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visium spatial tissue optimization kit  (10X Genomics)

 
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    10X Genomics visium spatial tissue optimization kit
    Visium Spatial Tissue Optimization Kit, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/visium+spatial+tissue+optimization+kit/pm42265746-67-8-6
    Average 86 stars, based on 1 article reviews
    visium spatial tissue optimization kit - by Bioz Stars, 2026-09
    86/100 stars

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    Related Articles

    Reverse Transcription:

    Article Title: A method utilizing chemical carcinogens and a Western diet to reliably induce advanced hepatocellular carcinoma in male and female mice.
    Article Snippet: .. Reverse transcription was performed using the 10X Genomics Visium Spatial Tissue Optimization Kit, relying on oligo-dt primers seeded in 55 μm diameter capture spots on the Visium slide. ..

    Article Title: Spatial multiomics reveals a subpopulation of fibroblasts associated with cancer stemness in human hepatocellular carcinoma.
    Article Snippet: Slides were finally taken on a Leica SCN400 F whole-slide scanner at 40 × resolution. .. After capturing ideal tissue morphology information and ensuring that RNA was not degraded (RIN ≥ 7), tissue permeabilization and reverse transcription were immediately conducted by a Visium Spatial Tissue Optimization Kit (10X Genomics). .. Finally, the library was prepared with secondstrand synthesis and denaturation and sequenced by NovaSeq 6000 (Illumina).

    Mutagenesis:

    Article Title: Integrative spatial analysis reveals a multi-layered organization of glioblastoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S3 for list of all primary antibodies used in CODEX panel N/A N/A Cy 2 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-225-152; RRID: AB_2340612 Cy 3 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-165-152; RRID: AB_2307443 Cy 3 AffiniPure Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat #712-165-153; RRID: AB_2340667 Cy 3 AffiniPure Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat #715-165-150: RRID: AB_2340813 Alexa Fluor 680 AffiniPure Donkey Anti-Goat IgG (H+L) Jackson ImmunoResearch Cat #705-625-147; RRID: AB_2340440 Biological samples Human glioblastoma samples University Hospital Zurich N/A Human glioblastoma and IDH mutant glioma samples Massachusetts General Hospital/Brigham and Women’s Hospital N/A Human glioblastoma organoid model BWH911 Dana Farber Cancer Institute N/A Chemicals, peptides, and recombinant proteins OCT Compound Scigen Cat #4586 Aqueous Eosin Y solution Millipore Sigma Cat #HT110216 Mayer’s Hematoxylin Millipore Sigma Cat #MHS16 Bluing Buffer Dako Cat #CS70230-2 SPRI Select Reagent Beckman Coulter Cat #B23318 DMEM/F-12 ThermoFisher Scientific Cat #11320033 MEM non-essential amino acids ThermoFisher Scientific Cat #11140050 Neurobasal medium ThermoFisher Scientific Cat # 21103049 Critical commercial assays Quick RNA Microprep Kit Zymo Cat #ZR-R1051 Tapestation RNA Screen Tape Agilent Cat #5067-5576 Tapestation High Sensitivity D5000 Screen Tape Agilent Cat #5067-5592 Tapestation High Sensitivity D1000 Screen Tape Agilent Cat #5067-5584 Visium Spatial Tissue Optimization Kit 10X Genomics Cat # PN-1000193 Visium Accessory Kit 10X Genomics Cat #PN-1000194 Dual Index Kit TT Set A 10X Genomics Cat #PN-1000215 Novaseq SP 100 Cycles Sequencing Kit Illumina Cat #20028401 Visium Spatial Gene Expression Slide and Reagent Kit 10X Genomics Cat # PN-1000184 FAST SYBR qPCR Master Mix KAPA Biosystems Cat # KK4600 NEBNext Library Quanit Kit for Illumina New England Biolabs Cat # E7630L Conjugation Kit Akoya Biosciences Cat # 7000009 Staining Kit Akoya Biosciences Cat # 7000008 CODEX buffer Akoya Biosciences Cat # 7000001 Nuclear stain Akoya Biosciences Cat # 7000003 Assay reagents Akoya Biosciences Cat # 7000002 Software and algorithms 10x Genomics SpaceRanger 1.0 and 1.1 10X Genomics N/A (Continued on next page) e1 Cell 187, 2485–2501.e1–e10, May 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Genomics Loupe Browser 5.0.1 10X Genomics N/A Seurat 4.3.0 Hao et al.52 https://github.com/cran/Seurat Scalop J. Laffy, Tirosh Lab https://github.com/jlaffy/scalop Cytoscape 3.9.1 Shannon et al.53 https://cytoscape.org QuPath Bankhead et al.54 https://qupath.github.io/ StarDist Schmidt et al.55 https://github.com/stardist/stardist imcRtools Eiling et al.56 https://github.com/BodenmillerGroup/imcRtools R 4.1.1 N/A https://cran.r-project.org/bin/ windows/base/old/4.1.1/ NMF Gaujoux, Seoighe et al.57 https://cran.r-project.org/ web/ packages/NMF/index.html MASS Venables WN, Ripley BD.

