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Cocktail of protease and phosphatase inhibitors

Manufactured by Thermo Fisher Scientific
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The Cocktail of protease and phosphatase inhibitors is a laboratory product designed to inhibit both protease and phosphatase enzymes. It is used to prevent the degradation of proteins during sample preparation and analysis processes.

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12 protocols using cocktail of protease and phosphatase inhibitors

1

STAT3 Phosphorylation in IgA Nephropathy

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To evaluate STAT3 phosphorylation in individual cell lines treated with IL-6 and JAK-STAT inhibitors, cells were plated in 6-well plates at 1 × 106 cells/well and treated with different concentrations of AZD1480 or Stattic for 1 hour, followed by addition of IL-6 at a final concentration of 40 ng/ml for 15 minutes. Cell lysates were prepared for Western blot analyses using M-PER lysis buffer with a cocktail of phosphatase and protease inhibitors (Thermo Fisher Scientific, Waltham, MA). To determine the long-term effects of IL-6 treatment on phosphorylation of STAT3, EBV-immortalized, IgA1-producing cell lines derived from cells in the peripheral blood of IgAN patients (IgAN-PB cells) and HC (HC-PB cells) were exposed to IL-6 at a final concentration of 40 ng/ml for 1, 3, and 48 hours in the presence or absence of JAK inhibitor AZD1480 (0.3- or 2-μM concentration).
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2

Protein Extraction and Western Blot Analysis

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The methods of protein extraction and Western blot were performed as previously described by Chiu et al. [11 (link)]. Briefly, the radioimmunoprecipitation assay (RIPA) buffer with a cocktail of phosphatase and protease inhibitors (Thermo Fisher Scientific, Waltham, MA, USA) was used for liver protein extraction. A BCA protein assay kit (Thermo Fisher Scientific, Waltham, MA, USA) was used to measure protein concentration. For immunoblotting, 50–100 μg of proteins were separated through 8–12% SDS-PAGE gel and then transferred to polyvinylidene difluoride membranes (Bio-Rad, Hercules, CA, USA). After blocking using 5% non-fat dry milk solution for 1 h, membranes were probed with primary antibodies specific for phosphorylated AMP-activated protein kinase α (p-AMPKα; #2531; 1:1000), AMPKα (#2532; 1:1000) (Cell Signaling Technology, Danvers, MA, USA), PPARγ (sc-7273; 1:1000), and GAPDH (sc-47724; 1:1000) (Santa Cruz Biotechnology, Santa Cruz, CA, USA) at 4 °C overnight. The membranes were then probed with horseradish peroxidase-conjugated secondary antibodies (Cell Signaling Technology, Danvers, MA, USA). An Enhanced Chemiluminescence kit (Bio-Rad) was used to detect the target protein expression, which was exposed to a Fujifilm X-ray film (Tokyo, Japan). The densitometry of target protein was analyzed by the Image J 1.8 software (National Institutes of Health, Bethesda, MD, USA).
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3

Hippocampus Protein Extraction and Analysis

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The hippocampus was taken out together with the inferior temporal cortex and prefrontal cortex (abbreviated hereafter as cortex). Then, we homogenized the tissue in neuronal Protein Extraction Reagent (Thermo Scientific, 87792) containing a cocktail of protease and phosphatase inhibitors (Thermo Scientific, 87786). Protein concentrations were determined using BCA protein assay (Thermo Scientific, 23227). Equal amounts of total protein were analyzed by 12% SDS-PAGE gels. Then, we transferred it to nitrocellulose (NC) membranes (Solarbio, Beijing, China). The primary antibodies rabbit anti-IDE (Abcam, 1: 1000) were used. Image Lab (Bio-Rad) was utilized for protein band densitometry.
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4

