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4 protocols using gel docking system

1

Protein Expression and Cytokine Profiling

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Tumor-containing tibiae and subcutaneous tumors were snap-frozen in liquid nitrogen. Frozen tibiae were homogenized in RIPA buffer (50 (link)) using a FastPrep-24 tissue homogenizer (MP Biomedicals). Prostate cancer cell lines were lysed using RIPA buffer as described previously (50 (link)). Total protein (10–20 μg) was separated by SDS-PAGE and transferred to PVDF membranes (Fisher). Membranes were blocked with 5% BSA-TBST and incubated with antibodies diluted in 5% BSA-TBST as previously described (50 (link)). Primary antibodies were detected using HRP-conjugated secondary antibodies (Sigma) by chemiluminescence using Quantity One imaging software on a Bio-Rad Gel Docking system. Antibodies listed in Supplementary Table S1.Equal amounts of protein from subcutaneous or tibiae tumors pooled from two mice were incubated with a 174-protein spotted human cytokine antibody array C2000 (Ray Biotech Inc) according to the manufacturer’s protocol.
An MMP-3 ELISA (R&D) that recognizes both the proenzyme and active form was performed on 24 h serum-starved PC3-NICD3 cells treated with or without Dox. Media were collected and concentrated (Ultracel-10k; Millipore) and equal volumes were used to quantify total MMP-3.
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2

Protein Expression and Cytokine Profiling

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Tumor-containing tibiae and subcutaneous tumors were snap-frozen in liquid nitrogen. Frozen tibiae were homogenized in RIPA buffer (50 (link)) using a FastPrep-24 tissue homogenizer (MP Biomedicals). Prostate cancer cell lines were lysed using RIPA buffer as described previously (50 (link)). Total protein (10–20 μg) was separated by SDS-PAGE and transferred to PVDF membranes (Fisher). Membranes were blocked with 5% BSA-TBST and incubated with antibodies diluted in 5% BSA-TBST as previously described (50 (link)). Primary antibodies were detected using HRP-conjugated secondary antibodies (Sigma) by chemiluminescence using Quantity One imaging software on a Bio-Rad Gel Docking system. Antibodies listed in Supplementary Table S1.Equal amounts of protein from subcutaneous or tibiae tumors pooled from two mice were incubated with a 174-protein spotted human cytokine antibody array C2000 (Ray Biotech Inc) according to the manufacturer’s protocol.
An MMP-3 ELISA (R&D) that recognizes both the proenzyme and active form was performed on 24 h serum-starved PC3-NICD3 cells treated with or without Dox. Media were collected and concentrated (Ultracel-10k; Millipore) and equal volumes were used to quantify total MMP-3.
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3

Western Blot Analysis of Protein Markers

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30–60μg of protein were separated on precast tris-glycine gels (Invitrogen) and transferred to PVDF membrane. Membranes were blocked with 5% BSA/TBST. Primary antibodies, after incubation in 5% BSA/TBST, were detected using HRP conjugated secondary antibodies in chemiluminescent solution using the Quantity One imaging software on a Bio-Rad Gel Docking system. Primary antibodies: Rabbit mAb Bnip3 (EPR4034) from Abcam, rabbit anti-P-AktSer473, rabbit mAb P-Akt308 (C31E5E), rabbit mAb Akt (pan) (C67E7), mouse mAb Histone H3 (96C10), rabbit mAb P-Ser555 ULK (D1H4, #5869), rabbit mAb ULK (D8H5, #8054), rabbit mAb P-AMPKα (Thr172) (40H9, #2535), and rabbit anti-AMPKα (#2532) from Cell Signaling Technology, rabbit anti-LC3B (NB100–2200) from Novus Biologicals, mouse mAb GAPDH from Millipore, rat anti-integrin α6 (GoH3) and mouse anti-HIF1α from BD Pharmingen, mouse mAb AR (441) from Santa Cruz, mouse anti-α tubulin and β-actin-HRP mouse mAb from Sigma-Aldrich), and rabbit anti-integrin α6 (AA6A, A6NT).12 (link), 35 (link)
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4

Western Blot Analysis of Protein Markers

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30–60μg of protein were separated on precast tris-glycine gels (Invitrogen) and transferred to PVDF membrane. Membranes were blocked with 5% BSA/TBST. Primary antibodies, after incubation in 5% BSA/TBST, were detected using HRP conjugated secondary antibodies in chemiluminescent solution using the Quantity One imaging software on a Bio-Rad Gel Docking system. Primary antibodies: Rabbit mAb Bnip3 (EPR4034) from Abcam, rabbit anti-P-AktSer473, rabbit mAb P-Akt308 (C31E5E), rabbit mAb Akt (pan) (C67E7), mouse mAb Histone H3 (96C10), rabbit mAb P-Ser555 ULK (D1H4, #5869), rabbit mAb ULK (D8H5, #8054), rabbit mAb P-AMPKα (Thr172) (40H9, #2535), and rabbit anti-AMPKα (#2532) from Cell Signaling Technology, rabbit anti-LC3B (NB100–2200) from Novus Biologicals, mouse mAb GAPDH from Millipore, rat anti-integrin α6 (GoH3) and mouse anti-HIF1α from BD Pharmingen, mouse mAb AR (441) from Santa Cruz, mouse anti-α tubulin and β-actin-HRP mouse mAb from Sigma-Aldrich), and rabbit anti-integrin α6 (AA6A, A6NT).12 (link), 35 (link)
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