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49 protocols using irdye 680lt goat anti mouse igg

1

Immunoblot Detection of Specific Proteins

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Specific proteins were detected using a Calretinin rabbit monoclonal antibody (ab92341) Abcam, diluted 1:500; a Calbidin-D-28K rabbit polyclonal antibody (C2724) Sigma, diluted 1:500; or a beta actin mouse monoclonal antibody (ab6276) Abcam, diluted 1:1000. IRDye 800CW goat anti-rabbit immunoglobulin G (IgG) or IRDye 680LT goat anti-mouse IgG (LI-COR Biosciences) secondary antibodies were used and the immunoblots were visualised using an Odyssey infrared imaging system (LI-COR Biosciences). Protein densitometry was determined using Image studio lite Software.
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2

Western Blot Analysis of Phospho-S6 Protein

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Total protein extracts were prepared by cell lysis in radioimmunoprecipitation assay buffer (RIPA lysis). A total of 100 μg total protein extracts were separated on polyacrylamid gel by electrophoresis (PAGE), transferred to a nitrocellulose membrane and incubated with mouse anti-phospho-S6 (Ser235/236) cupk43k (#14-9007-82, Invitrogen, Thermo Fisher Scientific), mouse anti-actin IgG (MAB 1501, Millipore, CA), followed by IRDye® 680LT goat anti-mouse IgG (LI-COR Biotechnology, BadHomburg, Germany). Membranes were scanned on a LI-COR Odyssey Infrared Scanner (LI-COR Biotechnology, Germany). Bands were quantified on Image Studio software. Three independent assays were performed. One representative blot is depicted.
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3

Western Blot Analysis of Cellular Proteins

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For Western blot analyses, 20 μg of total cellular proteins were added to each well of a 4–20% Mini-PROTEAN® TGX™ Precast Gel (Biorad, Mississauga, Canada cat# 4561093EDU) and electrophoresed at 95 volts for 5 min followed by 200 volts for 30 min. Proteins were transferred to a nitrocellulose membrane using the iBlot2 transfer stacks (Invitrogen, Waltham, MA, USA, cat#IB23001) and Invitrogen’s iBlot system. LI-COR TBS Odyssey buffer (LI-COR, Lincoln, NE, USA, cat#927-50100) was used to block the membranes for 1 h at room temperature. An overnight incubation at 4 °C with primary antibodies was followed by a 1-h incubation at room temperature with secondary antibodies. The membranes were imaged on the Odyssey FC imager (LI-COR, Lincoln, NE, USA). Quantification of proteins was performed using Image Studio Lite software from LI-COR. Primary antibodies: p53 (Santa Cruz Biotechnologies sc-126); BST2 (Santa Cruz Biotechnology, Dallas, TX, USA, cat# sc-390719); hTERT (Abcam, Cambridge, UK, cat# ab183105); UCHL1 (Santa Cruz Biotechnology, Dallas, TX, USA, cat#sc-58593); Vinculin (Abcam, Cambridge, UK, cat# ab73412); GAPDH (Invitrogen, Waltham, MA, USA, cat# MA5-15738). Secondary antibodies included IRDye® 680LT Goat anti-Mouse IgG (LI-COR, Lincoln, NE, USA, cat# 926-68020) and IRDye 800LT Goat anti-Rabbit IgG (LI-COR, Lincoln, NE, USA, cat# 926-32211)
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4

Immunoblot Analysis of Mitochondrial Proteins

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Specific proteins were detected using rabbit polyclonal antibodies against: MRPL44 (16394-1-AP), MRPL23 (11706-1-AP), TACO1 (21147-1-AP), MRPS35 (16457-1-AP), MRPS16 (16735-1-AP) (Proteintech, diluted 1:1,000), MRPS34 (Sigma HPA042112, diluted 1:1,000), and mouse monoclonal antibodies against: β-actin (8226), porin (14734), NDUFA9 (14713), complex II (14715), complex III (14745), COXI (14705), COXII (198286), COXIV (14744) and complex V subunit a (14748; Abcam, diluted 1:1,000), in Odyssey Blocking Buffer (Li-Cor). IR Dye 800CW Goat Anti-Rabbit IgG or IRDye 680LT Goat Anti-Mouse IgG (Li-Cor) secondary antibodies were used and the immunoblots were visualized using an Odyssey Infrared Imaging System (Li-Cor). Examples of uncropped blots are shown in the Supplementary Fig. 8. Tissue-specific analysis was performed using a Proteintech mouse tissue blot (Cat. No M10005).
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5

