Tissue:Article Title: Protocol for mechanical nuclei dissociation and isolation from frozen tissue and organoids for single-nucleus RNA sequencing.
Article Snippet: Note: If working with a tissue typically composed of a large number of cells (or more than 2 million cells), dilute the sample 1:10 in DNase/RNase-free water directly into the tube containing Trypan Blue prior to counting. .. Biological samples Mouse brain tissue C57BL/6 (hemisphere) This study N/A Human ESC-derived cerebral organoids* This study WIBR1 Chemicals, peptides, and recombinant proteins Anti-Nucleus MicroBeads Miltenyi Biotec Cat#130-132-997 Bovine serum albumin (BSA) Bio Basic Cat# A0903 DAPI Sigma-Aldrich Cat#D9542 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D8418 DNase I Solution STEMCELL Technologies Cat#07900 Hydrochloric acid Sigma-Aldrich Cat#H1758 Nuclei Extraction Buffer Miltenyi Biotec Cat130-128-024 Phosphate-buffered saline (D-PBS) Sigma-Aldrich Cat#P4474 RNase Inhibitor, Murine New England Biolabs Cat#M0314L Trypan Blue stain, 0.4% Thermo Fisher Scientific Cat#T10282 UltraPure DNase/RNase-Free Distilled Water Invitrogen Cat#10977-015 Critical commercial assays EVERCODE Nuclei Fixation v3 Parse Biosciences Cat#ECFN3300 STEMdiff Cerebral Organoid Kit STEMCELL Technologies Cat#08570 Software and algorithms BioRender BioRender https://www.biorender.com Other GentleMACS Dissociator Miltenyi Biotec Cat#130-093-235 GentleMACS C Tubes Miltenyi Biotec Cat#130-093-237 MACS MultiStand Miltenyi Biotec Cat#130-042-303 OctoMACS Separator Miltenyi Biotec Cat#130-042-109 MS Columns Miltenyi Biotec Cat#130-042-201 MACS SmartStrainers (100 μm) Miltenyi Biotec Cat#130-098-463 MACS SmartStrainers (70 μm) Miltenyi Biotec Cat#130-098-462 MACS SmartStrainers (30 μm) Miltenyi Biotec Cat#130-098-458 MACS Chill 15 Rack Miltenyi Biotec Cat#130-097-038 1.5 mL screw-cap microtubes Diamed Cat#DIATEC-2740 15 mL polypropylene conical tubes FroggaBio Cat#TB15-25 Disposable hemocytometer Incyto Cat#DHC-N01-5 Refrigerated centrifuge (15 mL and 1.5 mL rotors) Avantor Cat#76468-136; Cat#MP76533-878 Mr. Frosty freezing container Sigma-Aldrich Cat#CLS432001 25 mL reservoir Corning Cat#RES-V-25-S *Organoids differentiated using STEMdiff Cerebral Organoid Kit (key resource table). ..
Organoids:Article Title: Protocol for mechanical nuclei dissociation and isolation from frozen tissue and organoids for single-nucleus RNA sequencing.
Article Snippet: Note: If working with a tissue typically composed of a large number of cells (or more than 2 million cells), dilute the sample 1:10 in DNase/RNase-free water directly into the tube containing Trypan Blue prior to counting. .. Biological samples Mouse brain tissue C57BL/6 (hemisphere) This study N/A Human ESC-derived cerebral organoids* This study WIBR1 Chemicals, peptides, and recombinant proteins Anti-Nucleus MicroBeads Miltenyi Biotec Cat#130-132-997 Bovine serum albumin (BSA) Bio Basic Cat# A0903 DAPI Sigma-Aldrich Cat#D9542 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D8418 DNase I Solution STEMCELL Technologies Cat#07900 Hydrochloric acid Sigma-Aldrich Cat#H1758 Nuclei Extraction Buffer Miltenyi Biotec Cat130-128-024 Phosphate-buffered saline (D-PBS) Sigma-Aldrich Cat#P4474 RNase Inhibitor, Murine New England Biolabs Cat#M0314L Trypan Blue stain, 0.4% Thermo Fisher Scientific Cat#T10282 UltraPure DNase/RNase-Free Distilled Water Invitrogen Cat#10977-015 Critical commercial assays EVERCODE Nuclei Fixation v3 Parse Biosciences Cat#ECFN3300 STEMdiff Cerebral Organoid Kit STEMCELL Technologies Cat#08570 Software and algorithms BioRender BioRender https://www.biorender.com Other GentleMACS Dissociator Miltenyi Biotec Cat#130-093-235 GentleMACS C Tubes Miltenyi Biotec Cat#130-093-237 MACS MultiStand Miltenyi Biotec Cat#130-042-303 OctoMACS Separator Miltenyi Biotec Cat#130-042-109 MS Columns Miltenyi Biotec Cat#130-042-201 MACS SmartStrainers (100 μm) Miltenyi Biotec Cat#130-098-463 MACS SmartStrainers (70 μm) Miltenyi Biotec Cat#130-098-462 MACS SmartStrainers (30 μm) Miltenyi Biotec Cat#130-098-458 MACS Chill 15 Rack Miltenyi Biotec Cat#130-097-038 1.5 mL screw-cap microtubes Diamed Cat#DIATEC-2740 15 mL polypropylene conical tubes FroggaBio Cat#TB15-25 Disposable hemocytometer Incyto Cat#DHC-N01-5 Refrigerated centrifuge (15 mL and 1.5 mL rotors) Avantor Cat#76468-136; Cat#MP76533-878 Mr. Frosty freezing container Sigma-Aldrich Cat#CLS432001 25 mL reservoir Corning Cat#RES-V-25-S *Organoids differentiated using STEMdiff Cerebral Organoid Kit (key resource table). ..
Recombinant:Article Title: Protocol for mechanical nuclei dissociation and isolation from frozen tissue and organoids for single-nucleus RNA sequencing.
