://kampmannlab.ucsf.edu/ mageck-inc MATLAB MATLAB R2022a https://www.mathworks.com/products/ matlab.html Seurat Seurat v4.0 https://satijalab.org/seurat/ Fiji/ImageJ Fiji v2.8 RRID: SCR_002285 MetaXpress MetaXpress 6.7.2.290 RRID: SCR_016654 Custom code used for bulk RNA-seq, scRNA-seq, and calcium imaging data analysis https://github.com/lifan36/ Parra-Bravo-4R-P301S-2024 N/A CRISPRbrain Tian et al.36 https://www.crisprbrain.org/ ll Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015
Real-time Polymerase Chain Reaction:Article Title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation.
Article Snippet: HiFi Cas9 Nuclease V3 Integrated DNA Technologies Cat#1081060 Papain, Lyophilized Worthington Biochemical Cat#LS003118 DNase I Worthington Biochemical Cat#LS006333 TransIT-Lenti Transfection Reagent Mirus Bio Cat#MIR6600 Lipofectamine 3000 Thermo Fisher Scientific Cat#L3000015 Lenti-X Concentrator Takara Bio Cat#631232 Lentivirus Precipitation Solution Alstem Cat#VC125 Puromycin Thermo Fisher Scientific Cat#A1113803 Bovine Serum Albumin (BSA) Sigma Aldrich Cat#A7906 Janelia Fluor 549 analog JFX-549 HHMI Janelia Gift Clozapine N-oxide Tocris Cat#4936 NucRed Live 647 ReadyProbes Reagent Thermo Fisher Scientific Cat#R37106 iScript Reverse Transcription Supermix Bio-Rad Cat#1708840 Real-time PCR was performed using SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725270 FD Storage solution FD Neurotechnologies, Inc. Cat#PC101 Reveal Decloaker Biocare Medical Cat#RV1000M Hoescht 33342 Thermo Fisher Scientific Cat#62249 Critical commercial assays P3 Primary Cell 4D-Nucleofector X Kit S Lonza Cat#V4XP-303 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 QuickRNA MicroPrep Kit Zymo Research Cat#R1051 Illumina Stranded mRNA Prep Illumina Cat#20040532 Chromium Single Cell 30 Reagent Kits v3.1 10x Genomics Cat#PN-1000268 (Continued on next page) ll Cell 187, 1–19.e1–e13, May 9, 2024 e2 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Human Tau (Total) ELISA Kit Thermo Fisher Scientific Cat#KHB0042 NucleoBond Xtra Maxi EF Kit Macherey-Nagel Cat#740424.5 Laminin coated coverslips Neuvitro Corporation Cat#GG-12-15-Laminin ToxinSensor Chromogenic LAL Endotoxin Assay Kit GenScript Cat#L00350C VECTASHIELD Antifade Mounting Medium without DAPI Vector Laboratories Cat#H-1000-10 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories Cat#H-1200-10 NucleoSpin Blood L kit Macherey Nagel Cat#740954.20 MOM Immunodetection Kit Vector Laboratories CatBMK-2202 Deposited data Raw bulk RNA-seq data This paper GEO: GSE255902 Raw single-cell RNA-seq data This paper GEO: GSE255904 Experimental models: Cell lines Human: HEK293T line ATCC Cat#CRL-11268 Human: i3N iPSC line Wang et al.15 N/A Experimental models: Organisms/strains Mouse: Human Tau P301S (PS19) transgenic mice Jackson Laboratory Cat#008169 Oligonucleotides Primers for sequencing; see Table S1 This paper N/A Primers for qPCR; see Table S6 This paper N/A Recombinant DNA pCDH-EF1-FLPe Kazuhiro Oka Addgene #72262 psPAX Didier Trono Addgene #12260 pMD2.G Didier Trono Addgene #12259 pMDLg/pRRE Didier Trono Addgene #12251 pRSV-REV Didier Trono Addgene #12253 pC13N-CLYBL-CAG-dCas9-BFP-KRAB Martin Kampmann Addgene #127968 pMK1334 Martin Kampmann Addgene #127965 pFUGW-hSyn-jGCaMP8f This paper N/A PFUGW-hSyn-hM4D(Gi)-mCherry This paper N/A pFUGW-eGFP Manu Sharma Gift pFUGW-GFP-VAMP72-120 (VAMPDN) Manu Sharma Gift Software and algorithms R 4.2.2 The R project