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111 protocols using revert total protein stain

1

Quantitative Western Blot Analysis

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The protein concentration of homogenized samples was determined using Pierce BCA Protein Assay Kit (cat#23227, ThermoFisher Scientific, Waltham) and read on an EPOCH spectrophotometer (BioTek Instruments, Winoski, VT). The proteins (10 or 20 μg) were resolved by SDS-PAGE (12% Tris-HCL gels, Bio-Rad, Hercules, CA) and transferred to PVDF membranes. Membranes were stained with REVERT Total Protein Stain (LI-COR, Lincoln, NE) and reversed. PVDF membranes were then blocked in Intercept Blocking Buffer (TBS, LI-COR, Lincoln, NE) for 1 hr. All primary antibodies were probed overnight at 4°C (see Table 1 for dilutions) and followed by IRDye secondary antibodies (1:15,000, LI-COR). Blots were imaged using Odyssey Fc (700 and 800 nm, LI-COR). Optical densities of all bands and total protein stain were quantified using Image Studio software (LI-COR) and adjusted to background subtraction using the standard LI-COR Image Studio-defined parameters. Bands of interest (1 lane per independent brain sample) were normalized to REVERT Total Protein Stain using the lane normalization factor (LNF) recommended by LI-COR (Signal/LNF). Signal intensity deviates by channel (700 or 800 nm) and blot conditions, resulting in a range of values.
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2

Quantification of Anti-BSA Antibodies

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According to our results from ELISA BSA control wells we prepared a pool from plasma samples of four patients with high reactivity against native BSA. Immunodetection was performed according to the protocol of Mogues et al.26 (link) with a few modifications. To prove that the reactivity stems from high levels of specific antibodies against BSA (anti-BSA-Ab), 1 µg of BSA (Albumin Fraction V, IgG-free, Gibco) and 1 µg of HSA (Sigma Aldrich A5843), was blotted onto 0.2 µm nitrocellulose membrane using Minifold I Slot-blot system (Whatman). Protein loading was controlled with REVERT total protein stain from Li-COR. Membranes were blocked with 1% HSA in PBS for 2 h at RT, and washed in PBS-T (Tween-20 0.1%). The plasma pool was diluted 1:200 in PBS added to the membranes and incubated overnight at 4 °C. Then the membranes were washed and incubated with a secondary anti-human IgG antibody (Goat Anti-Human IgG (H + L), IRDye 800CW, Li-COR) for 1 h at RT, washed again and analyzed via Odyssey imaging system (Li-COR). Signal from IgG detection was standardized towards REVERT total protein stain from Li-COR.
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3

Western Blot Analysis of Cellular Proteins

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Proteins in cell lysates and immunoprecipitates in the NuPAGE LDS sample buffer were separated on either 4%-12% gradient or 10% SDS-PAGE and transferred onto a polyvinylidene difluoride membrane (Millipore). Blots were stained with REVERT Total Protein Stain (LI-COR) to verify equal loading and transfer of proteins, then blocked with Odyssey blocking buffer (LI-COR) at room temperature for 1 hour and incubated overnight at 4°C with the indicated antibodies in the Odyssey blocking buffer containing 0.05% TWEEN 20. After washing with PBS containing 0.05% TWEEN 20, the membrane was incubated with fluorescent-dye-labeled goat anti-mouse-IgG or goat anti-rabbit-IgG secondary antibodies (LI-COR). Immunoreactive protein bands were visualized using the LI-COR detection system. Immunoblots represent data from three independent experiments.
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4

Detailed Western Blot Protocol for Protein Analysis

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Western blot analysis was performed as described previously [60 (link)]. In brief, whole cell lysates were prepared by three cycles of freeze/thaw and then incubation on ice for 30 min in HEDG buffer (25 mM HEPES, pH 7.4, 1 mM EDTA, 1 mM DTT, 10% glycerol) containing 0.4 M KCl, 1 mM PMSF, and 2 µg/mL of leupeptin, followed by centrifugation (16,000× g for 10 min at 4 °C). BCA protein assay (Thermal Fisher, Waltham, MA, USA) was used to determine the protein content. Typically, 60 μg of lysates were used for Western blot analysis. The results were analyzed using a LI-COR CLx Odyssey imager. The amount of target proteins was normalized with β-actin or the total protein using the Revert total protein stain (LI-COR). Dilutions of antibodies were as follows: anti-AHR SA210, 1:4000; anti-LAMP2 H4B4, 1:200; anti-PR-B B-30, 1:200; anti-GFP B-2-AF790 conjugate, 1:200; anti-ERα F-10, 1:200; anti-HSC70 B-6, 1:200; anti-GAPDH G9545, 1:5000; anti-β-actin AM4302, 1:5000; all donkey secondary antibodies, 1:10,000.
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5

LYTAC-mediated protein analysis in cells

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Adherent cells were plated (100,000 cells/well in a 24-well plate) one day before the experiment. Cells were incubated with 250 μl of complete growth media with 10 nM LYTAC or controls for indicated time. Cells were then washed with DPBS 3 times and lysed with RIPA buffer supplemented with protease inhibitor cocktail (Roche), 0.1% Benzonase (Millipore-Sigma), and phosphatase inhibitor cocktail (Cell Signaling Technologies) on ice for 30 minutes. The cells were scraped, transferred to Eppendorf tubes, and spun down at 21,000g for 15 minutes at 4 °C. The supernatant was collected and the protein concentration was determined by BCA assay (Pierce). Equal amounts of lysates were loaded onto 4–12% Bis-Tris gel and separated by sodium dodecyl sulfate-polacrylamide gel electrophoresis (SDS-PAGE). Then, the gel was transferred onto a nitrocellulose membrane and stained with REVERT Total Protein Stain (LI-COR), then blocked with Odyssey Blocking Buffer (TBS) (LI-COR) for 1 hour at rt. The membrane was incubated with primary antibody overnight at 4 °C, washed 3 times with TBS-T. Subsequently, the membrane was incubated with secondary antibody for 1 hour at rt, and washed 3 times with TBS-T for visualization with an Odyssey CLx Imager (LI-COR). Image Studio (LI-COR) was used to quantify band intensities.
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6

