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18 protocols using p fak y397

1

Western Blot Analysis of Signaling Proteins

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Cells were lysed in RIPA buffer containing protease inhibitors and protein lysates were subjected to SDS–PAGE and immunoblot analysis as previously described [34 (link)]. Antibodies used include pSTAT5 (Cell Signaling #9314, 1:1000), total STAT5 (Cell Signaling #9363, 1:1000), β-tubulin (Cell Signaling # 2146S, 1:1000), pFAK Y397 (Cell Signaling, # 3283S, 1:1000), and total FAK (Cell Signaling #3285S, 1:1000).
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2

Antibody Protocol for Protein Quantification

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Antibodies against YAP1 (#14074), pYAPS127 (#4911), FAK (#3285), pFAKY397 (#8556), pERK (#4370), ERK (#9102), β-Arrestin1/2 (#4674), β-Actin (#4967) and GAPDH (#2118) were purchased from Cell Signaling Technology (Beverly, MA, USA). pYAPY357 (#ab62751) and CHRM3 (ab126168) was purchased from Abcam (Cambridge, UK). CHRM1 (#nbp1–87466) was purchased from Novus Biologicals, LLC (Centennial, CO, USA).
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3

Western Blot Analysis of Signaling Proteins

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Cultured cells were homogenized in RIPA buffer (Cell Signaling) containing protease inhibitors (Complete; Roche, IN, USA). Protein concentrations were measured using the Bradford protein assay (Bio-Rad), according to the manufacturer’s instructions. Protein samples (5 µg) was boiling for 5 min, then subjected to 13- or 17-wells of 5%–20% SDS-polyacrylamide Supersep Ace (Wako) gel electrophoresis. Gels that contains separated products were transferred to nitrocellulose membranes, followed by blocking with 5% nonfat dry milk in Tris-buffered saline containing 0.1% Tween 20. Nitrocellulose membranes then incubate overnight with primary antibodies for p-FAK (Y397) (1:1000, Cell Signaling), FAK (1:1000, Cell Signaling), p-ERK1/2 (T202/Y204) (1:1000, Cell Signaling), ERK1/2 (1:1000, Cell Signaling), p-Akt (S473) (1:1000, Cell Signaling), Akt (1:1000, Cell Signaling), and GAPDH (1:1000, Proteintech, IL, USA). After washing with Tris-buffered saline containing 0.1% Tween 20, membranes were incubated with secondary antibody for anti-rabbit or anti-mouse IgG horseradish peroxidase-conjugated (1:3000, Cell Signaling) for one hour at room temperature. Bands of target proteins were detected using an ECL detection system (Wako). ImageJ Fiji (NIH) was used to analyses the bands. Data are showed as the mean ± standard error of the mean (SEM). GAPDH was used as the loading control.
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4

Protein expression and signaling analysis

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Protein samples were electrophoresed on 6–12% SDS polyacrylamide gel and transferred to polyvinylidene difluoride membrane (PVDF, Merck Millipore). The PVDF was blocked in 5% nonfat milk and incubated with primary antibodies against ZNF488 (Abcam), Collagen IV (Abcam), integrin α5 (Abcam), p-FAK(Y397) (Cell Signaling Technology (CST)), FAK (CST), ERK 1/2(Cell Signaling Technology), p-ERK1/2 (CST), Akt (CST), p-Akt (CST), Cyclin D1 (Abcam), Cyclin D2 (Abcam), Cyclin E (C-19) (Santa Cruz), α-tubulin (CST) and Cleaved caspase 9 p10 (Santa Cruz) overnight at 4°C. The PVDF membrane was incubated with anti-mouse or rabbit IgG secondary antibodies. α-tubulin served as the loading control. The band on the PVDF membrane was observed using an electrochemiluminescence kit (Pierce).
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5

Molecular Marker Quantification Protocol

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Cleaved PARP (#5625), FAK (#130009), p-FAK (Y397) (#3283), and Cyclin D1 (#2922) were from Cell Signaling (Danvers, MA, USA). β-actin antibody (A2228) and fibronectin (AB1954) were from Sigma (St. Louis, MO, USA).
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6

Antibodies in Immunoblotting and Immunofluorescence

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The following antibodies were used at the indicated dilutions: PME‐1, Santa Cruz Biotechnology (Dallas, TX, USA) sc‐20086 (H‐226), Western blotting 1 : 1000; PME‐1, Santa Cruz Biotechnology sc‐25278 (B‐12), Immunohistochemistry 1 : 1000, Immunofluorescence 1 : 100; cleaved PARP‐1, Abcam (Cambridge, UK) ab32064 [E51], Western blotting 1 : 1000; GAPDH, HyTest 5G4‐6C5, Western blotting 1 : 5000; c‐MYC, Abcam ab32072 [Y69], Western blotting 1 : 1000; p‐Myc S62, Abcam ab78318, Western blotting 1 : 1000; AKT1/2/3, Cell Signaling Technology #9272, Western blotting 1 : 2000; p‐AKT S473, Cell Signaling Technology #4060, Western blotting 1 : 1000; Lamin‐A/C, Santa Cruz Biotechnology sc‐7292 (636), Immunofluorescence 1 : 250; Lamin‐A/C, Santa Cruz Biotechnology sc‐6215 (N‐18), Western blotting 1 : 1000; p‐Lamin‐A/C S392, Abcam ab58528, Western blotting 1 : 5000; EEA1, Santa Cruz Biotechnology sc‐137130 [G4], Immunofluorescence 1 : 100; p‐FAK Y397, Cell Signaling Technology #8556, Immunofluorescence 1 : 100; Histone H3K9me3, Cell Signaling Technology #13969 [D4W1U], Immunofluorescence 1 : 500; Histone H3K27me3, Cell Signaling Technology #9733 [C36B11], Immunofluorescence 1 : 500; PPP2R2A, Cell Signaling Technology #5689, Western blotting 1 : 1000.
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7

