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9 protocols using ab32363

1

Protein Expression and Regulation Assays

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Anti-C2EIP mouse antibody (previously used in14 ) was used to detect the expression of C2EIP protein in different tissues. In the flow cytometry and immunohistochemical assays, antibodies against CVH (Abcam, San Francisco, USA; ab27591) and C-KIT (Abcam, San Francisco, USA; ab32363) were used to label PGC. Antibodies against GST (Abcam, San Francisco, USA; ab19256) and C2EIP were used to test the accuracy of the GST pull-down experiment. PTCH2 antibody (Abcam, San Francisco, USA; ab194574) was used to examine protein cellular localization. Antibodies against PTCH2 (Abcam, San Francisco, USA; ab151775) were used for theco-IP experiment. Ubiquitylation antibody (Abcam, San Francisco, USA; ab139467) was used to determinethe ubiquitylation level of PTCH2under different treatments. TSA (MCE, Monmouth, USA; HY-15144) and 5-Zacd (MCE, Monmouth, USA; HY-10586)were used to inhibit deacetylation and methylation, respectively. The dual fluorescein test kit (Solarbio, Beijing, China; D0010) was used to measure the activity of promoter fragments.
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2

Culturing Human Papillary Thyroid Cancer Cells

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All human papillary thyroid cancer cell lines, including KTC-1, K1, KAT-5, K2, TPC-1, BCPAP, and BHP5-16, were purchased from Cell Bank of the Chinese Academy of Science (Wuhan, China). All cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco BRL, Grand Island, NY) containing with fetal bovine serum (Gibco BRL, Grand Island, NY) (10%), penicillin (100 U/mL) and streptomycin sulfate (100 µg/mL). Cells were maintained at 37 °C in a humidified atmosphere of 5% CO2 and 95% air.
TRIzol, Lipofectamine-3000, and Enzyme MIX were purchased from Invitrogen (Basel, Switzerland). Monoclonal antibodies (Abs) against human KIT (ab32363, 1:1000), β-actin (ab8226, 1:5000) and GAPDH (ab181602,1:5000) were purchased from Abcam. SiRNAs and negative control (siRNA-control) were purchased from Qiagen (Germany). Efficiency of RNA interferences was determined using qRT-PCR or western blotting analyses (Fig. 4E and Supplementary Fig. 3). MiR-146 precursor (Pre-miR-146), miR-146 oligonucleotide (anti-miR-146), and its corresponding control (pre-control and anti-control) were purchased from Ambion (Austin, TX, USA). Unless specified otherwise, all biochemical reagents were purchased from Sigma-Aldrich (St. Louis, MI).
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3

Immunohistochemical Profiling of Tumor Cells

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The 4-μm-thick sections were prepared from 10% FFPE tissue blocks for TFE3 IHC staining. All slides were exposed to 3% H2O2 for 10 minutes at room temperature to block endogenous peroxidase activity. TFE3 (HPA023881, Sigma, USA), cathepsin K (ab19027, Abcam, Cambridge, UK), CD10 (ab227640, Abcam, Cambridge, UK), CA-IX (ab107257, Abcam, Cambridge, UK), Vimentin (ab8978, Abcam, Cambridge, UK), CD117(ab32363, Abcam, Cambridge, UK), CK7 (ab181598, Abcam, Cambridge, UK) antibody were incubated with tumor sections in a humidified chamber at 4°C overnight, then the anti-mouse or anti-rabbit peroxidase-conjugated secondary antibody (EnVision™ Detection Kit, DAKO, Denmark) were used with the sections at 37°C for 30 minutes.
The result was evaluated in a semiquantitative manner by multiplying the staining intensity (0 = no staining, 1 = mild staining, 2 =moderate staining, and 3 = strong staining) by the percentage of immunoreactive tumor cells (0–100). The final immunostaining result was calculated as following: negative (0), score <25; weak positive (1+), score 26–100; moderate positive (2+), score 101–200; strong positive (3+), score 201–300.
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4

Immunofluorescence Staining Procedure for Cell Analysis

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Immunofluorescence staining was carried out according to the protocol as previously described.23 Briefly, control‐VPCs and MFS‐VPCs were fixed with formaldehyde for half an hour. Following permeation with 0.1% Triton X‐100 in PBS for 30 minutes, cells were stained with ki‐67 antibody (Abcam, ab15580), c‐kit antibody (Abcam, ab32363), γH2AX antibody (Abcam, ab81299) and incubated overnight at 4°C with a 1:100 dilution. After washing with PBS three times, cells were incubated with the secondary antibodies. Finally, the sample was mounted with DAPI and photographed. Images of five different view fields for each slide were captured randomly by a motorized inverted microscope and analysed using AxioVision (Zeiss). The percentage of positive cells was calculated in three independent experiments.
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5