    Recombinant:

    Article Title: Integrative spatial analysis reveals a multi-layered organization of glioblastoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S3 for list of all primary antibodies used in CODEX panel N/A N/A Cy 2 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-225-152; RRID: AB_2340612 Cy 3 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-165-152; RRID: AB_2307443 Cy 3 AffiniPure Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat #712-165-153; RRID: AB_2340667 Cy 3 AffiniPure Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat #715-165-150: RRID: AB_2340813 Alexa Fluor 680 AffiniPure Donkey Anti-Goat IgG (H+L) Jackson ImmunoResearch Cat #705-625-147; RRID: AB_2340440 Biological samples Human glioblastoma samples University Hospital Zurich N/A Human glioblastoma and IDH mutant glioma samples Massachusetts General Hospital/Brigham and Women’s Hospital N/A Human glioblastoma organoid model BWH911 Dana Farber Cancer Institute N/A Chemicals, peptides, and recombinant proteins OCT Compound Scigen Cat #4586 Aqueous Eosin Y solution Millipore Sigma Cat #HT110216 Mayer’s Hematoxylin Millipore Sigma Cat #MHS16 Bluing Buffer Dako Cat #CS70230-2 SPRI Select Reagent Beckman Coulter Cat #B23318 DMEM/F-12 ThermoFisher Scientific Cat #11320033 MEM non-essential amino acids ThermoFisher Scientific Cat #11140050 Neurobasal medium ThermoFisher Scientific Cat # 21103049 Critical commercial assays Quick RNA Microprep Kit Zymo Cat #ZR-R1051 Tapestation RNA Screen Tape Agilent Cat #5067-5576 Tapestation High Sensitivity D5000 Screen Tape Agilent Cat #5067-5592 Tapestation High Sensitivity D1000 Screen Tape Agilent Cat #5067-5584 Visium Spatial Tissue Optimization Kit 10X Genomics Cat # PN-1000193 Visium Accessory Kit 10X Genomics Cat #PN-1000194 Dual Index Kit TT Set A 10X Genomics Cat #PN-1000215 Novaseq SP 100 Cycles Sequencing Kit Illumina Cat #20028401 Visium Spatial Gene Expression Slide and Reagent Kit 10X Genomics Cat # PN-1000184 FAST SYBR qPCR Master Mix KAPA Biosystems Cat # KK4600 NEBNext Library Quanit Kit for Illumina New England Biolabs Cat # E7630L Conjugation Kit Akoya Biosciences Cat # 7000009 Staining Kit Akoya Biosciences Cat # 7000008 CODEX buffer Akoya Biosciences Cat # 7000001 Nuclear stain Akoya Biosciences Cat # 7000003 Assay reagents Akoya Biosciences Cat # 7000002 Software and algorithms 10x Genomics SpaceRanger 1.0 and 1.1 10X Genomics N/A (Continued on next page) e1 Cell 187, 2485–2501.e1–e10, May 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Genomics Loupe Browser 5.0.1 10X Genomics N/A Seurat 4.3.0 Hao et al.52 https://github.com/cran/Seurat Scalop J. Laffy, Tirosh Lab https://github.com/jlaffy/scalop Cytoscape 3.9.1 Shannon et al.53 https://cytoscape.org QuPath Bankhead et al.54 https://qupath.github.io/ StarDist Schmidt et al.55 https://github.com/stardist/stardist imcRtools Eiling et al.56 https://github.com/BodenmillerGroup/imcRtools R 4.1.1 N/A https://cran.r-project.org/bin/ windows/base/old/4.1.1/ NMF Gaujoux, Seoighe et al.57 https://cran.r-project.org/ web/ packages/NMF/index.html MASS Venables WN, Ripley BD.