Article Snippet: Note: If working with a tissue typically composed of a large number of cells (or more than 2 million cells), dilute the sample 1:10 in DNase/RNase-free water directly into the tube containing Trypan Blue prior to counting. .. Biological samples Mouse brain tissue C57BL/6 (hemisphere) This study N/A Human ESC-derived cerebral organoids* This study WIBR1 Chemicals, peptides, and recombinant proteins Anti-Nucleus MicroBeads Miltenyi Biotec Cat#130-132-997 Bovine serum albumin (BSA) Bio Basic Cat# A0903 DAPI Sigma-Aldrich Cat#D9542 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D8418 DNase I Solution STEMCELL Technologies Cat#07900 Hydrochloric acid Sigma-Aldrich Cat#H1758 Nuclei Extraction Buffer Miltenyi Biotec Cat130-128-024 Phosphate-buffered saline (D-PBS) Sigma-Aldrich Cat#P4474 RNase Inhibitor, Murine New England Biolabs Cat#M0314L Trypan Blue stain, 0.4% Thermo Fisher Scientific Cat#T10282 UltraPure DNase/RNase-Free Distilled Water Invitrogen Cat#10977-015 Critical commercial assays EVERCODE Nuclei Fixation v3 Parse Biosciences Cat#ECFN3300 STEMdiff Cerebral Organoid Kit STEMCELL Technologies Cat#08570 Software and algorithms BioRender BioRender https://www.biorender.com Other GentleMACS Dissociator Miltenyi Biotec Cat#130-093-235 GentleMACS C Tubes Miltenyi Biotec Cat#130-093-237 MACS MultiStand Miltenyi Biotec Cat#130-042-303 OctoMACS Separator Miltenyi Biotec Cat#130-042-109 MS Columns Miltenyi Biotec Cat#130-042-201 MACS SmartStrainers (100 μm) Miltenyi Biotec Cat#130-098-463 MACS SmartStrainers (70 μm) Miltenyi Biotec Cat#130-098-462 MACS SmartStrainers (30 μm) Miltenyi Biotec Cat#130-098-458 MACS Chill 15 Rack Miltenyi Biotec Cat#130-097-038 1.5 mL screw-cap microtubes Diamed Cat#DIATEC-2740 15 mL polypropylene conical tubes FroggaBio Cat#TB15-25 Disposable hemocytometer Incyto Cat#DHC-N01-5 Refrigerated centrifuge (15 mL and 1.5 mL rotors) Avantor Cat#76468-136; Cat#MP76533-878 Mr. Frosty freezing container Sigma-Aldrich Cat#CLS432001 25 mL reservoir Corning Cat#RES-V-25-S *Organoids differentiated using STEMdiff Cerebral Organoid Kit (key resource table). ..
Article Title: Protocol for minimized-bias profiling of liver and visceral adipose tissue in mice using integrated single-nucleus RNA sequencing.
Article Snippet: .. Biological samples Male wild-type C57BL/6J mice, 8 weeks old at diet initiation; tissues collected after 26 weeks of western diet feeding Janvier Labs Ethics approval #47097-2024012516265646 v4 Chemicals, peptides, and recombinant proteins PBS Gibco Cat#10010023 DMEM Gibco Cat#10566016 Absolute ethanol Major supplier N/A Nuclease-free water Major supplier N/A DAPI Staining Solution MILTENYI BIOTEC Cat#130-111-570 RNase inhibitor, 40000 U/mL New England Biolabs Cat#M0314 BD Stain Buffer (FBS) BD Biosciences Cat#554656 Proteinase K, 800 U/mL New England Biolabs Cat#P8107S Vybrant® DyeCycleTM Green Stain Thermo Fisher Cat#V35004 Critical commercial assays Nuclei Extraction Buffer MILTENYI BIOTEC Cat#130-128-024 Liver Dissociation Kit, mouse MILTENYI BIOTEC Cat130-105-807 Anti-Nucleus MicroBeads MILTENYI BIOTEC Cat#130-132-997 BD RhapsodyTM cDNA Kit BD Biosciences Cat#633773 BD RhapsodyTM Enhanced Cartridge Reagent Kit BD Biosciences Cat#667052 BD RhapsodyTM 8-Lane Cartridge BD Biosciences Cat#666262 BD RhapsodyTM WTA Amplification Kit BD Biosciences Cat#633801 QubitTM dsDNA HS Assay Kit Thermo Fisher Cat#Q32851 Agilent High Sensitivity DNA Kit Agilent Cat#5067-4626 MACS BSA Stock Solution MILTENYI BIOTEC Cat#130-091-376 BD® OMICS-One Dual Index Kit BD Biosciences Cat#571899 Agencourt® AMPure® XP magnetic beads Beckman Coulter Cat#A63880 Other LS Columns MILTENYI BIOTEC Cat#130-042-401 MACS SmartStrainers (30 μm) MILTENYI BIOTEC Cat#130-098-458 MACS SmartStrainers (70 μm) MILTENYI BIOTEC Cat#130-098-462 MACS SmartStrainers (100 μm) MILTENYI BIOTEC Cat#130-098-463 GentleMACS C Tubes MILTENYI BIOTEC Cat#130-093-237 Eppendorf® LoBind® Tubes BD Biosciences Cat#570751 Hemocytometer NANOENTEK Cat#DHC-N01 Hemocytometer adapter BD Biosciences Cat#633703 Centrifuge and rotor with adapters for 5-mL Falcon® tubes and 15-mL tubes. ..
Extraction:Article Title: Protocol for mechanical nuclei dissociation and isolation from frozen tissue and organoids for single-nucleus RNA sequencing.
