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6 protocols using sc 166685

1

Immunocytochemical Staining of Fibroblasts

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Fibroblasts were seeded on sterile glass coverslips and immunocytochemical staining was performed. Briefly, cells on coverslips were fixed with 4% paraformaldehyde for 10 minutes and then permeabilized with 0.5% Triton-X 100 for 5 minutes. Cells were then blocked for 1 hour with blocking solution (1% bovine serum albumin in phosphate-buffered saline [PBS]), followed by incubation with primary antibody against smoothened (SMO) (SC-166685; Santa Cruz Biotechnology, Santa Cruz, CA, USA) for 2 hours at room temperature. Subsequently, the cells were incubated with Alexa 594-conjugated antimouse IgG (A-11032, Invitrogen, Thermo Fisher Scientific Inc., Waltham, MA, USA) for 60 minutes at room temperature. To assess the subcellular organization of actin microfilaments, cells were incubated with rhodamine-conjugated phalloidin (Molecular Probes, Eugene, OR, USA) at a dilution of 1:200 (1.5 units/mL final concentration). The cells were then washed with PBS, and the coverslips were mounted on a glass slide in 10% Mowiol 4–88, 1 µg/mL 4′,6-diamidino-2-phenylindole dihydrochloride, and 25% glycerol in PBS. The cells were observed with a ZEISS FL Microscope Axiovert 200 (Zeiss, Oberkochen, Germany).
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2

Antibody Generation and Characterization

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Antibodies were generated against Myc (M4439, mouse monoclonal 1:200, Sigma-Aldrich), Ptch1 (sc-293416, mouse monoclonal 1:200, Santa Cruz), Ptch2 (PA1-46223, rabbit polyclonal 1:200, Invitrogen), Gas1 (AF2636, goat polyclonal 1:500, R&D; PA5-48298, rabbit polyclonal 1:500), Boc (AF2385, goat polyclonal 1:500, R&D; MAB20361, mouse monoclonal 1:500, R&D), Cdon (GTX105422, rabbit polyclonal 1:500, GeneTex), Smo (sc-166685, mouse monoclonal 1:200, Santa Cruz, A3274, rabbit polyclonal 1:200, ABclonal), Shh (sc-365112, mouse monoclonal 1:200, Santa Cruz), Gli3 (AF3690, goat polyclonal 1:200, R&D), WDR11 (ab175256, rabbit polyclonal 1:200, Abcam), SSEA1(MC-480, mouse monoclonal 1:200, DSHB), Stella (ab19878, rabbit polyclonal 1:200, Abcam), phospho-Src, (sc-166860, mouse monoclonal 1:500, Santa Cruz), phospho-Creb (sc-81486, mouse monoclonal 1:500, Santa Cruz), Arl13b (17711-1-AP, rabbit polyclonal 1:500, Proteintech), IFT88 (13967-1-AP, rabbit polyclonal 1:500, Proteintech), CEP164 (sc-515403, mouse monoclonal 1:200, Santa cruz), gamma‑tubulin (T6557, mouse monoclonal 1:500, Sigma), b-actin (4967L, rabbit polyclonal 1:500, CST). HRP-conjugated secondary antibodies used were goat anti-mouse IgG (sc-516102, 1:1000, Santa Cruz), goat anti-rabbit IgG (ab6721, 1:1000, Abcam), donkey anti-goat IgG (ab6741, 1:1000, Abcam).
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3

Antibodies for Ciliogenesis and Signaling

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The following primary antibodies were used: acetylated α-tubulin (T7451, diluted 1:2000 for immunofluorescence, Sigma), γ-tubulin (T6557, Sigma), FLAG (F1804, Sigma), HA (H3663, Sigma), CEP83 (HPA038161, Sigma), CEP164 (SAB3500022, Sigma), CEP290 (ab84870, Abcam), TALPID3 (24421-1-AP, Proteintech), ARL13b (17711-1-AP, Proteintech), FBF1 (11531-1-AP, Proteintech), TCTN1 (15004-1-AP, Proteintech), SCLT1 (14875-1-AP, Proteintech), IFT140 (17460-1-AP, Proteintech), β-actin (sc-47778, diluted 1:5000 for western blotting, Santa Cruz), SMO (sc-166685, Santa Cruz), CEP89 (ab204410, Abcam), ANKRD26 (GTX128255, GeneTex), polyglutamylated tubulin (ALX-804-885-C100, diluted 1:2000 for immunofluorescence, Enzo Life Sciences), GLI-3 (AF3690, R&D Systems), ODF2 (H00004957-M01, Abnova), and Polycystin-2 (Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center). The secondary antibodies were goat anti-mouse Alexa Fluor 488/594 or goat anti-rabbit Alexa Fluor 488/594 (1:1000 dilution). Primary antibodies were diluted 1:500 for immunofluorescence and 1:2000 for western blotting experiments unless otherwise specified. Uncropped versions of blots can be found in Supplementary Fig. 9.
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4