    Sequencing:

    Article Title: Integrative spatial analysis reveals a multi-layered organization of glioblastoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S3 for list of all primary antibodies used in CODEX panel N/A N/A Cy 2 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-225-152; RRID: AB_2340612 Cy 3 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-165-152; RRID: AB_2307443 Cy 3 AffiniPure Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat #712-165-153; RRID: AB_2340667 Cy 3 AffiniPure Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat #715-165-150: RRID: AB_2340813 Alexa Fluor 680 AffiniPure Donkey Anti-Goat IgG (H+L) Jackson ImmunoResearch Cat #705-625-147; RRID: AB_2340440 Biological samples Human glioblastoma samples University Hospital Zurich N/A Human glioblastoma and IDH mutant glioma samples Massachusetts General Hospital/Brigham and Women’s Hospital N/A Human glioblastoma organoid model BWH911 Dana Farber Cancer Institute N/A Chemicals, peptides, and recombinant proteins OCT Compound Scigen Cat #4586 Aqueous Eosin Y solution Millipore Sigma Cat #HT110216 Mayer’s Hematoxylin Millipore Sigma Cat #MHS16 Bluing Buffer Dako Cat #CS70230-2 SPRI Select Reagent Beckman Coulter Cat #B23318 DMEM/F-12 ThermoFisher Scientific Cat #11320033 MEM non-essential amino acids ThermoFisher Scientific Cat #11140050 Neurobasal medium ThermoFisher Scientific Cat # 21103049 Critical commercial assays Quick RNA Microprep Kit Zymo Cat #ZR-R1051 Tapestation RNA Screen Tape Agilent Cat #5067-5576 Tapestation High Sensitivity D5000 Screen Tape Agilent Cat #5067-5592 Tapestation High Sensitivity D1000 Screen Tape Agilent Cat #5067-5584 Visium Spatial Tissue Optimization Kit 10X Genomics Cat # PN-1000193 Visium Accessory Kit 10X Genomics Cat #PN-1000194 Dual Index Kit TT Set A 10X Genomics Cat #PN-1000215 Novaseq SP 100 Cycles Sequencing Kit Illumina Cat #20028401 Visium Spatial Gene Expression Slide and Reagent Kit 10X Genomics Cat # PN-1000184 FAST SYBR qPCR Master Mix KAPA Biosystems Cat # KK4600 NEBNext Library Quanit Kit for Illumina New England Biolabs Cat # E7630L Conjugation Kit Akoya Biosciences Cat # 7000009 Staining Kit Akoya Biosciences Cat # 7000008 CODEX buffer Akoya Biosciences Cat # 7000001 Nuclear stain Akoya Biosciences Cat # 7000003 Assay reagents Akoya Biosciences Cat # 7000002 Software and algorithms 10x Genomics SpaceRanger 1.0 and 1.1 10X Genomics N/A (Continued on next page) e1 Cell 187, 2485–2501.e1–e10, May 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Genomics Loupe Browser 5.0.1 10X Genomics N/A Seurat 4.3.0 Hao et al.52 https://github.com/cran/Seurat Scalop J. Laffy, Tirosh Lab https://github.com/jlaffy/scalop Cytoscape 3.9.1 Shannon et al.53 https://cytoscape.org QuPath Bankhead et al.54 https://qupath.github.io/ StarDist Schmidt et al.55 https://github.com/stardist/stardist imcRtools Eiling et al.56 https://github.com/BodenmillerGroup/imcRtools R 4.1.1 N/A https://cran.r-project.org/bin/ windows/base/old/4.1.1/ NMF Gaujoux, Seoighe et al.57 https://cran.r-project.org/ web/ packages/NMF/index.html MASS Venables WN, Ripley BD.

