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22 protocols using nonfat milk

1

Detailed Cell Culture Protocol

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DMEM/F12 medium (#11320033), fetal bovine serum (FBS, #10100147), PBS (#10010072), Penicillin–streptomycin (#15140122), and Lipofectamine® 3000 reagent (#L3000015) were obtained from Life Technologies Co. (Carlsbad, CA, USA). Dimethyl sulfoxide (DMSO, #2650), phenylmethylsulfonyl fluoride (PMSF, #P7626), 37% paraformaldehyde (#P6148), proteinase inhibitor (#P2714), glycine (#67419), horseradish peroxidase (HRP), and c-JUN inhibitor (SP600125, #S5567) were from Sigma-Aldrich (Darmstadt, Germany). Nonfat milk (#P0216), RIPA lysis buffer (#P0013B), RNase A (#ST578), RNase inhibitor (#R0102-2kU), and BCA Protein Assay Kit (#P0012S) were obtained from Beyotime Biotechnology (Shanghai, China). PVDF membrane (#3010040001) and Protein A/G magnetic beads (#LSKMAGT02) were purchased from Merck Millipore (Darmstadt, Germany). Primers used here were synthesized by TsingKe Biotechnology (Beijing, China), and the siRNAs used in this study were designed and synthesized by GenePharma (Shanghai, China). All chemicals and solutions were analytical reagent grade and all buffer components were endotoxin free or low endotoxin from Sigma-Aldrich, as available.
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2

Protein Extraction, Quantification, and Western Blot Analysis

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Protein extraction reagent (Beyotime) and BCA protein quantification reagent (Abcam, Cambridge, UK) were used for protein extraction and quantification respectively. WB was executed according to a previous report [29 (link)]. The extracted protein samples were separated using SDS-PAGE (Beyotime), followed by transferring to nitrocellulose membranes (Invitrogen). After blockage with nonfat milk (5%; Beyotime), the antibodies listed below were applied to incubate these membranes for 12–14 h at 4°C: Bcl-2 (ab194583, 1:1500, Abcam), Bax (ab32503, 1:1500, Abcam), glucose transport protein type 1 (GLUT1; ab150299, 1:3000, Abcam), LDHA (ab125683, 1:2000, Abcam), TXNRD1 (ab124954, 1:1500, Abcam) or β-actin (ab227387, 1:3000, Abcam). After incubation of the corresponding secondary antibody (ab205718, 1:6000, Abcam), protein blot visualization was achieved by an ECL reagent (Abcam). Analysis of relative levels of proteins was performed by densitometric analysis using Image J software (Bio-Rad).
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3

Protein Extraction and Western Blot Analysis

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The total cellular proteins were extracted with RIPA buffer (Beyotime). Equal amounts of protein (30 µg/lane) were separated on sodium dodecyl sulfate (SDS)-PAGE and then transferred to polyvinylidene fluoride (PVDF) membranes (Millipore, MA). After blocking with PBS buffer (Beyotime) containing 5% non-fat milk and 0.1% Tween 20 (Beyotime), membranes were incubated with primary antibody overnight at 4°C. Subsequently HRP-conjugated secondary antibodies were incubated for 1 hour at room temperature and developed with enhanced chemiluminescence (Beyotime).
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4