Article Snippet: Note: If working with a tissue typically composed of a large number of cells (or more than 2 million cells), dilute the sample 1:10 in DNase/RNase-free water directly into the tube containing Trypan Blue prior to counting. .. Biological samples Mouse brain tissue C57BL/6 (hemisphere) This study N/A Human ESC-derived cerebral organoids* This study WIBR1 Chemicals, peptides, and recombinant proteins Anti-Nucleus MicroBeads Miltenyi Biotec Cat#130-132-997 Bovine serum albumin (BSA) Bio Basic Cat# A0903 DAPI Sigma-Aldrich Cat#D9542 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D8418 DNase I Solution STEMCELL Technologies Cat#07900 Hydrochloric acid Sigma-Aldrich Cat#H1758 Nuclei Extraction Buffer Miltenyi Biotec Cat130-128-024 Phosphate-buffered saline (D-PBS) Sigma-Aldrich Cat#P4474 RNase Inhibitor, Murine New England Biolabs Cat#M0314L Trypan Blue stain, 0.4% Thermo Fisher Scientific Cat#T10282 UltraPure DNase/RNase-Free Distilled Water Invitrogen Cat#10977-015 Critical commercial assays EVERCODE Nuclei Fixation v3 Parse Biosciences Cat#ECFN3300 STEMdiff Cerebral Organoid Kit STEMCELL Technologies Cat#08570 Software and algorithms BioRender BioRender https://www.biorender.com Other GentleMACS Dissociator Miltenyi Biotec Cat#130-093-235 GentleMACS C Tubes Miltenyi Biotec Cat#130-093-237 MACS MultiStand Miltenyi Biotec Cat#130-042-303 OctoMACS Separator Miltenyi Biotec Cat#130-042-109 MS Columns Miltenyi Biotec Cat#130-042-201 MACS SmartStrainers (100 μm) Miltenyi Biotec Cat#130-098-463 MACS SmartStrainers (70 μm) Miltenyi Biotec Cat#130-098-462 MACS SmartStrainers (30 μm) Miltenyi Biotec Cat#130-098-458 MACS Chill 15 Rack Miltenyi Biotec Cat#130-097-038 1.5 mL screw-cap microtubes Diamed Cat#DIATEC-2740 15 mL polypropylene conical tubes FroggaBio Cat#TB15-25 Disposable hemocytometer Incyto Cat#DHC-N01-5 Refrigerated centrifuge (15 mL and 1.5 mL rotors) Avantor Cat#76468-136; Cat#MP76533-878 Mr. Frosty freezing container Sigma-Aldrich Cat#CLS432001 25 mL reservoir Corning Cat#RES-V-25-S *Organoids differentiated using STEMdiff Cerebral Organoid Kit (key resource table). ..
Article Title: SORLA up-regulation suppresses pathological effects in aged tauopathy mouse brain
Article Snippet: .. Three frozen 9 MO hippocampus tissue from WT, PS19, and SORLA TG/PS19 groups were pooled and lysed in Miltenyi nuclei extraction buffer containing RNase inhibitor (0.2 U/μl) using a gentleMACS Octo Dissociator (Program 4C_nuclei_1) according to the manufacturer’s protocol. .. Miltenyi Debris removal solution was applied to the nuclei suspension, and NeuN-AF488 and Olig2-AF647 were added to the samples and incubated on ice for 30 min.
Article Title: Tricuspid valve regurgitation accelerates heart failure via a cardio-intestinal innate immune circuit
Article Snippet: .. Snap-frozen cardiac tissue samples were transferred into 2 ml of ice-cold Nuclei Extraction Buffer (Miltenyi Biotec, #130-128-024) buffer supplemented with 0.2 U/μl RNAse inhibitor (Invitrogen, AM2696) in gentleMACS C Tubes (Miltenyi Biotec, #130-093-237). .. Tubes were placed on a gentleMACS Octo Dissociator (Miltenyi Biotec, #130-095-937), and the 4C_nuclei_1 program was run.
Article Title: Patient-derived tau-seeded human neuronal chimeras recapitulate mature Alzheimer’s tau pathology and uncover human-specific neuronal vulnerability
Article Snippet: Mice were euthanized and perfused with ice-cold DPBS, and the brains were quickly extracted and rinsed in the same buffer supplied with RiboGrip RNase inhibitor (Solis BioDyne, 0.8 U/μL). .. Brains were then dissociated and chopped into fine pieces before being transferred into Nuclei Extraction Buffer (Miltenyi Biotec, 130-128-024). .. Tissues were subsequently processed using gentleMACS dissociator (Miltenyi Biotec) following instructions.
Article Title: Protocol for minimized-bias profiling of liver and visceral adipose tissue in mice using integrated single-nucleus RNA sequencing.
Article Snippet: .. Biological samples Male wild-type C57BL/6J mice, 8 weeks old at diet initiation; tissues collected after 26 weeks of western diet feeding Janvier Labs Ethics approval #47097-2024012516265646 v4 Chemicals, peptides, and recombinant proteins PBS Gibco Cat#10010023 DMEM Gibco Cat#10566016 Absolute ethanol Major supplier N/A Nuclease-free water Major supplier N/A DAPI Staining Solution MILTENYI BIOTEC Cat#130-111-570 RNase inhibitor, 40000 U/mL New England Biolabs Cat#M0314 BD Stain Buffer (FBS) BD Biosciences Cat#554656 Proteinase K, 800 U/mL New England Biolabs Cat#P8107S Vybrant® DyeCycleTM Green Stain Thermo Fisher Cat#V35004 Critical commercial assays Nuclei Extraction Buffer MILTENYI BIOTEC Cat#130-128-024 Liver Dissociation Kit, mouse MILTENYI BIOTEC Cat130-105-807 Anti-Nucleus MicroBeads MILTENYI BIOTEC Cat#130-132-997 BD RhapsodyTM cDNA Kit BD Biosciences Cat#633773 BD RhapsodyTM Enhanced Cartridge Reagent Kit BD Biosciences Cat#667052 BD RhapsodyTM 8-Lane Cartridge BD Biosciences Cat#666262 BD RhapsodyTM WTA Amplification Kit BD Biosciences Cat#633801 QubitTM dsDNA HS Assay Kit Thermo Fisher Cat#Q32851 Agilent High Sensitivity DNA Kit Agilent Cat#5067-4626 MACS BSA Stock Solution MILTENYI BIOTEC Cat#130-091-376 BD® OMICS-One Dual Index Kit BD Biosciences Cat#571899 Agencourt® AMPure® XP magnetic beads Beckman Coulter Cat#A63880 Other LS Columns MILTENYI BIOTEC Cat#130-042-401 MACS SmartStrainers (30 μm) MILTENYI BIOTEC Cat#130-098-458 MACS SmartStrainers (70 μm) MILTENYI BIOTEC Cat#130-098-462 MACS SmartStrainers (100 μm) MILTENYI BIOTEC Cat#130-098-463 GentleMACS C Tubes MILTENYI BIOTEC Cat#130-093-237 Eppendorf® LoBind® Tubes BD Biosciences Cat#570751 Hemocytometer NANOENTEK Cat#DHC-N01 Hemocytometer adapter BD Biosciences Cat#633703 Centrifuge and rotor with adapters for 5-mL Falcon® tubes and 15-mL tubes. ..