Immunoblot and Immunofluorescence Protein Analysis

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Immunoblot analyses were performed using the following antibodies: FAK (Santa Cruz Biotechnology, Inc.), pFAKY397, Akt, pAktS473, HRP-linked anti-mouse IgG, HRP-linked anti-rabbit IgG (all Cell Signaling), IRDye® 680RD anti-mouse IgG, IRDye® 800CW anti-mouse IgG, IRDye® 680RD anti-rabbit IgG, and IRDye® anti-rabbit IgG (all LI-COR Biosciences). The mouse Abca1 antibody was a generous gift from Dr. David Castle (University of Virginia, Charlottesville, VA). Immunofluorescence staining was performed using rabbit anti-Salmonella (Thermo), donkey anti-rabbit AlexaFluor 488, and AlexaFluor 647 phalloidin (both Invitrogen).
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8

Immunofluorescence Analysis of FAK Phosphorylation

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MDA-MB 231 cells cultured on fibronectin-coated 6 well plates were serum deprived and then treated for 30 min with E2 and G1 alone or in combination with G15, as indicated. Then cells were washed three times with PBS, fixed in 4% paraformaldehyde for 15 min, permeabilized with 0.2% Triton X-100, washed three times with PBS and incubated overnight with or without (negative control) a rabbit primary antibody anti p-FAK (Y397) (Cell Signaling Technology, Milan, Italy). After incubation, the wells were extensively washed with PBS and incubated with donkey anti-rabbit IgG-FITC (1:300; purchased from Alexa Fluor, Life Technologies, Milan, Italy) for 1 h at room temperature. Finally, cells were washed with PBS and incubated in PBS buffer containing 4′, 6-diamidino-2-phenylindole dihydrochloride (DAPI), (1:1000), (Sigma-Aldrich, Milan, Italy) 10 min at room temperature for nuclear staining. FAs images were acquired on the Cytation 3 Cell Imaging Multimode Reader (BioTek, Winooski, VT) and analysed using the software Gen5 (BioTek, Winooski, VT).
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9

Western Blot Analysis of Signaling Proteins

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The following antibodies were obtained from Cell Signaling Technology (Danvers, MA, USA) : EGFR (#2232), pEGFR Y1068 (#2234), HER3 (#4754), pHER3 Y1197 (#4561), pBRAF S445 (#2696), MEK (#9126), pMEK S217/221 (#9154), ERK (#9102), pERK T202/Y204 (#9101), PDK1 (#3062), pPDK1 S241 (#3061), AKT (#9272), pAKT S473 (#9271), pAKT T308 (#9275), ribosomal protein S6 (#2317), pS6 S240/S244 (#5364), FAK (#3285), pFAK Y397 (#8556), SFKs (#2108), pSFKs Y416 (#2101), YES (#3201), Integrin Antibody Sampler Kit (#4749), PARP (#9542), E-cadherin (#3195), Vimentin (#3932), horseradish peroxidase (HRP)-conjugated anti-mouse (#7076) and HRP-conjugated anti-rabbit (#7074). The actin antibody (A2066) was purchased from Sigma-Aldrich. The BRAF antibody (sc-55522) was purchased from Santa Cruz Biotechnology (Dallas, TX, USA). For immunoblot, cells were harvested, washed in PBS, and lysed in RIPA buffer [50 mM Tris•HCl (pH 8.0), 150 mM sodium chloride, 5 mM magnesium chloride, 1% Triton X-100. 0.5% sodium deoxycholate, 0.1% SDS, 40 mM sodium fluoride, 1 mM sodium orthovanadate, and complete protease inhibitors (Roche Diagnostics, Indianapolis, IN, USA)]. Western Lightning ECL reagent (Perkin-Elmer) as used for signal detection. Phosphorylated bands were quantified using ImageJ software.
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10

Western Blot Analysis of Signaling Pathways

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Cells were washed once with PBS and lysed with RIPA buffer (150 mM NaCl, 50 nM Tris, 1% Triton-X-100, 0.5% sodium deoxycholate, and 0.1% SDS) containing protease and phosphatase inhibitors (Roche, Indianapolis, IN, USA). Cell lysates were centrifuged at 12,000 g for 5 min to isolate protein extracts. The protein concentration was measured using Bio-Rad Protein Assay reagent (Bio-Rad Laboratories, Hercules, CA, USA). The same amount of protein was loaded and separated by electrophoresis on SDS-polyacrylamide gels, and then transferred to nitrocellulose membranes. The membranes were blocked in 5% skim milk in Tris-buffered saline (TBS) containing 0.1% Tween 20 for 1 h at room temperature. The blocked membranes were then incubated with primary antibodies overnight at 4 °C with agitation followed by incubation with horseradish peroxidase-conjugated secondary antibodies for 1 h at room temperature. The blots were visualized using the Chemiluminescence Western Blot Detection System (BioSpectrum®600 Imaging System, Upland, CA, USA). Primary antibodies used are as follows: pErk, Erk, pJNK, JNK, pFAK (Y397), and FAK from Cell Signaling (Danvers, MA, USA), and GAPDH from Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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