https://www.r-project.org/ RStudio 2022.07.2 RStudio: Integrated Development for R. RStudio https://rstudio.com Gene set enrichment analysis (GSEA) Subramanian et al.70 https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp ClueGO Bindea et al.71; Shannon et al.72 https://apps.cytoscape.org/apps/cluego Adobe Illustrator Illustrator v26.5.2 https://www.adobe.com/products/ illustrator.html GraphPad Prism 6 Prism v9.2 https://www.graphpad.com FlowJo FlowJo v10 https://www.flowjo.com/ Cell Ranger- 6.1.2 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/what-is-cell-ranger (Continued on next page) ll e3 Cell 187, 1–19.e1–e13, May 9, 2024 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER NIS Elements AR 5.21.03 64-bit Nikon Instruments Inc. https://www.microscope.healthcare.nikon. com/products/software/nis-elements Bowtie- 0.12.9 Langmead et al.73 https://bowtie-bio.sourceforge.net/ index.shtml MAGeCK-iNC Tian et al.11 https://kampmannlab.ucsf.edu/ mageck-inc MATLAB MATLAB R2022a https://www.mathworks.com/products/ matlab.html Seurat Seurat v4.0 https://satijalab.org/seurat/ Fiji/ImageJ Fiji v2.8 RRID: SCR_002285 MetaXpress MetaXpress 6.7.2.290 RRID: SCR_016654 Custom code used for bulk RNA-seq, scRNA-seq, and calcium imaging data analysis https://github.com/lifan36/ Parra-Bravo-4R-P301S-2024 N/A CRISPRbrain Tian et al.36 https://www.crisprbrain.org/ ll Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015
Recombinant:Article Title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation.
Article Snippet: HiFi Cas9 Nuclease V3 Integrated DNA Technologies Cat#1081060 Papain, Lyophilized Worthington Biochemical Cat#LS003118 DNase I Worthington Biochemical Cat#LS006333 TransIT-Lenti Transfection Reagent Mirus Bio Cat#MIR6600 Lipofectamine 3000 Thermo Fisher Scientific Cat#L3000015 Lenti-X Concentrator Takara Bio Cat#631232 Lentivirus Precipitation Solution Alstem Cat#VC125 Puromycin Thermo Fisher Scientific Cat#A1113803 Bovine Serum Albumin (BSA) Sigma Aldrich Cat#A7906 Janelia Fluor 549 analog JFX-549 HHMI Janelia Gift Clozapine N-oxide Tocris Cat#4936 NucRed Live 647 ReadyProbes Reagent Thermo Fisher Scientific Cat#R37106 iScript Reverse Transcription Supermix Bio-Rad Cat#1708840 Real-time PCR was performed using SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725270 FD Storage solution FD Neurotechnologies, Inc. Cat#PC101 Reveal Decloaker Biocare Medical Cat#RV1000M Hoescht 33342 Thermo Fisher Scientific Cat#62249 Critical commercial assays P3 Primary Cell 4D-Nucleofector X Kit S Lonza Cat#V4XP-303 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 QuickRNA MicroPrep Kit Zymo Research Cat#R1051 Illumina Stranded mRNA Prep Illumina Cat#20040532 Chromium Single Cell 30 Reagent Kits v3.1 10x Genomics Cat#PN-1000268 (Continued on next page) ll Cell 187, 1–19.e1–e13, May 9, 2024 e2 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Human Tau (Total) ELISA Kit Thermo Fisher Scientific Cat#KHB0042 NucleoBond Xtra Maxi EF Kit Macherey-Nagel Cat#740424.5 Laminin coated coverslips Neuvitro Corporation Cat#GG-12-15-Laminin ToxinSensor Chromogenic LAL Endotoxin Assay Kit GenScript Cat#L00350C VECTASHIELD Antifade Mounting Medium without DAPI Vector Laboratories Cat#H-1000-10 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories Cat#H-1200-10 NucleoSpin Blood L kit Macherey Nagel Cat#740954.20 MOM Immunodetection Kit Vector Laboratories CatBMK-2202 Deposited data Raw bulk RNA-seq data This paper