Protein Quantification and Western Blotting of Chondrocytes

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The total protein of chondrocytes and cartilage explants was isolated and quantified using the BAC Protein Assay Reagent Kit (Pierce, Rockford, IL, USA). Fifteen micrograms of total protein was electrophoresed by 10% SDS PAGE under reducing conditions. After electrophoresis, the proteins were transferred onto an NC membrane (Beyotime Biotechnology, China) and probed with a polyclonal antibody against Smo (SC-166685, Santa Cruz, CA, USA), type II collagen, MMP-13 (SC-52658, SC-515284 Santa Cruz, CA, USA), type X collagen (ab49945 Abcam, USA), and Runx-2 (SC-390351 Santa Cruz, CA, USA). The antibody was diluted 1:500 in PBS-T containing 1% bovine serum albumin (BSA) (Sigma-Aldrich, St Louis, MO, USA). Horseradish peroxidase-conjugated secondary antibody IgG (H + L) (SC-2371, Santa Cruz, CA, USA) was diluted 1:2000 in PBS-T. Visualization of immunoreactive proteins was achieved using ECL Western blotting detection reagents (KWBIO, Beijing, China) and subsequently exposing the membrane to Kodak X-Omat AR film (Kodak, Rochester, NY). Band densities were quantified using Image Acquisition and Analysis Software (UVP, Upland, CA, USA).
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5

Comprehensive Immunostaining and Western Blot Protocol

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For immunostaining, rabbit anti-PMP70 (Invitrogen, PA1–650, 1:1,000), mouse anti-FLAG (Sigma-Aldrich, F1804, 1:2,000), anti-ACOX1 (ABclonal, A8091, 1:1,000), rabbit anti-MFF (Proteintech, 17090–1-AP, 1:2,000), mouse anti-PMP70 (Sigma-Aldrich, SAB4200181, 1:1000), rabbit anti-DRP1 (Abcam, ab219596, 1:1000), mouse anti-γ-Tubulin (Sigma-Aldrich, T6567, 1:2000), mouse anti-Acetylated-Tubulin (Sigma-Aldrich, T6793, 1:2000), rabbit anti-Arl13b (Proteintech, 17711–11-AP, 1:2000), mouse anti-SMO (Santa Cruz, sc-166685, 1:500). Specific secondary fluorescent antibodies were used, all conjugated to Alexa flour dyes (Invitrogen, 1:1000). For western blot analysis, rabbit anti-GFP (Invitrogen, A-11122, 1:1,000). Anti-rabbit horseradish peroxidase (HRP)-conjugated secondary antibody was used at a 1:10,000 dilution (Jackson ImmunoResearch, 111–035-1400).
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6

Cilia Characterization in RPE, 293T, and Primary Cells

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Retinal pigment epithelial (RPE) cells, 293T cells, and primary chondrocytes and osteoblasts were seeded onto poly L-lysine coated coverslips in 24-well plates. Confluent RPE and 293 T cells were serum-starved overnight to increase cilia lengths. All post-confluent cells were fixed in 4% PFA in PBS containing 0.1% Triton x-100 for 10 min at room temperature, then blocked in 1% Bovine Serum Albumin (Sigma, A9647) for 1 h. Primary antibodies against Arl13b (Proteintech, 17711–1-AP, 1:300), acetylated α-tubulin (Sigma T6557, 1:4000), THM2 (Custom-made Antibody, Proteintech S4132–2, 1:50), IFT81 (Proteintech, 11744–1-AP, 1:200), SMO (Santa Cruz, sc-166685, 1:50) were incubated with cells in 1% BSA overnight at 4°C. Cells were washed three times in PBS, then incubated with secondary antibody conjugated to Alexa Fluor 594 or Alexa Fluor 488 [Life Technologies, A-11005 (anti-mouse) and A-11008 (anti-rabbit), 1:500] for 1 h at room temperature. Cells were washed three times in PBS. Coverslips were inverted and mounted onto slides using DAPI Fluoromount-G (Electron Microscopy Services, 17984–24). RPE cells were imaged using a Nikon Eclipse TiE attached to an A1R-SHR confocal with an A1-DU4 detector and LU4 laser launch. All other cells were imaged using a Nikon 80i or Nikon TiS attached to a Nikon DS-Fi1 or QICAM FAST1934 camera, respectively.
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