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13 protocols using halt phosphatase inhibitor single use cocktail

1

Protein Extraction and Western Blot Analysis

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Pieces of whole liver were homogenized using a tissue homogenizer (TissueRuptor, Qiagen, Germantown, MD), followed by centrifugation. Protein extraction from cells or whole liver was performed using lysis buffer complemented with protease inhibitor (Complete Lysis M kit, Roche Diagnostics, Indianapolis, IN) and phosphatase inhibitor (Halt Phosphatase Inhibitor Single-Use Cocktail, Thermo Scientific, Waltham, MA). Protein concentration was measured using a Bio-Rad DC kit (Bio-Rad Laboratories, Hercules, CA) and lysates were then subjected to immunoblot analysis. Blots were developed with the ECL Detection System (Amersham, Pharmacia Biotech, Buckinghamshire, England). Densitometry of bands was performed with ImageJ software (rsbweb.nih.gov/ij, NIH, Bethesda, MD). Western blot membranes were incubated with the following primary antibodies: Rabbit anti-β-PDGFR (1:500) and anti-phospho-β-PDGFR (1:500) were obtained from Santa Cruz Biotechnology, Santa Cruz, CA, rabbit anti-CD31 (1:500), rabbit anti-Ki67 (1:2500), rabbit anti-Desmin (1:1000) and rabbit anti-Calnexin (1:3,000) were from Abcam, Cambridge, England). The reactions were detected with the Fujifilm LAS-4000 system (Fujifilm Life Science, Stamford, CT), using a horseradish peroxidase-conjugated secondary antibody (Anti-rabbit IgG, Cell Signaling, Danvers, MA).
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2

Analyzing Protein Expression in Cell Lysates

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After removing spent media and washing cells with cold phosphate buffered saline (PBS), the cells were incubated with cold Pierce RIPA lysis buffer (Thermo Scientific, Hudson, NH) containing Halt™ Protease Inhibitor Single-Use Cocktail, Halt™ Phosphatase Inhibitor Single-Use Cocktail (Thermo Scientific) and 1 mM dithiothreitol (DTT) for 15 min with occasional swirling. Then, the cells were scraped, homogenized with a 26-gauge needle and vortexed at the highest setting for 1 min; the lysates were cleared by centrifuging at 16,000 g at 4°C for 15 min. Protein concentration was determined with the bicinchoninic acid (BCA) method (BCA Protein Assay - Reducing Agent Compatible; Thermo Scientific). Proteins were separated on NuPAGE 4–12% Bis Tris gel electrophoresis (Life Technologies), and transferred to a nitrocellulose membrane (iBlot Gel Transfer Stacks Nitrocellulose; Life Technologies) using iBlot Gel Transfer Device (Life Technologies). The membrane was probed with monoclonal rabbit antibodies, anti-HMGCR (1:500, ab174830, Abcam Inc., Cambridge, MA), anti-vimentin (1:1000, ab92547, Abcam), and anti-E-cadherin (1:1000, 24E10, Cell Signaling Technology, Beverly, MA). A monoclonal mouse antibody to β-actin (1:500, ab8226, Abcam) was used as a loading control. Immunodetection was performed using the iBlot Western Detection chromogenic kit (Life Technologies).
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3

Protein Expression Profiling of ESCC Xenograft Tumors

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Proteins were extracted from ESCC xenograft tumors and small intestine tissue using Trident RIPA Lysis Buffer (GeneTex, Inc) with the addition of Halt™ Phosphatase Inhibitor Single-Use Cocktail (Thermo Scientific™) and Protease Inhibitor Cocktail (Sigma). Protein concentration was determined by BCA Protein Assay Kit (Thermo Scientific™). Antibodies for PARP (9532), Caspase-8 (9746), Caspase-9 (9502), Caspase-3 (9662), TNFR1 (3736), CYLD (8462), JNK (9252), p-JNK (4668), Apaf-1 (8969), Bax (5023), Bcl-2 (15071), Cytochrome c (4280), NF-κB (8242), and Myd88 (4283) were purchased from Cell Signaling. TLR4 antibody (ab13556) was obtained from Abcam. UltraSignal Hypersensitive ECL Western Blotting Substrate (4A Biotech, 4AW011-1000).
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4

Protein Extraction and Quantification

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Total protein was extracted using 1x RIPA buffer (Millipore, North Ryde, NSW) with 1 μL/mL protease inhibitor cocktail (Sigma-Aldrich, Castle Hill, NSW) and 10 μL/mL Halt Phosphatase Inhibitor Single-Use Cocktail (Thermo Scientific, Rockford, IL). Total protein content was determined using the BCA Protein Assay Kit (Pierce Biotechnology, Rockford, IL) according to the manufacturer's instructions.
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5

