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129 protocols using sds page sample loading buffer

1

Western Blot Assay for Protein Analysis

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For the tissue-based assay, the brains of three mice in each group were homogenized in RIPA buffer (Beyotime, Jiangsu, China) by a hand-held motor and kept on ice for 30 min to lyse the cells completely. The homogenates were then centrifuged at 14,000 × g at 4°C for 15 min. The supernatants were collected and protein concentration was determined using a BCA protein assay kit (Boster, Wuhan, China). Equal protein was mixed with 5 × SDS-PAGE sample loading buffer (Beyotime, Jiangsu, China) and boiled for 5 min at 99°C.
For the cell-based assay, cells were lysed with RIPA buffer (Beyotime, Jiangsu, China) according to the manufacturer’s instructions. Protein concentration was determined by a BCA protein assay kit (Boster, Wuhan, China) and equal protein concentrations were mixed with 5 × SDS-PAGE sample loading buffer (Beyotime, Jiangsu, China) and boiled for 5 min at 99°C.
All tissue and cell samples were fractionated using 10% SDS-PAGE and transferred to a PVDF membrane (Millipore). Membranes were incubated with primary antibodies overnight at 4°C, detected with HRP-conjugated secondary antibodies (Zhongshan Jinqiao Biology) and developed using an ECL chemiluminescence kit (Millipore). The optical density (OD) of each band was determined using Gel Pro Analyzer 6.0 (Media Cybernetics, Bethesda, MD, United States).
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2

Western Blot Analysis of Protein Extracts

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Western blot analysis was performed as previously reported [50 (link)]. Protein extracts of the tissues and cells were obtained using ice-cold RIPA lysis buffer (50 mM Tris pH 7.4, 150 mM NaCl, 1% Triton X-100, 1% sodium deoxycholate, 0.1% SDS, protease inhibitor [Beyotime, Shanghai, China]) containing phenylmethanesulfonyl fluoride (PMSF, Beyotime). Protein extracts were boiled in 5× SDS-PAGE sample loading buffer (Beyotime) for 10 min, and protein concentration was determined using a BCA protein assay kit (Beyotime). Up to 15 µg of protein were separated in SDS-PAGE gels (Beyotime) by electrophoresis, and proteins were transferred to polyvinylidene difluoride (PVDF) membranes (Solarbio, Beijing, China). After membrane blocking in 5% nonfat milk for 2–3 h, the membranes were incubated with the primary antibodies overnight at 4 °C and then washed three times for 30 min in TBST (Tris-buffered saline and Tween-20) before incubation with the secondary antibodies (ZB-2301; Beijing Zhongshan Golden Bridge Technology Co., Ltd., Beijing, China) conjugated with horseradish peroxidase for 2 h at room temperature. The membranes were washed three times with TBST and further quantified using chemiluminescence with a super enhancer ECL kit (Novland, Shanghai, China). The quantification of western blot bands was performed using ImageJ. All experiments were performed at least three time.
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3

Gut and Brain Tissue Protein Analysis

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The proteins of gut and brain tissues were extracted by cell lysis buffer for Western blot and IP (Beyotime, Nanjing, China) and a suitable amount of phenylmethanesulfonyl fluoride (PMSF) was added to prevent against protein degradation (Beyotime, Nanjing, China). Subsequently, the protein concentration was measured using a BCA Protein Assay Kit (Beyotime, Nanjing, China), and protein concentration was diluted to 30 μg/10 μL in cell lysis buffer for Western blot and IP with 5 × SDS-PAGE sample loading buffer (Beyotime, Nanjing, China). Following the protocol described in Wan et al. (2020) (link), protein expression levels from brain and gut tissues were detected targeting cyclin-dependent kinase inhibitor 2A (p16Ink4a), forkhead box O1 (FoxO1), glucagon-like peptide 1 receptor (GLP-1R), matrix metallopeptidase 2 (MMP2), glucagon-like peptide 1 (GLP-1), glucose transporter type 4 (GLUT4), insulin receptor (INSR), and c-Jun N-terminal kinases (JNK) (Beyotime, Nanjing, China).
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4

