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14 protocols using sc 8431

1

Immunohistochemical and Immunofluorescence Staining Protocol

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The following primary antibodies were used: anti-GFP (rabbit, 1:1,000, A11122, Molecular Probes), anti-GFP (mouse, 1:300, 2955, Cell Signaling), anti-K5 (rabbit, 1:3,000, PRB-160P, Covance), anti-K8 (mouse, 1:2,500, MMS-162P, Covance), anti-p63 (mouse, 1:200, sc-8431, Santa Cruz), anti-β-catenin (rabbit, 1:500, sc-7199, Santa Cruz), anti-β-catenin (mouse, 1:500, 610154, BD Transduction Laboratories), anti Ki67 (mouse, 1:1,000, NCL-ki67, Novacastra), anti-E-cadherin (mouse, 1:300, c20820, BD Transduction Laboratories), anti-androgen receptor (rabbit, 1:500, sc-816, Santa Cruz), anti-synaptophysin (rabbit, 1:500, 18-0130, Invitrogen), anti-BrdU (mouse, 1:200, 5292, Cell Signaling), and anti-Nkx3.1 (rabbit, 1:3,000, provided by Dr. Cory Abate-Shen, Columbia University, New York). The biotinylated anti-rabbit or anti-mouse secondary antibody (BA-1000 or BA-9200, Vector Laboratories), or anti-rabbit or anti-mouse conjugated to AlexaFluor488 or to AlexaFluor594 (Molecular Probes) secondary antibody was used for were used for immunohistochemistry or immunofluorescence staining, respectively.
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2

Immunostaining Protocol for Epithelial Markers

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Mouse monoclonal antibody against IL-33 (clone Nessy-1) (#ALX-804-840-C100) was purchased from Enzo. Rabbit polyclonal antibodies against KRT5 (#ab24647) and Ki-67 (#ab15580) were purchased from Abcam (Abcam, Cambridge, MA). Rabbit polyclonal antibody against KRT14 (#PRB-155P) was purchased from Covance (Covance, Princeton, NJ). Rabbit polyclonal antibody against KRT4 (#HPA034881) was purchased from Sigma (Sigma-Aldrich Corp, St. Louis, MO). Rabbit monoclonal antibodies against E-cadherin (#3195), p75 (#8238), and phospho-histone H3 (#3377) were purchased from Cell Signaling (Cell Signaling Technology, MA). Mouse monoclonal antibody against p63 (#sc-8431) was purchased from Santa Cruz (Santa Cruz Biotechnology, TX). Mouse monoclonal antibody against PCNA (#MAB424) was purchased from Millipore (Billerica, MA). Goat polyclonal antibody against IL-33 (#AF3625) was purchased from R&D (R&D Systems, Minneapolis, MN). Donkey anti-goat Alexa Fluor 488 (A11055), anti-rabbit Alexa Fluor 568 (A10042), and anti-mouse Alexa Fluor 647 (A31571) secondary antibodies were purchased from Life Technologies (Carlsbad, CA). Mouse anti-HSP90 (TA500494) and mouse anti-GAPDH (TA310153) primary antibodies were purchased from Origene (Rockville, MD).
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3

Quantifying Cellular Enzyme Activity

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Alkaline Phosphatase Activity Assay was performed on frozen sections. Immunohistochemistry analysis was carried out in paraformaldehyde fixed, paraffin sections with PGR (A0098, Dako) and TP63 (sc-8431, Santa Cruz) antibodies. Detail information is in the supplemental information.
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4

Immunohistochemical Profiling of Prostate Cancer

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The primary antibodies used and their subsequent dilutions were: anti-P16 (rabbit, 1:1000, SC-1207, Santa Cruz), anti-human AR (mouse, 1:250, sc-7305, Santa Cruz Biotechnology), anti-CK5 (rabbit, 2400, PRB-160P, Covance), anti-CK8 (mouse, 1:2000, MMS-162P, Covance), anti-p63 (mouse, 1:2000, sc-8431, Santa Cruz), anti Ki67 (mouse, 1:1000, NCL-ki67, Novacastra), anti-E-cadherin (mouse, 1:200, Cat. No. c20820, BD Transduction Laboratoriesc, Sparks, MD, United States), anti-mouse/ human androgen receptor (rabbit, 1:250, sc-816, Santa Cruz), anti-synaptophysin (rabbit, 1:100, Cat. No. 18–0130, Invitrogen), anti-SPP1 (rabbit, 1:200, Cat. No. 91655, Abcam, Cambridge, MA, USA), CD44 (Rat, 1:50, sc-18849, Santa Cruz) and anti-Vimentin (Chicken, 1:2000, Cat. No. 919101, Biolegend). The biotinylated anti-rabbit or anti-mouse secondary antibody (BA-1000 or BA-9200, Vector Laboratories), or anti-rabbit or anti-mouse conjugated to AlexaFluor488 or to AlexaFluor594 (Molecular Probes) secondary antibody that were used for IHC or IF staining, respectively.
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5