    Gene Expression:

    Article Title: Integrative spatial analysis reveals a multi-layered organization of glioblastoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S3 for list of all primary antibodies used in CODEX panel N/A N/A Cy 2 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-225-152; RRID: AB_2340612 Cy 3 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-165-152; RRID: AB_2307443 Cy 3 AffiniPure Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat #712-165-153; RRID: AB_2340667 Cy 3 AffiniPure Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat #715-165-150: RRID: AB_2340813 Alexa Fluor 680 AffiniPure Donkey Anti-Goat IgG (H+L) Jackson ImmunoResearch Cat #705-625-147; RRID: AB_2340440 Biological samples Human glioblastoma samples University Hospital Zurich N/A Human glioblastoma and IDH mutant glioma samples Massachusetts General Hospital/Brigham and Women’s Hospital N/A Human glioblastoma organoid model BWH911 Dana Farber Cancer Institute N/A Chemicals, peptides, and recombinant proteins OCT Compound Scigen Cat #4586 Aqueous Eosin Y solution Millipore Sigma Cat #HT110216 Mayer’s Hematoxylin Millipore Sigma Cat #MHS16 Bluing Buffer Dako Cat #CS70230-2 SPRI Select Reagent Beckman Coulter Cat #B23318 DMEM/F-12 ThermoFisher Scientific Cat #11320033 MEM non-essential amino acids ThermoFisher Scientific Cat #11140050 Neurobasal medium ThermoFisher Scientific Cat # 21103049 Critical commercial assays Quick RNA Microprep Kit Zymo Cat #ZR-R1051 Tapestation RNA Screen Tape Agilent Cat #5067-5576 Tapestation High Sensitivity D5000 Screen Tape Agilent Cat #5067-5592 Tapestation High Sensitivity D1000 Screen Tape Agilent Cat #5067-5584 Visium Spatial Tissue Optimization Kit 10X Genomics Cat # PN-1000193 Visium Accessory Kit 10X Genomics Cat #PN-1000194 Dual Index Kit TT Set A 10X Genomics Cat #PN-1000215 Novaseq SP 100 Cycles Sequencing Kit Illumina Cat #20028401 Visium Spatial Gene Expression Slide and Reagent Kit 10X Genomics Cat # PN-1000184 FAST SYBR qPCR Master Mix KAPA Biosystems Cat # KK4600 NEBNext Library Quanit Kit for Illumina New England Biolabs Cat # E7630L Conjugation Kit Akoya Biosciences Cat # 7000009 Staining Kit Akoya Biosciences Cat # 7000008 CODEX buffer Akoya Biosciences Cat # 7000001 Nuclear stain Akoya Biosciences Cat # 7000003 Assay reagents Akoya Biosciences Cat # 7000002 Software and algorithms 10x Genomics SpaceRanger 1.0 and 1.1 10X Genomics N/A (Continued on next page) e1 Cell 187, 2485–2501.e1–e10, May 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Genomics Loupe Browser 5.0.1 10X Genomics N/A Seurat 4.3.0 Hao et al.52 https://github.com/cran/Seurat Scalop J. Laffy, Tirosh Lab https://github.com/jlaffy/scalop Cytoscape 3.9.1 Shannon et al.53 https://cytoscape.org QuPath Bankhead et al.54 https://qupath.github.io/ StarDist Schmidt et al.55 https://github.com/stardist/stardist imcRtools Eiling et al.56 https://github.com/BodenmillerGroup/imcRtools R 4.1.1 N/A https://cran.r-project.org/bin/ windows/base/old/4.1.1/ NMF Gaujoux, Seoighe et al.57 https://cran.r-project.org/ web/ packages/NMF/index.html MASS Venables WN, Ripley BD.