Saline:Article Title: Protocol for mechanical nuclei dissociation and isolation from frozen tissue and organoids for single-nucleus RNA sequencing.
Article Snippet: Note: If working with a tissue typically composed of a large number of cells (or more than 2 million cells), dilute the sample 1:10 in DNase/RNase-free water directly into the tube containing Trypan Blue prior to counting. .. Biological samples Mouse brain tissue C57BL/6 (hemisphere) This study N/A Human ESC-derived cerebral organoids* This study WIBR1 Chemicals, peptides, and recombinant proteins Anti-Nucleus MicroBeads Miltenyi Biotec Cat#130-132-997 Bovine serum albumin (BSA) Bio Basic Cat# A0903 DAPI Sigma-Aldrich Cat#D9542 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D8418 DNase I Solution STEMCELL Technologies Cat#07900 Hydrochloric acid Sigma-Aldrich Cat#H1758 Nuclei Extraction Buffer Miltenyi Biotec Cat130-128-024 Phosphate-buffered saline (D-PBS) Sigma-Aldrich Cat#P4474 RNase Inhibitor, Murine New England Biolabs Cat#M0314L Trypan Blue stain, 0.4% Thermo Fisher Scientific Cat#T10282 UltraPure DNase/RNase-Free Distilled Water Invitrogen Cat#10977-015 Critical commercial assays EVERCODE Nuclei Fixation v3 Parse Biosciences Cat#ECFN3300 STEMdiff Cerebral Organoid Kit STEMCELL Technologies Cat#08570 Software and algorithms BioRender BioRender https://www.biorender.com Other GentleMACS Dissociator Miltenyi Biotec Cat#130-093-235 GentleMACS C Tubes Miltenyi Biotec Cat#130-093-237 MACS MultiStand Miltenyi Biotec Cat#130-042-303 OctoMACS Separator Miltenyi Biotec Cat#130-042-109 MS Columns Miltenyi Biotec Cat#130-042-201 MACS SmartStrainers (100 μm) Miltenyi Biotec Cat#130-098-463 MACS SmartStrainers (70 μm) Miltenyi Biotec Cat#130-098-462 MACS SmartStrainers (30 μm) Miltenyi Biotec Cat#130-098-458 MACS Chill 15 Rack Miltenyi Biotec Cat#130-097-038 1.5 mL screw-cap microtubes Diamed Cat#DIATEC-2740 15 mL polypropylene conical tubes FroggaBio Cat#TB15-25 Disposable hemocytometer Incyto Cat#DHC-N01-5 Refrigerated centrifuge (15 mL and 1.5 mL rotors) Avantor Cat#76468-136; Cat#MP76533-878 Mr. Frosty freezing container Sigma-Aldrich Cat#CLS432001 25 mL reservoir Corning Cat#RES-V-25-S *Organoids differentiated using STEMdiff Cerebral Organoid Kit (key resource table). ..
Staining:Article Title: Protocol for mechanical nuclei dissociation and isolation from frozen tissue and organoids for single-nucleus RNA sequencing.
Article Snippet: Note: If working with a tissue typically composed of a large number of cells (or more than 2 million cells), dilute the sample 1:10 in DNase/RNase-free water directly into the tube containing Trypan Blue prior to counting. .. Biological samples Mouse brain tissue C57BL/6 (hemisphere) This study N/A Human ESC-derived cerebral organoids* This study WIBR1 Chemicals, peptides, and recombinant proteins Anti-Nucleus MicroBeads Miltenyi Biotec Cat#130-132-997 Bovine serum albumin (BSA) Bio Basic Cat# A0903 DAPI Sigma-Aldrich Cat#D9542 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D8418 DNase I Solution STEMCELL Technologies Cat#07900 Hydrochloric acid Sigma-Aldrich Cat#H1758 Nuclei Extraction Buffer Miltenyi Biotec Cat130-128-024 Phosphate-buffered saline (D-PBS) Sigma-Aldrich Cat#P4474 RNase Inhibitor, Murine New England Biolabs Cat#M0314L Trypan Blue stain, 0.4% Thermo Fisher Scientific Cat#T10282 UltraPure DNase/RNase-Free Distilled Water Invitrogen Cat#10977-015 Critical commercial assays EVERCODE Nuclei Fixation v3 Parse Biosciences Cat#ECFN3300 STEMdiff Cerebral Organoid Kit STEMCELL Technologies Cat#08570 Software and algorithms BioRender BioRender https://www.biorender.com Other GentleMACS Dissociator Miltenyi Biotec Cat#130-093-235 GentleMACS C Tubes Miltenyi Biotec Cat#130-093-237 MACS MultiStand Miltenyi Biotec Cat#130-042-303 OctoMACS Separator Miltenyi Biotec Cat#130-042-109 MS Columns Miltenyi Biotec Cat#130-042-201 MACS SmartStrainers (100 μm) Miltenyi Biotec Cat#130-098-463 MACS SmartStrainers (70 μm) Miltenyi Biotec Cat#130-098-462 MACS SmartStrainers (30 μm) Miltenyi Biotec Cat#130-098-458 MACS Chill 15 Rack Miltenyi Biotec Cat#130-097-038 1.5 mL screw-cap microtubes Diamed Cat#DIATEC-2740 15 mL polypropylene conical tubes FroggaBio Cat#TB15-25 Disposable hemocytometer Incyto Cat#DHC-N01-5 Refrigerated centrifuge (15 mL and 1.5 mL rotors) Avantor Cat#76468-136; Cat#MP76533-878 Mr. Frosty freezing container Sigma-Aldrich Cat#CLS432001 25 mL reservoir Corning Cat#RES-V-25-S *Organoids differentiated using STEMdiff Cerebral Organoid Kit (key resource table). ..