Immunohistochemical Analysis of Xenograft Tumors

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The xenograft tumor specimens were fixed with 4% paraformaldehyde solution. Specimens were sectioned onto 4-μm slices after embedding with paraffin. Then, the slides were incubated with the primary antibody, including CD117 (ab32363, Abcam, USA), CD44 (37259, Cell Signaling Technology, USA), vimentin (5741, Cell Signaling Technology, USA), Ki67 (ab156956, Abcam, USA) at 4°C overnight and then washed three times with PBS. After incubation with the HRP polymer-conjugated secondary antibody for 1 h at room temperature, it was stained with a diaminobenzidine solution (DAB) for 3min and then stained with hematoxylin as a counterstain. Three random fields were imaged for each sample with a microscope.
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6

Adenomyosis Endometrial Innervation Analysis

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Adenomyosis eutopic endometrium and corresponding ectopic endometrium were collected during surgery. The diagnosis of adenomyosis was confirmed by imaging or histological examination. Samples were collected in the proliferative phase of the menstrual cycle. Sections were incubated with anti-c-kit antibody (dilution 1:200, ab32363, Abcam, Cambridge, MA, USA) and anti-PGP9.5 antibody (dilution 1:500, Z5116, Dako Cytomation, DenmarkA/S). Immunohistochemical assay was performed as previously described 24 (link). Individual nerve fibers were then counted under high power (× 200) to obtain a nerve count in a defined area. The average nerve count in five hot spots was calculated 25 (link).
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7

Immunohistochemical Analysis of Gastric Cancer

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Paraffin sections from the 200 cases of GC patients were dewaxed in xylene and ethanol. After cleaned in distilled water, the paraffin sections were pretreated with citrate buffer, pH 6.0 (CD177) and EDTA Antigen Retrieval Solution, pH 8.0 (CD4, CD8, CD20, CD56, CD68, and CD117) for 3 min at 120°C in a pressure cooker, and endogenous peroxidase was inhibited with 3% H2O2 in PBS for 10 min. Nonspecific actions in the sections were also blocked with goat serum (BOSTER, USA) for 1 h at room temperature. The sections were then incubated with the primary antibody overnight at 4°C, followed by incubation with the secondary antibody for 30 min at 37°C. Primary antibodies used were CD4 (ab183685, 1 : 1000, Abcam, Cambridge, MA, USA), CD8 (ab4055, 1 : 100, Abcam, Cambridge, MA, USA), CD20 (ab9475, 1 : 50, Abcam, Cambridge, MA, USA), CD56 (ab75813, 1 : 100, Abcam, Cambridge, MA, USA), CD68 (ab213363, 1 : 4000, Abcam, Cambridge, MA, USA), CD117 (ab32363, 1 : 400, Abcam, Cambridge, MA, USA), and CD177 (ab220279, 1 : 200, Abcam, Cambridge, MA, USA). Second antibodies used were goat anti-rabbit IgG (CD4, CD8, CD56, CD68, CD117, and CD177) and goat anti-mouse IgG (CD20). The chromogenic reaction was performed via diaminobenzidine (DAB) staining, and the staining intensity was measured using Image-Pro Plus version 6.2 software (Media Cybernetics, Rockville, Maryland, USA).
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8

Immunofluorescence Staining of Paraffin Sections

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The paraffin embedded tissues were cut into 5-μm sections, which were then processed for immunofluorescence staining. The antibodies included anti-c-kit (ab32363, Abcam; 1: 150), anti-HCN1 (ab176304, Abcam; 1: 150), goat anti-rabbit IgG H&L (Cy3®) pre-adsorbed (ab6939, Abcam; 1: 800), and anti-c-Myc [Y69] (FITC) (ab223913, Abcam; 1: 800) antibodies. After staining with DAPI in the dark, the images were observed and captured using a laser scanning confocal microscope.
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9

Immunohistochemical Analysis of Tryptase and c-kit

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Tissue blocks were prepared and sectioned at 4 μm using routine deparaffinization and rehydration procedures. Sections were incubated with anti-mouse tryptase primary antibody (dilution 1:800, ab2378, Abcam) and anti-rabbit c-kit primary antibody (dilution 1:200, ab32363, Abcam) for 60 min at room temperature. After washing with 1× PBS, the sections were incubated with Envision-labeled polymer-alkaline phosphatase mouse/rabbit (Envision/HRP/Mo, GK400105; Envision/HRP/ Rb, GK400305/15, Novocastra, Newcastle upon Tyne, UK) for 60 min. The antigen-antibody reaction was then visualized using diaminobenzidine as a chromogen (GK346810, Novocastra). After washing, the sections were counterstained with Mayer's hematoxylin, dehydrated and mounted with a mounting medium. Tonsils were used as a positive control, and HeLa-cultured cells were used as a negative control.
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