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12 protocols using tubulin t 9026

1

Whole-cell Protein Extraction and Immunoblot Analysis

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Whole-cell extracts were generated as described previously52 (link). In brief, cell monolayers were washed with ice-cold phosphate-buffered saline and then lysed in extraction buffer (1% (v/v) Triton X-100, 10 mm Tris-HCl, pH 7.4, 5 mm EDTA, 50 mm NaCl, 50 mm sodium fluoride, 2 mm Na3VO4, containing Complete™ inhibitor mix (Roche Applied Science) per 10 ml of buffer) and homogenised by passage through a 26-gauge needle six times. The lysate was incubated on ice for 10 min prior to centrifugation (14,000 rpm at 4 °C). Equal amounts of protein were resolved by SDS-PAGE using 4–12% gradient gel (Biorad) and then subjected to immunoblot analysis. Antigen-antibody interactions were detected with ECL-reagent (Amersham, UK). Proteins were detected using the following antibodies: ER (ERα(F-10) sc-8002, Santa Cruz Biotechnology) at 1:200, cyclin D1 (CST-2922, Cell Signalling Technology) at 1:1000, PGR (NCL-L-PGR, Novocastra) at 1:500, FOXA1 (Abcam; ab 5089) at 1:1000, GAPDH [6C5] (Abcam; ab 8245) at 1:2000 and Tubulin (T-9026, Sigma- Aldrich) at 1:5000. Uncropped immunoblots are show in Supplemental Fig. 7.
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2

DMEM-Based Cell Culture Protocol

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Dulbecco's Modified Eagle's Medium (DMEM), FBS, Penicillin/Streptomycin and Glutamine were all purchased from Life Technologies. BIRB796 (S1574), CB1954 (S7829), PLX-4072 (S1267), Vemurafenib (S1267) and ZSTK474 (S1072) were purchased from Selleckchem; Trametinib (HY-10999) was from Insight Biotechnologies; JNK inhibitor VIII (CAS 894804-07-0) was from Calbiochem; SCH772984 (S7101) was from Merck. Bovine serum albumin (BSA), DMSO and Doxycycline were purchased from Sigma. Vectashield (H-1200-10) was purchased from VectorLabs. The following antibodies were all purchased from Cell Signalling Technologies: p-S473 AKT (4060), Akt1 (2967), c-Jun (9165), p-T202/Y204 ERK1/2 (4370), ERK1/2 (9107), GFP (2955), p-S217/S221 MEK1/2 (9154), MEK1/2 (4694), p-T334 MAPKAPK2 (8753), MAPKAPK2 (3042). BRAF (3967S) was purchased from Santa Cruz. Tubulin (T9026) and β-actin (A5441) were purchased from Sigma and KRAS (12063-1-AP) was from ProteinTech. Horseradish peroxidase-conjugated secondary antibodies were from Bio-Rad and the enhanced chemiluminescence (ECL) system from GE Healthcare was used for detection. The Dylight™680 and Dylight™800 conjugated secondary antibodies were from Cell Signalling Technology.
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3

Antibody Usage for Protein Analysis

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The following antibodies (Ab) were used: ADAM10 purchased from Abcam ab39153 (Cambridge, UK), SAP97 from Stressgen ADI-VAM-PS005-D (San Diego, CA, USA), β2-Adaptin from BD Bioscience 610382 (NJ, USA), Tubulin T9026 and GluN2A M264 from Sigma-Aldrich, GluA1 75-327, PSD-95 75-028, GluN2B 75-097, and GFP 75-132 from Neuromab (Davis, CA, USA), GluA1-p845 04-1073 and 6E10 SIG39320-200 (Covance) from Millipore (Billenca, MA, USA), and GluN1 320500 from Thermo Fisher (Waltham, MA, USA). Peroxidase-conjugated secondary Abs were purchased from Bio-Rad (Hercules, CA, USA). AlexaFluor secondary Abs were purchased from Thermo Fisher.
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4

Western Blot Analysis of Cell Markers

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Western blot analysis was performed following standard protocols. Primary antibodies against CAP1 (sc-376286; dilution: 1:500, Santa Cruz), Tubulin (T9026; 1:5,000, Sigma), Flag (F7425; 1:1,000, Sigma), Myosin Heavy chain 1/2/4/6 (sc-32732; 1:1,000, Santa Cruz), GAPDH (5174S; 1:3,000, Cell Signaling), Myogenin (sc-12732; 1:1,000) and MyoD (MA1-41017; 1:1,000, Thermo Fisher Scientific) were incubated overnight at 4°C. Fluorophore-conjugated secondary antibodies IRDye 700 or IRDye 800 (1:15,000, LICOR Biosciences) were incubated for 1 h at room temperature. Imaging and quantifications were done using the Odyssey Image Scanner System with the software Image Studio V 3.1.4 (LI-COR Biosciences, Cambridge, United Kingdom), as described before (Werner et al., 2019 (link)).
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5