Article Title: Protocol for minimized-bias profiling of liver and visceral adipose tissue in mice using integrated single-nucleus RNA sequencing.
Article Snippet: .. Biological samples Male wild-type C57BL/6J mice, 8 weeks old at diet initiation; tissues collected after 26 weeks of western diet feeding Janvier Labs Ethics approval #47097-2024012516265646 v4 Chemicals, peptides, and recombinant proteins PBS Gibco Cat#10010023 DMEM Gibco Cat#10566016 Absolute ethanol Major supplier N/A Nuclease-free water Major supplier N/A DAPI Staining Solution MILTENYI BIOTEC Cat#130-111-570 RNase inhibitor, 40000 U/mL New England Biolabs Cat#M0314 BD Stain Buffer (FBS) BD Biosciences Cat#554656 Proteinase K, 800 U/mL New England Biolabs Cat#P8107S Vybrant® DyeCycleTM Green Stain Thermo Fisher Cat#V35004 Critical commercial assays Nuclei Extraction Buffer MILTENYI BIOTEC Cat#130-128-024 Liver Dissociation Kit, mouse MILTENYI BIOTEC Cat130-105-807 Anti-Nucleus MicroBeads MILTENYI BIOTEC Cat#130-132-997 BD RhapsodyTM cDNA Kit BD Biosciences Cat#633773 BD RhapsodyTM Enhanced Cartridge Reagent Kit BD Biosciences Cat#667052 BD RhapsodyTM 8-Lane Cartridge BD Biosciences Cat#666262 BD RhapsodyTM WTA Amplification Kit BD Biosciences Cat#633801 QubitTM dsDNA HS Assay Kit Thermo Fisher Cat#Q32851 Agilent High Sensitivity DNA Kit Agilent Cat#5067-4626 MACS BSA Stock Solution MILTENYI BIOTEC Cat#130-091-376 BD® OMICS-One Dual Index Kit BD Biosciences Cat#571899 Agencourt® AMPure® XP magnetic beads Beckman Coulter Cat#A63880 Other LS Columns MILTENYI BIOTEC Cat#130-042-401 MACS SmartStrainers (30 μm) MILTENYI BIOTEC Cat#130-098-458 MACS SmartStrainers (70 μm) MILTENYI BIOTEC Cat#130-098-462 MACS SmartStrainers (100 μm) MILTENYI BIOTEC Cat#130-098-463 GentleMACS C Tubes MILTENYI BIOTEC Cat#130-093-237 Eppendorf® LoBind® Tubes BD Biosciences Cat#570751 Hemocytometer NANOENTEK Cat#DHC-N01 Hemocytometer adapter BD Biosciences Cat#633703 Centrifuge and rotor with adapters for 5-mL Falcon® tubes and 15-mL tubes. ..
Software:Article Title: Protocol for mechanical nuclei dissociation and isolation from frozen tissue and organoids for single-nucleus RNA sequencing.
Article Snippet: Note: If working with a tissue typically composed of a large number of cells (or more than 2 million cells), dilute the sample 1:10 in DNase/RNase-free water directly into the tube containing Trypan Blue prior to counting. .. Biological samples Mouse brain tissue C57BL/6 (hemisphere) This study N/A Human ESC-derived cerebral organoids* This study WIBR1 Chemicals, peptides, and recombinant proteins Anti-Nucleus MicroBeads Miltenyi Biotec Cat#130-132-997 Bovine serum albumin (BSA) Bio Basic Cat# A0903 DAPI Sigma-Aldrich Cat#D9542 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D8418 DNase I Solution STEMCELL Technologies Cat#07900 Hydrochloric acid Sigma-Aldrich Cat#H1758 Nuclei Extraction Buffer Miltenyi Biotec Cat130-128-024 Phosphate-buffered saline (D-PBS) Sigma-Aldrich Cat#P4474 RNase Inhibitor, Murine New England Biolabs Cat#M0314L Trypan Blue stain, 0.4% Thermo Fisher Scientific Cat#T10282 UltraPure DNase/RNase-Free Distilled Water Invitrogen Cat#10977-015 Critical commercial assays EVERCODE Nuclei Fixation v3 Parse Biosciences Cat#ECFN3300 STEMdiff Cerebral Organoid Kit STEMCELL Technologies Cat#08570 Software and algorithms BioRender BioRender https://www.biorender.com Other GentleMACS Dissociator Miltenyi Biotec Cat#130-093-235 GentleMACS C Tubes Miltenyi Biotec Cat#130-093-237 MACS MultiStand Miltenyi Biotec Cat#130-042-303 OctoMACS Separator Miltenyi Biotec Cat#130-042-109 MS Columns Miltenyi Biotec Cat#130-042-201 MACS SmartStrainers (100 μm) Miltenyi Biotec Cat#130-098-463 MACS SmartStrainers (70 μm) Miltenyi Biotec Cat#130-098-462 MACS SmartStrainers (30 μm) Miltenyi Biotec Cat#130-098-458 MACS Chill 15 Rack Miltenyi Biotec Cat#130-097-038 1.5 mL screw-cap microtubes Diamed Cat#DIATEC-2740 15 mL polypropylene conical tubes FroggaBio Cat#TB15-25 Disposable hemocytometer Incyto Cat#DHC-N01-5 Refrigerated centrifuge (15 mL and 1.5 mL rotors) Avantor Cat#76468-136; Cat#MP76533-878 Mr. Frosty freezing container Sigma-Aldrich Cat#CLS432001 25 mL reservoir Corning Cat#RES-V-25-S *Organoids differentiated using STEMdiff Cerebral Organoid Kit (key resource table). ..