Immunohistochemical Profiling of Epithelial Markers

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The following primary antibodies were used: anti-GFP (Rabbit, 1:1,000, A11122, Molecular Probes), anti-GFP (mouse, 1:300, 2955, Cell Signaling), anti-GFP (Chicken, 1:2000, ab13970, Abcam), anti-K5 (rabbit, 1:3000, PRB-160P, Covance), anti-K8 (mouse, 1:2500, MMS-162P, Covance), anti-p63 (mouse, 1:200, sc-8431, Santa Cruz), anti-Ki67 (mouse, 1:1000, NCL-ki67, Novacastra), anti-E-cadherin (mouse, 1:300, c20820, BD Transduction Laboratories), anti-androgen receptor (rabbit, 1:500, sc-816, Santa Cruz). Biotinylated anti-rabbit or anti-mouse secondary antibodies (BA-1000 or BA-9200, Vector Laboratories) were used for immunohistochemistry experiments. For immunofluorescence studies AlexaFluor-conjugated anti-rabbit, anti-mouse or anti-chicken antibodies (Molecular Probes) were used.
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6

Immunohistochemical Analysis of Larval Tissues

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Larvae were anesthetized and fixed with 4% PFA overnight at 4°C. Standard antibody staining was performed. Antibodies used were: tp63 (1:100, Santa Cruz, sc-8431), Anti-Notch1 intracellular domain rabbit polyclonal (1:100, Abcam, AB_306525), Monoclonal a5 ATPase, (Na (+) K(+)) alpha subunit (5 ug/mL, Developmental Studies Hybridoma Bank, AB_2166869), and rabbit anti-GFP (1:500, Invitrogen, A11122). Antibody staining was counterstained with DAPI (5ug/mL) for 30 min at RT in the dark and washed three times with PBST before imaging.
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7

Kras/Lkb1 Mouse Lung Tumor Analysis

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Lung tumours (≥2 mm in diameter) were freshly dissected from male and female Kras/Lkb1 mice at 8–10 weeks post Ad-Cre treatment. These tumours were immediately cut into several pieces, one piece was used for HE and IHC inspection, and the rest pieces were snap-frozen separately for western blotting and real-time PCR analyses. Western blot assays were performed as previously described with antibodies against p63 (SC-8431, Santa Cruz, this antibody specifically recognizes DNp63; 1:200, 1 ng μl−1), Lox (L4669, Sigma; 1:800, 1.25 ng μl−1), SP-C (AB3786, Chemicon; 1:2,000) and Actin (C-1, Santa Cruz; 1:2,000, 0.1 ng μl−1). Total RNA and genomic DNA were prepared as previously described35 (link). Total RNA was retrotranscribed into first-strand cDNA using RevertAid First Strand cDNA Synthesis Kit (Fermentas). The cDNAs were then used for real-time PCR on a 7500 Fast Real-Time PCR System (Applied Biosystems) using SYBR-Green Master PCR mix (Toyobo). β-actin served as internal control. The primers for PCR were summarized in Supplementary Information (Supplementary Table 5).
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8

Quantitative Immunoblotting for IRF6 and p63

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Cells were lysed in RIPA buffer and homogenized with 26G syringe. Total protein (20–100 μg) was subjected to SDS/PAGE followed by immunoblotting with rabbit polyclonal anti-IRF6 (1:400, ab58915, Abcam), and mouse monoclonal anti-p63 (1:200, sc8431, Santa Cruz). Mouse monoclonal anti-γ-tubulin (1:10000, T6557, Sigma) was used for equal loading control. Quantification of the western images were done by Gel Analysis tool of ImageJ [29 (link)]. All protein levels were normalized to tubulin, and then each data was normalized to the control group within the experiment. Two-tailed Student’s t-test was used to calculate statistical significance.
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9

Histopathological and Immunohistochemical Lung Analysis

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For histologic assessment of lesions, formalin fixed lung tissue was paraffin embedded and cut into 5 micron thick sections. Three sections at least 100 microns apart were stained with hematoxylin and eosin (H&E) and scored to allow for adequate sampling of the lung. H&E staining was conducted using a standard protocol (28 ). Standard immunohistochemistry techniques were employed to stain for Ki-67, cytokeratin 5 & 6 (CK 5/6), thyroid transcription factor (TTF-1), p63, and F4/80 (26 (link)). The IHC technique used for VDR is similar to the IHC method cited above except that slides were processed with an ABC kit (Vector Labs) to enhance the visualization of VDR (18 ). Primary antibodies were used at the following concentrations: (VDR, 1:250 MA1-710 (Affinity Bio); p63, 1:1500 SC-8431 (Santa Cruz); TTF-1, 1:400 M3675 (Dako); and F4/80, 1:100 AB6640 (Abcam). See supplemental Figure 1 for immunohistochemistry controls.
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10

Protein Extraction and Western Blotting

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Cells were collected, washed with cold PBS, and resuspended in EBC250 lysis buffer (250 mM NaCl, 50 mM Tris [pH 8.0], 0.5% Nonidet P-40, 50 mM NaF, 0.5 mM Na3VO4, 1 mM phenylmethylsulfonyl fluoride [PMSF], 2 μg/mL aprotinin, and 2 μg/mL leupeptin). Equal amounts of protein were loaded onto gels, separated by SDS-PAGE, transferred to PVDF membranes (Millipore), and hybridized to the appropriate primary antibodies and HRP-conjugated secondary antibodies for subsequent detection via enhanced chemiluminescence. Antibody directed against actin (sc-8431) was purchased from Santa Cruz Biotech (CA, USA). Antibodies directed against phospho-AMPK (Thr172) (2535), AMPKα (2532) and PARP1 (9532) were purchased from Cell Signaling Technology (Danvers, MA, USA).
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