Recombinant:Article Title: Human cerebellar organoids with functional Purkinje cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-BARHL1 Atlas Antibodies Cat# HPA004809; RRID:AB_1078266 Rabbit polyclonal anti-SKOR2 Atlas Antibodies Cat# HPA046206; RRID:AB_2679588 Rabbit polyclonal anti-KIRREL2 Proteintech Cat# 10890-1-AP; RRID:AB_2130842 Goat polyclonal anti-SOX2 RD systems Cat# AF2018; RRID:AB_355110 Rabbit monoclonal anti-ATOH1 Abclonal Cat# A11477; RRID:AB_2861575 Mouse monoclonal anti-CALB1 Sigma-Aldrich Cat# C9848-100UL; RRID:AB_476894 Rabbit polyclonal anti-PAX6 Biolegend Cat# 901301; RRID:AB_2749901 Chemicals, peptides, and recombinant proteins Accutase Sigma 07922 AmphoB Gibco 15290018 Apo-transferrin Sigma T1147-100MG BDNF R&D Systems 248-BDB-050 BrainPhys Optimized Medium STEMCELL Technologies 05796 Bovine Serum Albumin (BSA) Sigma A0281 B-27 supplement Gibco 17504001 chemically defined lipid concentrate (CDLC) Gibco 11905031 CHIR Reprocell 04-0004 DMEM/F-12 Corning/Cytiva SH30023.FS Fluoromount EMS 50-259-73 F-12 medium Gibco 11-765-054 Geltrex Thermo Fisher Scientific A1413301 Glutamax Gibco 35050061 Heparin Sigma H314-25KU IMDM medium Gibco 12440053 insulin Sigma I9278-5ML Knockout Serum Replacement (KSR) Gibco 10828028 Matrigel Corning 354230 Mono-Thioglycerol Sigma M1753 mTeSR1medium Stem Cell Technologies 4309155 Neurobasal medium Gibco 21103049 NeuroCult SM1 Neuronal Supplement STEMCELL Technologies 05711 NMDA Tocris 0114 Noggin Peprotech 120-10C N2 supplement Gibco 17502001 Penicillin/streptomycin Corning SV30010 PTX Hello Bio HB0506 ROCK inhibitor STEMCELL Technologies 72302 SB431542 Selleckchem S1067 SYBR Green PCR Master Mix Thermo Fisher Scientific 4309155 Tetrodotoxin, TTX Tocris 1078 Tissue-Tek O.C.T. compound Sakura 62550 TritonX-100 Sigma T9284 (Continued on next page) e1 Cell Stem Cell 31, 39–51.e1–e6, January 4, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tween20 Sigma P9416 T3 Sigma T2877-250MG 2-Mercaptoethanol Gibco 21985023 Critical commercial assays RNeasy Mini kit Qiagen 74004 RevertAid First Strand cDNA Synthesis Kit Thermo Fisher Scientific K1621 Deposited data RNA-seq data of human cerebellar organoids (hCerOs) This paper GEO Accession: https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE247974 Atamian_et_al_2023_deposited figures and tables This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/preview/ 6hr4sgn4sx?a=1a6b251c-8d1e-4089-95e5-d5fad93a5c78 Supplementary Text This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/preview/ 6hr4sgn4sx?a=1a6b251c-8d1e-4089-95e5-d5fad93a5c78 RNA-seq data of developing human cerebellum Aldinger et al.37 dbGaP Study Accession: phs001908.v2.p1 Experimental models: Cell lines Human: PGP1 (Personal Genome Project 1) hiPSC Laboratory of Gorge Church hiPSC Human: PGP1-FOXG1 hiPSC Harvard Stem Cell institute hiPSC Human: WA09 (H9) hESC (NIH approval number NIHhESC-10-0062) WiCell hES Cell Line: H9 Human: 11a hiPSC Laboratory of Kevin Eggan hiPSC Human: D2 hiPSC Laboratory of Marcelo Coba hiPSC Oligonucleotides RT-PCR Primer Sequence See Mendeley Data Table 4 Recombinant DNA Plasmid: pAAV-CAG-SomaGCaMP6f2 Shemesh et al.63 Addgene catalog #158757 Plasmid: pAAV/L7-6-GFP-WPRE Nitta et al.65 Addgene catalog #126462 Software and algorithms Biorender https://www.biorender.com/ N/A Human + Organoid Integrated data code This paper https://github.com/quadratolab/ Cerebellar-Organoid-2023 ImageJ Schneider et al.62 https://imagej.nih.gov/ij/ MATLAB MathWorks 2022b Other Ultra-low attachment V-bottom Plates Sbio MS-9096VZ Ultra-low attachment 6-well dishes Corning 3471 10cm plates Avantor 10062–880
