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15 protocols using ba2913

1

Protein Extraction and Western Blot Analysis

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Total protein was extracted from cells or tissues using RIPA buffer (Beyotime) and quantified with an Easy II Protein Quantitative Kit (TransGen Biotech). The protein samples were subjected to SDS‐PAGE and then transferred onto polyvinylidene difluoride membranes. The membranes were blocked with 5% skim milk for 1 hour and incubated with primary antibodies against PARP1 (1:1000, PB9309, Boster Biological Technology), HMGB1 (1:1000, A00066‐1, Boster Biological Technology), Bcl‐2 (1:1000, A00040‐2, Boster Biological Technology), Bax (1:500, bs‐0127R, Bioss, Beijing, China), cleaved caspase‐3 (c‐Caspase3; 1:500, BA3257, Boster Biological Technology), acetylated lysine (1:500, MA1‐2021, Thermo Fisher), cytochrome C (1:500, bs‐0013R, Bioss), COX IV (1:2000, bsm‐52750R, Bioss) and GAPDH (1:1000, BA2913, Boster Biological Technology) overnight at 4°C. Then, HRP‐conjugated AffiniPure Goat Anti‐rabbit/mouse IgG secondary antibody (1:5000, Boster Biological Technology) was incubated for 1 hour. The EasySee® Western Blot Kit (TransGen Biotech) was used to detect the protein bands.
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2

Evaluating Kidney Histopathology and Protein Markers

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Paraffin-embedded kidney samples were cut into 4-μm-thick sections for hematoxylin and eosin (HE) staining and periodic acid-Schiff (PAS) staining to evaluate the incrassation of the glomerular mesangial matrix; the positive area was calculated as previously described [13 (link),14 (link)]. Picrosirius red staining was used to detect renal fibrosis as previously reported [15 (link)]. Frozen kidney samples were cut into 10-μm-thick sections for oil red O staining to evaluate the lipid accumulation.
The expression of CD36, adipophilin, and PPARα was detected using Western blotting. Kidney proteins were obtained via cold radioimmunoprecipitation assay lysis buffer (BL504A; Biosharp) with the addition of phenylmethylsulfonyl fluoride (BL507A; Biosharp) on ice and quantified using a bicinchoninic acid assay kit (P0012S; Beyotime). Western blotting was performed according to standard protocols. The following antibodies were used: anti-CD36 (1:1,000, bs-1100R, Bioss), anti-adipophilin (1:300, bs-1164R, Bioss), anti-PPARα (1:600, 15540-1-AP, Proteintech) and anti-GAPDH (1:1,500, BA2913, Boster).
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3

Western Blot Analysis of Autophagy and Inflammasome Proteins

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Proteins were extracted using RIPA buffer containing protease inhibitors and phosphatase inhibitors (Beyotime, China). Samples were homogenized on ice, centrifuged for supernatant at 12,000 g for 15 min at 4°C and heated to 100°C for 5 min. Protein extracts resuspended in sample loading buffer were separated by electrophoresis through 12% polyacrylamide gels and transferred to PVDF membranes (Millipore, USA). After blocking with 5% non-fat milk (Sangon Biotech Shanghai Co.,Ltd., China), membranes were incubated with primary antibodies anti-LC3 (4108S, CST, USA; 1: 1,000 dilution), anti-Beclin 1 (3738, CST, USA; 1: 1,000 dilution), anti-NLRP3 (15101S, CST, USA; 1: 1,000 dilution), anti-NLRC4 (ab201792, abcam, UK; 1: 1,000 dilution), anti-GAPDH (BA2913, Boster, China; 1: 1,000 dilution), anti-Tubulin (AF1216, Beyotime, China; 1: 1,000 dilution) and anti-Histone H3 (ab194681, abcam, UK; 1: 1,000 dilution) overnight at 4°C. Membranes were then washed and incubated with the horseradish peroxidase (HRP)-labeled goat anti-rabbit IgG (A0208, Beyotime, China; 1: 3,000 dilution) for 1 h at room temperature. Proteins were visualized using ECL luminescence reagent (Meilunbio, China). The gray-scale values of the bands were determined by Image J launcher broken symmetry software program (National Institutes of Health, Bethesda, MD, USA).
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4