GEO: GSE255902 Raw single-cell RNA-seq data This paper GEO: GSE255904 Experimental models: Cell lines Human: HEK293T line ATCC Cat#CRL-11268 Human: i3N iPSC line Wang et al.15 N/A Experimental models: Organisms/strains Mouse: Human Tau P301S (PS19) transgenic mice Jackson Laboratory Cat#008169 Oligonucleotides Primers for sequencing; see Table S1 This paper N/A Primers for qPCR; see Table S6 This paper N/A Recombinant DNA pCDH-EF1-FLPe Kazuhiro Oka Addgene #72262 psPAX Didier Trono Addgene #12260 pMD2.G Didier Trono Addgene #12259 pMDLg/pRRE Didier Trono Addgene #12251 pRSV-REV Didier Trono Addgene #12253 pC13N-CLYBL-CAG-dCas9-BFP-KRAB Martin Kampmann Addgene #127968 pMK1334 Martin Kampmann Addgene #127965 pFUGW-hSyn-jGCaMP8f This paper N/A PFUGW-hSyn-hM4D(Gi)-mCherry This paper N/A pFUGW-eGFP Manu Sharma Gift pFUGW-GFP-VAMP72-120 (VAMPDN) Manu Sharma Gift Software and algorithms R 4.2.2 The R project https://www.r-project.org/ RStudio 2022.07.2 RStudio: Integrated Development for R. RStudio https://rstudio.com Gene set enrichment analysis (GSEA) Subramanian et al.70 https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp ClueGO Bindea et al.71; Shannon et al.72 https://apps.cytoscape.org/apps/cluego Adobe Illustrator Illustrator v26.5.2 https://www.adobe.com/products/ illustrator.html GraphPad Prism 6 Prism v9.2 https://www.graphpad.com FlowJo FlowJo v10 https://www.flowjo.com/ Cell Ranger- 6.1.2 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/what-is-cell-ranger (Continued on next page) ll e3 Cell 187, 1–19.e1–e13, May 9, 2024 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER NIS Elements AR 5.21.03 64-bit Nikon Instruments Inc. https://www.microscope.healthcare.nikon. com/products/software/nis-elements Bowtie- 0.12.9 Langmead et al.73 https://bowtie-bio.sourceforge.net/ index.shtml MAGeCK-iNC Tian et al.11 https://kampmannlab.ucsf.edu/ mageck-inc MATLAB MATLAB R2022a https://www.mathworks.com/products/ matlab.html Seurat Seurat v4.0 https://satijalab.org/seurat/ Fiji/ImageJ Fiji v2.8 RRID: SCR_002285 MetaXpress MetaXpress 6.7.2.290 RRID: SCR_016654 Custom code used for bulk RNA-seq, scRNA-seq, and calcium imaging data analysis https://github.com/lifan36/ Parra-Bravo-4R-P301S-2024 N/A CRISPRbrain Tian et al.36 https://www.crisprbrain.org/ ll Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015
Software:Article Title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation.
Article Snippet: HiFi Cas9 Nuclease V3 Integrated DNA Technologies Cat#1081060 Papain, Lyophilized Worthington Biochemical Cat#LS003118 DNase I Worthington Biochemical Cat#LS006333 TransIT-Lenti Transfection Reagent Mirus Bio Cat#MIR6600 Lipofectamine 3000 Thermo Fisher Scientific Cat#L3000015 Lenti-X Concentrator Takara Bio Cat#631232 Lentivirus Precipitation Solution Alstem Cat#VC125 Puromycin Thermo Fisher Scientific Cat#A1113803 Bovine Serum Albumin (BSA) Sigma Aldrich Cat#A7906 Janelia Fluor 549 analog JFX-549 HHMI Janelia Gift Clozapine N-oxide Tocris Cat#4936 NucRed Live 647 ReadyProbes Reagent Thermo Fisher Scientific Cat#R37106 iScript Reverse Transcription Supermix Bio-Rad Cat#1708840 Real-time PCR was performed using SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725270 FD Storage solution FD Neurotechnologies, Inc. Cat#PC101 Reveal Decloaker Biocare Medical Cat#RV1000M Hoescht 33342 Thermo Fisher Scientific Cat#62249 Critical commercial assays P3 Primary Cell 4D-Nucleofector X Kit S Lonza Cat#V4XP-303 