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83 protocols using e cadherin

1

Protein Expression Analysis in Cell Lines

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Immunohistochemistry (IHC), immunofluorescence (IF) and western blot were performed following standard procedures. Antibodies applied to detect protein expressions in IHC and IF were Gli1 1:100 (sc-20687 Santa Cruz Biotechnology, Santa Cruz, CA), Gli2 1:150 (Abcam, Cambridge, MA), E-Cadherin 1:100 (EMD Millipore, Billerica, MA), and the cell proliferation marker Ki67 1:200 (Abcam, Cambridge, MA). Antibodies used in Western blot were Gli1 1:100 (sc-20687 Santa Cruz Biotechnology), Gli2 1:150 (Abcam, Cambridge, MA), E-Cadherin 1:100 (EMD Millipore), and Actin 1:500 (Sigma-Aldrich, St. Louis, MO). Total protein extraction was performed with M-PER Mammalian Protein Extraction Solution (Thermo Scientific, Waltham, MA), and 40 μg of protein extracts were analyzed by Western blotting.
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2

Lacrimal Gland Immunofluorescence Protocol

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Whole lacrimal glands were isolated and fixed for 20 minutes at room temperature in 4% paraformaldehyde. Glands were permealized in 0.2% Triton in PBS and blocked in 10% goat serum and 3% BSA for two hours. Glands were then incubated in primary antibodies for 2 hours at room temperature followed by an overnight incubation at 4°C. Antibodies included 1:300 for E-cadherin (Sigma U3294) and 1:200 for Ki67 (Abcam ab15580). Glands were thoroughly washed in 0.05% Tween in PBS followed by a 2-hour incubation in appropriate secondary antibodies (1:500, Life Technologies) and stained with DAPI. Glands imaged on a Leica SP5 confocal. Ki67 and DAPI were quantified using ImageJ (Abràmoff et al., 2004 ). Paraffin sections were de-paraffinized and boiled for 20 minutes in Citrate buffer, following by 1 hour blocking solution (10% chicken serum in PBST) and an overnight antibody at 4°C. Antibodies included 1:500 for E-cadherin (Sigma U3294) and 1:500 for Ki67 (Abcam ab15580). After washes in PBS, slides were incubated with secondary for 1 hour (1:500, Life Technologies) and stained with DAPI.
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3

Profiling Heat-Induced Molecular Changes

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Changes in the molecular properties of the heat-exposed cells were investigated using ICC, western blotting, and qRT-PCR. Five different primary antibodies (DAKO, Denmark), anti-E-cadherin (1 : 300), anti-CK8/18 (1 : 200), anti-vimentin (1 : 1000), anti-desmin (1 : 150), and anti-p53 (1 : 300), were employed for immunocytochemistry (ICC). The antibodies were applied to quantify the changes in EMT-related properties or demonstrate the cell death mechanism.
The changes in protein expression were further determined by western blotting. The expression of heat shock protein 70 (Hsp70, 1 : 1000, Merck Millipore, Germany), Hsp90 (1 : 500, Santa Cruz, CA, USA), E-cadherin (41 : 1000, Merck Millipore), and vimentin (1 : 1000, Merck Millipore) were quantified by comparing to that of β-actin (1 : 1000, Merck Millipore).
EMT-related genes were quantified using qRT-PCR. Primer sequences, including HSPA1A (Hs00359163_s1), CDH1 (Hs01023894_m1), VIM (Hs00958111_m1), TWIST1 (Hs01675818_s1), and GADPH (Hs02758991_g1), were purchased from Thermo Fisher Scientific. See ESI for additional details.
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4