Protein Expression Analysis in H9C2 Cells

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The H9C2 cells were lysed in RIPA buffer (P0013C, Beyondtime) containing 1 mM PMSF (ST505, Beyondtime). Total protein of 30 μg was subjected to electrophorese on 12–6% SDS-Page gels and transferred to PVDF membranes. Antibodies against β1AR (1:1000; cat. bs-0498R, Bioss), VEGF (1:800; cat. AF5131, Affinity), PGC-1α (1:1000, cat. bs-1832R, Bioss), and caspase3 (1:1000; cat. bs-0081R, Bioss) were used as primary antibodies. Rabbit IgG antibodies coupled to horseradish peroxidase (HRP) were used as secondary antibodies. GAPDH (1:1000; cat. BA2913, Boster) was used as loading control. An enhanced chemiluminescence (ECL) system was used for detection of protein bands.
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5

Proteomic Analysis of Urethral Tissue

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Based on a previously reported protocol [1 (link)], the dorsal neurovascular bundle and buck fascia were removed from the TA and urethra. The tissues and fibroblasts in each group were lysed in RIPA buffer (R0010, Solarbio, China). Twelve per cent SDS-PAGE was used to separate proteins (30 μg), and the separated proteins were transferred to PVDF membranes (EMD Millipore). Appropriate primary antibodies diluted with 5% BSA were incubated with the membranes overnight at 4 °C. The primary antibodies consisted of collagen 3 (1:800, AF5457, Affinity, China), Smad7 (1: 800, AF5147, Affinity, China), elastase-2B (1: 800, orb471854, Biorbyt, China), osteopontin (1: 800, AF0227, Affinity, China) and GAPDH (1:1000, BA2913, Boster, China). After 3 washes with TBS-0.01% Tween 20, the HRP-Affinipure goat anti-rabbit IgG (H + L) (1:500, BM3894, Boster, China) was incultured with the membranes for 2 h at 25 °C. After washing, the signals were visualized using enhanced chemiluminescence reagent (D085075, Bio-Rad, China).
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6

Quantification of Periostin Protein Levels by Western Blot

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Total cellular proteins were extracted by using RIPA and then subjected to Western blot experiments for quantification. In order to carry out Western blot experiments, total proteins were segregated using sodium-dodecyl sulfate polyacrylamide gel electrophoresis and transferred onto polyvinylidene difluoride membranes. After briefly washing, Tris-buffered saline with 1% Tween 20 containing 3% bovine serum albumin (BSA) was used for membrane blocking for 1 h. Then, the membranes were incubated with the primary antibodies including periostin (1:1000, ab152099, Abcam, USA) and GAPDH (1:1000, BA2913, Boster Biological Technology, China) overnight at 4 °C. The following day, the membranes were removed with tweezers and then washed in TBST three times and incubated with horseradish peroxidase (HRP)-conjugated goat anti-rabbit IgG (H+L) (1:3000, GB23303, Servicebio, China) at room temperature for 1 h. After washing with TBST again, the membranes were subjected to chemiluminescence by using an enhanced chemiluminescence substrate.
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7

Western Blot Analysis of Apoptosis Proteins

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After isolation from tissue or cell samples, total proteins were separated via SDS-PAGE and transferred onto PVDF membranes that were blocked with an appropriate solution for 1 h at room temperature. Blots were then probed for 2 h at room temperature with primary antibodies specific for Bax (1:1000, BA0315-2, Boster), Bcl-2 (1:1200, A00040-1, Boster), Cytochrome C (1:5000, ab133504, Abcam), DNAJB4 (0.1 µg/ml, ab254641, Abcam), and GAPDH (1:10,000, BA2913, Boster). Blots were then probed for 1 h at room temperature using Goat Anti-Rabbit IgG H&L (HRP) (1: 2000, ab6721, Abcam), after which they were washed, incubated in developer solution, and exposed to X-ray film to detect protein bands.
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8