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 QuickRNA MicroPrep Kit Zymo Research Cat#R1051 Illumina Stranded mRNA Prep Illumina Cat#20040532 Chromium Single Cell 30 Reagent Kits v3.1 10x Genomics Cat#PN-1000268 (Continued on next page) ll Cell 187, 1–19.e1–e13, May 9, 2024 e2 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Human Tau (Total) ELISA Kit Thermo Fisher Scientific Cat#KHB0042 NucleoBond Xtra Maxi EF Kit Macherey-Nagel Cat#740424.5 Laminin coated coverslips Neuvitro Corporation Cat#GG-12-15-Laminin ToxinSensor Chromogenic LAL Endotoxin Assay Kit GenScript Cat#L00350C VECTASHIELD Antifade Mounting Medium without DAPI Vector Laboratories Cat#H-1000-10 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories Cat#H-1200-10 NucleoSpin Blood L kit Macherey Nagel Cat#740954.20 MOM Immunodetection Kit Vector Laboratories CatBMK-2202 Deposited data Raw bulk RNA-seq data This paper GEO: GSE255902 Raw single-cell RNA-seq data This paper GEO: GSE255904 Experimental models: Cell lines Human: HEK293T line ATCC Cat#CRL-11268 Human: i3N iPSC line Wang et al.15 N/A Experimental models: Organisms/strains Mouse: Human Tau P301S (PS19) transgenic mice Jackson Laboratory Cat#008169 Oligonucleotides Primers for sequencing; see Table S1 This paper N/A Primers for qPCR; see Table S6 This paper N/A Recombinant DNA pCDH-EF1-FLPe Kazuhiro Oka Addgene #72262 psPAX Didier Trono Addgene #12260 pMD2.G Didier Trono Addgene #12259 pMDLg/pRRE Didier Trono Addgene #12251 pRSV-REV Didier Trono Addgene #12253 pC13N-CLYBL-CAG-dCas9-BFP-KRAB Martin Kampmann Addgene #127968 pMK1334 Martin Kampmann Addgene #127965 pFUGW-hSyn-jGCaMP8f This paper N/A PFUGW-hSyn-hM4D(Gi)-mCherry This paper N/A pFUGW-eGFP Manu Sharma Gift pFUGW-GFP-VAMP72-120 (VAMPDN) Manu Sharma Gift Software and algorithms R 4.2.2 The R project https://www.r-project.org/ RStudio 2022.07.2 RStudio: Integrated Development for R. RStudio https://rstudio.com Gene set enrichment analysis (GSEA) Subramanian et al.70 https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp ClueGO Bindea et al.71; Shannon et al.72 https://apps.cytoscape.org/apps/cluego Adobe Illustrator Illustrator v26.5.2 https://www.adobe.com/products/ illustrator.html GraphPad Prism 6 Prism v9.2 https://www.graphpad.com FlowJo FlowJo v10 https://www.flowjo.com/ Cell Ranger- 6.1.2 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ pipelines/latest/what-is-cell-ranger (Continued on next page) ll e3 Cell 187, 1–19.e1–e13, May 9, 2024 Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER NIS Elements AR 5.21.03 64-bit Nikon Instruments Inc. https://www.microscope.healthcare.nikon. com/products/software/nis-elements Bowtie- 0.12.9 Langmead et al.73 https://bowtie-bio.sourceforge.net/ index.shtml MAGeCK-iNC Tian et al.11 https://kampmannlab.ucsf.edu/ mageck-inc MATLAB MATLAB R2022a https://www.mathworks.com/products/ matlab.html Seurat Seurat v4.0 https://satijalab.org/seurat/ Fiji/ImageJ Fiji v2.8 RRID: SCR_002285 MetaXpress MetaXpress 6.7.2.290 RRID: SCR_016654 Custom code used for bulk RNA-seq, scRNA-seq, and calcium imaging data analysis https://github.com/lifan36/ Parra-Bravo-4R-P301S-2024 N/A CRISPRbrain Tian et al.36 https://www.crisprbrain.org/ ll Please cite this article in press as: Parra Bravo et al., Human iPSC 4R tauopathy model uncovers modifiers of tau propagation, Cell (2024), https://doi.org/10.1016/j.cell.2024.03.015
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