Comprehensive Protein Expression Analysis

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Immunohistochemistry, immunofluorescence and western blot were performed following standard procedures. Antibodies applied to detect protein expressions in IHC and IF were Gli1 (sc-20687 Santa Cruz Biotechnology, Santa Cruz, CA) at 1:100, Shh (ab 50515 Abcam, Cambridge, MA) at 1:100, Smo (ab 72130 Abcam) at 1:200, Ptch1 (Santa Cruz that Biotechnology,) and E-Cadherin (EMD Millipore) Smo (Sigma, St. Louis, MO) at 1:100, E-Cadherin (sc-7870, Santa Cruz Biotechnology) at 1:100, and β-catenin (BD Biosciences, San Jose, California) at 1:400. Antibodies used in Western blot were Gli (C68H3, Abcam) at 1:1000, E-Cad (HECD-1 MED Milliopore, Darmstadt, Germany) at 1:1000 and Actin (A5441, Sigma) at 1:5000. Total protein extraction was performed with M-PER Mammalian Protein Extraction Solution (Thermo Scientific, Waltham, MA), and 40ug of proteins were analyzed in Western blot.
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5

Investigating GC Cell Line Interactions

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Human GC cell lines AGS, SGC7901, HGC-27(Beijing qualityard biotechnology Co., Ltd.) were purchased from the ATCC and routinely checked for mycoplasma contamination using the Vazyme Mycoplasma detection kit. Nude mice were purchased from SLAC Laboratory Animal Center. primers were designed based on the sequences of THUMPD3-AS1, miR-1297, BCAT1, U6 (internal control) and β-actin (internal control) and synthesized by Merck. Fet al bovine serum, Dulbecco’s modified Eagle’s medium (DMEM), streptomycin, β-actin antibody, recombinant basement membrane and Transwell were purchased from Merck. CCK-8 reagent, trypsin, penicillin and streptomycin, and phosphate-buffered saline (PBS) were purchased from MCE and Dual luciferase reporter assay kits and BCA kits were purchased from abcam and Merck. N-cadherin, E-cadherin and glyceraldehyde-3-phosphate dehydrogenase antibodies were purchased from Merck.
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6

Western Blot Analysis of Epithelial-Mesenchymal Transition

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Total protein was extracted from cells using RIPA buffer (Thermo Fisher Scientific, Inc.) and quantified using a Bicinchoninic Acid Protein Assay kit (Thermo Fisher Scientific, Inc.). A total of 50 µg of protein was loaded per lane. Proteins were separated via 10% SDS-PAGE and transferred to PVDF membranes (EMD Millipore), which were blocked with 5% skim milk at room temperature for 1 h. Subsequently, the membranes were incubated overnight at 4˚C with primary antibodies targeted against: E-Cadherin (cat. no. 14472; 1:1,000; Cell Signaling Technology, Inc.), Vimentin (cat. no. 5741; 1:1,000; Cell Signaling Technology, Inc.) and β-Actin (cat. no. 4970; 1:1,000; Cell Signaling Technology, Inc.). Following primary incubation, the membranes were incubated for 1 h at room temperature with HRP-conjugated anti-mouse IgG (cat. no. 7076; 1:2,000; Cell Signaling Technology, Inc.) and anti-rabbit IgG (cat. no. 7074; 1:2,000; Cell Signaling Technology, Inc.) secondary antibodies. Protein bands were visualized using an enhanced chemiluminescence reagent (Bio-Rad Laboratories, Inc.) with ChemiDoc MP imaging system (Bio-Rad Laboratories, Inc.). Densitometry was measured using Image Lab Touch Software, version 2.4 (Bio-Rad Laboratories, Inc.). β-Actin was used as the loading control.
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7

Immunoblot Analysis of Chick Embryonic Signaling

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This was performed as described (Flentke et al. 2011 ). Antibodies were directed against Snail2 (#27568, 1:1000; Abcam), CyclinD1 (#100–1939 1:1000; Novus), Bcl2 (#610538, 1:1000; BD Biosciences), PUMA (#SPC-166, 1:2000; StressMarq Biosciences, Victoria, BC), p53 (#SC-99, 1:2000; Santa Cruz), E-cadherin (#07–697, 1:1000, EMD Millipore), and GAPDH (#G8795, 1:50,000, Sigma, St. Louis MO). Vendors confirmed the immunizing peptide sequence is conserved in chick. For some western blots, bands were normalized against GAPDH and visualized using infrared dye-conjugated secondary antibodies and the Odyssey system (LiCor); GAPDH protein content is unaffected by alcohol in this model (Flentke et al. 2011 ). For other western blots, bands were instead normalized against total protein content per lane (Revert™ Total Protein Stain; LiCor, # 926–11021), visualized using chemiluminescence with horseradish peroxidase secondary antibodies, and imaged with the Azure Biosystems C600 system (Dublin, CA). Experiments were performed in triplicate and analyzed pools of 8–10 dissected headfolds per lane.
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8