    Real-time Polymerase Chain Reaction:

    Article Title: Integrative spatial analysis reveals a multi-layered organization of glioblastoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S3 for list of all primary antibodies used in CODEX panel N/A N/A Cy 2 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-225-152; RRID: AB_2340612 Cy 3 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-165-152; RRID: AB_2307443 Cy 3 AffiniPure Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat #712-165-153; RRID: AB_2340667 Cy 3 AffiniPure Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat #715-165-150: RRID: AB_2340813 Alexa Fluor 680 AffiniPure Donkey Anti-Goat IgG (H+L) Jackson ImmunoResearch Cat #705-625-147; RRID: AB_2340440 Biological samples Human glioblastoma samples University Hospital Zurich N/A Human glioblastoma and IDH mutant glioma samples Massachusetts General Hospital/Brigham and Women’s Hospital N/A Human glioblastoma organoid model BWH911 Dana Farber Cancer Institute N/A Chemicals, peptides, and recombinant proteins OCT Compound Scigen Cat #4586 Aqueous Eosin Y solution Millipore Sigma Cat #HT110216 Mayer’s Hematoxylin Millipore Sigma Cat #MHS16 Bluing Buffer Dako Cat #CS70230-2 SPRI Select Reagent Beckman Coulter Cat #B23318 DMEM/F-12 ThermoFisher Scientific Cat #11320033 MEM non-essential amino acids ThermoFisher Scientific Cat #11140050 Neurobasal medium ThermoFisher Scientific Cat # 21103049 Critical commercial assays Quick RNA Microprep Kit Zymo Cat #ZR-R1051 Tapestation RNA Screen Tape Agilent Cat #5067-5576 Tapestation High Sensitivity D5000 Screen Tape Agilent Cat #5067-5592 Tapestation High Sensitivity D1000 Screen Tape Agilent Cat #5067-5584 Visium Spatial Tissue Optimization Kit 10X Genomics Cat # PN-1000193 Visium Accessory Kit 10X Genomics Cat #PN-1000194 Dual Index Kit TT Set A 10X Genomics Cat #PN-1000215 Novaseq SP 100 Cycles Sequencing Kit Illumina Cat #20028401 Visium Spatial Gene Expression Slide and Reagent Kit 10X Genomics Cat # PN-1000184 FAST SYBR qPCR Master Mix KAPA Biosystems Cat # KK4600 NEBNext Library Quanit Kit for Illumina New England Biolabs Cat # E7630L Conjugation Kit Akoya Biosciences Cat # 7000009 Staining Kit Akoya Biosciences Cat # 7000008 CODEX buffer Akoya Biosciences Cat # 7000001 Nuclear stain Akoya Biosciences Cat # 7000003 Assay reagents Akoya Biosciences Cat # 7000002 Software and algorithms 10x Genomics SpaceRanger 1.0 and 1.1 10X Genomics N/A (Continued on next page) e1 Cell 187, 2485–2501.e1–e10, May 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Genomics Loupe Browser 5.0.1 10X Genomics N/A Seurat 4.3.0 Hao et al.52 https://github.com/cran/Seurat Scalop J. Laffy, Tirosh Lab https://github.com/jlaffy/scalop Cytoscape 3.9.1 Shannon et al.53 https://cytoscape.org QuPath Bankhead et al.54 https://qupath.github.io/ StarDist Schmidt et al.55 https://github.com/stardist/stardist imcRtools Eiling et al.56 https://github.com/BodenmillerGroup/imcRtools R 4.1.1 N/A https://cran.r-project.org/bin/ windows/base/old/4.1.1/ NMF Gaujoux, Seoighe et al.57 https://cran.r-project.org/ web/ packages/NMF/index.html MASS Venables WN, Ripley BD.

