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14 protocols using dca protein assay kit

1

Quantifying Cellular Cytotoxicity and Protein Interactions

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HEK293T cells were transiently transfected and inhibitor treated as indicated. OCI-AML2 and MV-4-11 cells were plated in 6-well culture plates at 1.0 × 106 cells/well and treated with VbP as indicated. Supernatants were analyzed for LDH levels using the Pierce LDH Cytotoxicity Assay Kit (Life Technologies). LDH levels were quantified relative to a lysis control where cells were lysed in 80 μL of a 9% Triton X-100 solution. For FLAG immunoprecipitation, cell pellets were lysed in Tris-Buffered Saline (TBS) with 0.5% NP-40 on ice for 20 min and centrifuged at 20000 x g for 10 min. The soluble fraction was retained, and protein concentrations were normalized to 1 mg/mL using the DCA Protein Assay kit (Bio-Rad). Lysates were incubated with 40 μL of anti-FLAG-M2 agarose resin (Sigma) overnight at 4°C. After washing 3 × 1 mL with PBS, bound proteins were eluted by incubating resin with 100 μL of PBS containing 150 ng/ μL 3 × -FLAG peptide for 1 h at 4°C. An equal volume of 2 × sample loading dye was added to the eluate and incubated at 95°C for 10 min. For immunoblotting, cells were washed 2 × in PBS (pH = 7.4), resuspended in PBS, and lysed by sonication. Protein concentrations were determined and normalized using the DCA Protein Assay kit (Bio-Rad). The samples were separated by SDS-PAGE, immunoblotted, and visualized using the Odyssey Imaging System (Li-Cor).
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2

Quantifying Cellular Cytotoxicity and Protein Interactions

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HEK293T cells were transiently transfected and inhibitor treated as indicated. OCI-AML2 and MV-4-11 cells were plated in 6-well culture plates at 1.0 × 106 cells/well and treated with VbP as indicated. Supernatants were analyzed for LDH levels using the Pierce LDH Cytotoxicity Assay Kit (Life Technologies). LDH levels were quantified relative to a lysis control where cells were lysed in 80 μL of a 9% Triton X-100 solution. For FLAG immunoprecipitation, cell pellets were lysed in Tris-Buffered Saline (TBS) with 0.5% NP-40 on ice for 20 min and centrifuged at 20000 x g for 10 min. The soluble fraction was retained, and protein concentrations were normalized to 1 mg/mL using the DCA Protein Assay kit (Bio-Rad). Lysates were incubated with 40 μL of anti-FLAG-M2 agarose resin (Sigma) overnight at 4°C. After washing 3 × 1 mL with PBS, bound proteins were eluted by incubating resin with 100 μL of PBS containing 150 ng/ μL 3 × -FLAG peptide for 1 h at 4°C. An equal volume of 2 × sample loading dye was added to the eluate and incubated at 95°C for 10 min. For immunoblotting, cells were washed 2 × in PBS (pH = 7.4), resuspended in PBS, and lysed by sonication. Protein concentrations were determined and normalized using the DCA Protein Assay kit (Bio-Rad). The samples were separated by SDS-PAGE, immunoblotted, and visualized using the Odyssey Imaging System (Li-Cor).
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3

Protein Extraction and Western Blot Analysis

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Cells were washed 2 × in PBS (pH = 7.4), resuspended in PBS, and lysed by sonication. Protein concentrations were determined and normalized using the DCA Protein Assay kit (Bio-Rad). To prepare supernatant western blotting samples of N/TERT-1 keratinocytes, spent media of each treatment were combined, centrifuged at 400 g for 3 min, and the supernatant was precipitated by addition of four sample volumes of acetone at −20°C overnight followed by centrifugation at 3000 g for 30 min at 4°C and decanting. Protein pellets were then suspended in 1X PBS and combined 1:1 with 2X sample loading buffer before heating to 97°C for 10 min.
Samples were run on NuPAGE 4 to 12%, Bis-Tris, 1.0 mM, Midi Protein Gel (Invitrogen) for 45–60 min at 175 V. Gels were transferred to nitrocellulose with the Trans-Blot Turbo Transfer System (BIO-RAD). Membranes were blocked with Intercept (TBS) Blocking Buffer (LI-COR) for 30 min at ambient temperature, before incubating with primary antibody overnight at 4°C. Blots were washed 3 times with TBST buffer before incubating with secondary antibody for 60 min at ambient temperature. Blots were washed 3 times, rinsed with water, and imaged via Odyssey CLx (LI-COR).
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4

Inflammasome Activation Assay Protocol

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Cell lines (1.0 × 106 cells) were seeded in 6-well plates and treated with DMSO or compounds as described. THP-1 cells were also treated with LPS (10 μg/mL) for 24 h. After 24 h, LPS-primed cells were treated with nigericin (20 μM) for 30 minutes. For primary cell western blots, primary cells were thawed and seeded in 6 well plates at 3 × 106 – 4 × 106 cells/well. Seeded primary cells were treated with DMSO or Val-boroPro for 24 h. Cells were washed 2x in PBS (pH = 7.4), resuspended in PBS, and lysed by sonication. Protein concentrations were determined using the DCA Protein Assay kit (Bio-Rad). The samples were separated by SDS-PAGE, immunoblotted, and visualized using the Odyssey Imaging System (Li-Cor).
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5

