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12 protocols using phospho yaps127

1

Sprague Dawley Rat Biochemical Assay

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Male Sprague Dawley (SD) rats were obtained from Charles River. Culture media and additives were obtained from Invitrogen. All chemicals were obtained from Sigma unless otherwise stated. BAY60-6583 was from Tocris. Antibodies to YAP, phospho-YAPS127, phospho-YAPS397, TAZ, pan-TEAD and phospho-Retinoblastoma protein were from Cell Signalling Technologies. Anti-BrDU antibody was from Sigma.
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2

Investigating YAP Signaling Modulation

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Crenolanib (Selleck Chemicals) and Dasatinib (TSZ Chemicals) was added to cells at final concentrations from 0.1–10μM. The following primary antisera were used for immunoblot analysis: PDGF Receptor (28E1 Cell Signaling, Danvers, MA), actin (C-11 Santa Cruz, Dallas, TX), phospho YAPY357 (ab62751 abcam, Cambridge, MA), phospho YAPS127 (4911 Cell Signaling), total YAP (63.7 Santa Cruz), lamin B1 (D8P3U Cell Signaling), GAPDH (MAB374 Millipore, Temecula, CA), phospho SrcY416 (2101 Cell Signaling), Src (L4A1 Cell Signaling), and Mcl-1 (S-19 Santa Cruz). The following primary monoclonal antibodies were used for immunofluorescence: total YAP (63.7 Santa Cruz) and anti-FLAG M2 (F1804 Sigma Adrich). For ChIP immunoprecipitation assays we employed an anti-YAP monoclonal antibody (63.7 Santa Cruz). ProLong Antifade with 4′,6-diamidino-2-phenylindole (DAPI, Life Technologies) was used for nuclear staining. The following primers used are listed in Table 1.
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3

Antibody-based analysis of Hippo pathway

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Antibodies against YAP (#4912), YAP/TAZ (#8418), phospho-YAP S127 (#4911), LATS1 (#3477, 1:200), phospho-LATS1 Thr1079 (#9159, 1:200), MOB1 (#3863), phosphor-MOB1T35 (#8699), MST1 (#3682) were purchased from Cell Signaling, USA, anti-14:3:3 ε (sc-393177), TAZ (sc-48805), Ubiquitin (sc-8017) and Lamin B1 (sc-377001) were from SantaCruz Biotechnology. Anti-LATS1 ab70562 (abcam) and anti-MOB1A/B sc-161867 (Santa Cruz) were used in the mouse cell line with 1:500 dilution. Anti-Hsp27 (1:5000) was from ENZO lifesciences. MG132 was from Millipore (#474791).
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4

Western Blot Analysis of Kidney Proteins

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Western blot analysis was performed on stage E13.5 Nf2UB−/− kidneys or cultured YapUB-OE kidneys following doxycycline induction. Unless stated otherwise each western blot lane represents one animal (two kidneys). Kidneys were mechanically homogenized and lysed in RIPA buffer supplemented with proteasome and phosphatase inhibitors. Western blot analysis was performed following standard protocols with the following primary antibodies: CALBINDIN (C9848, Sigma, 1:1,000), BAF155 (SC-9748, SantaCruz Biotechnology, 1:2,000), GAPDH (R9545, Sigma, 1:7,500), HA (11867423001, Roche, 1:1,000), LATS1 (#3477, Cell Signaling Technology, 1:1,000), MST1 (#3682, Cell Signaling Technology, 1:2,000), NF2 (HPA003097, Sigma Prestige Antibodies, 1:2,000), phosho-LATS1 S909 (#9157, Cell Signaling Technology, 1:500), phospho-MST1/2 T183/T180 (#3681, Cell Signaling Technology, 1:2,000), phospho-YAP S127 (#4911, Cell Signaling Technology, 1:2,000) and YAP (sc-101199, SantaCruz Biotechnology, 1:2,000). All uncropped western blots can be found in Supplementary Fig. 8.
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5

Density-Dependent Protein Expression Analysis

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Cells were grown at either high or low density in culture and then lysed. Proteins extracted from the lysates were separated by SDS-PAGE and immunoblotted with anti-vimentin (Dako, Carpinteria, CA), beta-catenin (BD Biosciences, San Jose, CA), actin (Millipore, Billerica, MA), E-Cadherin, Stat3, phospho-Stat3, NFκB, phospho-NFκB, IκBα, phospho-IκBα, phospho-YAP (S127) (Cell Signaling, Boston, MA), and YAP (Santa Cruz, Dallas, TX).
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6

Western Blot Analysis of Signaling Proteins

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Cells were lysed in ice-cold radioimmunoprecipitation assay (RIPA) buffer supplemented with a protease and phosphatase inhibitor cocktail (Roche). Whole-cell extracts were incubated with the indicated antibodies and protein A/G beads (Santa Cruz Biotechnology) overnight. The beads were washed with RIPA buffer three times and then boiled in SDS loading buffer. For Western blotting, cell extracts were separated by SDS-PAGE. After Western transfer, membranes were probed with antibodies against DDK (Origene ta50011), GFP (Santa Cruz biotechnology sc-101536), Glut3 (Santa Cruz biotechnology sc-74399), HA (Santa Cruz biotechnology sc-393579), PKM2 (Cell Signaling #3198), phospho-PKM2(Y705) (Cell Signaling #3827), YAP (Cell Signaling #12395), phospho-YAP(S127) (Cell Signaling #13008), actin (GeneTex GTX11003) and lamin C (GeneTex GTX101127). Bands were detected with an enhanced chemiluminescence system (Millipore). Western blotting was performed at least three times, and representative experiments are shown. Quantification was carried out using ImageJ software.
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7

