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pn 1000186 visium library construction kit 10x genomics cat  (10X Genomics)

 
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    10X Genomics pn 1000186 visium library construction kit 10x genomics cat
    Pn 1000186 Visium Library Construction Kit 10x Genomics Cat, 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/libraries+visium/pm39471809-238-65-70
    Average 86 stars, based on 1 article reviews
    pn 1000186 visium library construction kit 10x genomics cat - by Bioz Stars, 2026-10
    86/100 stars

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    Article Title: Region- and cell type-specific changes in gene expression in the cerebellum after classical fear conditioning.
    Article Snippet: The sections were mounted onto the active capture areas of 10x Genomics Visium slides (10x Genomics, PN 1000184) and stored in airtight containers at −80°C until Visium library preparation.

    Sequencing:

    Article Title: Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics.
    Article Snippet: .. In order to assess concordance of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics, we sequenced three 10x Genomics Visium libraries of FFPE ovarian tumor tissues. ..

    Article Title: Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis
    Article Snippet: Following amplification, the cDNA was purified using SPRISelect beads (Agilent, Santa Clara, CA). .. The Visium Library Construction Kit (10X Genomics) was then used to generate Illumina-compatible sequencing libraries with approximately 25% of the total cDNA yield. cDNA amplicon size was optimized, and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. .. The NovaSeq 6000 sequencer (Illumina, San Diego, CA) was used to sequence the amplified libraries on an SP flow cell of 28x10x10x90 to obtain approximately 50,000 reads per spot for each capture area covered by tissue, according to the sequencing requirements in the Visium Spatial Gene Expression manual.

    Spatial Transcriptomics:

    Article Title: Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics.
    Article Snippet: .. In order to assess concordance of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics, we sequenced three 10x Genomics Visium libraries of FFPE ovarian tumor tissues. ..

    Formalin-fixed Paraffin-Embedded:

    Article Title: Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics.
    Article Snippet: .. In order to assess concordance of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics, we sequenced three 10x Genomics Visium libraries of FFPE ovarian tumor tissues. ..

    Article Title: Dissecting Sex‐Specific Pathology in K18‐hACE2 Transgenic Mice Infected With Different SARS‐CoV‐2 Variants
    Article Snippet: .. Visium libraries were prepared according to the Visium Spatial Gene Expression for FFPE User Guide (10x Genomics) and were sequenced at Baylor Genomics and RNA Profiling Core using NextSeq. ..

    Gene Expression:

    Article Title: Dissecting Sex‐Specific Pathology in K18‐hACE2 Transgenic Mice Infected With Different SARS‐CoV‐2 Variants
    Article Snippet: .. Visium libraries were prepared according to the Visium Spatial Gene Expression for FFPE User Guide (10x Genomics) and were sequenced at Baylor Genomics and RNA Profiling Core using NextSeq. ..