Quantifying UCP1 Protein Levels in Pregnant Mouse Adipose

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Samples of extraperitoneal adipose tissue from pregnant mice were collected on the 18th day of pregnancy and stored at −80°C until use. For total protein extraction, protein concentration was measured using Pierce BCA Protein Assay Kit. The proteins were separated on SDS-PAGE and transferred to the PVDF membrane using Trans-Blot Turbo semidry transfer system (Bio-Rad). The membrane was incubated with the following primary antibodies (UCP1, 1:1000; β-action, 1:1000) from cell signaling technology diluted in blocking buffer overnight at 4°C. Normalization of the signals was done using REVERT total protein stain (LI-COR). PVDF film was placed in SuperSingal chemiluminescent reagent for 2 minutes. BiospectrumAC gel imaging analysis system was used to scan and save the analysis pictures.
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7

Quantifying Yeast Mitochondrial Respiratory Proteins

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To quantify respiratory chain subunit proteins, western blot analysis was performed in biological triplicate with mitochondrial protein extracts using IRDye 800CW goat anti-mouse and anti-rabbit secondary antibodies (LI-COR) imaged on a Typhoon scanner. Revert™ total protein stain (LI-COR) was used for western blot normalization. Respiratory chain complexes from 10 μg of n-dodecyl-β-d-maltoside (DDM)-solubilized yeast mitochondria were resolved using blue native polyacrylamide gel electrophoresis (BN-PAGE; Invitrogen BN1001) according to the manufacturer's protocols. Proteins were transferred to a polyvinyldifluoridene (PVDF) membrane (Millipore Immobilon-FL), then western blot analysis was performed and the proteins were quantified by the same method as for the subunit proteins. Primary antibodies used were anti-Cox1 mouse monoclonal antibody (mAb; 1D6E1A8), anti-Cox2 mouse mAb (4B12A5), anti-Cox3 mouse mAb (DA5BC4) obtained from Abcam, anti-Cob rabbit polyclonal (97505)—a gift from Brian Robinson (31 (link)), anti-Atp2 rabbit polyclonal—a gift from Alexander Tzagoloff (32 (link)) and anti-Atp6 rabbit polyclonal—a gift from Jean Velours (33 (link)).
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8

Western Blot Antibodies for OXPHOS

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Antibodies used for Western blot included the Total OXPHOS Human WB Antibody Cocktail (#ab1104a1; Abcam), anti-Aco2 (#ab110321; Abcam), anti-4E-BP1 (#9644; Cell Signaling) and anti-phospho-4E-BP1 (#2855; Cell Signaling), anti-EF-1α1/2 (#sc-377439; Santa Cruz), anti-Hsp60 (#ab59457; Abcam), anti-Hsp70 (#ab47455; Abcam), anti-Hsp90 (#16F1; Enzo), anti-Mdh2 (#sc-293474; Santa Cruz), anti-Mia40 (#sc-365137; Santa Cruz), anti-rpS6 (#ab40820, Abcam); anti-phospho-rpS6 (#ab65748; Abcam), anti-SMAC (#ab8114; Abcam), anti-Tim22 (#14927-1-AP; Proteintech), anti-ubiquitin (#701339; Thermo Scientific), and anti-VDAC (#sc-390996; Santa Cruz). Total proteins were stained with REVERT Total Protein Stain (#926-11011; LI-COR).
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9

Quantitative Western Blot Normalization

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Proteins within a lane were normalized to either total protein (REVERT Total Protein Stain, LI-COR) or to a housekeeping protein (LI-COR Western Blot Normalization Handbook). Western blots were quantitated using Image Studio Software (LI-COR). All westerns were reproduced in at least three independent experiments.
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10

Comprehensive Western Blotting Methodology

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Western blotting was conducted as previously described33 (link),37 (link),41 (link),52 (link),53 (link). The following primary antibodies were used in this study: α-actin (Cell signaling #4976L), SLC25A1 (Proteintech #15235-1-AP), SLC13A5 (Santa Cruz #sc293277), AT-1 (Aviva System Biology #ARP43888_P050), Acetylated Lysine (Cell Signaling #cs9441L), ACLY (Abcam #ab40793), Calnexin (Novus #NB100-1974). Donkey anti-rabbit or goat anti-mouse IRDye 800CW and 680RD-conjugated secondary antibodies (LI-COR Biosciences, #926-32213, #926-32210, #926-68073, #926-68070) were used for infrared imaging (LI-COR Odyssey Infrared Imaging System; LI-COR Biosciences). For enriched liver ER and nuclear Western blotting, target proteins were normalized to total protein staining with the Revert Total Protein Stain (LI-COR Biosciences, #926-11021) performed before immunodetection. Original uncropped Western blot images included in the manuscript can be found in Supplementary Fig. 9.
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