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12 protocols using af4001

1

Protein Expression Profiling in Cardiovascular and Immune Cells

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Total proteins were extracted from heart tissues or RAW264.7 cell lysates and supplemented with a cocktail of protease inhibitors and phosphatase inhibitors. Proteins were quantified to an equivalent amount, separated by SDS-PAGE gel, and electro-transferred to a PVDF membrane. Having been blocked in 5% skimmed milk, membranes were incubated with antibodies: anti-LFA-1 (ITGAL, Affinity Biosciences. DF5625, 1:1000), anti-p-JNK (Affinity Biosciences. AF3318, 1:1000), anti-total JNK (Affinity Biosciences. AF6138, 1:1000), anti-p-ERK (Affinity Biosciences. AF1015, 1:1000), anti-total ERK (Affinity Biosciences. AF0155, 1:1000), anti-p-p38(Affinity Biosciences. AF4001, 1:1000), anti-total p38 (Affinity Biosciences. AF6456, 1:1000) and GAPDH. The loading control was GAPDH (Proteintech, 60004-1-lg, 1:10000). Western blot bands were analyzed with the ChemiDicTM XRS + Imaging System (Bio-Rad Laboratories, Hercules, CA, USA), and the densities were quantified with Multi Gauge Software of Science Lab 2006 (FUJIFILM Corporation, Tokyo, Japan).
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2

Articular Cartilage Protein Analysis

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Articular cartilage (0.1 g) was weighed and lysed for 30 min on ice with RIPA lysis buffer containing PMSF (R0010). The supernatant was obtained by centrifugation for 20 min at 4 ℃ and 12,000 rpm, that is, the total protein. The protein concentration was measured by a BCA protein assay kit (PC0020, Solarbio). Equal amounts of protein samples were separated by SDS‒PAGE and then transferred to PVDF membranes (IPVH00010, Millipore). The membrane was blocked with 5% skim milk at room temperature for 1 h and then incubated with antibodies against p38MAPK (AF6456, Affinity), p-p38MAPK (AF4001, Affinity), MMP1 (AF0209, Affinity), MMP13 (AF5355, Affinity) and beta actin (AF7018, Affinity) overnight at 4 °C. Then, the membrane was incubated with the secondary antibody at room temperature for 2 h. The protein bands were detected by ECL reagent (WBKLS0100, Millipore) and observed by a Bio-Rad chemiluminescence imaging system (Chemidoc XRS+, Bio-Rad). ImageJ software was used to quantify the scanned image.
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3

Analysis of Uterine Protein Expression

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After treatment, the uterine tissues (myometrium and endometrium) were lysed with RIPA buffer. After isolation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), the proteins were transferred to polyvinylidene difluoride (PVDF) membranes. After blocking by 5% defatted milk powder, the membranes were incubated with the primary antibodies against tubulin alpha antibody (AF7010, 1 : 5000, Affinity, USA), ERK1/2 antibody (AF0155, 1 : 1000, Affinity, USA), phospho-ERK1/2 (Thr202/Tyr204) antibody (ab92946, 1 : 500, Affinity, USA), JNK1/2/3 antibody (AF6318, 1 : 500, Affinity, USA), phospho-ERK1/2 (Tyr204) antibody (AF1014, 1 : 500, Affinity, USA), p38 MAPK antibody (AF6456, 1 : 500, Affinity, USA), and phospho-p38 MAPK (Thr180/Tyr182) antibody (AF4001, 1 : 500, Affinity, USA) at 4°C for 24 h. After washing with PBS, the membranes were incubated with the secondary antibodies at room temperature for another 2 h. Lastly, the signals of protein bands were developed with enhanced chemiluminescence (ECL).
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4

Western Blot Analysis of Heart Tissue Proteins

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Protein lysates were harvested from heart tissues. The proteins were separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred onto polyvinylidene difluoride (PVDF, MilliporeSigma, Burlington, MA, USA) membranes. After being blocked with 5% non-at milk, the membranes were incubated with the following primary antibodies: anti-IFIT3 (1:1,000; A3924, ABclonal), anti-JNK (1:1,000; AF6318, Affinity, Changzhou, China), anti-p-JNK (1:1,000; AF3318, Affinity), p38 (1:1,000; AF6456, Affinity), p-p38 (1:1,000; AF4001, Affinity), ERK (1:1,000; AF0155, Affinity), p-ERK (1:1,000; AF1015, Affinity), collagen I (1:1,000; AF0134, Affinity), collagen III (1:1,000; AF0136, Affinity), α-SMA (1:1,000; AF1032, Affinity), and anti-β-actin (1:1,000; sc-47778, Santa Cruz Biotechnology, Dallas, TX, USA) at 4°C overnight. Next, the membranes were incubated with horseradish peroxidase (HRP) goat anti-rabbit IgG and HRP goat anti-mouse IgG (1:5,000; A0208/A0216, Beyotime) at 37°C for 45 min. Finally, the protein bands were visualized by using enhanced chemiluminescence liquid (ECL, Beyotime), and the OD values were analyzed by a Gel-Pro Analyzer (Liuyi, Beijing, China).
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5