    Article Title: Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Polyclonal Anti-AREG LSBio Cat#LS-B13911; RRID:AB_3106998 Mouse Monoclonal Anti-actin (Smooth Muscle)(aSMA) (Clone 1A4) Dako Cat#M0851; RRID: AB_2223500 Mouse Monoclonal Anti-Beta-Catenin (Clone 14) Cell Marque Cat#224M-14; RRID: AB_1158971 Rabbit Monoclonal Anti-Bmi-1 (Clone D20B7) Cell Signaling Technologies Cat#6964; RRID: AB_10828713 Rabbit Monoclonal Anti-CD11b (Clone EP45) BioSB Cat#BSB6441; RRID: AB_3107001 Rabbit Monoclonal Anti-CD3 (Clone EP449E) Invitrogen Cat#MA5-14482; RRID: AB_10985777 Mouse Monoclonal Anti-CD34 Class II (Clone QBEnd10) Dako Cat#M716529-2; RRID: AB_2063006 Mouse Monoclonal Anti-E-Cadherin (Clone 36) BD Biosciences Cat#610182; RRID: AB_397581 Rabbit Monoclonal Anti-EGFR (Clone D38B1) Cell Signaling Technologies Cat#:4267; RRID: AB_2864406 Rabbit Polyclonal Anti-Epcam Abcam Cat#71916; RRID:AB_1603782 Rabbit Monoclonal Anti-Fibroblast Activation Protein (FAP) (Clone EPR20021) Abcam Cat#:207178; RRID:AB_2864720 Guinea Pig Polyclonal Anti-Keratin 14 Progen Cat#03-GP-CK14; RRID:AB_1541011 Mouse Monoclonal Anti-Keratin 18/8 (Clone C51) Cell Signalling Technologies Cat#4546; RRID:AB_2134843 Rabbit Polyclonal Anti-non-muscle Myosin Heavy Chain II-A (Myh9) Biolegend Cat#909802; RRID:AB_291638 Mouse Monoclonal Anti-pan-Cytokeratin (Clone C11) Abcam Cat#ab7753; RRID:AB_306047 Mouse Monoclonal Anti-Pan-Cytokeratin (Clone AE1/AE3) Invitrogen Cat#MA5-13156; RRID:AB_10983023 Rabbit Monoclonal Anti-PDGF Receptor Beta (Clone 28E1) Cell Signalling Technologies Cat#3169; RRID:AB_2162497 Rabbit Monoclonal Anti-Slug (Clone C19G7) Cell Signalling Technologies Cat#9585; RRID:AB_2239535 Rabbit Monoclonal Anti-Sox2 (Clone D6D9) Cell Signalling Technologies Cat#3579; RRID:AB_2195767 Rat Monoclonal Anti-Tenascin C (Clone 578) R&D Cat#MAB2138; RRID:AB_2203818 MouseMonoclonal Anti-vimentin (Clone V9) Santa Cruz Biotechnology Cat#sc-6260; RRID:AB_628437 Biological Samples HNSCC Tumor Microarray 2005–2010 Auria Biobank pathology archive; Routila et al.35 AB15-7642 HNSCC Tumor Microarray 2005–2015 Auria Biobank pathology archive; Mylly et al.36 AB19-6863, ABTMA21-06 (Continued on next page) ll OPEN ACCESS Cell 187, 1–18.e1–e9, December 12, 2024 e1 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Freshly Resected Human HNSCC Tissue Helsinki University Hospital Head and Neck Center N/A Chemicals, Peptides, and Recombinant Proteins A83-01 Tocris Bioscience Cat#2939 TGFß1 R&D Cat#7754-BH Gefitinib Sigma Cat# SML1657 Critical Commercial Assays Lenti-X Packaging Single Shots (VSV-G) Takara Bio Cat#631276 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#PN-1000184 Visium Spatial Gene Expression Reagent Kit 10x Genomics Cat# PN-1000186 Visium Library Construction Kit 10x Genomics Cat#PN-1000190 BD Rhapsody WTA Reagent Kit BD Cat#633802 Illumina NextSeq 500 High Output Kit v2.5 Illumina Cat#20024908 Deposited Data Spatial RNA Sequencing of Eight Tongue Squamous Cell Carcinomas This paper GEO: GSE251902 Single-Cell RNA Sequencing of Human Tongue Squamous Cell Carcinomas in Spheroid Culture with and without Human Cancer Associated Fibroblasts This paper GEO: GSE252265 Experimental Models: Cell Lines UTSCC25 Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC47 Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC74a Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC76a Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A HNSCC Patient-Derived CancerAssociated Fibroblast Line Kaukonen et al.38 N/A Patient-Derived ‘‘Healthy’’ Non-cancerAssociated Fibroblast Line Kaukonen et al.38 N/A UTSCC74-eGFP Tagged Human Tongue Squamous Cell Carcinoma This paper N/A UTSCC76-eGFP Tagged Human Tongue Squamous Cell Carcinoma This paper N/A CAF-MCherry Tagged Human HNSCCDerived Cancer-Associated Fibroblast This paper N/A Experimental Models: Organisms/Strains Mouse: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ Jackson Laboratory Strain#005557; RRID:IMSR_JAX:005557 Recombinant DNA PLVX-EF1a-IRES-mCherry Takara Bio Cat# 631987 pLVX-EF1a-pIRES-EGFP This paper N/A Software and Algorithms AnnData v0.9.1 Virshup et al.39 https://anndata.readthedocs.io/en/latest/ index.html (Continued on next page) ll OPEN ACCESS e2 Cell 187, 1–18.e1–e9, December 12, 2024 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article ..

    Recombinant:

