Mouse anti rptpβ ζ

For detection of protein-protein interactions, in situ PLA was performed. The components used (Duolink PLA Technology, Sigma-Aldrich) were as follows: anti-mouse PLA plus probe, anti-rabbit PLA minus probe, anti-goat PLA minus probe and Detection Reagents Orange. HUVEC were grown on chamber slides (Ibidi^® μ-Chamber 12 well on glass slides, Martinsried, Germany) till they reached 80% confluence. Following fixation and blocking, the cells were incubated with the primary antibodies: mouse anti-RPTPβ/ζ (1:250, #610180, BD Biosciences), rabbit anti-CDK5 (1:100 in TBS-T; #sc-173, Santa Cruz Biotechnology), mouse anti-CDK5 (1:100 in TBS-T; #H00001020-M01A, Abnova, Taipei, Taiwan), goat anti-p35 (1:100 in TBS-T; #sc-31102, Santa Cruz Biotechnology). Subsequently, the cells were incubated with secondary antibodies conjugated with oligonucleotides, after hybridization and ligation of which, the DNA was amplified resulting in red fluorescence signals. Nuclei were counterstained with Draq5; cells were mounted with Mowiol 4–88 and visualized with Leica SP5 confocal microscope. Estimation of nuclei and cytoplasm size was performed using the Duolink ImageTool software. To calculate the total number of spots per cell, an algorithmic procedure was used as previously described^{55 (link)}.

For detection of protein-protein interactions, in situ PLA was performed. The components used (Sigma) were as follows: anti-mouse PLA plus probe, anti-rabbit PLA minus probe and Detection Reagents Orange. HUVEC or U87MG cells were grown on μ-Chamber 12 well on glass slides (Ibidi©, Martinsried, Germany). After reaching 80% confluence or after appropriate treatment of cells, the assay was performed according to the manufacturer’s instructions. Briefly, after fixation and blocking, cells were incubated with the primary antibodies: mouse anti-VEGF (1:250), rabbit anti-VEGF (1:250), rabbit anti-Flk-1 (1:250), mouse anti-Flk-1 (1:250), mouse anti-NCL (1:50), goat anti-RPTPβ/ζ (1:250) (all from Santa Cruz Biotechnology Inc.), mouse anti-α_νβ₃ (1:500; Merck Millipore), mouse anti-PTN (1:500; Abnova, Heidelberg, Germany) and mouse anti-RPTPβ/ζ (1:250; BD Biosciences). Subsequently, cells were incubated with secondary antibodies conjugated with oligonucleotides. After hybridization and ligation of the oligonucleotides, the DNA was amplified. A detection mixture detected the amplicons, resulting in red fluorescence signals. Nuclei were counterstained with Draq5; cells were mounted with Mowiol 4–88 and visualized at room temperature with Leica SP5 confocal microscope.

Proteins were analyzed by SDS-PAGE and transferred to Immobilon P membranes. Blocking was performed by incubating the membranes with Tris-buffered saline (TBS) pH 7.4 with 0.05% Tween (TBS-T), containing either 5% nonfat dry milk or 3% BSA. Membranes were incubated with primary antibodies for 16 h at 4°C under continuous agitation, washed 3 times with TBS-T, and incubated with secondary antibodies for 1 h at room temperature. Primary antibodies used were mouse anti-Flk-1 (1:500), goat anti-β₃ (1:500), mouse anti-VEGF (1:500), rabbit anti-phospho-β₃(Y773) (1:1,000; Santa Cruz Biotechnology Inc.), mouse anti-RPTPβ/ζ (1:500; BD Biosciences), rabbit anti-c-Src (1:1,000; Merck Millipore), rabbit anti-phospho-c-Src(Y418) (1:1,000; Acris Antibodies GmbH) and rabbit anti-non-phospho-c-Src (1:1,000; Cell Signaling Technology Inc.). Detection of immunoreactive bands was performed using the enhanced chemiluminescence detection kit (Pierce Biotechnology, Rockford, IL, USA). Protein levels were quantified using the ImagePC image analysis software (Scion Corp., Frederick, MD, USA).