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10 protocols using sc 1661

1

Immunohistochemical Identification of Vascular Cells

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VSMCs, macrophages and proliferating cells were identified by immunohistochemistry for α-smooth muscle cell actin (Sigma, A2547, 3.1 µg/ml)and desmin (R&D Systems, AF3844, 5 µg/ml), Griffonia Simplicifolia Lectin-1 (GSL, Vector, B-1205, 2.5 µg/ml) and CD68 (LSBio, LS-C343891, 1 µg/ml) and proliferating cell nuclear antigen (PCNA, abcam 18197, 1 µg/ml) and Ki67 (DAKO, M7249, 3.8 ug/ml), respectively, as described previously14 (link),24 (link). Cleaved caspase-3 (R&D Systems, AF835, 10 µg/ml) as described previously14 (link),24 (link)) and cleaved PARP (abcam, ab32064, 4.8 µg/ml) were used to identify apoptotic cells. Briefly, antigen retrieval was performed by boiling in citrate buffer, blocking step was with 5% goat serum, the primary antibody for cleaved PARP was added and incubated overnight at 4 °C. Biotinylated anti-rabbit secondary antibody was utilised, followed by Extravidin-HRP and DAB (3,3′-diaminobenzidine). Nuclei were counterstained with haematoxylin. Immunohistochemistry for a marker of cellular senescence, p16 (Santa Cruz, sc-1661, 2 µg/ml) was performed as described previously27 (link). Non-immune immunoglobulin controls were performed for all protocols by substituting the primary antibody with non-immune immunoglobulin of the same species and at the same concentration (Supplementary Figure 3).
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2

Skin Protein Extraction and Analysis

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Mouse skin was homogenized in ice cold lysis buffer (50 mm Tris–HCl, pH 7.5, 150 mm NaCl, 0.5% NP40, 20% glycerol) with freshly added proteases and phosphatases inhibitor cocktails (Roche, Vienna, Austria). The homogenate was centrifuged at 15 000 g for 30 min at 4°C. The supernatant was collected and the aliquots were stored at −70°C. The protein content was measured by Bradford assay. Equal amounts of protein were subjected to electrophoresis on 4–12% NuPage gels (Invitrogen, Carlsbad, CA, USA) in 1× MOPS running buffer and then transferred to PVDF membrane. The PVDF membranes were subsequently blocked with 3% non‐fat milk in 1% Tween 20–PBS buffer for 1 h at room temperature. PVDF membranes were incubated with the following primary antibodies: Pso4/Prp19 (SNEV) (1:1000, A300‐102A, Bethyl Lab); γ‐H2AX (1:1000, ab26350; Abcam, Cambridge, UK); p16INK4a (1:200, SC‐1661; Santa Cruz); MMP‐13 (1:500, ab75606; Abcam); beta‐actin (1:10 000, A5441; Sigma‐Aldrich); and gapdh (1:1000, sc‐25778; Santa Cruz) overnight at 4°C. Thereafter, incubation with secondary antibodies Alexa 680 – (1:10 000; Life Technologies, Carlsbad, CA, USA) or Infrared 800‐conjugated (1:10 000; Lincoln, Nebraska, USA) was performed for 1 h at room temperature. Detection was performed using an Odyssey Infrared scanner, and the optical density of the bands was measured using Image Studio software vs. 2.1 (Licor).
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3

Western Blot Analysis of Skin Proteins

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Total protein was extracted from mouse skin tissues using ice-cold RIPA lysis buffer (Beyotime) containing a protease inhibitor mixture (Roche). The total protein content was quantified using the BCA method. Protein samples were subjected to Mini-PROTEAN® TGX Stain-Free™ Precast 10% or 12% gels (Bio-Rad) and transferred to 0.2 µm PVDF membranes (Millipore) using the Trans-Blot Turbo Transfer Pack and Trans-Blot Turbo Transfer System (Bio-Rad). PVDF membranes were incubated with primary antibody overnight at 4°C, followed by HRP-coupled secondary antibody for 1 h at room temperature. Bio-Rad ChemDoc MP was used for Western blot data collection and analysis. The primary antibodies used in this study were Tgf-β (1:1000; ab215715, Abcam), IL-6 (1:1000; ab9324, Abcam), γ-H2AX (1:1000; ab81299, Abcam) and p16 (1:1000; sc1661, Santa Cruz).
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4