    Article Title: Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Polyclonal Anti-AREG LSBio Cat#LS-B13911; RRID:AB_3106998 Mouse Monoclonal Anti-actin (Smooth Muscle)(aSMA) (Clone 1A4) Dako Cat#M0851; RRID: AB_2223500 Mouse Monoclonal Anti-Beta-Catenin (Clone 14) Cell Marque Cat#224M-14; RRID: AB_1158971 Rabbit Monoclonal Anti-Bmi-1 (Clone D20B7) Cell Signaling Technologies Cat#6964; RRID: AB_10828713 Rabbit Monoclonal Anti-CD11b (Clone EP45) BioSB Cat#BSB6441; RRID: AB_3107001 Rabbit Monoclonal Anti-CD3 (Clone EP449E) Invitrogen Cat#MA5-14482; RRID: AB_10985777 Mouse Monoclonal Anti-CD34 Class II (Clone QBEnd10) Dako Cat#M716529-2; RRID: AB_2063006 Mouse Monoclonal Anti-E-Cadherin (Clone 36) BD Biosciences Cat#610182; RRID: AB_397581 Rabbit Monoclonal Anti-EGFR (Clone D38B1) Cell Signaling Technologies Cat#:4267; RRID: AB_2864406 Rabbit Polyclonal Anti-Epcam Abcam Cat#71916; RRID:AB_1603782 Rabbit Monoclonal Anti-Fibroblast Activation Protein (FAP) (Clone EPR20021) Abcam Cat#:207178; RRID:AB_2864720 Guinea Pig Polyclonal Anti-Keratin 14 Progen Cat#03-GP-CK14; RRID:AB_1541011 Mouse Monoclonal Anti-Keratin 18/8 (Clone C51) Cell Signalling Technologies Cat#4546; RRID:AB_2134843 Rabbit Polyclonal Anti-non-muscle Myosin Heavy Chain II-A (Myh9) Biolegend Cat#909802; RRID:AB_291638 Mouse Monoclonal Anti-pan-Cytokeratin (Clone C11) Abcam Cat#ab7753; RRID:AB_306047 Mouse Monoclonal Anti-Pan-Cytokeratin (Clone AE1/AE3) Invitrogen Cat#MA5-13156; RRID:AB_10983023 Rabbit Monoclonal Anti-PDGF Receptor Beta (Clone 28E1) Cell Signalling Technologies Cat#3169; RRID:AB_2162497 Rabbit Monoclonal Anti-Slug (Clone C19G7) Cell Signalling Technologies Cat#9585; RRID:AB_2239535 Rabbit Monoclonal Anti-Sox2 (Clone D6D9) Cell Signalling Technologies Cat#3579; RRID:AB_2195767 Rat Monoclonal Anti-Tenascin C (Clone 578) R&D Cat#MAB2138; RRID:AB_2203818 MouseMonoclonal Anti-vimentin (Clone V9) Santa Cruz Biotechnology Cat#sc-6260; RRID:AB_628437 Biological Samples HNSCC Tumor Microarray 2005–2010 Auria Biobank pathology archive; Routila et al.35 AB15-7642 HNSCC Tumor Microarray 2005–2015 Auria Biobank pathology archive; Mylly et al.36 AB19-6863, ABTMA21-06 (Continued on next page) ll OPEN ACCESS Cell 187, 1–18.e1–e9, December 12, 2024 e1 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Freshly Resected Human HNSCC Tissue Helsinki University Hospital Head and Neck Center N/A Chemicals, Peptides, and Recombinant Proteins A83-01 Tocris Bioscience Cat#2939 TGFß1 R&D Cat#7754-BH Gefitinib Sigma Cat# SML1657 Critical Commercial Assays Lenti-X Packaging Single Shots (VSV-G) Takara Bio Cat#631276 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#PN-1000184 Visium Spatial Gene Expression Reagent Kit 10x Genomics Cat# PN-1000186 Visium Library Construction Kit 10x Genomics Cat#PN-1000190 BD Rhapsody WTA Reagent Kit BD Cat#633802 Illumina NextSeq 500 High Output Kit v2.5 Illumina Cat#20024908 Deposited Data Spatial RNA Sequencing of Eight Tongue Squamous Cell Carcinomas This paper GEO: GSE251902 Single-Cell RNA Sequencing of Human Tongue Squamous Cell Carcinomas in Spheroid Culture with and without Human Cancer Associated Fibroblasts This paper GEO: GSE252265 Experimental Models: Cell Lines UTSCC25 Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC47 Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC74a Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC76a Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A HNSCC Patient-Derived CancerAssociated Fibroblast Line Kaukonen et al.38 N/A Patient-Derived ‘‘Healthy’’ Non-cancerAssociated Fibroblast Line Kaukonen et al.38 N/A UTSCC74-eGFP Tagged Human Tongue Squamous Cell Carcinoma This paper N/A UTSCC76-eGFP Tagged Human Tongue Squamous Cell Carcinoma This paper N/A CAF-MCherry Tagged Human HNSCCDerived Cancer-Associated Fibroblast This paper N/A Experimental Models: Organisms/Strains Mouse: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ Jackson Laboratory Strain#005557; RRID:IMSR_JAX:005557 Recombinant DNA PLVX-EF1a-IRES-mCherry Takara Bio Cat# 631987 pLVX-EF1a-pIRES-EGFP This paper N/A Software and Algorithms AnnData v0.9.1 Virshup et al.39 https://anndata.readthedocs.io/en/latest/ index.html (Continued on next page) ll OPEN ACCESS e2 Cell 187, 1–18.e1–e9, December 12, 2024 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article ..

    RNA Sequencing:

    Article Title: Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Polyclonal Anti-AREG LSBio Cat#LS-B13911; RRID:AB_3106998 Mouse Monoclonal Anti-actin (Smooth Muscle)(aSMA) (Clone 1A4) Dako Cat#M0851; RRID: AB_2223500 Mouse Monoclonal Anti-Beta-Catenin (Clone 14) Cell Marque Cat#224M-14; RRID: AB_1158971 Rabbit Monoclonal Anti-Bmi-1 (Clone D20B7) Cell Signaling Technologies Cat#6964; RRID: AB_10828713 Rabbit Monoclonal Anti-CD11b (Clone EP45) BioSB Cat#BSB6441; RRID: AB_3107001 Rabbit Monoclonal Anti-CD3 (Clone EP449E) Invitrogen Cat#MA5-14482; RRID: AB_10985777 Mouse Monoclonal Anti-CD34 Class II (Clone QBEnd10) Dako Cat#M716529-2; RRID: AB_2063006 Mouse Monoclonal Anti-E-Cadherin (Clone 36) BD Biosciences Cat#610182; RRID: AB_397581 Rabbit Monoclonal Anti-EGFR (Clone D38B1) Cell Signaling Technologies Cat#:4267; RRID: AB_2864406 Rabbit Polyclonal Anti-Epcam Abcam Cat#71916; RRID:AB_1603782 Rabbit Monoclonal Anti-Fibroblast Activation Protein (FAP) (Clone EPR20021) Abcam Cat#:207178; RRID:AB_2864720 Guinea Pig Polyclonal Anti-Keratin 14 Progen Cat#03-GP-CK14; RRID:AB_1541011 Mouse Monoclonal Anti-Keratin 18/8 (Clone C51) Cell Signalling Technologies Cat#4546; RRID:AB_2134843 Rabbit Polyclonal Anti-non-muscle Myosin Heavy Chain II-A (Myh9) Biolegend Cat#909802; RRID:AB_291638 Mouse Monoclonal Anti-pan-Cytokeratin (Clone C11) Abcam Cat#ab7753; RRID:AB_306047 Mouse Monoclonal Anti-Pan-Cytokeratin (Clone AE1/AE3) Invitrogen Cat#MA5-13156; RRID:AB_10983023 Rabbit Monoclonal Anti-PDGF Receptor Beta (Clone 28E1) Cell Signalling Technologies Cat#3169; RRID:AB_2162497 Rabbit Monoclonal Anti-Slug (Clone C19G7) Cell Signalling Technologies Cat#9585; RRID:AB_2239535 Rabbit Monoclonal Anti-Sox2 (Clone D6D9) Cell Signalling Technologies Cat#3579; RRID:AB_2195767 Rat Monoclonal Anti-Tenascin C (Clone 578) R&D Cat#MAB2138; RRID:AB_2203818 MouseMonoclonal Anti-vimentin (Clone V9) Santa Cruz Biotechnology Cat#sc-6260; RRID:AB_628437 Biological Samples HNSCC Tumor Microarray 2005–2010 Auria Biobank pathology archive; Routila et al.35 AB15-7642 HNSCC Tumor Microarray 2005–2015 Auria Biobank pathology archive; Mylly et al.36 AB19-6863, ABTMA21-06 (Continued on next page) ll OPEN ACCESS Cell 187, 1–18.e1–e9, December 12, 2024 e1 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Freshly Resected Human HNSCC Tissue Helsinki University Hospital Head and Neck Center N/A Chemicals, Peptides, and Recombinant Proteins A83-01 Tocris Bioscience Cat#2939 TGFß1 R&D Cat#7754-BH Gefitinib Sigma Cat# SML1657 Critical Commercial Assays Lenti-X Packaging Single Shots (VSV-G) Takara Bio Cat#631276 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#PN-1000184 Visium Spatial Gene Expression Reagent Kit 10x Genomics Cat# PN-1000186 Visium Library Construction Kit 10x Genomics Cat#PN-1000190 BD Rhapsody WTA Reagent Kit BD Cat#633802 Illumina NextSeq 500 High Output Kit v2.5 Illumina Cat#20024908 Deposited Data Spatial RNA Sequencing of Eight Tongue Squamous Cell Carcinomas This paper GEO: GSE251902 Single-Cell RNA Sequencing of Human Tongue Squamous Cell Carcinomas in Spheroid Culture with and without Human Cancer Associated Fibroblasts This paper GEO: GSE252265 Experimental Models: Cell Lines UTSCC25 Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC47 Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC74a Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC76a Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A HNSCC Patient-Derived CancerAssociated Fibroblast Line Kaukonen et al.38 N/A Patient-Derived ‘‘Healthy’’ Non-cancerAssociated Fibroblast Line Kaukonen et al.38 N/A UTSCC74-eGFP Tagged Human Tongue Squamous Cell Carcinoma This paper N/A UTSCC76-eGFP Tagged Human Tongue Squamous Cell Carcinoma This paper N/A CAF-MCherry Tagged Human HNSCCDerived Cancer-Associated Fibroblast This paper N/A Experimental Models: Organisms/Strains Mouse: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ Jackson Laboratory Strain#005557; RRID:IMSR_JAX:005557 Recombinant DNA PLVX-EF1a-IRES-mCherry Takara Bio Cat# 631987 pLVX-EF1a-pIRES-EGFP This paper N/A Software and Algorithms AnnData v0.9.1 Virshup et al.39 https://anndata.readthedocs.io/en/latest/ index.html (Continued on next page) ll OPEN ACCESS e2 Cell 187, 1–18.e1–e9, December 12, 2024 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article ..