Antibody Selection and Use Guidelines

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The following antibodies were used in this study and were purchased from Santa Cruz Biotechnology unless otherwise noted (including dilutions/amounts used for immunofluorescence, Western blot [WB], and immunoprecipitation [IP]): ERα (HC-20 rabbit; 1:100 immunofluorescence, 1:200 WB; 3 µg IP), ERα (F-10 mouse; 3 µg IP), β1-integrin (LM534 mouse; 1:100 immunofluorescence; EMD Millipore), β1-integrin (M-106 rabbit; 1:300 WB; 3 µg IP), E-cadherin (H-108 rabbit; 1:1,000 WB), β-actin (C4 mouse; 1:10,000 WB), Rab11 (H-87 rabbit; 1:200 WB), Rab7 (sc-376362 mouse; 1:100 immunofluorescence), and caveolin 1 (sc-53564 mouse; 1:600 immunofluorescence; 1:200 WB). LAMP-1 (ab25630 mouse; 1:20 immunofluorescence), clathrin (ab2731 mouse; 1:500 immunofluorescence), and Lamin B1 (ab133741 rabbit; 1:243 immunofluorescence) were purchased from Abcam; and clathrin-HC (clone 23 mouse; 610500; 1:1,000 WB) was purchased from BD. HC-20 peptide was purchased from Santa Cruz Biotechnology. Secondary antibodies used for WB (1:5,000) were goat anti–mouse HRP-conjugated (AP308P) and goat anti–rabbit HRP conjugated (AP132P) purchased from EMD Millipore. Secondary antibodies used for immunofluorescence (1:500) were goat anti–mouse and goat anti–rabbit Alexa Fluor 488–, 555–, and 647–conjugated antibodies, all purchased from Thermo Fisher Scientific.
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9

Immunohistochemistry of Neural Crest Markers

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This was performed on paraffin-embedded tissue sections or neural crest explants as described (Flentke et al. 2011 ), evaluating 3–5 embryos per treatment and 5–7 hindbrain sections per embryo. Antibodies were directed against Snail2 (#27568, 1:1000, AbCam), E-cadherin (#07–697, 1:1000, EMD Millipore), and p53 (#SC-99, 1:2000, Santa Cruz). Isotype-directed secondary antibodies were conjugated with Alexa488. Nuclei were visualized using DAPI stain. All images were photographed using the same exposure.
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10

Evaluation of Cell Signaling Proteins

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The cells were washed with phosphate-buffered saline (PBS) and lysed in radioimmunoprecipitation assay (RIPA) buffer containing protease inhibitors (Sigma-Aldrich, St. Lois, MO, USA). Western blot analyses were conducted as previously described [15 (link)]. Antibodies to the following proteins were used: ZEB1 and ZEB2 (Novusbio, Littleton, CO, USA), cyclin-D1 (Merck, Darmstadt, Germany), N-Cadherin (Merck), E-cadherin (Merck), vimentin (Merck), CD200 (R&D systems, Minneapolis, MN, USA), CD200R1 (R&D systems), c-Myc (Cell Signaling Technology, Danvers, MA, USA), β-catenin (Merck), Fibronectin (Merck), and β-actin (Santa Cruz, Dallas, TX, USA). For flow cytometry analysis, all cells (1 × 107) or dissociated tumors were incubated for 15 min in the dark with anti-mouse CD16/CD32 antibody (BD Biosciences, San Diego, CA, USA). Cells (1 × 107) were incubated for 30 min with anti-human CD200 PE-Cy7-conjugated antibody (BD Biosciences) or anti-mouse CD200 PE-conjugated antibody (BioLegend, San Diego, CA, USA). After washing again with FACS buffer, the MEER cell lines were resuspended in FACS buffer and analyzed. Densitometry readings/intensity ratio of each band was performed by using ImageJ software (ImageJ, NIH, Bethesda, MD, USA). Details information of western blot could be found in Supplementary Figure S7.
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