Cardiac Protein Expression Analysis

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Proteins were extracted from cardiac tissues and cells with RIPA lysis buffer. After centrifugation, the supernatant was collected as the total protein. Each 20 μg protein was separated by electrophoresis using 10% SDS-PAGE and then transferred to PVDF membranes (Bio-Rad Laboratories, Inc.). The membranes were blocked with 5% BSA in TBST for 1 h at room temperature, followed by incubation with primary antibodies including anti-CRIF1 (dilution 1:2,000, ab226244, Abcam, UK), anti-p27 (dilution 1:5,000, ab32034, Abcam), anti-p21 (dilution 1:1,000, ab109199, Abcam), anti-p16 (dilution 1:1,000, sc-1661, Santa Cruz Biotechnology, USA), anti-peroxidasin (PXDN; dilution 1:1,000, orb544131, Biorbyt, UK), anti-Flag (dilution 1:1,000, ab205606, Abcam), anti-Myc (dilution 1:1,000, ab9106, Abcam) and anti-GAPDH (dilution 1:2,500, ab9485, Abcam) at 4° C overnight. Thereafter, after incubation with goat anti-rabbit horseradish peroxidase-conjugated secondary antibody (dilution 1:2,000, ab6721, Abcam) for 2 h at room temperature, membranes were detected by an enhanced chemiluminescence (ECL) detection system (Beyotime Institute of Biotechnology, Shanghai, China) and the density of the bands was determined using ImageJ software (NIH, Bethesda, MD, USA).
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5

Immunoblotting Protocol for Mitochondrial and Cell Cycle Proteins

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Immunoblotting was performed as described previously [7 (link)]. The following specific primary antibodies were used against p16 (sc-74400, 1:200; sc-1661, 1:500), SOD1 (sc-11407, 1:500), SOD2 (sc-30080, 1:200), ND4 (sc-20499-R, 1:200), PGC-1α (sc-13067, 1:200), PGC-1β (sc-373771, 1:200), PRC (sc-135516, 1:200), TFAM (sc-166965, 1:200), and Rb (sc-102, 1:500) obtained from Santa Cruz Biotechnology (Santa Cruz, CA). When the p16 antibodies were no longer available from Santa Cruz, we used a different antibody (NA29, 1:100) from EMD Millipore (Billerica, MA). The β-actin antibody was used at a 1:1000 dilution and obtained from Sigma-Aldrich (A-3853, St. Louis, MO, USA). The ATP5A (ab14746, 1;200), UQCRC2 (ab14745, 1:200), and tubulin (ab21058, 1:5000) antibodies were obtained from Abcam (Cambridge, MA). The SDHA antibody (MS 204M) was used at a 1:200 dilution and obtained from Mitoscience (Eugene, OR). The VDAC antibody (PAI-954A) was used at a 1:200 dilution and obtained from ABR Affinity Bioreagents (Golden, CO). The phospho-Rb (8180S, 1:1000), CDK4 (12790S, 1:1000), and CDK6 (3136S, 1:500) antibodies were obtained from Cell Signaling Technology (Beverly, MA).
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6

Immunofluorescence and Immunohistochemistry Staining

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For immunofluorescence staining, cultured cells and sections were incubated with rabbit anti- VDR (Abcam, ab3508) at 4 °C overnight followed by using Alexa Fluor Plus 594 goat anti-rabbit IgG (H+L) secondary antibody (Invitrogen, A32740, 1:500 dilution) to detect immunoreactivity. For Immunohistochemistry staining, dewaxed and rehydrated paraffin-embedded sections were incubated with 6% hydrogen peroxide to block endogenous peroxidase activity and then washed in PBS (pH 7.6). The slides were then incubated with the primary antibodies, including rabbit anti-VDR (Abcam, ab3508), rabbit anti-β-gal (Abcam, ab616), rabbit anti-Collagen II (Abcam, ab34712), mouse anti-Collagen X (Abcam, ab49945), rabbit anti-Mmp13 (Proteintech, 18165-1-AP) and mouse anti-p16 (Santa Cruz, sc-1661) overnight at 4 °C. After rinsing with PBS for 15 min, sections were incubated with secondary antibody (biotinylated goat anti-rabbit IgG and goat anti-mouse IgG, Sigma). Sections were then washed and incubated with the Vectastain Elite ABC reagent (Vector Laboratories) for 30 minutes. Staining was done using 3,3-diaminobenzidine (2.5 mg/ml) followed by counterstaining with Mayer's hematoxylin.
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7