Knock-Out:Article Title: Human cerebellar organoids with functional Purkinje cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-BARHL1 Atlas Antibodies Cat# HPA004809; RRID:AB_1078266 Rabbit polyclonal anti-SKOR2 Atlas Antibodies Cat# HPA046206; RRID:AB_2679588 Rabbit polyclonal anti-KIRREL2 Proteintech Cat# 10890-1-AP; RRID:AB_2130842 Goat polyclonal anti-SOX2 RD systems Cat# AF2018; RRID:AB_355110 Rabbit monoclonal anti-ATOH1 Abclonal Cat# A11477; RRID:AB_2861575 Mouse monoclonal anti-CALB1 Sigma-Aldrich Cat# C9848-100UL; RRID:AB_476894 Rabbit polyclonal anti-PAX6 Biolegend Cat# 901301; RRID:AB_2749901 Chemicals, peptides, and recombinant proteins Accutase Sigma 07922 AmphoB Gibco 15290018 Apo-transferrin Sigma T1147-100MG BDNF R&D Systems 248-BDB-050 BrainPhys Optimized Medium STEMCELL Technologies 05796 Bovine Serum Albumin (BSA) Sigma A0281 B-27 supplement Gibco 17504001 chemically defined lipid concentrate (CDLC) Gibco 11905031 CHIR Reprocell 04-0004 DMEM/F-12 Corning/Cytiva SH30023.FS Fluoromount EMS 50-259-73 F-12 medium Gibco 11-765-054 Geltrex Thermo Fisher Scientific A1413301 Glutamax Gibco 35050061 Heparin Sigma H314-25KU IMDM medium Gibco 12440053 insulin Sigma I9278-5ML Knockout Serum Replacement (KSR) Gibco 10828028 Matrigel Corning 354230 Mono-Thioglycerol Sigma M1753 mTeSR1medium Stem Cell Technologies 4309155 Neurobasal medium Gibco 21103049 NeuroCult SM1 Neuronal Supplement STEMCELL Technologies 05711 NMDA Tocris 0114 Noggin Peprotech 120-10C N2 supplement Gibco 17502001 Penicillin/streptomycin Corning SV30010 PTX Hello Bio HB0506 ROCK inhibitor STEMCELL Technologies 72302 SB431542 Selleckchem S1067 SYBR Green PCR Master Mix Thermo Fisher Scientific 4309155 Tetrodotoxin, TTX Tocris 1078 Tissue-Tek O.C.T. compound Sakura 62550 TritonX-100 Sigma T9284 (Continued on next page) e1 Cell Stem Cell 31, 39–51.e1–e6, January 4, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tween20 Sigma P9416 T3 Sigma T2877-250MG 2-Mercaptoethanol Gibco 21985023 Critical commercial assays RNeasy Mini kit Qiagen 74004 RevertAid First Strand cDNA Synthesis Kit Thermo Fisher Scientific K1621 Deposited data RNA-seq data of human cerebellar organoids (hCerOs) This paper GEO Accession: https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE247974 Atamian_et_al_2023_deposited figures and tables This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/preview/ 6hr4sgn4sx?a=1a6b251c-8d1e-4089-95e5-d5fad93a5c78 Supplementary Text This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/preview/ 6hr4sgn4sx?a=1a6b251c-8d1e-4089-95e5-d5fad93a5c78 RNA-seq data of developing human cerebellum Aldinger et al.37 dbGaP Study Accession: phs001908.v2.p1 Experimental models: Cell lines Human: PGP1 (Personal Genome Project 1) hiPSC Laboratory of Gorge Church hiPSC Human: PGP1-FOXG1 hiPSC Harvard Stem Cell institute hiPSC Human: WA09 (H9) hESC (NIH approval number NIHhESC-10-0062) WiCell hES Cell Line: H9 Human: 11a hiPSC Laboratory of Kevin Eggan hiPSC Human: D2 hiPSC Laboratory of Marcelo Coba hiPSC Oligonucleotides RT-PCR Primer Sequence See Mendeley Data Table 4 Recombinant DNA Plasmid: pAAV-CAG-SomaGCaMP6f2 Shemesh et al.63 Addgene catalog #158757 Plasmid: pAAV/L7-6-GFP-WPRE Nitta et al.65 Addgene catalog #126462 Software and algorithms Biorender https://www.biorender.com/ N/A Human + Organoid Integrated data code This paper https://github.com/quadratolab/ Cerebellar-Organoid-2023 ImageJ Schneider et al.62 https://imagej.nih.gov/ij/ MATLAB MathWorks 2022b Other Ultra-low attachment V-bottom Plates Sbio MS-9096VZ Ultra-low attachment 6-well dishes Corning 3471 10cm plates Avantor 10062–880
