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Fig. 2. Differential fibroblast gene expression and secreted protein analysis. (A) Hierarchical clustering of 1948 differentially expressed gene probes in MRC5, CAF7, and CAF12 (A; see Materials and Methods for scoring procedure). (B and C) IGF1R pathway components that were significantly (P < 0.05 by two-tailed, two-sample unequal variance t tests) differentially expressed in either CAF7 or CAF12 compared with MRC5 (each n = 3 biological replicates; B) and in PC9GR compared with PC9 cells (n = 3; C). (D) Comparison of 2330 proteins identified by secretome analysis based on the average abundance (ave riBAQ) of each protein in CAF7 and CAF12 (n = 6) and the ratio of each protein identified in CAF7 and CAF12 compared with MRC5 (n = 3). Dashed lines indicate the top 2.5% most abundant secreted proteins and a ratio of 1.5-fold increased or decreased. (E) Log2 ratio of each secreted protein identified in CAF7 and CAF12 compared with MRC5 and significance of these differences. Dashed lines indicate a log2 ratio of ±0.58 (1.5-fold increased or decreased) and −log(P value) greater than 1.3 (P < 0.05 by a two-tailed, two-sample equal variance t test), comparing the riBAQ values for CAF7 and CAF12 to the riBAQ values for MRC5 from (D). (F) Western blot analysis of total protein levels of <t>IGFBP5,</t> IGFBP6, and IGFBP7 in the indicated cell lines. Actin, loading control (LI-COR scans in fig. S9). Dashed line indicates removed lanes. Blot shown is representative of two biological replicates.
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Fig. 2. Differential fibroblast gene expression and secreted protein analysis. (A) Hierarchical clustering of 1948 differentially expressed gene probes in MRC5, CAF7, and CAF12 (A; see Materials and Methods for scoring procedure). (B and C) IGF1R pathway components that were significantly (P < 0.05 by two-tailed, two-sample unequal variance t tests) differentially expressed in either CAF7 or CAF12 compared with MRC5 (each n = 3 biological replicates; B) and in PC9GR compared with PC9 cells (n = 3; C). (D) Comparison of 2330 proteins identified by secretome analysis based on the average abundance (ave riBAQ) of each protein in CAF7 and CAF12 (n = 6) and the ratio of each protein identified in CAF7 and CAF12 compared with MRC5 (n = 3). Dashed lines indicate the top 2.5% most abundant secreted proteins and a ratio of 1.5-fold increased or decreased. (E) Log2 ratio of each secreted protein identified in CAF7 and CAF12 compared with MRC5 and significance of these differences. Dashed lines indicate a log2 ratio of ±0.58 (1.5-fold increased or decreased) and −log(P value) greater than 1.3 (P < 0.05 by a two-tailed, two-sample equal variance t test), comparing the riBAQ values for CAF7 and CAF12 to the riBAQ values for MRC5 from (D). (F) Western blot analysis of total protein levels of <t>IGFBP5,</t> IGFBP6, and IGFBP7 in the indicated cell lines. Actin, loading control (LI-COR scans in fig. S9). Dashed line indicates removed lanes. Blot shown is representative of two biological replicates.
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Fig. 2. Differential fibroblast gene expression and secreted protein analysis. (A) Hierarchical clustering of 1948 differentially expressed gene probes in MRC5, CAF7, and CAF12 (A; see Materials and Methods for scoring procedure). (B and C) IGF1R pathway components that were significantly (P < 0.05 by two-tailed, two-sample unequal variance t tests) differentially expressed in either CAF7 or CAF12 compared with MRC5 (each n = 3 biological replicates; B) and in PC9GR compared with PC9 cells (n = 3; C). (D) Comparison of 2330 proteins identified by secretome analysis based on the average abundance (ave riBAQ) of each protein in CAF7 and CAF12 (n = 6) and the ratio of each protein identified in CAF7 and CAF12 compared