    Single Cell:

    Article Title: Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Polyclonal Anti-AREG LSBio Cat#LS-B13911; RRID:AB_3106998 Mouse Monoclonal Anti-actin (Smooth Muscle)(aSMA) (Clone 1A4) Dako Cat#M0851; RRID: AB_2223500 Mouse Monoclonal Anti-Beta-Catenin (Clone 14) Cell Marque Cat#224M-14; RRID: AB_1158971 Rabbit Monoclonal Anti-Bmi-1 (Clone D20B7) Cell Signaling Technologies Cat#6964; RRID: AB_10828713 Rabbit Monoclonal Anti-CD11b (Clone EP45) BioSB Cat#BSB6441; RRID: AB_3107001 Rabbit Monoclonal Anti-CD3 (Clone EP449E) Invitrogen Cat#MA5-14482; RRID: AB_10985777 Mouse Monoclonal Anti-CD34 Class II (Clone QBEnd10) Dako Cat#M716529-2; RRID: AB_2063006 Mouse Monoclonal Anti-E-Cadherin (Clone 36) BD Biosciences Cat#610182; RRID: AB_397581 Rabbit Monoclonal Anti-EGFR (Clone D38B1) Cell Signaling Technologies Cat#:4267; RRID: AB_2864406 Rabbit Polyclonal Anti-Epcam Abcam Cat#71916; RRID:AB_1603782 Rabbit Monoclonal Anti-Fibroblast Activation Protein (FAP) (Clone EPR20021) Abcam Cat#:207178; RRID:AB_2864720 Guinea Pig Polyclonal Anti-Keratin 14 Progen Cat#03-GP-CK14; RRID:AB_1541011 Mouse Monoclonal Anti-Keratin 18/8 (Clone C51) Cell Signalling Technologies Cat#4546; RRID:AB_2134843 Rabbit Polyclonal Anti-non-muscle Myosin Heavy Chain II-A (Myh9) Biolegend Cat#909802; RRID:AB_291638 Mouse Monoclonal Anti-pan-Cytokeratin (Clone C11) Abcam Cat#ab7753; RRID:AB_306047 Mouse Monoclonal Anti-Pan-Cytokeratin (Clone AE1/AE3) Invitrogen Cat#MA5-13156; RRID:AB_10983023 Rabbit Monoclonal Anti-PDGF Receptor Beta (Clone 28E1) Cell Signalling Technologies Cat#3169; RRID:AB_2162497 Rabbit Monoclonal Anti-Slug (Clone C19G7) Cell Signalling Technologies Cat#9585; RRID:AB_2239535 Rabbit Monoclonal Anti-Sox2 (Clone D6D9) Cell Signalling Technologies Cat#3579; RRID:AB_2195767 Rat Monoclonal Anti-Tenascin C (Clone 578) R&D Cat#MAB2138; RRID:AB_2203818 MouseMonoclonal Anti-vimentin (Clone V9) Santa Cruz Biotechnology Cat#sc-6260; RRID:AB_628437 Biological Samples HNSCC Tumor Microarray 2005–2010 Auria Biobank pathology archive; Routila et al.35 AB15-7642 HNSCC Tumor Microarray 2005–2015 Auria Biobank pathology archive; Mylly et al.36 AB19-6863, ABTMA21-06 (Continued on next page) ll OPEN ACCESS Cell 187, 1–18.e1–e9, December 12, 2024 e1 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Freshly Resected Human HNSCC Tissue Helsinki University Hospital Head and Neck Center N/A Chemicals, Peptides, and Recombinant Proteins A83-01 Tocris Bioscience Cat#2939 TGFß1 R&D Cat#7754-BH Gefitinib Sigma Cat# SML1657 Critical Commercial Assays Lenti-X Packaging Single Shots (VSV-G) Takara Bio Cat#631276 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#PN-1000184 Visium Spatial Gene Expression Reagent Kit 10x Genomics Cat# PN-1000186 Visium Library Construction Kit 10x Genomics Cat#PN-1000190 BD Rhapsody WTA Reagent Kit BD Cat#633802 Illumina NextSeq 500 High Output Kit v2.5 Illumina Cat#20024908 Deposited Data Spatial RNA Sequencing of Eight Tongue Squamous Cell Carcinomas This paper GEO: GSE251902 Single-Cell RNA Sequencing of Human Tongue Squamous Cell Carcinomas in Spheroid Culture with and without Human Cancer Associated Fibroblasts This paper GEO: GSE252265 Experimental Models: Cell Lines UTSCC25 Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC47 Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC74a Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC76a Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A HNSCC Patient-Derived CancerAssociated Fibroblast Line Kaukonen et al.38 N/A Patient-Derived ‘‘Healthy’’ Non-cancerAssociated Fibroblast Line Kaukonen et al.38 N/A UTSCC74-eGFP Tagged Human Tongue Squamous Cell Carcinoma This paper N/A UTSCC76-eGFP Tagged Human Tongue Squamous Cell Carcinoma This paper N/A CAF-MCherry Tagged Human HNSCCDerived Cancer-Associated Fibroblast This paper N/A Experimental Models: Organisms/Strains Mouse: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ Jackson Laboratory Strain#005557; RRID:IMSR_JAX:005557 Recombinant DNA PLVX-EF1a-IRES-mCherry Takara Bio Cat# 631987 pLVX-EF1a-pIRES-EGFP This paper N/A Software and Algorithms AnnData v0.9.1 Virshup et al.39 https://anndata.readthedocs.io/en/latest/ index.html (Continued on next page) ll OPEN ACCESS e2 Cell 187, 1–18.e1–e9, December 12, 2024 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article ..

