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nuclei extraction buffer miltenyi biotec  (Miltenyi Biotec)


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    Structured Review

    Miltenyi Biotec nuclei extraction buffer miltenyi biotec
    Nuclei Extraction Buffer Miltenyi Biotec, supplied by Miltenyi Biotec, used in various techniques. Bioz Stars score: 96/100, based on 120 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/extraction+buffer/Nuclei+Extraction+Buffer/pm42804364-61-53-56
    Average 96 stars, based on 120 article reviews
    nuclei extraction buffer miltenyi biotec - by Bioz Stars, 2026-11
    96/100 stars

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    Related Articles

    Tissue:

    Article Title: Single-nucleus transcriptomic analysis reveals subfield-specific cell-to-cell synaptic reorganisation of the mouse hippocampus in focal temporal lobe epilepsy.
    Article Snippet: Qualitative images were processed using ImageJ version 1.54 by Fiji [27]. .. Frozen ipsilateral hippocampal tissue samples were placed in 2 ml of Nuclei Extraction Buffer (Miltenyi, 130- 128-024) containing 0.2 U/μl RNAse inhibitor (Enzymatics, Y9240L) inside gentleMACS C Tubes (Miltenyi, 130-093-23) and then dissociated using a gentleMACS octo dissociator (Miltenyi, 130-096-427) with the preinstalled “Nuclei 4 C” program. .. The lysate was filtered through 100 μm MACS SmartStrainers (Miltenyi, 130- 098-463) and centrifuged at 300 x g for 5 min at 4 °C.

    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: VEGFR-2 blocker induces pulmonary vascular disease in rats with CRISPR-edited human non-deficient G6PD polymorphism: role of 3D genomic modifications and DNA methylation.
    Article Snippet: Department of Pharmacology, New York Medical College, Valhalla, New York, USA Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA Department of Cardiology, Heart and Vascular Institute, Westchester Medical Center, Valhalla, New York, USA

    Extraction:

    Article Title: Single-nucleus transcriptomic analysis reveals subfield-specific cell-to-cell synaptic reorganisation of the mouse hippocampus in focal temporal lobe epilepsy.
    Article Snippet: Qualitative images were processed using ImageJ version 1.54 by Fiji [27]. .. Frozen ipsilateral hippocampal tissue samples were placed in 2 ml of Nuclei Extraction Buffer (Miltenyi, 130- 128-024) containing 0.2 U/μl RNAse inhibitor (Enzymatics, Y9240L) inside gentleMACS C Tubes (Miltenyi, 130-093-23) and then dissociated using a gentleMACS octo dissociator (Miltenyi, 130-096-427) with the preinstalled “Nuclei 4 C” program. .. The lysate was filtered through 100 μm MACS SmartStrainers (Miltenyi, 130- 098-463) and centrifuged at 300 x g for 5 min at 4 °C.

    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: VEGFR-2 blocker induces pulmonary vascular disease in rats with CRISPR-edited human non-deficient G6PD polymorphism: role of 3D genomic modifications and DNA methylation.
    Article Snippet: Department of Pharmacology, New York Medical College, Valhalla, New York, USA Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA Department of Cardiology, Heart and Vascular Institute, Westchester Medical Center, Valhalla, New York, USA

    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: Molecular Signatures of HIV‐Induced Neuroinflammation and Neurodegeneration in Human Cerebral Organoids: Identification of Therapeutic Targets for NeuroHIV
    Article Snippet: .. For single‐nucleus ATAC sequencing (snATAC‐seq), nuclei were isolated using Nuclei Extraction Buffer (130‐128‐024, Miltenyi Biotec) supplemented with a protease inhibitor cocktail (5892791001; Roche). ..

    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: Single-cell and spatial omics reveals region-specific plasticity and therapeutic vulnerabilities in metastatic high-risk neuroblastoma
    Article Snippet: .. Snap-frozen human NBL specimens were lysed in ice-cold nuclei lysis buffer (Nuclei Extraction Buffer (Miltenyi Biotec) containing dithiothreitol (DTT) (Sigma-Aldrich) and (RNase) inhibitor (Sigma-Aldrich) for 5 min on a gentleMACS Octo Dissociator at 4°C with agitation. ..

    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). ..

    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). ..

    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). ..

    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). ..

    Isolation:

    Article Title: VEGFR-2 blocker induces pulmonary vascular disease in rats with CRISPR-edited human non-deficient G6PD polymorphism: role of 3D genomic modifications and DNA methylation.
    Article Snippet: Department of Pharmacology, New York Medical College, Valhalla, New York, USA Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA Department of Cardiology, Heart and Vascular Institute, Westchester Medical Center, Valhalla, New York, USA

    Article Title: Molecular Signatures of HIV‐Induced Neuroinflammation and Neurodegeneration in Human Cerebral Organoids: Identification of Therapeutic Targets for NeuroHIV
    Article Snippet: .. For single‐nucleus ATAC sequencing (snATAC‐seq), nuclei were isolated using Nuclei Extraction Buffer (130‐128‐024, Miltenyi Biotec) supplemented with a protease inhibitor cocktail (5892791001; Roche). ..

    Sequencing:

    Article Title: Molecular Signatures of HIV‐Induced Neuroinflammation and Neurodegeneration in Human Cerebral Organoids: Identification of Therapeutic Targets for NeuroHIV
    Article Snippet: .. For single‐nucleus ATAC sequencing (snATAC‐seq), nuclei were isolated using Nuclei Extraction Buffer (130‐128‐024, Miltenyi Biotec) supplemented with a protease inhibitor cocktail (5892791001; Roche). ..

    Protease Inhibitor:

    Article Title: Molecular Signatures of HIV‐Induced Neuroinflammation and Neurodegeneration in Human Cerebral Organoids: Identification of Therapeutic Targets for NeuroHIV
    Article Snippet: .. For single‐nucleus ATAC sequencing (snATAC‐seq), nuclei were isolated using Nuclei Extraction Buffer (130‐128‐024, Miltenyi Biotec) supplemented with a protease inhibitor cocktail (5892791001; Roche). ..

    Lysis:

    Article Title: Single-cell and spatial omics reveals region-specific plasticity and therapeutic vulnerabilities in metastatic high-risk neuroblastoma
    Article Snippet: .. Snap-frozen human NBL specimens were lysed in ice-cold nuclei lysis buffer (Nuclei Extraction Buffer (Miltenyi Biotec) containing dithiothreitol (DTT) (Sigma-Aldrich) and (RNase) inhibitor (Sigma-Aldrich) for 5 min on a gentleMACS Octo Dissociator at 4°C with agitation. ..



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