    Conjugation Assay:

    Article Title: Integrative spatial analysis reveals a multi-layered organization of glioblastoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S3 for list of all primary antibodies used in CODEX panel N/A N/A Cy 2 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-225-152; RRID: AB_2340612 Cy 3 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-165-152; RRID: AB_2307443 Cy 3 AffiniPure Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat #712-165-153; RRID: AB_2340667 Cy 3 AffiniPure Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat #715-165-150: RRID: AB_2340813 Alexa Fluor 680 AffiniPure Donkey Anti-Goat IgG (H+L) Jackson ImmunoResearch Cat #705-625-147; RRID: AB_2340440 Biological samples Human glioblastoma samples University Hospital Zurich N/A Human glioblastoma and IDH mutant glioma samples Massachusetts General Hospital/Brigham and Women’s Hospital N/A Human glioblastoma organoid model BWH911 Dana Farber Cancer Institute N/A Chemicals, peptides, and recombinant proteins OCT Compound Scigen Cat #4586 Aqueous Eosin Y solution Millipore Sigma Cat #HT110216 Mayer’s Hematoxylin Millipore Sigma Cat #MHS16 Bluing Buffer Dako Cat #CS70230-2 SPRI Select Reagent Beckman Coulter Cat #B23318 DMEM/F-12 ThermoFisher Scientific Cat #11320033 MEM non-essential amino acids ThermoFisher Scientific Cat #11140050 Neurobasal medium ThermoFisher Scientific Cat # 21103049 Critical commercial assays Quick RNA Microprep Kit Zymo Cat #ZR-R1051 Tapestation RNA Screen Tape Agilent Cat #5067-5576 Tapestation High Sensitivity D5000 Screen Tape Agilent Cat #5067-5592 Tapestation High Sensitivity D1000 Screen Tape Agilent Cat #5067-5584 Visium Spatial Tissue Optimization Kit 10X Genomics Cat # PN-1000193 Visium Accessory Kit 10X Genomics Cat #PN-1000194 Dual Index Kit TT Set A 10X Genomics Cat #PN-1000215 Novaseq SP 100 Cycles Sequencing Kit Illumina Cat #20028401 Visium Spatial Gene Expression Slide and Reagent Kit 10X Genomics Cat # PN-1000184 FAST SYBR qPCR Master Mix KAPA Biosystems Cat # KK4600 NEBNext Library Quanit Kit for Illumina New England Biolabs Cat # E7630L Conjugation Kit Akoya Biosciences Cat # 7000009 Staining Kit Akoya Biosciences Cat # 7000008 CODEX buffer Akoya Biosciences Cat # 7000001 Nuclear stain Akoya Biosciences Cat # 7000003 Assay reagents Akoya Biosciences Cat # 7000002 Software and algorithms 10x Genomics SpaceRanger 1.0 and 1.1 10X Genomics N/A (Continued on next page) e1 Cell 187, 2485–2501.e1–e10, May 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Genomics Loupe Browser 5.0.1 10X Genomics N/A Seurat 4.3.0 Hao et al.52 https://github.com/cran/Seurat Scalop J. Laffy, Tirosh Lab https://github.com/jlaffy/scalop Cytoscape 3.9.1 Shannon et al.53 https://cytoscape.org QuPath Bankhead et al.54 https://qupath.github.io/ StarDist Schmidt et al.55 https://github.com/stardist/stardist imcRtools Eiling et al.56 https://github.com/BodenmillerGroup/imcRtools R 4.1.1 N/A https://cran.r-project.org/bin/ windows/base/old/4.1.1/ NMF Gaujoux, Seoighe et al.57 https://cran.r-project.org/ web/ packages/NMF/index.html MASS Venables WN, Ripley BD.