    Software:

    Article Title: Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Polyclonal Anti-AREG LSBio Cat#LS-B13911; RRID:AB_3106998 Mouse Monoclonal Anti-actin (Smooth Muscle)(aSMA) (Clone 1A4) Dako Cat#M0851; RRID: AB_2223500 Mouse Monoclonal Anti-Beta-Catenin (Clone 14) Cell Marque Cat#224M-14; RRID: AB_1158971 Rabbit Monoclonal Anti-Bmi-1 (Clone D20B7) Cell Signaling Technologies Cat#6964; RRID: AB_10828713 Rabbit Monoclonal Anti-CD11b (Clone EP45) BioSB Cat#BSB6441; RRID: AB_3107001 Rabbit Monoclonal Anti-CD3 (Clone EP449E) Invitrogen Cat#MA5-14482; RRID: AB_10985777 Mouse Monoclonal Anti-CD34 Class II (Clone QBEnd10) Dako Cat#M716529-2; RRID: AB_2063006 Mouse Monoclonal Anti-E-Cadherin (Clone 36) BD Biosciences Cat#610182; RRID: AB_397581 Rabbit Monoclonal Anti-EGFR (Clone D38B1) Cell Signaling Technologies Cat#:4267; RRID: AB_2864406 Rabbit Polyclonal Anti-Epcam Abcam Cat#71916; RRID:AB_1603782 Rabbit Monoclonal Anti-Fibroblast Activation Protein (FAP) (Clone EPR20021) Abcam Cat#:207178; RRID:AB_2864720 Guinea Pig Polyclonal Anti-Keratin 14 Progen Cat#03-GP-CK14; RRID:AB_1541011 Mouse Monoclonal Anti-Keratin 18/8 (Clone C51) Cell Signalling Technologies Cat#4546; RRID:AB_2134843 Rabbit Polyclonal Anti-non-muscle Myosin Heavy Chain II-A (Myh9) Biolegend Cat#909802; RRID:AB_291638 Mouse Monoclonal Anti-pan-Cytokeratin (Clone C11) Abcam Cat#ab7753; RRID:AB_306047 Mouse Monoclonal Anti-Pan-Cytokeratin (Clone AE1/AE3) Invitrogen Cat#MA5-13156; RRID:AB_10983023 Rabbit Monoclonal Anti-PDGF Receptor Beta (Clone 28E1) Cell Signalling Technologies Cat#3169; RRID:AB_2162497 Rabbit Monoclonal Anti-Slug (Clone C19G7) Cell Signalling Technologies Cat#9585; RRID:AB_2239535 Rabbit Monoclonal Anti-Sox2 (Clone D6D9) Cell Signalling Technologies Cat#3579; RRID:AB_2195767 Rat Monoclonal Anti-Tenascin C (Clone 578) R&D Cat#MAB2138; RRID:AB_2203818 MouseMonoclonal Anti-vimentin (Clone V9) Santa Cruz Biotechnology Cat#sc-6260; RRID:AB_628437 Biological Samples HNSCC Tumor Microarray 2005–2010 Auria Biobank pathology archive; Routila et al.35 AB15-7642 HNSCC Tumor Microarray 2005–2015 Auria Biobank pathology archive; Mylly et al.36 AB19-6863, ABTMA21-06 (Continued on next page) ll OPEN ACCESS Cell 187, 1–18.e1–e9, December 12, 2024 e1 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Freshly Resected Human HNSCC Tissue Helsinki University Hospital Head and Neck Center N/A Chemicals, Peptides, and Recombinant Proteins A83-01 Tocris Bioscience Cat#2939 TGFß1 R&D Cat#7754-BH Gefitinib Sigma Cat# SML1657 Critical Commercial Assays Lenti-X Packaging Single Shots (VSV-G) Takara Bio Cat#631276 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#PN-1000184 Visium Spatial Gene Expression Reagent Kit 10x Genomics Cat# PN-1000186 Visium Library Construction Kit 10x Genomics Cat#PN-1000190 BD Rhapsody WTA Reagent Kit BD Cat#633802 Illumina NextSeq 500 High Output Kit v2.5 Illumina Cat#20024908 Deposited Data Spatial RNA Sequencing of Eight Tongue Squamous Cell Carcinomas This paper GEO: GSE251902 Single-Cell RNA Sequencing of Human Tongue Squamous Cell Carcinomas in Spheroid Culture with and without Human Cancer Associated Fibroblasts This paper GEO: GSE252265 Experimental Models: Cell Lines UTSCC25 Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC47 Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC74a Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC76a Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A HNSCC Patient-Derived CancerAssociated Fibroblast Line Kaukonen et al.38 N/A Patient-Derived ‘‘Healthy’’ Non-cancerAssociated Fibroblast Line Kaukonen et al.38 N/A UTSCC74-eGFP Tagged Human Tongue Squamous Cell Carcinoma This paper N/A UTSCC76-eGFP Tagged Human Tongue Squamous Cell Carcinoma This paper N/A CAF-MCherry Tagged Human HNSCCDerived Cancer-Associated Fibroblast This paper N/A Experimental Models: Organisms/Strains Mouse: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ Jackson Laboratory Strain#005557; RRID:IMSR_JAX:005557 Recombinant DNA PLVX-EF1a-IRES-mCherry Takara Bio Cat# 631987 pLVX-EF1a-pIRES-EGFP This paper N/A Software and Algorithms AnnData v0.9.1 Virshup et al.39 https://anndata.readthedocs.io/en/latest/ index.html (Continued on next page) ll OPEN ACCESS e2 Cell 187, 1–18.e1–e9, December 12, 2024 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article ..