Protein Expression Analysis in Gastric Cancer Cells

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Total protein were collected from AGS and NCI-N87 cells in a radioimmunoprecipitation assay buffer (Beijing Solarbio Science and Technology Co., Ltd.). The protein concentration was determined using a BCA protein assay kit (Pierce; Thermo Fisher Scientific, Inc.). A total of 30 µg protein was separated on 10% SDS-PAGE gels, followed by transfer of electrophoresed proteins onto nitrocellulose membranes. The membranes were blocked with 5% non-fat milk (Beyotime Biotechnology, Beijing, China) and incubated with primary antibodies, including GPX4 (no. 52455, 1:1,000, Cell Signaling Technology, Inc.), xCT (no. 12691, 1:1,000, Cell Signaling Technology, Inc.), NCOA4 (no. 66849; 1:1,000; Abcam), FTH-1 (no. 4393; 1:1,000; Abcam), and GAPDH (cat. no. 5174, 1:4,000, Cell Signaling Technology, Inc.), at 4°C overnight. Subsequently, the cells were incubated with the corresponding peroxidase-conjugated secondary antibodies (both 1:5,000; cat. no. ZB-2301 and ZB-2305; Beijing Zhongshan Golden Bridge Biotechnology Co.). The protein bands were detected using enhanced chemiluminescence reagent (EMD Millipore). Relative protein expression was normalized to GAPDH. All the experiments were repeated three times. ImageJ 1.43b software (National Institutes of Health) was used for the densitometry analysis.
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5

Quantification of Immune Proteins in Mouse Ear Tissue

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RIPA buffer was used to lyse mouse ear tissue samples as above, after which protein levels therein were measured via BCA assay. Equal protein amounts were then separated via 6-15% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to polyvinylidene fluoride (PVDF) membranes (Thermo Fisher Scientific, MA, USA). These blots were then blocked for 2 hours using 5% non-fat milk (Beyotime, Shanghai, China) in 0.1% Tween 20 in tris-buffered saline (TBS-T) at 26 °C. They were then incubated overnight at 4 °C while being constantly shaken with primary antibodies specific to β-actin (HRP-60008, Proteintech, IL, USA), TLR3 (ab62566, Abcam, Cambridge, MA, USA), IL-13Rα1 (ab79277, Abcam, Cambridge, MA, USA), or TSLP (ab115700, Abcam, Cambridge, MA, USA). Blots were then washed repeatedly, probed for 2 hours with secondary horseradish peroxidase (HRP)-conjugated goat anti-rabbit IgG antibody (ab205718, Abcam, Cambridge, MA, USA), with β-actin being assessed as a loading control. Protein bands were then detected using enhanced chemiluminescence (ECL) detection reagents (Thermo Fisher Scientific, MA, USA) with a Tanon 5200 automatic chemiluminescence image analysis system (Tanon, Shanghai, China).
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6

Western Blot Protein Expression Analysis

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The total cellular proteins were extracted with RIPA buffer (Beyotime). Equal amounts of protein (30 μg/lane) were separated on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and then transferred to polyvinylidene fluoride membranes (Millipore, Burlington, MA). After blocking with PBS buffer (Beyotime) containing 5% non-fat milk and 0.1% Tween 20 (Beyotime), membranes were incubated with primary antibody over-night at 4℃. Subsequently HRP-conjugated secondary antibodies were incubated for 1 hour at room temperature and developed with enhanced chemiluminesence (Beyotime). All antibodies used were listed in S1 Table.
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7

Western Blotting of ATC Cells

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Western blotting assays of ATC cells were implemented at 48 h after treatment. First of all, ATC cells were lysed by RIPA comprising 1 mM PMSF (Selleck, USA) and the concentration of total proteins was quantified using the bicinchoninic acid kit (Beyotime, China). Secondly, 40 μg of proteins was separated by SDS-PAGE and transferred onto a nitrocellulose membrane (Pall, USA). Then, membranes were blocked using 5% nonfat milk (Beyotime, China), hatched with primary antibodies overnight at 4°C, and subsequently incubated with secondary antibody (1:10,000) (Affinity, China) for 1 h at 37°C. Finally, blots were detected via ECL-PLUS kit (Beyotime, China) and analyzed using ImageJ software (version 1.8.0, NIH). The primary antibodies used in this study were bought from Abcam (Cambridge, USA) and listed as follows: anti-AKIP1 (1:500, ab135996), anti-p-PI3K (1:1,000, ab182651), anti-PI3K (1:1,500, ab86714), anti-p-AKTSer473 (1:1,000, ab81283), anti-AKT (1:1,500, ab8805), anti-β-catenin (1:1,000, ab68813), anti-GAPDH (1:5,000, ab181602), and anti-Histone H3 (1:5,000, ab1791).
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8