Protein Expression Analysis by Western Blot

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Total proteins were extracted using radioimmunoprecipitation assay lysis buffer containing proteinase inhibitors (No. 04693159001, Roche Diagnostics, Switzerland), and phosphatase inhibitors (No. 04906845001, Roche), separated by sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE), transferred to polyvinylidene difluoride (PVDF) membranes, and analyzed by immunoblotting. Primary antibodies against the following proteins were used: TH (66334-1-Ig, Proteintech), protein kinase A (PKA) (AF5450, Affinity (China)), p-HSL (AF8026, Affinity), hormone-sensitive lipase (HSL) (AF6403, Affinity), p-p38 mitogen-activated protein kinase (MAPK) (AF4001, Affinity), p38 MAPK (AF6456, Affinity), PGC1α (AF5395, Affinity), UCP1 (NB100-2828, Novus Biologicals), and GAPDH (60004-1-Ig, Proteintech). The antibodies were diluted 1:1,000 with PBS. The membranes were then incubated with a peroxidase-conjugated secondary antibody (BS13278, Bioworld (China); SA00001-1, Proteintech; SA00001-3, Proteintech), and antibody-specific signals were detected by enhanced chemiluminescence and quantified using the Automatic Chemiluminescence Imaging System (Complex 2000; Nanjing PuoAoXin Biotechnology, China).
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6

Western Blot Analysis of Cellular Proteins

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ARPE‐19 cells were lysed in a lysis buffer to extract total protein, and the protein concentration was measured by a bicinchoninic acid assay kit (Beyotime, Shanghai, China). Samples were loaded and separated in 10% Bis‐Tris‐polyacrylamide electrophoresis gels. Then, the proteins were transferred to PVDF membranes, which were blocked with 5% nonfat milk followed by incubation with primary antibodies at 4 °C overnight. After incubation with the secondary antibody for 1 h, the Western blot signals were detected by ECL Plus reagents. ImageJ was used to analyze the protein bands. Primary antibodies against Occludin (1:800, Cat No. 17590‐1‐AP), TLR4 (1:800, Cat No. 66350‐1‐Ig), p65 (1:500, Cat No. 10745‐1‐AP), JNK (1:500, Cat No. 24164‐1‐AP), p‐JNK (1:500, Cat No. 80024‐1‐RR) and MYD88 (1:800, Cat No: 23230‐1‐AP) were purchased from Proteintech. Antibodies against p‐p65 (1:1000, AF2006), GADD45G (1:1000, A10286), p‐p38 (1:1000, AF4001), p38 (1:1000, AF6456), GAPDH (1:3000, AF7021), β‐actin (1:3000, AF7018) and OR11H1 (1:1000, DF5186) were purchased from Affinity.
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7

Western Blot Analysis of Signaling Proteins

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Splenocytes were lysed in fresh extraction buffer (Sigma-Aldrich, St. Louis, MO,
USA) supplemented with a protease inhibitor and phosphatase inhibitor (Gold
Biotechnology, St. Louis, MO, USA). The extracted proteins (20 μg) were
separated on a 15% SDS-polyacrylamide gel and electroblotted onto a
polyvinylidene fluoride membrane. The membrane was blocked using 5% milk
dissolved in TBST for 60 min at 20–25°C and incubated overnight at 4°C with
primary antibodies against p-p38 (AF4001, Affinity Biosciences, Changzhou,
China), p38 (AF6456, Affinity Biosciences) p-p65 (AF2006, Affinity Biosciences),
p65 (AF5006, Affinity Biosciences), p-IκBα (AF2002, Affinity Biosciences) and
IκBα (AF5002, Affinity Biosciences). The membranes were then washed with TBST
and incubated with goat anti-mouse IgG (1:1000; HAF007, R&D Systems, Inc.,
Minneapolis, MN, USA) and goat anti-rabbit IgG (1:1000; HAF008, R&D Systems,
Inc., Minneapolis, MN, USA). Bound antibodies were detected using an
electrochemiluminescence detection system (Amersham Life Science, Arlington
Heights, IL, USA). β-Actin was used as the control and to ensure equal protein
loading.
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8