Magnetic Cell Separation:Article Title: Protocol for mechanical nuclei dissociation and isolation from frozen tissue and organoids for single-nucleus RNA sequencing.
Article Snippet: Note: If working with a tissue typically composed of a large number of cells (or more than 2 million cells), dilute the sample 1:10 in DNase/RNase-free water directly into the tube containing Trypan Blue prior to counting. .. Biological samples Mouse brain tissue C57BL/6 (hemisphere) This study N/A Human ESC-derived cerebral organoids* This study WIBR1 Chemicals, peptides, and recombinant proteins Anti-Nucleus MicroBeads Miltenyi Biotec Cat#130-132-997 Bovine serum albumin (BSA) Bio Basic Cat# A0903 DAPI Sigma-Aldrich Cat#D9542 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D8418 DNase I Solution STEMCELL Technologies Cat#07900 Hydrochloric acid Sigma-Aldrich Cat#H1758 Nuclei Extraction Buffer Miltenyi Biotec Cat130-128-024 Phosphate-buffered saline (D-PBS) Sigma-Aldrich Cat#P4474 RNase Inhibitor, Murine New England Biolabs Cat#M0314L Trypan Blue stain, 0.4% Thermo Fisher Scientific Cat#T10282 UltraPure DNase/RNase-Free Distilled Water Invitrogen Cat#10977-015 Critical commercial assays EVERCODE Nuclei Fixation v3 Parse Biosciences Cat#ECFN3300 STEMdiff Cerebral Organoid Kit STEMCELL Technologies Cat#08570 Software and algorithms BioRender BioRender https://www.biorender.com Other GentleMACS Dissociator Miltenyi Biotec Cat#130-093-235 GentleMACS C Tubes Miltenyi Biotec Cat#130-093-237 MACS MultiStand Miltenyi Biotec Cat#130-042-303 OctoMACS Separator Miltenyi Biotec Cat#130-042-109 MS Columns Miltenyi Biotec Cat#130-042-201 MACS SmartStrainers (100 μm) Miltenyi Biotec Cat#130-098-463 MACS SmartStrainers (70 μm) Miltenyi Biotec Cat#130-098-462 MACS SmartStrainers (30 μm) Miltenyi Biotec Cat#130-098-458 MACS Chill 15 Rack Miltenyi Biotec Cat#130-097-038 1.5 mL screw-cap microtubes Diamed Cat#DIATEC-2740 15 mL polypropylene conical tubes FroggaBio Cat#TB15-25 Disposable hemocytometer Incyto Cat#DHC-N01-5 Refrigerated centrifuge (15 mL and 1.5 mL rotors) Avantor Cat#76468-136; Cat#MP76533-878 Mr. Frosty freezing container Sigma-Aldrich Cat#CLS432001 25 mL reservoir Corning Cat#RES-V-25-S *Organoids differentiated using STEMdiff Cerebral Organoid Kit (key resource table). ..
Article Title: Transcriptional plasticity of ventral tegmental area neurons induced after cessation of chronic cocaine exposure is required for incubation of cocaine seeking
Article Snippet: .. For single nucleus RNA sequencing (snRNA-seq) experiments, the nuclei fraction was pelleted and resuspended in MACS nuclei separation buffer (Miltenyi Biotec, 130-128-024). .. For single nucleus RNA sequencing (snRNA-seq) experiments, the nuclei fraction was pelleted and resuspended in MACS nuclei separation buffer (Miltenyi Biotec, 130-128-024).
Article Title: Protocol for minimized-bias profiling of liver and visceral adipose tissue in mice using integrated single-nucleus RNA sequencing.
Article Snippet: .. Biological samples Male wild-type C57BL/6J mice, 8 weeks old at diet initiation; tissues collected after 26 weeks of western diet feeding Janvier Labs Ethics approval #47097-2024012516265646 v4 Chemicals, peptides, and recombinant proteins PBS Gibco Cat#10010023 DMEM Gibco Cat#10566016 Absolute ethanol Major supplier N/A Nuclease-free water Major supplier N/A DAPI Staining Solution MILTENYI BIOTEC Cat#130-111-570 RNase inhibitor, 40000 U/mL New England Biolabs Cat#M0314 BD Stain Buffer (FBS) BD Biosciences Cat#554656 Proteinase K, 800 U/mL New England Biolabs Cat#P8107S Vybrant® DyeCycleTM Green Stain Thermo Fisher Cat#V35004 Critical commercial assays Nuclei Extraction Buffer MILTENYI BIOTEC Cat#130-128-024 Liver Dissociation Kit, mouse MILTENYI BIOTEC Cat130-105-807 Anti-Nucleus MicroBeads MILTENYI BIOTEC Cat#130-132-997 BD RhapsodyTM cDNA Kit BD Biosciences Cat#633773 BD RhapsodyTM Enhanced Cartridge Reagent Kit BD Biosciences Cat#667052 BD RhapsodyTM 8-Lane Cartridge BD Biosciences Cat#666262 BD RhapsodyTM WTA Amplification Kit BD Biosciences Cat#633801 QubitTM dsDNA HS Assay Kit Thermo Fisher Cat#Q32851 Agilent High Sensitivity DNA Kit Agilent Cat#5067-4626 MACS BSA Stock Solution MILTENYI BIOTEC Cat#130-091-376 BD® OMICS-One Dual Index Kit BD Biosciences Cat#571899 Agencourt® AMPure® XP magnetic beads Beckman Coulter Cat#A63880 Other LS Columns MILTENYI BIOTEC Cat#130-042-401 MACS SmartStrainers (30 μm) MILTENYI BIOTEC Cat#130-098-458 MACS SmartStrainers (70 μm) MILTENYI BIOTEC Cat#130-098-462 MACS SmartStrainers (100 μm) MILTENYI BIOTEC Cat#130-098-463 GentleMACS C Tubes MILTENYI BIOTEC Cat#130-093-237 Eppendorf® LoBind® Tubes BD Biosciences Cat#570751 Hemocytometer NANOENTEK Cat#DHC-N01 Hemocytometer adapter BD Biosciences Cat#633703 Centrifuge and rotor with adapters for 5-mL Falcon® tubes and 15-mL tubes. ..
