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A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and <t>AXL.</t> The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots <t>showing</t> <t>IRF1</t> protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.
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A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and <t>AXL.</t> The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots <t>showing</t> <t>IRF1</t> protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.
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A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and <t>AXL.</t> The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots <t>showing</t> <t>IRF1</t> protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.
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A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and <t>AXL.</t> The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots <t>showing</t> <t>IRF1</t> protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.
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A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and <t>AXL.</t> The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots <t>showing</t> <t>IRF1</t> protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.
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A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and <t>AXL.</t> The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots <t>showing</t> <t>IRF1</t> protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.
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A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and <t>AXL.</t> The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots <t>showing</t> <t>IRF1</t> protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.
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A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and <t>AXL.</t> The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots <t>showing</t> <t>IRF1</t> protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.
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A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and <t>AXL.</t> The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots <t>showing</t> <t>IRF1</t> protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.
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A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and <t>AXL.</t> The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots <t>showing</t> <t>IRF1</t> protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.
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A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and <t>AXL.</t> The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots <t>showing</t> <t>IRF1</t> protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.
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A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and AXL. The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots showing IRF1 protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.

Journal: Nature Communications

Article Title: The molecular and functional landscape of resistance to immune checkpoint blockade in melanoma

doi: 10.1038/s41467-023-36979-y

Figure Lengend Snippet: A ssGSEA score for Reactome_IFNγ_Signaling in BSA control and IFNγ-treated PD1 PROG cell lines with ( n = 6; orange) and without ( n = 15; blue, not including SCC16-0016) intrinsic IFNγ activity. The dotted line aligns with the lowest ssGSEA score in the IFNγ-treated PD1 PROGs, and solid lines indicate the median ssGSEA scores. B Subset of top-scoring gene sets (GSEA Pre-Ranked; Hallmark gene set collection and melanoma-specific transcriptome signatures) in PD1 PROGs with ( n = 6) compared to without ( n = 15) intrinsic IFNγ activity (Supplementary Data ). C Hierarchical clustering of PD1 PROG cell lines ( n = 22) with Euclidean distance based on protein expression of Melan-A, MITF, SOX10, and AXL. The transcriptome melanoma clusters defined according to ref. are also shown. PD1 PROG cell lines with intrinsic IFNγ signaling ( n = 6) are highlighted in red. D Plots showing IRF1 protein expression (derived from the densitometric normalized protein data after log 2 transformation and z score calculation) in PD1 PROGs with ( n = 6) and without ( n = 5) intrinsic IFNγ activity. The relative cell surface expression (median fluorescence intensity stained divided by fluorescence minus one control, MFI/FMO) of PD-L1, PD-L2, and MHC-I in PD1 PROGs with ( n = 6) and without ( n = 16) intrinsic IFNγ activity. Data compared using two-sided Mann–Whitney test, p -values shown. E Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1, dotted line) in control (BSA)-treated PD1 PROGs with (IFNγ-high; n = 6) or without (IFNγ-low; n = 15) intrinsic IFNγ signaling are highlighted in red. The comparison of secreted cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). F Differentially expressed secreted cytokines (FDR-adjusted p -value < 0.1) in control (BSA)-treated PD1 PROGs versus IFNγ-treated PD1 PROG cell lines ( n = 21; 1000 U IFNγ/ml for 24) are highlighted in red. The comparison of cytokine expression was performed using log 2 transformed fluorescence intensity values (Supplementary Data ). Source data are provided as a Source Data file.

Article Snippet: Western blots were probed with antibodies against ß2-microglobulin (1:1000; D8P1H; Cell Signaling Technology; Cat No. 12851), CIITA (1:1000; Cell Signaling Technology; Cat No. 3793), STAT1 (1:1000; 9H2; Cell Signaling Technology; Cat No. 9176), phospho-STAT1 Ser727 (1:1000; D3B7; Cell Signaling Technology; Cat No. 8826), JAK1 (1:1000, Cell Signaling Technology; Cat No. 3332), JAK2 (1:1000, E4Y4D; Cell Signaling Technology; Cat No. 74987), IRF1 (1:1000; D5E4; Cell Signaling Technology; Cat No. 8478), AXL (1:200; R&D systems; Cat No. AF154), MLANA/Mart-1 (1:1000; Cell Signaling Technology; Cat No. 34511), MITF (1:1000; C5; Calbiochem; Cat No. OP126L), SOX10 (1:1000; D5V9L; Cell Signaling Technology; Cat No. 89356), and ß-Actin (1:6000; AC-74; Sigma-Aldrich; Cat No. A5316).

Techniques: Control, Activity Assay, Expressing, Derivative Assay, Transformation Assay, Fluorescence, Staining, MANN-WHITNEY, Comparison

Journal: Cell Reports

Article Title: Quantitative Proteomics Analysis of Lytic KSHV Infection in Human Endothelial Cells Reveals Targets of Viral Immune Modulation

doi: 10.1016/j.celrep.2020.108249

Figure Lengend Snippet:

Article Snippet: Mouse Anti-Human Axl monoclonal antibody , R and D Systems , Cat# MAB154; RRID: AB_2062558.

Techniques: Purification, Control, Virus, Recombinant, Mass Spectrometry, Sample Prep, Transfection, SYBR Green Assay, Sequencing, CRISPR, Plasmid Preparation, Software