    Staining:

    Article Title: Integrative spatial analysis reveals a multi-layered organization of glioblastoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S3 for list of all primary antibodies used in CODEX panel N/A N/A Cy 2 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-225-152; RRID: AB_2340612 Cy 3 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-165-152; RRID: AB_2307443 Cy 3 AffiniPure Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat #712-165-153; RRID: AB_2340667 Cy 3 AffiniPure Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat #715-165-150: RRID: AB_2340813 Alexa Fluor 680 AffiniPure Donkey Anti-Goat IgG (H+L) Jackson ImmunoResearch Cat #705-625-147; RRID: AB_2340440 Biological samples Human glioblastoma samples University Hospital Zurich N/A Human glioblastoma and IDH mutant glioma samples Massachusetts General Hospital/Brigham and Women’s Hospital N/A Human glioblastoma organoid model BWH911 Dana Farber Cancer Institute N/A Chemicals, peptides, and recombinant proteins OCT Compound Scigen Cat #4586 Aqueous Eosin Y solution Millipore Sigma Cat #HT110216 Mayer’s Hematoxylin Millipore Sigma Cat #MHS16 Bluing Buffer Dako Cat #CS70230-2 SPRI Select Reagent Beckman Coulter Cat #B23318 DMEM/F-12 ThermoFisher Scientific Cat #11320033 MEM non-essential amino acids ThermoFisher Scientific Cat #11140050 Neurobasal medium ThermoFisher Scientific Cat # 21103049 Critical commercial assays Quick RNA Microprep Kit Zymo Cat #ZR-R1051 Tapestation RNA Screen Tape Agilent Cat #5067-5576 Tapestation High Sensitivity D5000 Screen Tape Agilent Cat #5067-5592 Tapestation High Sensitivity D1000 Screen Tape Agilent Cat #5067-5584 Visium Spatial Tissue Optimization Kit 10X Genomics Cat # PN-1000193 Visium Accessory Kit 10X Genomics Cat #PN-1000194 Dual Index Kit TT Set A 10X Genomics Cat #PN-1000215 Novaseq SP 100 Cycles Sequencing Kit Illumina Cat #20028401 Visium Spatial Gene Expression Slide and Reagent Kit 10X Genomics Cat # PN-1000184 FAST SYBR qPCR Master Mix KAPA Biosystems Cat # KK4600 NEBNext Library Quanit Kit for Illumina New England Biolabs Cat # E7630L Conjugation Kit Akoya Biosciences Cat # 7000009 Staining Kit Akoya Biosciences Cat # 7000008 CODEX buffer Akoya Biosciences Cat # 7000001 Nuclear stain Akoya Biosciences Cat # 7000003 Assay reagents Akoya Biosciences Cat # 7000002 Software and algorithms 10x Genomics SpaceRanger 1.0 and 1.1 10X Genomics N/A (Continued on next page) e1 Cell 187, 2485–2501.e1–e10, May 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Genomics Loupe Browser 5.0.1 10X Genomics N/A Seurat 4.3.0 Hao et al.52 https://github.com/cran/Seurat Scalop J. Laffy, Tirosh Lab https://github.com/jlaffy/scalop Cytoscape 3.9.1 Shannon et al.53 https://cytoscape.org QuPath Bankhead et al.54 https://qupath.github.io/ StarDist Schmidt et al.55 https://github.com/stardist/stardist imcRtools Eiling et al.56 https://github.com/BodenmillerGroup/imcRtools R 4.1.1 N/A https://cran.r-project.org/bin/ windows/base/old/4.1.1/ NMF Gaujoux, Seoighe et al.57 https://cran.r-project.org/ web/ packages/NMF/index.html MASS Venables WN, Ripley BD.