Antibody-Based Kinase Inhibitor Profiling

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The primary antibodies against pEGFR (Y1173, #4407), pERK1/2 (T202/Y204, #9101), ERK1/2 (#4695), pAKT (S473, #9271), AKT (#9272), MCM2 (#3619), pRNA-II (S2/5; #4735), RNA-II (#2629), and p-pRb (S780, # 9307) were commercially supplied from Cell Signaling TECHNOLOGY®, EGFR (sc-03), pRb (sc-102), CDK4 (sc-601), Cyclin D1 (sc-20,044) from Santa Cruz BIOTECHNOLOGY®, cdc7 (ab10535) and pMCM2 (S40/41; ab70371) from Abcam® and Tubulin (T-9026) from Sigma®. Secondary antibodies included Cy5-conjugated anti-mouse and horseradish peroxidase (HRP) anti-mouse or anti-rabbit (Jackson ImmunoResearch). Individual kinase inhibitors lapatinib (S2111), gefitinib (S1025), erlotinib (S7786) and PHA-767491 (S2742), plus the previously described 273-kinase inhibitor library (L1200), were purchased from Selleckchem® (Munich, Germany) and dissolved in DMSO solution at 10 mM [22 (link)]. TAK-931 and BAY-1143572 were purchased from MedChemExpress (Sollentuna, Sweden).
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6

Profiling mTOR Pathway Activation

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Antibodies used include UCH-L1 (3524), raptor (2280), rictor (9476), 4EBP1 (2845), p4EBP1T70 (5078), p4EBP1T37/46 (2855), p4EBP1S65 (9451), pS6K (9208), S6K (49D7), AKT (4691), pAKTS473 (4060), eIF4A (C32B4), eIF4E (C46H6), anti-DYKDDDDK Tag (8146), anti-MYC tag (9B11) from Cell Signaling Inc. (Danvers, MA, USA), anti-HA (3F10, Roche Applied Science, Indianapolis, IN, USA) tubulin (T9026) from Sigma, mTOR (A301-143a), PHLPP (A300-660A) from Bethyl Laboratories (Montgomery, TX, USA), eIF4G (ab31217) from Abcam. Immunoprecipitations were performed as described using lysates prepared with 0.3% CHAPS (mTOR/rictor/raptor)4 (link),30 (link), 0.5% NP40 (BioID2-UCHL1, UCHL1-HA) or 1% SDS (raptor for detection of FLAG-Ub)4 (link). Immobilized m7GTP (AC-155) was from Jena Bioscience (Jena, Germany). M7GTP pulldowns were performed as described3 (link).
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7

Investigating MAPK Signaling in Mice

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LPS (E. coli EH100) was from Enzo Life Sciences. PGE2, PF04418948 and ONO-AE3-208 were from Cayman Chemical. Antibodies used in western blotting were from Santa Cruz (COX-2, sc-1745; DUSP1, sc-373841), Cell Signaling Technology (phosphorylated MAPK p38, #9211), Sigma Aldrich (tubulin, T9026 and β-actin, A1978). Flow cytometry antibodies against EP2 and EP4 were from Cayman Chemical (16684 and 16625). All other reagents were from Sigma Aldrich. The generation of Dusp1−/−, Zfp36aa/aa and Dusp1−/−: Zfp36aa/aa mouse strains was previously described37 (link). All strains were back-crossed to C57/BL6J for at least ten generations.
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8

Analyzing EGFR Mutant Cell Signaling

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EGFR L858R and EGFR L858M/L861Q NIH-3T3 cells were plated at 1×106 cells per 10-cm plate and treated with the indicated concentrations of inhibitors for 6 hours the following day. After 6 hours of treatment, cells were washed with PBS and lysed with NP40 buffer (Calbiochem) supplemented with Complete Mini protease inhibitor and PhosSTOP phosphatase inhibitors (Roche). Lysates were separated by SDS-PAGE gel, transferred to nitrocellulose membranes, and probed the following antibodies: phospho-EGFR(Y1068) (3777), total EGFR (2232) (Cell Signaling), and tubulin (T9026) (Sigma Aldrich). Densitometry was measured using ImageJ. Samples were normalized to tubulin before determining the ratio of phospho-EGFR in treated versus untreated samples.
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9

Quantification of ETS Transcription Factors

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RNA levels were measured by quantitative reverse transcription-PCR as described previously [15 (link)], using primers in Additional file 4: Table S1.
Whole-cell extracts of equivalent cell number were separated by SDS-PAGE and blotted to nitrocellulose. Antibodies for immunoblotting were: ERK (sc-94) and pERK (sc-7383) from Santa Cruz Biotechnology, ETV5 (ab102010) and ETV1 (ab81086) from Abcam, pAKT (S473) and pMEK (9121) from Cell Signaling, Tubulin (T-9026) from Sigma, ETV4 (ARP32263_P050) from Aviva Systems Biology, and ERG (9FY) from Biocare Medical.
Purification of His-tagged ETS proteins for antibody validation was as described previously [49 (link)]. DNA binding activity was verified by EMSA. Concentration was calculated by comparison to BSA standards on Coomassie stained 10% SDS-PAGE gels.
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10

Antibody Sources for PTK6 Analysis

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Human PTK6 C-18 (SC-1188) and human PTK6 G6 (SC-166171) were obtained from Santa Cruz Biotechnologies (Santa Cruz, CA); phospho-PTK6 Tyr-342 (P-Y342) (09-144) was purchased from Millipore (Billerica, MA), and rabbit IgG from Vector Laboratories (Burlingame, CA). Antibodies against β-actin (A-5441) and α-tubulin (T-9026) were from Sigma-Aldrich(St. Louis, MO).
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