with MRC5 (n = 3). Dashed lines indicate the top 2.5% most abundant secreted proteins and a ratio of 1.5-fold increased or decreased. (E) Log2 ratio of each secreted protein identified in CAF7 and CAF12 compared with MRC5 and significance of these differences. Dashed lines indicate a log2 ratio of ±0.58 (1.5-fold increased or decreased) and −log(P value) greater than 1.3 (P < 0.05 by a two-tailed, two-sample equal variance t test), comparing the riBAQ values for CAF7 and CAF12 to the riBAQ values for MRC5 from (D). (F) Western blot analysis of total protein levels of <t>IGFBP5,</t> IGFBP6, and IGFBP7 in the indicated cell lines. Actin, loading control (LI-COR scans in fig. S9). Dashed line indicates removed lanes. Blot shown is representative of two biological replicates.
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Fig. 2. Differential fibroblast gene expression and secreted protein analysis. (A) Hierarchical clustering of 1948 differentially expressed gene probes in MRC5, CAF7, and CAF12 (A; see Materials and Methods for scoring procedure). (B and C) IGF1R pathway components that were significantly (P < 0.05 by two-tailed, two-sample unequal variance t tests) differentially expressed in either CAF7 or CAF12 compared with MRC5 (each n = 3 biological replicates; B) and in PC9GR compared with PC9 cells (n = 3; C). (D) Comparison of 2330 proteins identified by secretome analysis based on the average abundance (ave riBAQ) of each protein in CAF7 and CAF12 (n = 6) and the ratio of each protein identified in CAF7 and CAF12 compared with MRC5 (n = 3). Dashed lines indicate the top 2.5% most abundant secreted proteins and a ratio of 1.5-fold increased or decreased. (E) Log2 ratio of each secreted protein identified in CAF7 and CAF12 compared with MRC5 and significance of these differences. Dashed lines indicate a log2 ratio of ±0.58 (1.5-fold increased or decreased) and −log(P value) greater than 1.3 (P < 0.05 by a two-tailed, two-sample equal variance t test), comparing the riBAQ values for CAF7 and CAF12 to the riBAQ values for MRC5 from (D). (F) Western blot analysis of total protein levels of <t>IGFBP5,</t> IGFBP6, and IGFBP7 in the indicated cell lines. Actin, loading control (LI-COR scans in fig. S9). Dashed line indicates removed lanes. Blot shown is representative of two biological replicates.
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Fig. 2. Differential fibroblast gene expression and secreted protein analysis. (A) Hierarchical clustering of 1948 differentially expressed gene probes in MRC5, CAF7, and CAF12 (A; see Materials and Methods for scoring procedure). (B and C) IGF1R pathway components that were significantly (P < 0.05 by two-tailed, two-sample unequal variance t tests) differentially expressed in either CAF7 or CAF12 compared with MRC5 (each n = 3 biological replicates; B) and in PC9GR compared with PC9 cells (n = 3; C). (D) Comparison of 2330 proteins identified by secretome analysis based on the average abundance (ave riBAQ) of each protein in CAF7 and CAF12 (n = 6) and the ratio of each protein identified in CAF7 and CAF12 compared with MRC5 (n = 3). Dashed lines indicate the top 2.5% most abundant secreted proteins and a ratio of 1.5-fold increased or decreased. (E) Log2 ratio of each secreted protein identified in CAF7 and CAF12 compared with MRC5 and significance of these differences. Dashed lines indicate a log2 ratio of ±0.58 (1.5-fold increased or decreased) and −log(P value) greater than 1.3 (P < 0.05 by a two-tailed, two-sample equal variance t test), comparing the riBAQ values for CAF7 and CAF12 to the riBAQ values for MRC5 from (D). (F) Western blot analysis of total protein levels of IGFBP5, IGFBP6, and IGFBP7 in the indicated cell lines. Actin, loading control (LI-COR scans in fig. S9). Dashed line indicates removed lanes. Blot shown is representative of two biological replicates.

