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5 protocols using anti pdgf d

1

Brain Immunohistochemistry Analysis Post-ICH

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Twenty-four hours after ICH, mice were perfused under deep anesthesia with 100 ml of ice-cold PBS followed by perfusion with 30 ml formalin (10%). The brains were removed and fixed in formalin at 4 °C for a minimum of 3 days. Samples were then dehydrated with 30% sucrose in PBS and sectioned with cryostat (CM3050S; Leica Microsystems) in 10 µm coronal slices. Anti-PDGFR-β antibody (1:100, Santa Cruz), anti-PDGF-D (1:100, Santa Cruz), anti-MPO (1:100, Santa Cruz), anti-Macrophages/Monocytes (1:100, Millipore), anti-Iba1 antibody (1:100, Abcam), anti-NeuN (1:100, Abcam), anti-GFAP (1:100, Abcam) were incubated separately or double staining overnight at 4 °C. It was then incubated with the appropriate fluorescence conjugated secondary antibodies (1:200, Jackson Immunoresearch, West Grove, PA). The slices were visualized underneath a fluorescence microscope (Olympus BX51, Olympus Optical Co. Ltd., Japan), and pictures were taken with MagnaFire SP 2.1B software (Olympus, Melville, NY).
Macrophages and microglia were stained with ED1 and Iba-1 stains and these two types of cells were distinguished by their morphology as previously described (Power et al., 2003 (link)). Macrophage positive cells were quantified in the perihematoma region at 24 h using 12 fields per slide.
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2

Protein Expression Analysis by Western Blot

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Thirty (30) micrograms of protein was loaded on SDS-PAGE gel. After being electrophoresed, proteins were transferred to a nitrocellulose membrane. The membrane was blocked and incubated with the primary antibody overnight at 4 °C. The primary antibodies were: anti-p-PDGFR-β (1:1000, Santa Cruz), anti-PDGF-D (1:1000, Santa Cruz), anti-MPO (1:1000, Santa Cruz), anti-TNF-α (1:1000, Santa Cruz). The nitrocellulose membranes were incubated with secondary antibodies (1:8000, Santa Cruz) for 1 h at room temperature. Immunoblots were then probed with an ECL Plus chemiluminescence reagent kit (Amersham Biosciences, Arlington Heights, IL) and visualized with the image system (Bio-Rad, Versa Doc, model 4000). All data were analyzed using Image J software.
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3

Protein Expression Analysis Protocol

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Protein extraction was performed using RIPA lysis buffer with a cocktail of protease and phosphatase inhibitors (Thermo Fisher Scientific, cat: A32961). Lysates were separated using SDS-PAGE under reducing conditions and transferred onto a PVDF membrane (Bio-Rad, cat: 162-0177). Membranes were blocked using 5% defatted milk and immunoblotted with the primary antibodies overnight at 4°C, followed by incubation with the secondary antibodies conjugated with horseradish peroxidase (HRP). The following antibodies were used: anti-PDGFRα (CST, cat: 3169), anti-PDGFRβ (CST, cat: 3174), anti-NRP1 (Abcam, cat: ab81321), anti-PDGF-D (Santa Cruz, cat: sc137030), anti-PDGF-D (R&D, AF1159), anti-C1q (Abcam, cat: ab235454), and anti-C3 (Abcam, cat: 200999). Bands were detected using a Syngene GBOX/CHEMI-XT16 device.
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4

Regulation of Tumor Angiogenesis by KLF5

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Human umbilical vein endothelial cells (HuVECs) were purchased from Life Technologies and cultured in Medium 200 with low serum growth supplement (LSGS) (Carlsbad, CA). PC-3 and DU 145 human prostate cancer cell lines and the 293 T human embryonic kidney cell line were purchased from American Type Culture Collection (ATCC) (Manassas, VA), and propagated following ATCC’s instructions.
SiRNA against KLF5 (SiKLF5), developed in a previous study [64 (link)] with the sequence of AAGCUCACCUGAGGACUCATT, was used to knock down KLF5 in human cells at a concentration of 150 nM or as indicated in related figures. The control siRNA (siCtrl), AAUUCUCCGAACGUGUCACGUTT, was purchased from Thermo Fisher (Waltham, MA) used to bring the siRNA concentration to the same in concentration gradient RNAi assay.
PI3K inhibitors Wortmannin and LY294002 were purchased from Cell Signaling Technology (Danvers, MA), and dissolved in dimethyl sulfoxide (DMSO).
Antibodies used in this study included the following: anti-HIF1α and anti-PDGF-B from Novus Biologicals (Littleton, CO), anti-PDGF-D from Santa Cruz (Santa Cruz, CA), anti-phospho-AKT (S473), anti-AKT, anti-phospho-EGFR (Y1068), anti-EGFR, anti-phospho-ERK1/2 and anti-ERK1/2 from Cell Signaling Technology, anti-VEGF and anti-CD31 from Abcam (Cambridge, MA), and anti-β-actin from Sigma. The antibody against KLF5 has been described previously [23 (link)].
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5

Comprehensive Protein Analysis Workflow

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Western blots were performed by separating proteins on SDS-PAGE gels followed by protein transfer to PVDF membranes (Bio-Rad). The antibodies used were: anti-PDGFD (sc-137030, Santa Cruz), anti-SOX2 (AF-2018, R&D), anti-BRACHYURY (sc-166962, Santa Cruz), anti-ERKs (4696, Cell Signaling Technology), anti-Phospho ERKs (4370, Cell Signaling Technology), anti-PDGFR-β (3169, Cell Signaling Technology), anti-Phospho PDGFR-β (Tyr1021) (2227, Cell Signaling Technology), anti-PECAM1 (222783, Abcom), anti-Phospho STAT3 (9145, Cell Signaling Technology), anti-STAT3 (9139, Cell Signaling Technology), anti-KDR (9698, Cell Signaling Technology), anti-HSP90 (7411, Cell Signaling Technology), anti-TUBULIN (RM2007, Ray Antibody), anti-β-ACTIN (RM2001, Ray Antibody), anti-GAPDH (70-Mab5465-040, MultiSciences), anti-HISTONE 3 (GB13102-1, Servicebio), Goat anti-mouse IgG (GAM0072, MultiSciences), Goat anti-rabbit IgG (GAR0072, MultiSciences), Rabbit anti-goat IgG (RAG0072, MultiSciences), anti-PDGFB (PA1-27394, Invitrogen), anti-uPA (17968-1-AP, Proteintech) and anti-PLASMIN (66399-1-Ig, Proteintech). The bands were visualized using a GBOX-CHEMI-XX8 device (SYNGENE).
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