Protein Extraction and Western Blot Analysis

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For extraction of protein, RIPA lysis buffer (Keygen) was used to lyse cells or tissues. After measuring the protein concentration using a BCA protein assay kit (Abcam), electrophoresis was performed with SDS‐PAGE to separate the protein. Next, the protein was transferred onto PVDF membranes (Invitrogen), followed by blocking in nonfat milk (5%; Beyotime). After that, the membranes were probed with primary antibodies (overnight, 4°C). The primary antibodies containing Cyclin D1 (1:1000, ab226977), MMP9 (1:2000, ab76003), PDL1 (1:1000, ab205921) and GAPDH (1:2000, ab9485) were all provided by Abcam. After incubation with secondary antibody (1:3000, ab205718, Abcam), enhanced chemiluminescence reagent (Abcam) was used to visualize the blot signal.
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9

Western Blot Analysis Protocol

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After treated as indicated, cells were collected and lysed on ice for 10 min with the lysis buffer, which contained 0.2 M Tris–HCl (pH 6.8), 3 mM SDS (Aladdin, Shanghai, China), 2% glycerol (Kelong, Chengdu, China), 0.2% mercaptoethanol (Sigma-Aldrich, Missouri, USA), 60 μM bromophenol blue (Solarbio, Beijing, China), 1 mM PMSF (Phenylmethyl sulfonyl fluoride) (Beyotime Biotechnology, Shanghai, China) and 1% protease inhibitor cocktail (APExBIO, Houston, USA). The proteins were separated on 12% or 15% SDS-PAGE gels and transferred to PVDF (polyvinylidene difluoride) membranes (0.22 μM) (Millipore, Massachusetts, USA). After blocking for 1 h at 4 °C with 8% nonfat milk (Beyotime Biotechnology, Shanghai, China) in TTBS (150 mM NaCl, 20 mM Tris-HCl, 0.1% Tween-20, pH 7.5), the membranes were incubated with the primary antibodies for 6 h at 4 °C and with HRP-conjugated secondary antibody goat anti-rabbit IgG (H&L) or rabbit anti-mouse IgG (H&L) for 1 h at 4 °C. The protein bands were visualized using the ultra-sensitive ECL chemiluminescence kit (Beyotime Biotechnology, Shanghai, China) by UNIVERSAL HOOD II gel imager (Bio-Rad, USA). The images were analyzed by using image lab 6.0 software (BIO-RAD, USA).
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10

Western Blot Analysis of sEV Proteins

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Cells and sEV samples were lysed with a Radio Immunoprecipitation Assay (RIPA, Beyotime Biotechnology, China) with phenylmethanesulfonyl fluoride (PMSF) (10 μL/1 mL) (Beyotime Biotechnology, China). The protein concentration was measured by a BCA assay (Beyotime Biotechnology, China). Then, the protein solution was mixed with loading buffer (Beyotime Biotechnology, China) and boiled at 95 °C for 10 min. Proteins were separated with SDS‒PAGE (Shanghai Epizyme Biomedical Technology, China) and transferred to a 0.45 μm polyvinylidenedifluoride (PVDF) membrane (Millipore, American). After that, the membranes were blocked with 5% (w/v) nonfat milk (Beyotime Biotechnology, China) for 90 min and incubated with primary antibody followed by secondary antibody. The primary antibodies used for immunoblotting were anti-pirb (1:1000, R&D Systems, MAB2754), anti-actin (1:1000, Invitrogen, MA5-15,739), anti-GM130 (1:1000, Abcam, ab52649), anti-CD63 (1:1000, Abcam, ab134045), anti-CD9 (1:1000, Abcam, ab92726), and anti-Alix (1:500, Santa Cruz, sc-53540). The secondary antibodies used for immunoblotting were anti-mouse IgG, HRP-linked antibody (1:2000, CST, 7076) and anti-rabbit, IgG, HRP-linked antibody (1:2000, CST, 7074).
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