SYBR Green Assay:Article Title: Human cerebellar organoids with functional Purkinje cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-BARHL1 Atlas Antibodies Cat# HPA004809; RRID:AB_1078266 Rabbit polyclonal anti-SKOR2 Atlas Antibodies Cat# HPA046206; RRID:AB_2679588 Rabbit polyclonal anti-KIRREL2 Proteintech Cat# 10890-1-AP; RRID:AB_2130842 Goat polyclonal anti-SOX2 RD systems Cat# AF2018; RRID:AB_355110 Rabbit monoclonal anti-ATOH1 Abclonal Cat# A11477; RRID:AB_2861575 Mouse monoclonal anti-CALB1 Sigma-Aldrich Cat# C9848-100UL; RRID:AB_476894 Rabbit polyclonal anti-PAX6 Biolegend Cat# 901301; RRID:AB_2749901 Chemicals, peptides, and recombinant proteins Accutase Sigma 07922 AmphoB Gibco 15290018 Apo-transferrin Sigma T1147-100MG BDNF R&D Systems 248-BDB-050 BrainPhys Optimized Medium STEMCELL Technologies 05796 Bovine Serum Albumin (BSA) Sigma A0281 B-27 supplement Gibco 17504001 chemically defined lipid concentrate (CDLC) Gibco 11905031 CHIR Reprocell 04-0004 DMEM/F-12 Corning/Cytiva SH30023.FS Fluoromount EMS 50-259-73 F-12 medium Gibco 11-765-054 Geltrex Thermo Fisher Scientific A1413301 Glutamax Gibco 35050061 Heparin Sigma H314-25KU IMDM medium Gibco 12440053 insulin Sigma I9278-5ML Knockout Serum Replacement (KSR) Gibco 10828028 Matrigel Corning 354230 Mono-Thioglycerol Sigma M1753 mTeSR1medium Stem Cell Technologies 4309155 Neurobasal medium Gibco 21103049 NeuroCult SM1 Neuronal Supplement STEMCELL Technologies 05711 NMDA Tocris 0114 Noggin Peprotech 120-10C N2 supplement Gibco 17502001 Penicillin/streptomycin Corning SV30010 PTX Hello Bio HB0506 ROCK inhibitor STEMCELL Technologies 72302 SB431542 Selleckchem S1067 SYBR Green PCR Master Mix Thermo Fisher Scientific 4309155 Tetrodotoxin, TTX Tocris 1078 Tissue-Tek O.C.T. compound Sakura 62550 TritonX-100 Sigma T9284 (Continued on next page) e1 Cell Stem Cell 31, 39–51.e1–e6, January 4, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tween20 Sigma P9416 T3 Sigma T2877-250MG 2-Mercaptoethanol Gibco 21985023 Critical commercial assays RNeasy Mini kit Qiagen 74004 RevertAid First Strand cDNA Synthesis Kit Thermo Fisher Scientific K1621 Deposited data RNA-seq data of human cerebellar organoids (hCerOs) This paper GEO Accession: https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE247974 Atamian_et_al_2023_deposited figures and tables This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/preview/ 6hr4sgn4sx?a=1a6b251c-8d1e-4089-95e5-d5fad93a5c78 Supplementary Text This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/preview/ 6hr4sgn4sx?a=1a6b251c-8d1e-4089-95e5-d5fad93a5c78 RNA-seq data of developing human cerebellum Aldinger et al.37 dbGaP Study Accession: phs001908.v2.p1 Experimental models: Cell lines Human: PGP1 (Personal Genome Project 1) hiPSC Laboratory of Gorge Church hiPSC Human: PGP1-FOXG1 hiPSC Harvard Stem Cell institute hiPSC Human: WA09 (H9) hESC (NIH approval number NIHhESC-10-0062) WiCell hES Cell Line: H9 Human: 11a hiPSC Laboratory of Kevin Eggan hiPSC Human: D2 hiPSC Laboratory of Marcelo Coba hiPSC Oligonucleotides RT-PCR Primer Sequence See Mendeley Data Table 4 Recombinant DNA Plasmid: pAAV-CAG-SomaGCaMP6f2 Shemesh et al.63 Addgene catalog #158757 Plasmid: pAAV/L7-6-GFP-WPRE Nitta et al.65 Addgene catalog #126462 Software and algorithms Biorender https://www.biorender.com/ N/A Human + Organoid Integrated data code This paper https://github.com/quadratolab/ Cerebellar-Organoid-2023 ImageJ Schneider et al.62 https://imagej.nih.gov/ij/ MATLAB MathWorks 2022b Other Ultra-low attachment V-bottom Plates Sbio MS-9096VZ Ultra-low attachment 6-well dishes Corning 3471 10cm plates Avantor 10062–880