Immunoblotting Analysis of Signaling Pathways

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Cells were lysed in RIPA lysis and extraction buffer (Thermo Fisher Scientific, Cat.#89900) containing 1xprotease inhibitors (Roche, Cat.#11-836-145-001) and phosphatase inhibitor (50 μM NaF and 100 μM Na3VO4). Immunoblotting was performed as described(33 (link)) using antibodies that specifically recognize MET (Cell Signaling Technology, Cat.#8198), Phospho-MET (Cell Signaling Technology, Cat.#3077), STING (Cell Signaling Technology, Cat.#13647), CD73 (Cell Signaling Technology, Cat.#13160), TBK1 (Cell Signaling Technology, Cat.#3013), Phospho-TBK1 (Cell Signaling Technology, Cat.#5483), IRF3 (Cell Signaling Technology, Cat.#11904), phospho-IRF3 (Cell Signaling Technology, Cat.#4947), STAT1 (Cell Signaling Technology, Cat.#9172), phosphor-STAT1 (Cell Signaling Technology, Cat.#9167), ERK(Cell Signaling Technology, Cat.#9107), phosphor-ERK (Cell Signaling Technology, Cat.#4370), AKT(Cell Signaling Technology, Cat.#9272), phosphor-AKT(Cell Signaling Technology, Cat.#4060), FRA1 (Abcam, Cat.#124722), phospho-FRA1 (Cell Signaling Technology, Cat.#5841), cGAS(Cell Signaling Technology, Cat.#15102), and β-actin (Cell Signaling Technology, Cat.#3700). Secondary antibodies were from LICOR Bioscience: IRDye 680LT Goat anti-Mouse IgG (#926–68020), IRDye 800CW Goat anti-Rabbit IgG (#926–32211). Imaging of blots are was performed using LICOR Odyssey system.
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6

Quantifying IKZF1, IKZF2, and GSPT1 Proteins

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Primary and secondary antibodies used included
anti-IKZF1 at 1:1000 dilution (Cell signaling, #14859), anti-IKZF2
at 1:1000 dilution (Cell Signaling, #42427), anti-GSPT1 at 1:2000
dilution (Sigma, hpa052488), anti-Actin at 1:5000 dilution (Abcam,
ab8226), IRDye 680LT Goat anti-Mouse IgG (Licor, 926-68020), and IRDye
800CW Goat anti-Rabbit IgG at 1:5000 dilution (Licor, 926-32211) were
used as secondary antibodies.
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7

Immunoblotting and Immunofluorescence Assay Protocol

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Blebbistatin (B05060), low-endotoxin BSA (A8806), PA (P9767), and Y27632 (Y0503) were from Sigma Aldrich (St. Louis, MO), while cis-PO/palmitoleic acid (10009871) was from Cayman Chemicals (Ann Arbor, MI). Antibodies used for immunoblotting were α-actinin (Millipore Sigma; A7811), β-actin (Cell Signaling; 4790), α-catenin (ThermoFisher; 13-9700), β-catenin (BD Biosciences; 610153), VE-cadherin (Santa Cruz; 9989), RhoA (Santa Cruz; c-418), IRDye 800CW goat anti-rabbit immunoglobulin G (IgG) (LI-COR; 9253211), and IRDye 680LT goat anti-mouse IgG (92668070). Antibodies and reagents used for immunofluorescence were α-catenin (ThermoFisher; 13-9700), β-catenin (BD Biosciences; 610153), DAPI (4’,6-Diamidino-2-phenylindole, dihydrochloride; ThermoFisher; D1306), GM130 (BD Biosciences; 610823), phospho-MLC (Cell Signaling; 3674), phalloidin (Alexa Fluor 555) (ThermoFisher; A34055), phospho-YAP S127 (Abcam; 76252), YAP (Cell Signaling 14074), VE-cadherin (Santa Cruz; 9989), goat anti-rabbit IgG secondary antibody (Alexa Fluor 488) (ThermoFisher; A11008), goat anti-mouse IgG secondary antibody (Alexa Fluor 647) (ThermoFisher; A21235). Dako fluorescence mounting medium (S3023) was from Aligent. Y227632 (Y0503) was from Millipore Sigma (Burlington, MA). The plasmid encoding GFP–β-actin was kindly provided by Sergio Grinstein (Hospital for Sick Children, Toronto, Ontario, Canada).
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8