Comprehensive Cell Signaling Antibody Panel

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Antibodies against phospho-S6K(T389) (#9205), S6K (#9202), phospho-4E-BP1(T37/46) (#9459), 4E-BP1 (#9452), phospho-Akt(S473) (#9271), phospho-Akt(T308) (#9275), Akt (#9272), phospho-TSC2(T1462) (#3611), phospho-TSC2(S1387) (#5584), phospho-TSC2(S1254) (#3616), TSC2 (#4308), mTOR (#2983), phospho-GSK3β(Ser9) (#5558), phospho-p38(T180/Y182) (#9216), p38 (#9212), phospho-MAPKAPK2(T222) (#3316), phospho-ERK1/2(T202/Y204) (#4370), ERK1/2 (#4695), phospho-AMPKβ1(S108) (#4181), phospho-p90RSK(S380) (#9341), phospho-Erk5(T218/Y220) (#3371), phospho-CaMKII(T286) (#3361), phospho-MST1(T183)/MST2(T180) (#3681), and phospho-YAP(S127) (#4911) proteins were purchased from Cell Signaling Technology. An antibody against phospho-TSC2(S664) was purchased from Abcam (ab133465). The mouse LAMP2 (ABL-93) antibody was obtained from Developmental Studies Hybridoma Bank. A monoclonal antibody recognizing human and mouse α-tubulin (#T9026) and an anti-FLAG (M2) (#F1804) antibody were purchased from Sigma. All antibodies were used in 1:1000 dilution for western blotting, except for the phospho-ERK, total ERK, TSC2, and p38 antibodies that were used in 1:2000.
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8

Investigating YAP Signaling Pathway

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Dasatinib (Selleckchem), KW-2449 (Selleckchem), sodium orthovanadate (Sigma), and/or latrunculin A (Abcam) was added to cells at final concentrations from 0.1–10 µM per experimental design. The following primary antisera were used for immunoblot analysis: actin (C-11 Santa Cruz, Dallas, TX), phospho YAPY357 (ab62751 abcam, Cambridge, MA), phospho YAPS127 (4911 Cell Signaling), total YAP (63.7 Santa Cruz, 4912 CST), lamin B1 (D8P3U Cell Signaling), GAPDH (MAB374 Millipore, Temecula, CA), phospho SRCY416 (2101 Cell Signaling), SRC (L4A1 Cell Signaling), YES (3201 Cell Signaling), LCK (2657 Cell Signaling), FYN (4023 Cell Signaling), LYN (44 Santa Cruz), LATS1 (C66B Cell Signaling), phospho LATS1 (S909 Cell Signaling) and MCL-1 (S-19 Santa Cruz). The following primary monoclonal antibody were used for immunofluorescence and/or immunohistochemistry: total YAP (63.7 Santa Cruz), phospho YAPY357 (ab62751 abcam, Cambridge, MA), SOX9 (AB5535 Millipore) and anti-FLAG M2 (F1804 Sigma Adrich). ProLong Antifade with 4’,6-diamidino-2-phenylindole (DAPI, Life Technologies) was used for nuclear staining.
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9

Antibody Sources for Signaling Pathway Analysis

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Antibodies against IL-6 were obtained from Ab Cam (Cat# 191194), CD11B were acquired from Novus Biologicals (Cat# NB110-89474), and RALGDS from Abiocode (Cat# R1857-vp). Antibodies for Phospho-ERK (Cat# 9101), ERK (Cat# 9102), Phospho-AKT-Ser473 (Cat# 9271), Phospho-YAP-S127 (Cat# 4911), YAP (Cat# 4912), and Mouse and Rabbit secondary antibodies (Cat# 7076 and 7074) were obtained from Cell Signaling Technologies (Boston, MA). Epitope tag antibodies detecting GFP were purchased from Santa Cruz (Cat# SC-9996) and HA from Covance (Cat# MMS-101P). RASSF1A rabbit antibody was generated by Prosci (Poway CA) against the peptide “ELRELAPAGRAGKGRTRLER”.
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10

Immunofluorescence Analysis of YAP Signaling

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EMT6 cells were seeded on glass coverslips in a 24-well plate and incubated O/N for attachment. After indicated treatments, samples were washed with 1X PBS and fixed with 4% PFA for 20 min. Then, Triton-X (0.5%) was used to permeabilize the cells for 20 min on a shaker. Samples were blocked with 3% BSA for 1 h on a shaker, washed three times with 1X PBS, and incubated with the following antibodies Phospho-YAP (S127) (Cell Signaling 13008), YAP (Cell Signaling 4912), or calreticulin (Cell Signaling D3E6) O/N on shaker at 4°C. The following day samples were washed and incubated for 1 h on a shaker with DyLight 488 Donkey anti-rabbit IgG (minimal x-reactivity) antibody (BioLegend 406404). After incubation, samples were washed and incubated with Flash Phalloidin Red 594 (BioLegend 424203) for 30 min on a shaker. Lastly, samples were washed and mounted in ProLong Glass Antifade Mountant with NucBlue Stain (Thermo Fisher P36981) and stored in the dark until imaging.
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