Polymerase Chain Reaction:Article Title: Human cerebellar organoids with functional Purkinje cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-BARHL1 Atlas Antibodies Cat# HPA004809; RRID:AB_1078266 Rabbit polyclonal anti-SKOR2 Atlas Antibodies Cat# HPA046206; RRID:AB_2679588 Rabbit polyclonal anti-KIRREL2 Proteintech Cat# 10890-1-AP; RRID:AB_2130842 Goat polyclonal anti-SOX2 RD systems Cat# AF2018; RRID:AB_355110 Rabbit monoclonal anti-ATOH1 Abclonal Cat# A11477; RRID:AB_2861575 Mouse monoclonal anti-CALB1 Sigma-Aldrich Cat# C9848-100UL; RRID:AB_476894 Rabbit polyclonal anti-PAX6 Biolegend Cat# 901301; RRID:AB_2749901 Chemicals, peptides, and recombinant proteins Accutase Sigma 07922 AmphoB Gibco 15290018 Apo-transferrin Sigma T1147-100MG BDNF R&D Systems 248-BDB-050 BrainPhys Optimized Medium STEMCELL Technologies 05796 Bovine Serum Albumin (BSA) Sigma A0281 B-27 supplement Gibco 17504001 chemically defined lipid concentrate (CDLC) Gibco 11905031 CHIR Reprocell 04-0004 DMEM/F-12 Corning/Cytiva SH30023.FS Fluoromount EMS 50-259-73 F-12 medium Gibco 11-765-054 Geltrex Thermo Fisher Scientific A1413301 Glutamax Gibco 35050061 Heparin Sigma H314-25KU IMDM medium Gibco 12440053 insulin Sigma I9278-5ML Knockout Serum Replacement (KSR) Gibco 10828028 Matrigel Corning 354230 Mono-Thioglycerol Sigma M1753 mTeSR1medium Stem Cell Technologies 4309155 Neurobasal medium Gibco 21103049 NeuroCult SM1 Neuronal Supplement STEMCELL Technologies 05711 NMDA Tocris 0114 Noggin Peprotech 120-10C N2 supplement Gibco 17502001 Penicillin/streptomycin Corning SV30010 PTX Hello Bio HB0506 ROCK inhibitor STEMCELL Technologies 72302 SB431542 Selleckchem S1067 SYBR Green PCR Master Mix Thermo Fisher Scientific 4309155 Tetrodotoxin, TTX Tocris 1078 Tissue-Tek O.C.T. compound Sakura 62550 TritonX-100 Sigma T9284 (Continued on next page) e1 Cell Stem Cell 31, 39–51.e1–e6, January 4, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tween20 Sigma P9416 T3 Sigma T2877-250MG 2-Mercaptoethanol Gibco 21985023 Critical commercial assays RNeasy Mini kit Qiagen 74004 RevertAid First Strand cDNA Synthesis Kit Thermo Fisher Scientific K1621 Deposited data RNA-seq data of human cerebellar organoids (hCerOs) This paper GEO Accession: https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE247974 Atamian_et_al_2023_deposited figures and tables This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/preview/ 6hr4sgn4sx?a=1a6b251c-8d1e-4089-95e5-d5fad93a5c78 Supplementary Text This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/preview/ 6hr4sgn4sx?a=1a6b251c-8d1e-4089-95e5-d5fad93a5c78 RNA-seq data of developing human cerebellum Aldinger et al.37 dbGaP Study Accession: phs001908.v2.p1 Experimental models: Cell lines Human: PGP1 (Personal Genome Project 1) hiPSC Laboratory of Gorge Church hiPSC Human: PGP1-FOXG1 hiPSC Harvard Stem Cell institute hiPSC Human: WA09 (H9) hESC (NIH approval number NIHhESC-10-0062) WiCell hES Cell Line: H9 Human: 11a hiPSC Laboratory of Kevin Eggan hiPSC Human: D2 hiPSC Laboratory of Marcelo Coba hiPSC Oligonucleotides RT-PCR Primer Sequence See Mendeley Data Table 4 Recombinant DNA Plasmid: pAAV-CAG-SomaGCaMP6f2 Shemesh et al.63 Addgene catalog #158757 Plasmid: pAAV/L7-6-GFP-WPRE Nitta et al.65 Addgene catalog #126462 Software and algorithms Biorender https://www.biorender.com/ N/A Human + Organoid Integrated data code This paper https://github.com/quadratolab/ Cerebellar-Organoid-2023 ImageJ Schneider et al.62 https://imagej.nih.gov/ij/ MATLAB MathWorks 2022b Other Ultra-low attachment V-bottom Plates Sbio MS-9096VZ Ultra-low attachment 6-well dishes Corning 3471 10cm plates Avantor 10062–880
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