Protein Quantification and Characterization

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WBY paste was provided by Tsingtao Brewery Co., Ltd. (Huangshi, Hubei). BCA protein concentration determination kit, SDS-PAGE gel quick preparation kit, SDS-PAGE electrophoresis buffer, coomassie brilliant blue R–250 and 5× SDS-PAGE sample loading buffer were purchased from Beyotime Institute of Biotechnology Co., Ltd. M5 Prestained Plus Protein Ladder (10–250 kDa) with 40 kD was obtained from Mei5 Biotechology. CO., Ltd. (Beijing, China). Trypsin (1:250) and alkaline protease (1:20,000) were purchased from Saiguo biotech CO., Ltd. (Guangzhou, China) and Solarbio Science and Technology CO., Ltd. (Beijing, China), respectively. Methanol acid, sulfuric acid, hydrochloric acid, glacial acetic acid, ethanol, ferrous sulfate, hydrogen peroxide, salicylic acid, DPPH, ABTS, potassium persulfate, PBS (pH 7.4), disodium edetate, and pyrogallic acid were obtained from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China). All chemicals used in this study were of analytical grade (AR) or guaranteed grade (GR).
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5

Western Blot Analysis of Neuro-2a Cells

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Neuro-2a cells were lysed in ice-cold RIPA Lysis Buffer. The protein concentration of each sample was determined by the bicinchoninic acid (BCA) protein assay (Pierce Biotechnology, Rockford, IL, USA). The samples were denatured by adding 5 × SDS-PAGE Sample Loading Buffer (Beyotime institute of biotechnology, China) and heating for 10 min at 100 °C. Equal amounts of protein were separated by10%–15% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and then transferred electrophoretically to polyvinylidene fluoride(PVDF) membranes (Millipore, Billerica, MA, USA). After blocking with 5% non-fat milk in Tris-buffered saline (50 mM TRIS-HCl, pH 7.5, 150 mM NaCl) containing 0.2% Tween 20, the membranes were probed with antibodies against the following proteins: LC3B (Sigma, L7543), SQSTM1/P62 (Abcam, ab56416), cleaved caspase-3 (CST, 9661), HIF-1α (Novus, NB100-105), PINK1 (Novus, BC100-494), BNIP3 (Abcam, ab109362), and β-actin (Proteintech, 60008-1-Ig). Following incubation with secondary anti-mouse (Proteintech, SA00001-1) or anti-rabbit (Proteintech, SA00001-2)antibodies, protein bands were visualized using enhanced chemiluminescence(ECL) blotting detection reagents (Millipore, WBKLS0500).
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6

Exosomal Protein Verification Protocol

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Western Blot was performed to verify three markers (HSP70, CD63 and CD81) to confirm successful exosome isolation. Exosomal proteins were isolated according to the instruction of Urine Exosome RNA Isolation Kit (47200, Norgen Biotek, Canada), and 80μl of Cell lysis buffer for Western and IP (P0013, Beyotime, China) and 20μl 5×SDS-PAGE Sample Loading Buffer (P0015, Beyotime, China) were used to resolve exosomal proteins. The mixtures containing exosomal proteins (approximately 20 μl total volume) were heated to 100°C on thermocycler for 5 minutes to fully denature the proteins. The process of western blot was performed according to the standard steps and the PVDF membranes were incubated with primary antibody anti-HSP70 antibody, anti-CD9 antibody and anti-CD81 antibody (EXOAB-KIT-1, SBI, USA) at 4°C overnight and subsequently with goat anti-rabbit IgG H&L secondary antibody (ab175773, Abcam, UK) at room temperature for one hour. The fluorescence detection was performed on the the Li-COR Odyssey Infrared Imaging System (Li-COR Biosciences, USA).
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7