Journal: Science signaling

Article Title: IGF-binding proteins secreted by cancer-associated fibroblasts induce context-dependent drug sensitization of lung cancer cells.

doi: 10.1126/scisignal.abj5879

Figure Lengend Snippet: Fig. 2. Differential fibroblast gene expression and secreted protein analysis. (A) Hierarchical clustering of 1948 differentially expressed gene probes in MRC5, CAF7, and CAF12 (A; see Materials and Methods for scoring procedure). (B and C) IGF1R pathway components that were significantly (P < 0.05 by two-tailed, two-sample unequal variance t tests) differentially expressed in either CAF7 or CAF12 compared with MRC5 (each n = 3 biological replicates; B) and in PC9GR compared with PC9 cells (n = 3; C). (D) Comparison of 2330 proteins identified by secretome analysis based on the average abundance (ave riBAQ) of each protein in CAF7 and CAF12 (n = 6) and the ratio of each protein identified in CAF7 and CAF12 compared with MRC5 (n = 3). Dashed lines indicate the top 2.5% most abundant secreted proteins and a ratio of 1.5-fold increased or decreased. (E) Log2 ratio of each secreted protein identified in CAF7 and CAF12 compared with MRC5 and significance of these differences. Dashed lines indicate a log2 ratio of ±0.58 (1.5-fold increased or decreased) and −log(P value) greater than 1.3 (P < 0.05 by a two-tailed, two-sample equal variance t test), comparing the riBAQ values for CAF7 and CAF12 to the riBAQ values for MRC5 from (D). (F) Western blot analysis of total protein levels of IGFBP5, IGFBP6, and IGFBP7 in the indicated cell lines. Actin, loading control (LI-COR scans in fig. S9). Dashed line indicates removed lanes. Blot shown is representative of two biological replicates.

Article Snippet: Antibodies were from Abcam: -SMA (ab32575, RRID:AB_722538; 1:1000); from BD Pharmingen: vimentin (550513, RRID:AB_393716; 1:1000); from Cell Signaling Technology: E-cadherin (3195, RRID:AB_2291471; 1:1000), p-EGFR Tyr1068 (aka Tyr1092) (2234, RRID:AB_331701; 1:1000), EGFR (4267, RRID:AB_2246311; 1:1000), p-AKT Ser473 (9271, RRID:AB_329825; 1:500), p-AKT Thr308 (13038, RRID:AB_2629447; 1:1000), AKT (9272, RRID:AB_329827; 1:1000), p-p44/42 MAPK (ERK1/2) Thr202/Tyr204 (4370, RRID:AB_ 2315112; 1:2000), p-IGF1R Tyr1131/InsR Tyr1146 (3021, RRID:AB_ 331578; 1:500), IGF1R (9750, RRID:AB_10950969, 1:1000), p-FAK Tyr397 (8556, RRID:AB_10891442; 1:1000), FAK (13009, RRID:AB_2798086; 1:1000), PARP1 (9542, RRID:AB_2160739; 1:1000), cleaved caspase-3 (9661, RRID:AB_2341188; 1:1000), and -tubulin (2125, RRID:AB_2619646; 1:1000); from R&D Systems: IGFBP5 (AF875, RRID:AB_355678; 1:2000), IGFBP6 (AF876, RRID:AB_355679; 1:2000), and IGFBP7 (AF1334, RRID:AB_2264436; 1:400); from Sigma-Aldrich: -actin (A5441, RRID:AB_476744; 1:15,000) and MAPK (ERK1/2) (M5670, RRID:AB_477216; 1:10,000); and from Thermo Fisher Scientific: pan-cytokeratin (MA5-12231, RRID:AB_10980711; 1:50).

Techniques: Gene Expression, Two Tailed Test, Comparison, Western Blot, Control

Fig. 3. Effect of modulation of IGF1R pathway components on EGFR-mutant NSCLC cells. Viability as determined by CTG of PC9GR cells plated in RPMI10 con- taining (A) rhIGFBP5 (n = 6), (B) rhIGFBP6 (n = 6), or (C) rhIGFBP7 (n = 7) (10 g/ml) and treated after 24 hours with 100 nM osimertinib for 72 hours. One hundred percent viability is set to total luminescence in DMSO-treated cells plated in RPMI10 con- taining PBS. PBS treatments (DMSO and osimertinib) in (A) and (B) are the same as IGFBP5, and six experiments were performed in parallel. (D) Viability as determined by CTG of PC9GR cells plated in RPMI10 containing IGF1 or IGF2 (100 ng/ml) and treated 24 hours later with osimertinib (100 nM for 72 hours). One hundred percent viability was set to total luminescence in DMSO-treated cells plated in RPMI10 con- taining 0.1% BSA/PBS as buffer control. n = 6 experiments. (E) Viability as determined by CTG of PC9GR cells plated in 1:1 RPMI10:siCM (from CAF12 cells in which IGFBP5 was silenced) and treated 24 hours later with osimertinib (100 nM for 72 hours). One hundred percent viability is set to total luminescence in DMSO-treated cells plated in 1:1 RPMI10:si-non targeting (NT) CM. n = 7 experiments. A representative Western blot confirming knockdown efficiency is shown. Technical replicates within each experiment in (A) to (E) were averaged before determining the means ± SD and significance across all biological replicates (n). P < 0.05 by unpaired t test with single pooled variance.