Immunohistochemical Analysis of Lung Proteins

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Immunohistochemistry was performed after dewaxing and rehydration. Lung slices were pretreated with an EDTA-antigen retrieval buffer in a microwave oven, and endogenous peroxidase in tissue was quenched with 3% H2O2 for 10 min. Lung slices were blocked with 20% normal fetal bovine serum for 30 min at 37 °C, then incubated with primary and secondary antibodies. The primary antibodies were utilized: anti-FSTL1 (1:200, ab71548, Abcam), anti-collagen I (1:200, BA2023, BOSTER), anti-SMA (1:400, BA0002, BOSTER), anti-P62 (1:200, ab56416, Abcam), anti-LC3B (1:200, ab48394, Abcam), and anti-GAPDH (1:400, BA2913, BOSTER). The staining was performed using the PV-9000 kit (Zhongshan Golden Bridge Biotechnology Co, China). After dehydrating and mounting, slices were observed under a microscope. For the expression of each protein, three slices of IHC were used to calculate the average optical density (AOD) per sample. Quantification of IHC was also performed using ImageJ.
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9

Quantification of Thrombospondin Proteins

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Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was selected as the loading control. Tissue was homogenized in protein extraction reagent (Keygen, China). The obtained homogenate was centrifuged at 12,000 rpm for 30 min at 4 °C. The protein samples collected from the supernatant were separated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) at 8% concentration and transferred to 0.45-μm polyvinylidene difluoride membranes, which were subsequently blocked with TBST buffer for 2 h at 37 °C. The membranes were probed with primary rabbit anti-TSP1 (1:1000, MA5-13,398, Thermo Fisher Scientific, USA), rabbit anti-TSP2 (1:600, PA5-97,117, Thermo Fisher Scientific, USA), rabbit anti-TSP4 (1:1000, ab156258, Abcam, USA), and rabbit anti-GAPDH (1:2000, BA2913, Boster, USA) antibodies for 12 h at 4 °C. Next, the membranes were incubated with a horseradish peroxidase (HRP)-conjugated secondary goat anti-rabbit antibody (1:10,000, BA1054, Boster, USA) for 1 h at 37 °C. The immunoreactive bands were visualized with a chemiluminescent substrate (Thermo Fisher Scientific, USA). The optical densities (ODs) of the bands on the Western blots were quantified using Fiji software (USA). The relative expression levels of specific proteins were normalized and calculated as the optical density of the specific protein band/OD of the GAPDH band.
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10

Protein Expression Analysis of Lung Tissues

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Lung tissues samples, washed with 0.01 M PBS, were lysed in ice-cold RIPA buffer containing sodium phosphate (20 mM, pH7.4), NaCl (150 mM), 1% NP-40, 0.1% SDS, and 0.5% deoxycholic acid with sodium orthovanadate (1 mM) and protease inhibitor cocktail (Roche). After centrifuging the samples at 12,000 g for 15 min, the supernatants were collected. The total amount of protein was quantified using the Pierce BCA Protein Assay Kit. 30 μg of total protein each were separated by 10% SDS polyacrylamide gel electrophoresis and blotted into PVDF membranes. Then the membranes were probed with primary and secondary antibodies sequentially. The primary antibodies were utilized: anti-FSTL1 (1:1000, ab71548, Abcam), anti-collagen I (1:1000, BA2023, BOSTER), anti-SMA (1:1000, BA0002, BOSTER), anti-P62 (1:1000, ab56416, Abcam), anti-LC3B (1:1000, ab48394, Abcam), and anti-GAPDH (1:1000, BA2913, BOSTER). The densitometry of bands was performed by ImageJ software (version 1.46).
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