Mass Spectrometry:Article Title: Protocol for mechanical nuclei dissociation and isolation from frozen tissue and organoids for single-nucleus RNA sequencing.
Article Snippet: Note: If working with a tissue typically composed of a large number of cells (or more than 2 million cells), dilute the sample 1:10 in DNase/RNase-free water directly into the tube containing Trypan Blue prior to counting. .. Biological samples Mouse brain tissue C57BL/6 (hemisphere) This study N/A Human ESC-derived cerebral organoids* This study WIBR1 Chemicals, peptides, and recombinant proteins Anti-Nucleus MicroBeads Miltenyi Biotec Cat#130-132-997 Bovine serum albumin (BSA) Bio Basic Cat# A0903 DAPI Sigma-Aldrich Cat#D9542 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D8418 DNase I Solution STEMCELL Technologies Cat#07900 Hydrochloric acid Sigma-Aldrich Cat#H1758 Nuclei Extraction Buffer Miltenyi Biotec Cat130-128-024 Phosphate-buffered saline (D-PBS) Sigma-Aldrich Cat#P4474 RNase Inhibitor, Murine New England Biolabs Cat#M0314L Trypan Blue stain, 0.4% Thermo Fisher Scientific Cat#T10282 UltraPure DNase/RNase-Free Distilled Water Invitrogen Cat#10977-015 Critical commercial assays EVERCODE Nuclei Fixation v3 Parse Biosciences Cat#ECFN3300 STEMdiff Cerebral Organoid Kit STEMCELL Technologies Cat#08570 Software and algorithms BioRender BioRender https://www.biorender.com Other GentleMACS Dissociator Miltenyi Biotec Cat#130-093-235 GentleMACS C Tubes Miltenyi Biotec Cat#130-093-237 MACS MultiStand Miltenyi Biotec Cat#130-042-303 OctoMACS Separator Miltenyi Biotec Cat#130-042-109 MS Columns Miltenyi Biotec Cat#130-042-201 MACS SmartStrainers (100 μm) Miltenyi Biotec Cat#130-098-463 MACS SmartStrainers (70 μm) Miltenyi Biotec Cat#130-098-462 MACS SmartStrainers (30 μm) Miltenyi Biotec Cat#130-098-458 MACS Chill 15 Rack Miltenyi Biotec Cat#130-097-038 1.5 mL screw-cap microtubes Diamed Cat#DIATEC-2740 15 mL polypropylene conical tubes FroggaBio Cat#TB15-25 Disposable hemocytometer Incyto Cat#DHC-N01-5 Refrigerated centrifuge (15 mL and 1.5 mL rotors) Avantor Cat#76468-136; Cat#MP76533-878 Mr. Frosty freezing container Sigma-Aldrich Cat#CLS432001 25 mL reservoir Corning Cat#RES-V-25-S *Organoids differentiated using STEMdiff Cerebral Organoid Kit (key resource table). ..
Lysis:
RNA Sequencing:Article Title: Transcriptional plasticity of ventral tegmental area neurons induced after cessation of chronic cocaine exposure is required for incubation of cocaine seeking
Article Snippet: .. For single nucleus RNA sequencing (snRNA-seq) experiments, the nuclei fraction was pelleted and resuspended in MACS nuclei separation buffer (Miltenyi Biotec, 130-128-024). .. For single nucleus RNA sequencing (snRNA-seq) experiments, the nuclei fraction was pelleted and resuspended in MACS nuclei separation buffer (Miltenyi Biotec, 130-128-024).
Western Blot:Article Title: Protocol for minimized-bias profiling of liver and visceral adipose tissue in mice using integrated single-nucleus RNA sequencing.
Article Snippet: .. Biological samples Male wild-type C57BL/6J mice, 8 weeks old at diet initiation; tissues collected after 26 weeks of western diet feeding Janvier Labs Ethics approval #47097-2024012516265646 v4 Chemicals, peptides, and recombinant proteins PBS Gibco Cat#10010023 DMEM Gibco Cat#10566016 Absolute ethanol Major supplier N/A Nuclease-free water Major supplier N/A DAPI Staining Solution MILTENYI BIOTEC Cat#130-111-570 RNase inhibitor, 40000 U/mL New England Biolabs Cat#M0314 BD Stain Buffer (FBS) BD Biosciences Cat#554656 Proteinase K, 800 U/mL New England Biolabs Cat#P8107S Vybrant® DyeCycleTM Green Stain Thermo Fisher Cat#V35004 Critical commercial assays Nuclei Extraction Buffer MILTENYI BIOTEC Cat#130-128-024 Liver Dissociation Kit, mouse MILTENYI BIOTEC Cat130-105-807 Anti-Nucleus MicroBeads MILTENYI BIOTEC Cat#130-132-997 BD RhapsodyTM cDNA Kit BD Biosciences Cat#633773 BD RhapsodyTM Enhanced Cartridge Reagent Kit BD Biosciences Cat#667052 BD RhapsodyTM 8-Lane Cartridge BD Biosciences Cat#666262 BD RhapsodyTM WTA Amplification Kit BD Biosciences Cat#633801 QubitTM dsDNA HS Assay Kit Thermo Fisher Cat#Q32851 Agilent High Sensitivity DNA Kit Agilent Cat#5067-4626 MACS BSA Stock Solution MILTENYI BIOTEC Cat#130-091-376 BD® OMICS-One Dual Index Kit BD Biosciences Cat#571899 Agencourt® AMPure® XP magnetic beads Beckman Coulter Cat#A63880 Other LS Columns MILTENYI BIOTEC Cat#130-042-401 MACS SmartStrainers (30 μm) MILTENYI BIOTEC Cat#130-098-458 MACS SmartStrainers (70 μm) MILTENYI BIOTEC Cat#130-098-462 MACS SmartStrainers (100 μm) MILTENYI BIOTEC Cat#130-098-463 GentleMACS C Tubes MILTENYI BIOTEC Cat#130-093-237 Eppendorf® LoBind® Tubes BD Biosciences Cat#570751 Hemocytometer NANOENTEK Cat#DHC-N01 Hemocytometer adapter BD Biosciences Cat#633703 Centrifuge and rotor with adapters for 5-mL Falcon® tubes and 15-mL tubes. ..