Western Blot Analysis of Femoral Tissues

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For western blot analysis, proteins were extracted from femoral tissues using RIPA Buffer (20101ES60, Yeasen, China). We used the BCA kit (BI-WB005, SBJBIO, China) for protein quantification. After electrophoresis, the protein was loaded onto PVDF membranes (PW0034, Leagene, China). Next, 5% bovine serum albumin (BL-082, SBJBIO, China) was added to seal the membranes (37 °C, 60 min). The membranes were then immersed in primary antibodies (4 °C, overnight) and subsequently in anti-rabbit secondary antibodies (31,466, Invitrogen, USA) or anti-mouse secondary antibodies (S0002, Affinity, USA) at 37 °C for 60 min. Protein visualization was performed using an ECL reagent (GK10008, GlpBio, USA) on an eZwest Lite Auto Imaging System (Genscript, USA). The primary antibodies of Nrf2 (1:2000, AF0639), heme oxygenase 1 (HO-1) (1:2000, AF5393), phospho-IKB alpha (Ser32/Ser36, 1:2000, AF2002), IKB alpha (1:2000, AF5002), phospho-NF-kB p65 (Ser536, 1:2000, AF2006), NF-kB p65 (1:2000, AF5006), phospho-extracellular regulated protein kinases ½ (ERK1/2) (Tyr204, 1:2000, AF1014), ERK1/2 (1:2000, AF0155), phospho-p38 mitogen-activated protein kinase (MAPK) (Thr180/Tyr182, 1:500, AF4001), p38 MAPK (1:1000, AF6456), and GAPDH (1:20,000, AF7021) were obtained from Affinity (USA). GAPDH was used as the loading control.
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9

Protein Expression Analysis in Hippocampal Tissue and SH-SY5Y Cells

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The mice were administered 1% pentobarbital sodium and decapitated. Then, bilateral hippocampal tissues were immediately collected. SH-SY5Y cells were collected after exposure. Cells and lysed tissues in RIPA buffer supplemented with protease and phosphatase inhibitors were collected. Protein concentrations were measured with BCA reagent (P0006, Beyotime Biotechnology, China). Protein samples (20 μg) were separated by SDS‒PAGE (10% separation gel) and transferred to a PVDF membrane (Merck and Co., Inc., Whitehouse Station, NJ, United States, Germany). After blocking with TBST containing 5% nonfat milk for 1 h, the membranes were incubated with Gpx4 (ab125066, 1:1000; Abcam), Hmox-1 (ab189491, 1:2000; Abcam), P2rx7 (ab259942, 1:1000, Abcam), phospho-Erk1/2 (AF1015, 1:1000; Affinity Biosciences), Erk1/2 (AF0155, 1:1000; Affinity Biosciences), phospho-p38 (AF4001, 1:1000; Affinity Biosciences), p38 (AF6456, 1:1000; Affinity Biosciences), phospho-Jnk (AF3318, 1:1000; Affinity Biosciences), and Jnk (AF6318, 1:1000; Affinity Biosciences) overnight at 4 °C. The next day, following three washes in TBST, the membranes were incubated with horseradish peroxidase (HRP)-conjugated anti-rabbit IgG (A0208, 1:2000, Beyotime) or anti-mouse IgG (A0216, 1:2000, Beyotime) at room temperature for 1 h. The protein levels were normalized to GAPDH (#5174, 1:1000, Cell Signaling Technology).
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10

Comprehensive Western Blot Assay Protocol

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Western blot assay was performed as described by Sale et al [19 (link)]. Total proteins were extracted from cells using RIPA lysate (R0010, Solarbio) containing phenylmethylsulfonyl fluoride protease inhibitor (PMSF, P0100, Solarbio). Then, protein concentration was detected with a BCA kit (PC0020, Solarbio). After separated by 5-10% SDS-PAGE, transferred to the PVDF membrane, blocked by nonfat milk (A600669, Sangon Biotech, China), proteins on the membrane were incubated overnight at 4°C with the primary antibodies: iNOS (1: 1000, A0312, Abclonal, China), COX-2 (1: 2000, A1253, Abclonal), MMP-1 (1: 2000, A1191, Abclonal and 1: 1000, DF6325, Affinity), MMP-3 (1: 2000, A11418, Abclonal), MMP-13 (1: 2000, A11148, Abclonal and 1: 1000, AF5355, Affinity), p-ERK1/2 (1: 1000, AF1015, Affinity, China), ERK1/2 (1: 1000, AF0155, Affinity), p-p38 (1: 500, AF4001, Affinity), p38 (1: 500, AF6456, Affinity), p-JNK (1: 1000, AF3318, Affinity), JNK (1: 500, AF6318, Affinity), p-p65 (1: 1000, AF2006, Affinity), p65 (1: 1000, AF5006, Affinity), and GAPDH (1: 10,000, 60,004-1-Ig, Proteintech, China). Next, the membrane was incubated with appropriate secondary antibody. Finally, membranes were detected by Western electrogenerated chemiluminescence (ECL) Substrate (D1010, Solarbio) and the images were analyzed by Gel-pro analyzer software (Media Cybernetics, CA, USA).
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