Protein Expression Analysis of Purine Biosynthesis Enzymes

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To assess protein expression of the 2×Strep-tagged fusions, 293T cells grown in normal medium were seeded at 4 × 105 cells per well in a 6-well plate. At 70–80% confluency, cells were transfected with 4.0 μg of pCI-neo-Strep-tag II plasmid in a 1:2.5 ratio with Lipofectamine 2000 as according to manufacturer’s protocol. After 48 h of expression, cells were harvested by trypsinization, washed once with 1× Dulbecco’s phosphate buffered saline (DPBS), and lysed in 100 μL of lysis buffer [50 mM sodium phosphate dibasic pH 8.0, 300 mM sodium chloride, 5% (v/v) glycerol, 1% (v/v) Triton X-100, 1× Halt phosphatase inhibitor single-use cocktail (Thermo-Fisher Scientific), and 1× Halt protease inhibitor cocktail (ThermoFisher Scientific)] for 30 min on ice. Soluble lysate (40 μg for PPAT and PFAS detection and 30 μg for remaining proteins) was separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE, 8% polyacrylamide gel), transferred to a PVDF membrane, and probed for the presence of PPAT (LifeSpan Biosciences, catalog no.: LSC80815), GART (Bethyl Laboratories, catalog no.: A304-311A), PFAS (Bethyl Laboratories, catalog no.: A304-220A), PAICS (Bethyl Laboratories, catalog no.: A304-546A), ADSL (Bethyl Laboratories, catalog no.: A304-778A), or ATIC (Bethyl Laboratories, catalog no.: A304-271A).
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6

Immunoprecipitation of Tyrosine-Phosphorylated AXL

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IP was performed using Protein A-Sepherose 4A beads (Life Technologies). Low salt IP-lysis buffer was enriched with Halt Phosphatase Inhibitor Single-Use Cocktail (Thermo Scientific) and Halt Protease Inhibitor Single-Use Cocktail (Thermo Scientific). Immuncomplexes were prepared with 200 μg protein and 1:50 dilution of anti-AXL (C89E7) rabbit antibody (Cell Signaling). Assay was performed according to previous protocol (14). Detection of RTK-AXL phosphorylation was determined using antibody 4G10 mouse anti-tyrosine antibody (Max Planck Institute of Biochemistry, Dilution 1:2.000).
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7

Comprehensive Protein Extraction and Quantification

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Dulbecco’s phosphate-buffered saline, Halt Protease Inhibitor Cocktail, Halt Phosphatase Inhibitor Single-Use Cocktail, Pierce BCA Protein Assay Kit, and Trypsin/EDTA solution were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Amphotericin B, penicillin G, and RIPA Buffer were purchased from Sigma-Aldrich Inc. (St. Luis, MO, USA). NC-Slides A8, Solution 3, and Via1-Cassettes were obtained from ChemoMetec (Lillerød, Denmark). Growth media (DMEM and RPMI 1640) and fetal bovine serum were acquired from CytoGen (Zgierz, Poland). Neomycin sulfate was obtained from 1Amara (Kraków, Poland). The remaining chemicals were purchased from POCH S.A. (Gliwice, Poland).
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8

Protein Quantification in Myotube Lysates

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Myotubes were lyzed in RIPA buffer (Merck-Millipore, VIC) with 1 μL/mL protease inhibitor cocktail (Sigma-Aldrich) and 10 μL/mL Halt Phosphatase Inhibitor Single-Use Cocktail (Thermo Scientific, Rockford, IL, United States). Protein concentrations were determined using the bicinchoninic acid (BCA) Protein Assay Kit (Thermo Scientific) according to the manufacturer’s protocol, and absorbance was measured at 562 nm on a Synergy 2 Microplate Reader (BioTek, Winooski, VT, United States).
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9

Cell Lysis Protocol for Protein Analysis

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In general, cells were seeded in 12-well plates and lysed at the indicated time points in 30 μl lysis buffer (100 mM Tris-HCl, pH 8.0, 250 mM NaCl, 0.5% Nonidet P-40, cOmplete protease inhibitor (Roche) and Halt™ Phosphatase Inhibitor Single-Use Cocktail (Thermo Scientific)). The cell lysates were processed as described by Eichwald et al., 2004 [24 (link)].
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10

Western Blot Protocol for Protein Detection

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Cells were lysed in RIPA Lysis and Extraction Buffer supplemented with cOmplete Protease Inhibitor Cocktail (Roche, catalog no. 04693124001) and Halt Phosphatase Inhibitor Single-Use Cocktail (Thermo Fisher Scientific, catalog no. 78428). Protein extracts were then separated by electrophoresis on a 4%–15% precast SDS polyacrylamide gel (Bio-Rad, catalog no. 4561084 or 4561086). Separated proteins in the gel were then transferred onto a polyvinylidene difluoride membrane (Bio-Rad, catalog no. 1620177) under 100 V for 75 minutes. After transfer, blot was blocked with 5% nonfat dry milk in TBS with 0.1% Tween 20 detergent (TBST) and then stained with the primary antibody. Horseradish peroxidase–conjugated secondary antibodies were used for all Western blots. Signals were detected using Pierce ECL Western Blotting Substrate (Thermo Fisher Scientific, catalog no. 32106). Information of the primary antibodies is included in Supplementary Table S2.
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