Tissue Preparation and Immunohistochemistry

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Following excision, tumors were fixed in 10% formalin and embedded in paraffin for sectioning. Standard H&E technique was used for all sections. Serial sections were stained for Ki67 (1:50, catalog number 550609, BD Bioscience, San Jose, CA), p16 (1:100, catalog number sc-1661, Santa Cruz Biotechnology, Dallas, TX) and vimentin (1:700, catalog number ab45939, Abcam, Cambridge, MA).
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8

Immunofluorescent Staining of p16INK4a in Skin Samples

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Immunofluorescent staining was performed as described elsewhere [37 (link)]. Briefly, paraffin-embedded slides of skin samples obtained on Day 16 post-wounding were processed with 1 h heating at 60°C, deparaffinization in xylene, rehydration in graded ethanol, 15 min antigen retrieval in citrate buffer, 15 min cell permeation using 0.3% Triton x-100 and 2 h of unspecific antigen blocking using 10% goat serum, and then were incubated with primary antibodies against p16INK4a (1 : 50; sc-1661, Santa Cruz Biotechnology) at 4°C overnight. The next day, the slides were washed three times with PBS and incubated with Alexa Fluor 647 fluorescence secondary antibody (1 : 200, Invitrogen) for 1 h in dark at room temperature. Next, the slides were stained with DAPI (4',6-diamidino-2-phenylindole) and mounted. Finally, immunofluorescence images were recorded using confocal microscope (Leica, Germany).
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9

Immunohistochemical Analysis of p16 and p21

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Tissue sections were treated with blocking solution for 30 min. Afterwards, the sections underwent an overnight incubation at 4 °C with primary antibodies targeting p16 (sc-1661, 1:500, Santa Cruz), and p21 (sc-397, 1:500, Santa Cruz). Following three washes with PBS, the sections was stained with 3,3-diaminobiphenylamine (DAB, Sigma) and hematoxylin (Beyotime). Finally, images of the stained sections were acquired utilizing an Olympus BX51 fluorescence microscope (Tokyo, Japan).
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10

Immunohistochemical Analysis of Tissue Samples

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Paraffin-embedded tissue blocks were cut into 5-μm sections in preparation for immunohistochemistry analysis. Histochemistry H&E staining and fluorescence immunohistochemistry were performed as described [58 (link), 59 (link)]. The following primary antibodies used for immunofluorescence were purchased from Abcam, Cambridge, MA: beta actin, GAPDH, rabbit anti-ALDH1A1 (1:100, #ab52492,); rabbit anti-ALDH2 (1:200 #ab 108306); mouse anti-BubR1 (1:200, #ab54894); ); rabbit anti-p38α (1:1000, #ab7952); rabbit anti-COX2 (1:200, #ab15191); rabbit anti-protein-HNE (1:500, #HNE11-S, Alpha Diagnostic International, San Antonio, TX); rabbit anti-iNOS (1:500, #ab15323); mouse anti-p16Ink4a (F-12) (1:200, #sc-1661, Santa Cruz Biotech, Dallas, TX); rabbit anti-p19Arf (M-167) (1:200, #sc-1063, Santa Cruz Biotech); and rabbit anti-phosph-p38αMAPK (Thr180/Tyr182) (D3F9) (1:250, #4511, Cell Signaling Technology, Danvers, MA). The sections were visualized using an Olympus BX53 digital microscope. Representative images of interest were acquired using the Olympus CellSense program.
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