Adipose Tissue Protein Extraction and Analysis

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Proteins were isolated from visceral adipose tissues using T-PER Mammalian Protein Extraction Reagent (Thermo Scientific) as indicated by the manufacturer, in the presence of a cocktail of protease and phosphatase inhibitors (Thermo Scientific). Protein content was determined by the bicinchoninic acid protein assay (Thermo Scientific) and 70 μg of proteins were separated with SDS-PAGE under reducing conditions. The separated proteins were then electrophoretically transferred to a nitrocellulose membrane (BioRad). Proteins of interest were revealed with specific antibodies: Ob Antibody (H-146) sc-9014 (Santa Cruz) and anti-β actin (Sigma-Aldrich). The immunostaining was detected using horseradish peroxidase-conjugated anti-rabbit or anti-mouse immunoglobulin (Novex), bands were revealed by the SuperSignal Substrate (Pierce), detected using the C-Digit Blot Scanner and quantified by densitometry using the Image Studio software (all from Li-Cor).
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5

Regulation of Iron Homeostasis in ARPE-19 Cells

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ARPE-19 cells were cultured in 6-well culture dishes for two days and then treated with 2,5-DHBA (250 µM) or deferiprone (250 µM) for 16 h and then the cells were used for preparation of RNA and protein extracts. Untreated cells were used as the control. Steady-state levels of TfR1 mRNA were monitored by RT-PCR and qPCR. To determine the ferritin levels, protein was extracted from the cells using the lysis buffer (10 mM Tris/HCl buffer, pH 7.6, 50 mM NaCl, 1% Triton X-100, 5 mM ethylenediamine tetraacetate) containing a cocktail of protease and phosphatase inhibitors (Thermo Scientific, Waltham, MA, USA). The levels of ferritin (heavy chain H as well as light chain L) were monitored by Western blot using specific antibodies. β-Actin was used as the internal control for protein loading in Western blot analysis.
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6

Quantitative Immunoblotting of Immune Signaling

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Cell lysates were prepared using radioimmunoprecipitation assay (RIPA) buffer (Thermo Fisher) supplemented with a cocktail of protease and phosphatase inhibitors (Thermo Fisher) on ice. Protein concentration was determined with a BCA protein assay (Pierce, catalog no. 23227). Gel electrophoresis was performed on 4 to 12% Bis-Tris NuPAGE gel (Invitrogen) and transferred onto polyvinylidene difluoride membranes according to the manufacturer’s instructions (iBLOT2; Life Technologies). Membranes were blotted with the following primary antibodies: Banf1 (BAF antibody A-11 [Santa Cruz, sc-166324]; 1:500), Irf3 (CST 4302; 1:1,000), cGAS (CST 31659; 1:1,000), Irf1 (CST 8478; 1:1,000), Aim2 (CST 63660; 1:1,000), Ddx41 (CST 15076; 1:1,000), Pqbp1 (Proteintech 16264-1-AP; 1:500), γH2AX (phospho S139) (Abcam, ab26350 [1:5,000] or CST 9718 [1:1,000]), H2AX (CST 2595; 1:1,000), actin (CST 3700; 1:3,000) and STING (CST 13647; 1:1,000). Horseradish peroxidase-conjugated goat anti-rabbit (Pierce, 31460; 1:5,000) or anti-mouse (Sigma, A8924; 1:5,000) IgG was used as a secondary antibody. Protein bands were visualized with chemiluminescence substrate (Thermo Fisher, 34577) and autoradiograph film (MIDSCI).
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7

Western Blot Analysis of Protein Samples

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Protein was obtained from skeletal muscle tissue or L6 myotubes using radioimmunoprecipitation assay buffer containing a cocktail of protease and phosphatase inhibitors (Thermo Fisher Scientific). Protein concentrations were determined with a BCA Protein Assay Kit (Thermo Fisher Scientific). Equal amounts of protein (35 μg) from each sample were separated by 10% SDS-PAGE and were subsequently transferred onto polyvinylidene difluoride membranes (Millipore Corporation, Bedford, MA, USA). Antigens were visualized by sequential treatment with specific antibodies, secondary antibodies conjugated to horseradish peroxidase, and an enhanced chemiluminescence substrate kit (Millipore Corporation). The intensities of bands were quantified by densitometry using ImageJ software (NIH, Bethesda, MD, USA).
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8