    Software:

    Article Title: Integrative spatial analysis reveals a multi-layered organization of glioblastoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S3 for list of all primary antibodies used in CODEX panel N/A N/A Cy 2 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-225-152; RRID: AB_2340612 Cy 3 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch Cat #711-165-152; RRID: AB_2307443 Cy 3 AffiniPure Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat #712-165-153; RRID: AB_2340667 Cy 3 AffiniPure Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat #715-165-150: RRID: AB_2340813 Alexa Fluor 680 AffiniPure Donkey Anti-Goat IgG (H+L) Jackson ImmunoResearch Cat #705-625-147; RRID: AB_2340440 Biological samples Human glioblastoma samples University Hospital Zurich N/A Human glioblastoma and IDH mutant glioma samples Massachusetts General Hospital/Brigham and Women’s Hospital N/A Human glioblastoma organoid model BWH911 Dana Farber Cancer Institute N/A Chemicals, peptides, and recombinant proteins OCT Compound Scigen Cat #4586 Aqueous Eosin Y solution Millipore Sigma Cat #HT110216 Mayer’s Hematoxylin Millipore Sigma Cat #MHS16 Bluing Buffer Dako Cat #CS70230-2 SPRI Select Reagent Beckman Coulter Cat #B23318 DMEM/F-12 ThermoFisher Scientific Cat #11320033 MEM non-essential amino acids ThermoFisher Scientific Cat #11140050 Neurobasal medium ThermoFisher Scientific Cat # 21103049 Critical commercial assays Quick RNA Microprep Kit Zymo Cat #ZR-R1051 Tapestation RNA Screen Tape Agilent Cat #5067-5576 Tapestation High Sensitivity D5000 Screen Tape Agilent Cat #5067-5592 Tapestation High Sensitivity D1000 Screen Tape Agilent Cat #5067-5584 Visium Spatial Tissue Optimization Kit 10X Genomics Cat # PN-1000193 Visium Accessory Kit 10X Genomics Cat #PN-1000194 Dual Index Kit TT Set A 10X Genomics Cat #PN-1000215 Novaseq SP 100 Cycles Sequencing Kit Illumina Cat #20028401 Visium Spatial Gene Expression Slide and Reagent Kit 10X Genomics Cat # PN-1000184 FAST SYBR qPCR Master Mix KAPA Biosystems Cat # KK4600 NEBNext Library Quanit Kit for Illumina New England Biolabs Cat # E7630L Conjugation Kit Akoya Biosciences Cat # 7000009 Staining Kit Akoya Biosciences Cat # 7000008 CODEX buffer Akoya Biosciences Cat # 7000001 Nuclear stain Akoya Biosciences Cat # 7000003 Assay reagents Akoya Biosciences Cat # 7000002 Software and algorithms 10x Genomics SpaceRanger 1.0 and 1.1 10X Genomics N/A (Continued on next page) e1 Cell 187, 2485–2501.e1–e10, May 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Genomics Loupe Browser 5.0.1 10X Genomics N/A Seurat 4.3.0 Hao et al.52 https://github.com/cran/Seurat Scalop J. Laffy, Tirosh Lab https://github.com/jlaffy/scalop Cytoscape 3.9.1 Shannon et al.53 https://cytoscape.org QuPath Bankhead et al.54 https://qupath.github.io/ StarDist Schmidt et al.55 https://github.com/stardist/stardist imcRtools Eiling et al.56 https://github.com/BodenmillerGroup/imcRtools R 4.1.1 N/A https://cran.r-project.org/bin/ windows/base/old/4.1.1/ NMF Gaujoux, Seoighe et al.57 https://cran.r-project.org/ web/ packages/NMF/index.html MASS Venables WN, Ripley BD.



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    Journal: JCI Insight

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    Techniques: Comparison, Expressing, Control, Modification, Marker, Single Cell, RNA Sequencing, MANN-WHITNEY