    Imaging:

    Article Title: Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Polyclonal Anti-AREG LSBio Cat#LS-B13911; RRID:AB_3106998 Mouse Monoclonal Anti-actin (Smooth Muscle)(aSMA) (Clone 1A4) Dako Cat#M0851; RRID: AB_2223500 Mouse Monoclonal Anti-Beta-Catenin (Clone 14) Cell Marque Cat#224M-14; RRID: AB_1158971 Rabbit Monoclonal Anti-Bmi-1 (Clone D20B7) Cell Signaling Technologies Cat#6964; RRID: AB_10828713 Rabbit Monoclonal Anti-CD11b (Clone EP45) BioSB Cat#BSB6441; RRID: AB_3107001 Rabbit Monoclonal Anti-CD3 (Clone EP449E) Invitrogen Cat#MA5-14482; RRID: AB_10985777 Mouse Monoclonal Anti-CD34 Class II (Clone QBEnd10) Dako Cat#M716529-2; RRID: AB_2063006 Mouse Monoclonal Anti-E-Cadherin (Clone 36) BD Biosciences Cat#610182; RRID: AB_397581 Rabbit Monoclonal Anti-EGFR (Clone D38B1) Cell Signaling Technologies Cat#:4267; RRID: AB_2864406 Rabbit Polyclonal Anti-Epcam Abcam Cat#71916; RRID:AB_1603782 Rabbit Monoclonal Anti-Fibroblast Activation Protein (FAP) (Clone EPR20021) Abcam Cat#:207178; RRID:AB_2864720 Guinea Pig Polyclonal Anti-Keratin 14 Progen Cat#03-GP-CK14; RRID:AB_1541011 Mouse Monoclonal Anti-Keratin 18/8 (Clone C51) Cell Signalling Technologies Cat#4546; RRID:AB_2134843 Rabbit Polyclonal Anti-non-muscle Myosin Heavy Chain II-A (Myh9) Biolegend Cat#909802; RRID:AB_291638 Mouse Monoclonal Anti-pan-Cytokeratin (Clone C11) Abcam Cat#ab7753; RRID:AB_306047 Mouse Monoclonal Anti-Pan-Cytokeratin (Clone AE1/AE3) Invitrogen Cat#MA5-13156; RRID:AB_10983023 Rabbit Monoclonal Anti-PDGF Receptor Beta (Clone 28E1) Cell Signalling Technologies Cat#3169; RRID:AB_2162497 Rabbit Monoclonal Anti-Slug (Clone C19G7) Cell Signalling Technologies Cat#9585; RRID:AB_2239535 Rabbit Monoclonal Anti-Sox2 (Clone D6D9) Cell Signalling Technologies Cat#3579; RRID:AB_2195767 Rat Monoclonal Anti-Tenascin C (Clone 578) R&D Cat#MAB2138; RRID:AB_2203818 MouseMonoclonal Anti-vimentin (Clone V9) Santa Cruz Biotechnology Cat#sc-6260; RRID:AB_628437 Biological Samples HNSCC Tumor Microarray 2005–2010 Auria Biobank pathology archive; Routila et al.35 AB15-7642 HNSCC Tumor Microarray 2005–2015 Auria Biobank pathology archive; Mylly et al.36 AB19-6863, ABTMA21-06 (Continued on next page) ll OPEN ACCESS Cell 187, 1–18.e1–e9, December 12, 2024 e1 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Freshly Resected Human HNSCC Tissue Helsinki University Hospital Head and Neck Center N/A Chemicals, Peptides, and Recombinant Proteins A83-01 Tocris Bioscience Cat#2939 TGFß1 R&D Cat#7754-BH Gefitinib Sigma Cat# SML1657 Critical Commercial Assays Lenti-X Packaging Single Shots (VSV-G) Takara Bio Cat#631276 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#PN-1000184 Visium Spatial Gene Expression Reagent Kit 10x Genomics Cat# PN-1000186 Visium Library Construction Kit 10x Genomics Cat#PN-1000190 BD Rhapsody WTA Reagent Kit BD Cat#633802 Illumina NextSeq 500 High Output Kit v2.5 Illumina Cat#20024908 Deposited Data Spatial RNA Sequencing of Eight Tongue Squamous Cell Carcinomas This paper GEO: GSE251902 Single-Cell RNA Sequencing of Human Tongue Squamous Cell Carcinomas in Spheroid Culture with and without Human Cancer Associated Fibroblasts This paper GEO: GSE252265 Experimental Models: Cell Lines UTSCC25 Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC47 Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC74a Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A UTSCC76a Human Tongue Squamous Cell Carcinoma Auria Biobank; Routila et al.37 N/A HNSCC Patient-Derived CancerAssociated Fibroblast Line Kaukonen et al.38 N/A Patient-Derived ‘‘Healthy’’ Non-cancerAssociated Fibroblast Line Kaukonen et al.38 N/A UTSCC74-eGFP Tagged Human Tongue Squamous Cell Carcinoma This paper N/A UTSCC76-eGFP Tagged Human Tongue Squamous Cell Carcinoma This paper N/A CAF-MCherry Tagged Human HNSCCDerived Cancer-Associated Fibroblast This paper N/A Experimental Models: Organisms/Strains Mouse: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ Jackson Laboratory Strain#005557; RRID:IMSR_JAX:005557 Recombinant DNA PLVX-EF1a-IRES-mCherry Takara Bio Cat# 631987 pLVX-EF1a-pIRES-EGFP This paper N/A Software and Algorithms AnnData v0.9.1 Virshup et al.39 https://anndata.readthedocs.io/en/latest/ index.html (Continued on next page) ll OPEN ACCESS e2 Cell 187, 1–18.e1–e9, December 12, 2024 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article ..