Journal: Science signaling

Article Title: IGF-binding proteins secreted by cancer-associated fibroblasts induce context-dependent drug sensitization of lung cancer cells.

doi: 10.1126/scisignal.abj5879

Figure Lengend Snippet: Fig. 3. Effect of modulation of IGF1R pathway components on EGFR-mutant NSCLC cells. Viability as determined by CTG of PC9GR cells plated in RPMI10 con- taining (A) rhIGFBP5 (n = 6), (B) rhIGFBP6 (n = 6), or (C) rhIGFBP7 (n = 7) (10 g/ml) and treated after 24 hours with 100 nM osimertinib for 72 hours. One hundred percent viability is set to total luminescence in DMSO-treated cells plated in RPMI10 con- taining PBS. PBS treatments (DMSO and osimertinib) in (A) and (B) are the same as IGFBP5, and six experiments were performed in parallel. (D) Viability as determined by CTG of PC9GR cells plated in RPMI10 containing IGF1 or IGF2 (100 ng/ml) and treated 24 hours later with osimertinib (100 nM for 72 hours). One hundred percent viability was set to total luminescence in DMSO-treated cells plated in RPMI10 con- taining 0.1% BSA/PBS as buffer control. n = 6 experiments. (E) Viability as determined by CTG of PC9GR cells plated in 1:1 RPMI10:siCM (from CAF12 cells in which IGFBP5 was silenced) and treated 24 hours later with osimertinib (100 nM for 72 hours). One hundred percent viability is set to total luminescence in DMSO-treated cells plated in 1:1 RPMI10:si-non targeting (NT) CM. n = 7 experiments. A representative Western blot confirming knockdown efficiency is shown. Technical replicates within each experiment in (A) to (E) were averaged before determining the means ± SD and significance across all biological replicates (n). P < 0.05 by unpaired t test with single pooled variance.

Article Snippet: Antibodies were from Abcam: -SMA (ab32575, RRID:AB_722538; 1:1000); from BD Pharmingen: vimentin (550513, RRID:AB_393716; 1:1000); from Cell Signaling Technology: E-cadherin (3195, RRID:AB_2291471; 1:1000), p-EGFR Tyr1068 (aka Tyr1092) (2234, RRID:AB_331701; 1:1000), EGFR (4267, RRID:AB_2246311; 1:1000), p-AKT Ser473 (9271, RRID:AB_329825; 1:500), p-AKT Thr308 (13038, RRID:AB_2629447; 1:1000), AKT (9272, RRID:AB_329827; 1:1000), p-p44/42 MAPK (ERK1/2) Thr202/Tyr204 (4370, RRID:AB_ 2315112; 1:2000), p-IGF1R Tyr1131/InsR Tyr1146 (3021, RRID:AB_ 331578; 1:500), IGF1R (9750, RRID:AB_10950969, 1:1000), p-FAK Tyr397 (8556, RRID:AB_10891442; 1:1000), FAK (13009, RRID:AB_2798086; 1:1000), PARP1 (9542, RRID:AB_2160739; 1:1000), cleaved caspase-3 (9661, RRID:AB_2341188; 1:1000), and -tubulin (2125, RRID:AB_2619646; 1:1000); from R&D Systems: IGFBP5 (AF875, RRID:AB_355678; 1:2000), IGFBP6 (AF876, RRID:AB_355679; 1:2000), and IGFBP7 (AF1334, RRID:AB_2264436; 1:400); from Sigma-Aldrich: -actin (A5441, RRID:AB_476744; 1:15,000) and MAPK (ERK1/2) (M5670, RRID:AB_477216; 1:10,000); and from Thermo Fisher Scientific: pan-cytokeratin (MA5-12231, RRID:AB_10980711; 1:50).

Techniques: Mutagenesis, Control, Western Blot, Knockdown