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5 protocols using chemiluminescent substrate

1

Nuclear Protein-DNA Interaction Analysis

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Nuclear extracts were prepared from Hela cells transfected with 10 μg of WT KLF13‐pcDNA3.1 or mutant KLF13‐pcDNA3.1 by using the NE‐PER Nuclear and Cytoplasmic Extraction Reagents (Thermo Scientific, Rockford, IL) according to the manufacturer's instructions. Oligonucleotide probes used for electrophoretic mobility shift analysis were synthesized, purified, and 5′ end‐labeled with biotin. For the binding reactions, biotinylated probes (0.2 pmol) were incubated with nuclear extracts (5 μg) and the binding buffer (Beyotime Biotechnology, Shanghai, China) for 20 minutes at room temperature. Of note, unlabeled cold probes (20 pmol) were preincubated with the nuclear extracts for 10 minutes. The mixture was fractionated on a 6% nondenaturing polyacrylamide gel in 0.5× Tris‐borate‐EDTA buffer at 100 V for 1 hour, transferred to a nylon membrane (Beyotime Biotechnology) in ice‐cold 0.5× Tris‐borate‐EDTA buffer at 380 mA for 30 minutes, and crosslinked by ultraviolet irradiation for 20 minutes. The biotin‐labeled probe was detected by using the streptavidin‐horseradish peroxidase conjugate and the chemiluminescent substrate (Beyotime Biotechnology) according to the manufacturer's instructions.
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2

Western Blot Protein Detection

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Protein was harvested using lysis buffer, and a BCA assay was applied to determine the protein concentration. Next, we separated 20 μg of protein using sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) and transferred protein to a polyvinylidene difluoride (PVDF) membrane (Millipore, MA). After blocking, membranes were incubated with primary antibodies as indicated and with horseradish peroxidase (HRP)-conjugated secondary antibodies. Membranes were developed using a chemiluminescent substrate (Beyotime, China). The antibodies used are listed in Additional file 1: Table S3.
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3

Western Blot Analysis of UPR Proteins

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Protein was extracted from the cultured cells using RIPA buffer. A total of 30 μg proteins were separated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). Then, proteins were transferred to polyvinylidene difluoride (PVDF) membranes. The membranes were blocked in TBST containing 5% skimmed milk, and incubated with the primary antibodies including: anti-GRP78 (1:1000; Sigma Aldrich), anti-PERK (1:1000; Sigma Aldrich), anti-p-PERK (1:500; Sigma Aldrich), anti-eIF2α (1:1000; Abcam, Cambridge, UK), anti-p-eIF2α (1:500; Abcam), anti-ATF4 (1:1000; Sigma Aldrich), anti-CHOP (1:500; Sigma Aldrich), anti-SIRT1 (1:1000; CST, Beverly, USA), anti-Bcl-2 (1:1000; Proteintech, Wuhan, China), Bax (1:1000; Proteintech), anti-Mcl-1(1:1000; Sigma), anti-caspase 3 (1:1000; CST), anti-caspase 9 (1:1000; CST), anti-cleaved caspase 3 (1:500; Sigma Aldrich), and anti-β-actin (1:1000; Origene, Rockville, USA), followed by incubation with the corresponding horseradish peroxidase (HRP)-conjugated secondary antibodies. Finally, chemiluminescent substrate (Beyotime) was used for signal visualization and detection. The density of each band was normalized to its respective loading control (β-actin). The immunoblots were quantified by densitometric analysis.
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4

Western Blot Protein Quantification

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The protein concentration of the samples was quantified using a BCA protein assay kit (Beyotime, China). The proteins were separated by SDS-PAGE and transferred to nitrocellulose (NC) membranes. The membranes were blocked with 5% skim milk plus 0.05% (v/v) Tween 20 (PBST) for 1 hour at room temperature. The membranes were incubated with the indicated primary antibodies overnight at 4°C and then incubated with horseradish peroxidase (HRP)-conjugated goat anti-mouse IgG (H+L) or HRP-conjugated goat anti-rabbit IgG for 1 h at room temperature. The membranes were washed three times with PBST for 5 min after each incubation step. Detection was performed using a chemiluminescent substrate (Beyotime, China) according to the manufacturer’s instructions.
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5

Western Blot Analysis of Protein Modifications

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For western blot analysis, protein homogenates from heart tissues or cells were separated by SDS-PAGE and transferred to a PVDF membrane. After blocking with 5% non-fat milk for 2 h, the membrane was incubated with antibodies against DLD (Abcam), P300 (Abcam), 2-hydroxyisobutyryl-lysine (Hangzhou Jingjie Biotechnology Co., Ltd), Flag (Sigma), HA (Sigma), and β-actin (Abcam). Subsequently, the membrane was incubated with HRP-conjugated secondary antibodies (Beyotime Biotechnology) and developed using a chemiluminescent substrate (Beyotime Biotechnology).
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