Amplification:Article Title: Protocol for minimized-bias profiling of liver and visceral adipose tissue in mice using integrated single-nucleus RNA sequencing.
Article Snippet: .. Biological samples Male wild-type C57BL/6J mice, 8 weeks old at diet initiation; tissues collected after 26 weeks of western diet feeding Janvier Labs Ethics approval #47097-2024012516265646 v4 Chemicals, peptides, and recombinant proteins PBS Gibco Cat#10010023 DMEM Gibco Cat#10566016 Absolute ethanol Major supplier N/A Nuclease-free water Major supplier N/A DAPI Staining Solution MILTENYI BIOTEC Cat#130-111-570 RNase inhibitor, 40000 U/mL New England Biolabs Cat#M0314 BD Stain Buffer (FBS) BD Biosciences Cat#554656 Proteinase K, 800 U/mL New England Biolabs Cat#P8107S Vybrant® DyeCycleTM Green Stain Thermo Fisher Cat#V35004 Critical commercial assays Nuclei Extraction Buffer MILTENYI BIOTEC Cat#130-128-024 Liver Dissociation Kit, mouse MILTENYI BIOTEC Cat130-105-807 Anti-Nucleus MicroBeads MILTENYI BIOTEC Cat#130-132-997 BD RhapsodyTM cDNA Kit BD Biosciences Cat#633773 BD RhapsodyTM Enhanced Cartridge Reagent Kit BD Biosciences Cat#667052 BD RhapsodyTM 8-Lane Cartridge BD Biosciences Cat#666262 BD RhapsodyTM WTA Amplification Kit BD Biosciences Cat#633801 QubitTM dsDNA HS Assay Kit Thermo Fisher Cat#Q32851 Agilent High Sensitivity DNA Kit Agilent Cat#5067-4626 MACS BSA Stock Solution MILTENYI BIOTEC Cat#130-091-376 BD® OMICS-One Dual Index Kit BD Biosciences Cat#571899 Agencourt® AMPure® XP magnetic beads Beckman Coulter Cat#A63880 Other LS Columns MILTENYI BIOTEC Cat#130-042-401 MACS SmartStrainers (30 μm) MILTENYI BIOTEC Cat#130-098-458 MACS SmartStrainers (70 μm) MILTENYI BIOTEC Cat#130-098-462 MACS SmartStrainers (100 μm) MILTENYI BIOTEC Cat#130-098-463 GentleMACS C Tubes MILTENYI BIOTEC Cat#130-093-237 Eppendorf® LoBind® Tubes BD Biosciences Cat#570751 Hemocytometer NANOENTEK Cat#DHC-N01 Hemocytometer adapter BD Biosciences Cat#633703 Centrifuge and rotor with adapters for 5-mL Falcon® tubes and 15-mL tubes. ..
Magnetic Beads:Article Title: Protocol for minimized-bias profiling of liver and visceral adipose tissue in mice using integrated single-nucleus RNA sequencing.
Article Snippet: .. Biological samples Male wild-type C57BL/6J mice, 8 weeks old at diet initiation; tissues collected after 26 weeks of western diet feeding Janvier Labs Ethics approval #47097-2024012516265646 v4 Chemicals, peptides, and recombinant proteins PBS Gibco Cat#10010023 DMEM Gibco Cat#10566016 Absolute ethanol Major supplier N/A Nuclease-free water Major supplier N/A DAPI Staining Solution MILTENYI BIOTEC Cat#130-111-570 RNase inhibitor, 40000 U/mL New England Biolabs Cat#M0314 BD Stain Buffer (FBS) BD Biosciences Cat#554656 Proteinase K, 800 U/mL New England Biolabs Cat#P8107S Vybrant® DyeCycleTM Green Stain Thermo Fisher Cat#V35004 Critical commercial assays Nuclei Extraction Buffer MILTENYI BIOTEC Cat#130-128-024 Liver Dissociation Kit, mouse MILTENYI BIOTEC Cat130-105-807 Anti-Nucleus MicroBeads MILTENYI BIOTEC Cat#130-132-997 BD RhapsodyTM cDNA Kit BD Biosciences Cat#633773 BD RhapsodyTM Enhanced Cartridge Reagent Kit BD Biosciences Cat#667052 BD RhapsodyTM 8-Lane Cartridge BD Biosciences Cat#666262 BD RhapsodyTM WTA Amplification Kit BD Biosciences Cat#633801 QubitTM dsDNA HS Assay Kit Thermo Fisher Cat#Q32851 Agilent High Sensitivity DNA Kit Agilent Cat#5067-4626 MACS BSA Stock Solution MILTENYI BIOTEC Cat#130-091-376 BD® OMICS-One Dual Index Kit BD Biosciences Cat#571899 Agencourt® AMPure® XP magnetic beads Beckman Coulter Cat#A63880 Other LS Columns MILTENYI BIOTEC Cat#130-042-401 MACS SmartStrainers (30 μm) MILTENYI BIOTEC Cat#130-098-458 MACS SmartStrainers (70 μm) MILTENYI BIOTEC Cat#130-098-462 MACS SmartStrainers (100 μm) MILTENYI BIOTEC Cat#130-098-463 GentleMACS C Tubes MILTENYI BIOTEC Cat#130-093-237 Eppendorf® LoBind® Tubes BD Biosciences Cat#570751 Hemocytometer NANOENTEK Cat#DHC-N01 Hemocytometer adapter BD Biosciences Cat#633703 Centrifuge and rotor with adapters for 5-mL Falcon® tubes and 15-mL tubes. ..
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