Transient Transfection and Inhibitor Assay

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HEK 293T cells were transiently transfected and inhibitor treated as indicated. THP-1 cells were plated in six-well culture plates at 5.0 × 105 cells/well and treated with VbP as indicated. 15 min before the conclusion of cell transfection experiments, 80 μl of a 9% Triton X-100 solution was added to designated lysis control wells of a six-well culture plate to completely lyse the cell contents. Supernatants were analyzed for LDH activity using the Pierce LDH Cytotoxicity Assay Kit (Life Technologies). For immunoblotting, the cells were washed 2× in PBS (pH = 7.4), resuspended in PBS, and lysed by sonication. Protein concentrations were determined using the DCA Protein Assay Kit (Bio-Rad). The serum-free supernatants were concentrated using the Amicon Ultra-15 3-kD molecular weight cutoff centrifugal filter unit before immunoblotting. The samples were separated by SDS–PAGE, immunoblotted, and visualized using the Odyssey Imaging System (LI-COR).
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6

THP-1 and RAW 264.7 Cells Stress Assay

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THP-1 cells (7 × 106 cells/plate) were seeded in 10 cm dishes and treated with DMSO, Val-boroPro (2 μM), etoposide (50 μM), bortezomib (2 μM), cycloheximide (2 μM), and staurosporine (100 nM) for 48 hours. THP-1 cells were also treated with LPS (10 μg/mL) for 48 h. After 48 h, LPS-primed cells were treated with nigericin (20 μM) for 30 minutes. RAW 264.7 cells (7 × 106 cells/plate) were seeded overnight in 10 cm dishes then treated with DMSO, Val-boroPro (2 μM), and etoposide (50 μM) for 24 h. Cells were washed 2x in PBS (pH = 7.4), resuspended in PBS, and lysed by sonication. Protein concentrations were determined using the DCA Protein Assay kit (Bio-Rad). The samples were separated by SDS-PAGE, immunoblotted, and visualized using the Odyssey Imaging System (Li-Cor).
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7

Cytotoxicity Assay and Immunoblotting

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HEK 293T cells were transiently transfected and treated with inhibitors as indicated. MV4;11, THP-1, RAW264.7 and J774.1 cells were plated in 12-well culture plates at 5 × 105 cells per well and treated as indicated. N/TERT-1 and HEKa cells were plated in 12-well culture plates at 1 × 105 cells per well until they reached 70% confluence and were treated as indicated. Supernatants were analyzed for LDH activity using the Pierce LDH cytotoxicity assay kit (Life Technologies). LDH activity was quantified relative to a lysis control where cells were lysed in 80 μl of a 9% Triton X-100 solution. For immunoblotting, cells were washed twice in PBS (pH 7.4), resuspended in PBS and lysed by sonication. Protein concentrations were determined and normalized using the DCA protein assay kit (Bio-Rad). The samples were separated by SDS–PAGE, immunoblotted, and visualized using the Odyssey imaging system (Li-Cor).
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8

Protein Stability Analysis in HEK293T Cells

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HEK293T cells were transiently transfected with 2 μg of indicated constructs. After 16-20 h, cells were harvested. Cells were washed 2 × in PBS (pH = 7.4), resuspended in PBS, and lysed by sonication. Protein concentrations were determined using the DCA Protein Assay kit (Bio-Rad) and normalized to 1 mg/mL. 48 μL of lysate was mixed with 12 μL of trypsin or proteinase K at the final indicated concentrations for 30 min at room temperature. The reaction was stopped by adding 60 μL of 2 × SDS-PAGE sample loading buffer and incubating samples for 10 min at 95°C. The samples were separated by SDS-PAGE, immunoblotted, and visualized using the Odyssey Imaging System (Li-Cor).
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9

Cell Lysis and Protein Extraction

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HEK 293T and THP-1 were purchased from ATCC. HEK 293T cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) with L-glutamine and 10% fetal bovine serum (FBS). THP-1 cells were grown in Roswell Park Memorial Institute (RPMI) medium 1640 with L-glutamine and 10% FBS. All cells were grown at 37°C in a 5% CO2 atmosphere incubator. Cells were washed 2 × in PBS (pH=7.4), resuspended in PBS, and lysed by sonication. Lysates were buffered exchanged using a Slide-A-Lyzer dialysis cassette (10 K MWCO, Thermo-Fisher Scientific) in 500 ml of cold PBS buffer and overnight. The protein concentration of the lysates were determined using the DCA Protein Assay kit (Bio-Rad) and either immediately used or frozen at −80°C.
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10

Cell Line Treatment and Analysis

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HEK293T cells were transiently transfected and treated with inhibitors, as indicated. MV4;11, OCI AML2, THP-1, and RAW264.7 cells were plated in 12-well culture plates at 5 × 105 cells/well and treated, as indicated. Supernatants were analyzed for LDH activity using the Pierce LDH Cytotoxicity Assay Kit (Life Technologies). LDH activity was quantified relative to a lysis control where cells were lysed in 80 μL of a 9% Triton X-100 solution. For immunoblotting, cells were washed 2× in PBS (pH = 7.4), resuspended in PBS, and lysed by sonication. Protein concentrations were determined and normalized using the DCA Protein Assay kit (Bio-Rad). The samples were separated by SDS-PAGE, immunoblotted, and visualized using the Odyssey Imaging System (Li-Cor).
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