Western Blot Analysis of Antiestrogen Response

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Approximately 350,000 cells per well were treated with 100 nM antiestrogen for 24 h in serum-free medium in 12-well plates. Cells were lysed with RIPA buffer (#89901) supplemented with a cocktail of protease and phosphatase inhibitors (#78410), both from ThermoFisher Scientific. Whole protein extracts were separated on 10% SDS–PAGE TGX gels (#5671035) and transferred to nitrocellulose membranes (#1704159), both from BioRad. Blots were incubated with either 1:1000 dilution of D12 ERα (#sc-8005), or 1:2000 dilution of β-actin (#sc-47778) primary antibodies, followed by 1:2000 dilution of goat anti-mouse-HRP secondary antibody (#sc-2005) (all antibodies from Santa Cruz Biotechnology). Signal was detected with Super Signal Femto chemiluminescent reagent (ThermoFisher Scientific, #34095) and ERα bands normalized to β-actin to control for differences in loading. Imaging was performed on FluorChem Imager by Alpha Innotech. Data shown in figures are representative experiments reproduced at least three times in independent Western assays. An uncropped image of the immunoblot is shown in Supplementary Fig. 5.
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9

Mass Spectrometry-Based Protein Identification

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Hela-S3 cells (1 × 107) were suspended in 1ml of cold IP buffer containing cocktail of protease and phosphatase inhibitors (Thermo; 78441) and subjected to homogenization at 4°C in a Bioruptor Plus (Diagenode) using a 30 s on-off cycle for 10 min at low intensity followed by centrifugation at 12 000 × g for 15 min in 4°C. IP reaction was performed according to ChIP protocol and proteins were recovered from beads by incubating them with 50 μl 0.1% Trifluoroacetic acid (TFA) for 3 min at room temperature. Samples were transferred to a fresh Eppendorf tube and immediately neutralized by adding 1M NH4HCO3 solution to a final 0.1M concentration and then were reduced, alkylated and trypsin-digested as described earlier (9 (link)). Liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of peptides was performed on a LTQ-Orbitrap Elite mass spectrometer (Thermo Scientific) coupled with a nanoAcquity (Waters Corporation) LC system. Acquired MS/MS raw data files were pre-processed with Mascot Distiller (version 2.5.1, Matrix Science) and searched against the SwissProt Homo Sapiens database (release 2015.11).
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10

UCP1 and GLUT4 Quantification in Rat Tissues

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The UCP1 levels in the BAT and GLUT4 in the iWAT of 7-month-old rats were determined using Western blot analysis. Tissue samples were disrupted by homogenization in RIPA buffer containing a cocktail of protease and phosphatase inhibitors (Thermo Fisher, Rockford, IL, USA) at 4 °C using a weight-to-volume ratio of 1:5. To obtain the supernatant, which was used for protein analysis, the homogenate was centrifuged at 7500× g for 2 min at 4 °C. The quantification of total protein was performed with a BCA protein assay kit (Pierce, Rockford, IL, USA).
Then, 10 µg and 75 µg of total protein for BAT and iWAT, respectively, were processed and separated utilizing 10% SDS-polyacrylamide gel electrophoresis, as previously described [13 (link)]. A rabbit polyclonal anti-UCP1 antibody (GTX10983, GeneTex, Irvine, CA, USA) and a mouse polyclonal anti-GLUT4 antibody (#2213, Cell Signaling Technology, Danvers, MA, USA) were used. An Odyssey Infrared Imaging System (Li-COR Biosciences, Lincoln, NE, USA) was employed for analysis. β-actin and/or HSP90 (#3700 and #4877, respectively, Cell Signaling Technology) were the reference proteins.
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