Western Blot Analysis of β-Catenin Signaling

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SW480 cells at 1 × 106 cells/mL were treated with different concentrations of inhibitors for 24 h. Cells were lysed in buffer containing 50 mM Tris (pH 7.4), 150 mM NaCl, 1% Nonidet P-40, 0.5% sodium deoxycholate, 0.1% SDS, and protease inhibitors. After centrifugation at 12,000 rpm for 20 min at 4 °C, the supernatant was loaded onto an 8% SDS polyacrylamide gel for electrophoretic analysis. Separated proteins were transferred onto nitrocellulose membranes for immunoblot analysis. The antibodies against total β-catenin (610153, BD Biosciences, most of which is phosphorylated β-catenin and represents the E-cadherin bound pool), the active form of β-catenin (ABC, 05–665, EMD Millipore, dephosphorylated at positions S37 and T41 of β-catenin), cyclin D1 (sc-853, Santa Cruz Biotechnology, Inc.), c-myc (D84C12, Cell Signaling), and β-tubulin (sc-55529, Santa Cruz Biotechnology, Inc.) were incubated with the membranes overnight at 4 °C, respectively. IRDye 680LT goat antimouse IgG (827–11080, LiCOR) or IRDye 800CW goat antirabbit IgG (827–08365, LiCOR) was used as the secondary antibody. The images were detected by the Odyssey Infrared Imaging System (LiCOR). Experiments were performed in duplicate.
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9

Western Blot Analysis of Ifit1, Ifit2/3, and GAPDH

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Cell lysates were separated in 12.5% SDS-PAGE and transferred to 0.45-μm nitrocellulose membrane by semi-dry blotting. Membranes were blocked in 5% milk phosphate buffered saline with 0.1% tween-20 (PBS-T) and primary antibodies were incubated in 5% BSA PBS-T at 4°C overnight. Anti-Ifit1 (Santa Cruz, sc-134949, rabbit polyclonal) was used at 1:500, anti-Ifit2/3 (ProteinTech, 12604-1-AP, rabbit polyclonal) was used at 1:800 and anti-GAPDH (Invitrogen, AM4300, mouse monoclonal) was used at 1:8000. Blots were incubated with IRDye 680LT Goat anti-Mouse IgG (Li-Cor, 926-68020) and IRDye 800CW Donkey anti-Rabbit IgG (Li-Cor, 926-32213) secondary antibodies at 1:10000 in PBS-T, for 1 hour at room temperature, then imaged on an Odyssey CLx Imaging System (Li-Cor).
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10

Immunoblotting Analysis of Tumor Proteins

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Portions of harvested tumors were resuspended at 100 mg/mL in RIPA buffer supplemented with protease and phosphatase inhibitors. Next, we homogenized these tumor samples with pestles in tubes, and then sonicated the samples for 10 s at 50% amplitude on a Fisherbrand Model 120 Sonic Dismembrator. Cells cultured on dishes were collected by scraping in 1× PBS and lysed in RIPA buffer supplemented with protease and phosphatase inhibitors. Proteins from lysates were separated on a 10% SDS-PAGE gel and transferred to a nitrocellulose membrane using the iBlot 2 dry blotting system (Invitrogen IB21001).
Membranes were incubated overnight at 4°C with the following antibodies: Phospho-Rb (Ser807/811) (D20B12) XP Rabbit mAb (Cell Signaling Technology #8516), Purified Mouse Anti-Human Retinoblastoma Protein Clone G3–245 (BD Biosciences 554136), Monoclonal ANTI-FLAG M2 antibody produced in mouse (Sigma-Aldrich F1804), E2F-1 Antibody (Cell Signaling Technology #3742), and mouse monoclonal β-Actin Antibody N-21 (Santa Cruz Biotechnology sc-130656). The primary antibodies were detected using the fluorescently labeled secondary antibodies IRDye 680LT Goat anti-Mouse IgG (LI-COR 926–68020) and IRDye 800CW Goat anti-Rabbit IgG (LI-COR 926–32211). Membranes were imaged on a LI-COR Odyssey CLx and analyzed with LI-COR ImageStudio software.
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