    Amplification:

    Article Title: Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis
    Article Snippet: Following amplification, the cDNA was purified using SPRISelect beads (Agilent, Santa Clara, CA). .. The Visium Library Construction Kit (10X Genomics) was then used to generate Illumina-compatible sequencing libraries with approximately 25% of the total cDNA yield. cDNA amplicon size was optimized, and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. .. The NovaSeq 6000 sequencer (Illumina, San Diego, CA) was used to sequence the amplified libraries on an SP flow cell of 28x10x10x90 to obtain approximately 50,000 reads per spot for each capture area covered by tissue, according to the sequencing requirements in the Visium Spatial Gene Expression manual.

    Construct:

    Article Title: Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis
    Article Snippet: Following amplification, the cDNA was purified using SPRISelect beads (Agilent, Santa Clara, CA). .. The Visium Library Construction Kit (10X Genomics) was then used to generate Illumina-compatible sequencing libraries with approximately 25% of the total cDNA yield. cDNA amplicon size was optimized, and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. .. The NovaSeq 6000 sequencer (Illumina, San Diego, CA) was used to sequence the amplified libraries on an SP flow cell of 28x10x10x90 to obtain approximately 50,000 reads per spot for each capture area covered by tissue, according to the sequencing requirements in the Visium Spatial Gene Expression manual.

    Ligation:

    Article Title: Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis
    Article Snippet: Following amplification, the cDNA was purified using SPRISelect beads (Agilent, Santa Clara, CA). .. The Visium Library Construction Kit (10X Genomics) was then used to generate Illumina-compatible sequencing libraries with approximately 25% of the total cDNA yield. cDNA amplicon size was optimized, and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. .. The NovaSeq 6000 sequencer (Illumina, San Diego, CA) was used to sequence the amplified libraries on an SP flow cell of 28x10x10x90 to obtain approximately 50,000 reads per spot for each capture area covered by tissue, according to the sequencing requirements in the Visium Spatial Gene Expression manual.

    Polymerase Chain Reaction:

    Article Title: Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis
    Article Snippet: Following amplification, the cDNA was purified using SPRISelect beads (Agilent, Santa Clara, CA). .. The Visium Library Construction Kit (10X Genomics) was then used to generate Illumina-compatible sequencing libraries with approximately 25% of the total cDNA yield. cDNA amplicon size was optimized, and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. .. The NovaSeq 6000 sequencer (Illumina, San Diego, CA) was used to sequence the amplified libraries on an SP flow cell of 28x10x10x90 to obtain approximately 50,000 reads per spot for each capture area covered by tissue, according to the sequencing requirements in the Visium Spatial Gene Expression manual.



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    Journal: JCI Insight

    Article Title: A potent inhibitor of PAI-1, MDI-2517, mitigates disease severity in a preclinical systemic sclerosis model

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    Figure Lengend Snippet: ( A ) Comparison of SERPINE1 expression in SSc and healthy control skin biopsy samples from the GEO dataset ( GSE58095 ). ( B ) Correlation analysis of modified Rodnan skin scores (mRSS) versus SERPINE1 expression from the data in A . ( C ) Enriched signature for expression of extracellular matrix (ECM) genes along with expression of the myofibroblast marker COL8A1 , and SERPINE1 (PAI-1) expression in SSc skin on the 10x Visium spatial platform (data representative of n = 4). ( D ) Violin plots of SERPINE1 expression in controls versus SSc skin across single-cell RNA-seq data from different cellular populations (top) and fibroblast subsets (bottom) ( n = 18 healthy controls, n = 22 SSc patients). ( E ) Enriched biological processes in SERPINE1 + versus SERPINE1 – COL8A1 myofibroblasts. ( F ) IHC of PAI-1 in SSc skin biopsy (data representative of n = 6). ( G ) IHC of PAI-1 in skin biopsy from a healthy volunteer. Scale bars: 500 μm on overall biopsy, 50 μm on the insets. **** P < 0.0001 by 2-tailed Mann-Whitney test in A . P = 0.0003 by Spearman’s r correlation test in B .

    Article Snippet: Optimization of tissue permeabilization was performed on 20 μm sections using a Visium Spatial Tissue Optimization Reagents Kit (10x Genomics), which established an optimal permeabilization time of 9 minutes.

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