Western Blot Analysis of Cochlear Proteins

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Cochleae from 10 newborn mice or two adult mice were dissected in cold PBS and lyzed in a homogenizer with 100 μl RIPA lysis buffer (Medium, Hangzhou Fu De Biological Technology) and 1 μl 100× protease inhibitor cocktail (Hangzhou Fu De Biological Technology). The homogenates were centrifuged at 13,000 × g at 4°C for 15 min, mixed with 5× SDS-PAGE sample loading buffer (Beyotime Biotechnology), boiled for 15 min, and subjected to SDS-polyacrylamide gel electrophoresis and blotted onto a PVDF membrane. The bound primary antibodies were detected by HRP-conjugated secondary antibodies using the ECL detection system. The following primary antibodies were used: Arhgef6 monoclonal antibody (rabbit, 1:1,000 dilution, CST), PAK1 polyclonal antibody (rabbit, 1:1,000 dilution, Abcam), phospho-PAK1(Thr423)/PAK2(Thr402) polyclonal antibody (rabbit, 1:500 dilution, CST, 2601), and GAPDH monoclonal antibody (mouse, 1:5,000 dilution, Millipore).
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8

Extraction and Separation of Proteins

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Collected cells or renal tissues were lysed with RIPA lysis buffer (Beyotime Biotechnology, Shanghai, China) on ice. The cell or tissue lysing reagents were collected, centrifuged at 14,000× g for 10 min at 4 °C, and mixed with 5 × SDS-PAGE Sample Loading Buffer (Beyotime Biotechnology, Shanghai, China). Proteins were separated by 10~15% SDS-PAGE and then transferred to polyvinylidene fluoride (PVDF) microporous membranes as described [43 (link)]. Membranes were subsequently developed with ECL reagent, and chemiluminescent signals were acquired using Tanon 5200 ChemiDoc imager (Shanghai Tianeng Technology Co., Ltd., Shanghai, China).
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9

Protein Isolation and Western Blot Analysis

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The entire protein content was isolated from cells utilizing RIPA lysis buffer (Beyotime, P0013B), enriched with a mixture of protease inhibitors (Roche, 11,697,498,001). Subsequently, the lysates were subjected to centrifugation at 12,000 revolutions per minute for 30 min at 4 °C and the supernatant was collected. Nuclear/cytoplasmic protein fractionation was performed as described below. The protein concentration was ascertained using Pierce™ BCA Protein Assay Kit (Thermo Fisher Scientific, 23,225), following the manufacturer's prescribed procedures. Subsequently, equal quantities of protein samples were mixed with one-fourth the amount of 5 × SDS-PAGE sample loading buffer (Beyotime, p0015) and heated for 10 min at 100 °C to allow for protein denaturation. The protein mixture was then loaded onto the gel and separated by SDS-PAGE. It was later transferred to a polyvinylidene difluoride membrane (Millipore Sigma, IPVH00010), with a pore size of 0.45 µm, and blocked for 2 h at room temperature in TBST-5% milk. After the membranes were incubated with the appropriate primary antibodies followed by secondary antibodies, the target protein bands were visualized using an Enhanced Chemiluminescence kit (Thermo Fisher Scientific, 32,132).
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10

Optimized Western Blot Protein Extraction and Detection

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Western blot (WB) experiments were conducted as previously described [29 (link)]. In brief, utilizing the Nuclear and Cytoplasmic Protein Extraction Kit (Thermo Fisher Scientific, USA), cytoplasmic and nuclear proteins were isolated. Protein concentrations were measured by a BCA kit (Beyotime Biotechnology, Shanghai, China) followed by adjusting them to a uniform concentration. The protein samples were mixed with a 5× SDS-PAGE sample loading buffer (Beyotime Biotechnology, Shanghai, China), followed by a 95 °C water bath for 5 min. Equal amounts of samples were separated on 10% SDS-poly-acrylamide gels. The proteins were then transferred onto polyvinylidene difluoride (PVDF) membranes and blocked with 5% bovine serum albumin for 1 h. The blots were allowed to incubate with the relevant primary antibodies for 12 h at a temperature of 4℃. Following the washing process, secondary antibodies were allowed to incubate for one hour at 25 °C before the blots were developed using Odyssey Infrared Imaging (Bio-Rad).
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