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14 protocols using af1027

1

Investigating Protein Expression in Lacrimal Fluid

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Clinical LF specimens (non-LFH group:LFH group = 2:2) were snap-frozen in liquid nitrogen and stored at −80°C for Western blotting. Total protein from each LF specimen was extracted in RIPA lysis buffer (Santa Cruz) and quantified using the BCA assay (Pierce). After denaturation, proteins specimens were separated using gel electrophoresis on 8%–12% SDS-PAGE, and then were transferred onto PVDF membranes (Roche Applied Science, Indianapolis, IN, USA). Using 5% nonfat dry milk for 2 hours at room temperature, The membranes were blocked in 5% nonfat dry milk for 2 h and then incubated overnight at 4°C with the following primary antibodies: Beclin1 (1:500; AF5128, Affinity), P62 (1:500; AF5384, Affinity), FN1 (1:500; AF5335, Affinity), TGFβ1 (1:500; AF1027, Affinity), NGF (1:500; AF5172, Affinity), HMOX1 (1:500; AF5393, Affinity), CAT (1:500; DF7545, Affinity), SIRT1 (1:500; TU365233, Abmart), and GAPDH (1:5000; AP0063, Bioworld). After, the membranes were incubated with goat anti-rabbit IgG (H+L) HRP secondary antibody (1:5000; RM3002, Rayantibody) for 2 h at room temperature. The proteins bands were detected using an enhanced chemiluminescence kit (KF005, Affinity), and chemiluminescence signals were quantified with Image Lab statistical software (Bio-Rad, Hercules, CA, USA).
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2

Immunohistochemical Analysis of Pancreatic Cancer

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Pancreatic cancer tissues and adjacent normal pancreatic tissues were obtained from pancreatic cancer patients. The research protocols were approved by the Research Ethics Committee of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine (ID: 20210728-31). All participants gave written consent authorizing the analysis of their tissue samples and medical information for scientific research.
After dewaxing and rehydration, tissue sections were put in EDTA solution, and antigen recovery was performed at 100°C for 30 min. After natural cooling to room temperature, an endogenous peroxidase blocker was used to block endogenous peroxidase activity for 15 min. After washing twice in PBS, tissue sections were incubated with the primary antibody anti-ADAMTS12 (ab203102, Abcam); anti-CD 163 (ab182422, Abcam); or anti-TGF beta 1 (AF1027, Affinity), at 4°C overnight. The next day, the tissue sections were washed twice in PBS and were then incubated with a secondary antibody at room temperature for 1 h. The immunohistochemical reactions were visualized with 3,3,0-diaminobenzidine (DAB), and hematoxylin was used for nuclear staining in all tissue sections. The protein levels were evaluated based on the percentage of positive cells and staining intensity (0, negative; 1+, weak; 2+, moderate; 3+, strong).
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3

Western Blot Quantification of TGF-β and Smad4

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To isolate the total proteins, U251 cells were lysed in radioimmunoprecipitation assay (RIPA) buffer (Beyotime). The protein samples were segregated by 10% SDS-PAGE, which were then deposited onto polyvinylidene difluoride membranes. After that, the membranes were blocked with 5% nonfat milk for 1 h before being incubated with primary antibodies anti-TGF-β (1 : 2000, AF1027, Affinity, Cincinnati, OH, USA) or anti-Smad4 (1 : 2000, AF5247, Affinity) for 12 h at 4°C. GAPDH was regarded as an internal control (1 : 3000, AF7021, Affinity). After being washed with Tris-buffered saline with Tween 20 (TBST), the membranes were further treated with a secondary antibody (HRP-IgG, 1 : 2000, ab205718, Abcam, Cambridge, England) for 1 h at 25°C in the dark. An ECL kit (Pierce, Rockford, IL, USA) was used to visualize the protein bands, which were then photographed using a Gel imaging system (Tanon 3500, Shanghai, China).
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4

Immunohistochemical and Collagen Analysis

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Tissues were harvested and fixed with 10% formalin and embedded in paraffin. Serial sections (4 μm) were prepared and stained with H&E and immunohistochemistry (IHC). For IHC, tissue sections were subjected to antigen retrieval and incubation with primary antibody against CCL2 (BF0556, Affinity), TGF-β (AF1027, Affinity), IL-1β (AF5103, Affinity), IL-6 (DF6087, Affinity), or IL-10 (DF6894, Affinity), followed by incubation with a peroxidase-conjugated goat anti-rabbit IgG (KIT-9706, Maixin-Bio) secondary antibody, and the immunoreactivity was detected with an UltraSensitive™ Streptavidin-Peroxidase Kit (KIT-9710, Mai Xin, China) according to the manufacturer's protocol. The collagen content was assessed by Sirius Red (365548, Sigma). For immunofluorescence (IF), cryosections (4 μm) were prepared from freshly frozen liver tissues and incubated with antibodies specific for mouse CD68 (137005, Biolegend), CD31-antibody (102432, Biolegend), TIE2 (124008, Biolegend), or phos-NF-κB (Affinity, AF5006). Photomicrographs were produced using a confocal microscope and corresponding software (Zeiss). Image Pro Plus 6.0 software was used for quantitative analysis.
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5

Western Blot Analysis of Fibrosis Markers

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Tissue protein samples were prepared in RIPA buffer (Beyotime Biotechnology, Haimen, China) containing phosphatase inhibitor and protease inhibitor cocktails (Roche Applied Science, Indianapolis, IN, USA). Samples containing 20 μg of protein were subjected to sodium dodecyl sulphate‐polyacrylamide gel electrophoresis, and the proteins were then transferred to a polyvinylidene difluoride membrane. The membrane was blocked with Tris‐buffered saline‐Tween with 5% bovine serum albumin and incubated at 4°C overnight with primary antibodies against α‐SMA (1:1000; AF1032, Affinity Biosciences), Collagen I (1:1000; AF7001, Affinity Biosciences), TGF‐β1 (1:1000; AF1027, Affinity Biosciences), eNOS (1:1000; AF0096, Affinity Biosciences), nNOS (1:1000; AF6249, Affinity Biosciences) or β‐actin (1:1000; 20536‐1‐AP, Proteintech, China). After hybridization of secondary antibodies (1:5000 or 1:10000; ProMab, USA), the immunoreactive proteins were detected through an enhanced chemiluminescence detection system (Pierce, Thermo Fisher Scientific, Rockford, IL, USA).
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6

Western Blot Profiling of Protein Expression

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Proteins were extracted by mixing RIPA lysate (R0010, Solarbio) and PMSF (P0100, Solarbio). The concentrations of proteins were assayed by the BCA kit (PC0020, Solarbio). According to different molecular weights, 5% concentrated gel and 8% separation gel concentrations were used in the SDS-PAGE. After transferred to a PVDF membrane, the proteins were blocked by prepared 5% (M/V) BSA (Biosharp, BS043, China) in TBST buffer for 1 h and incubated overnight at 4 °C with the following primary antibodies: α-SMA (1: 500), COL-I (1: 500, AF0134, Affinity), TGF-β1 (1: 1000, AF1027, Affinity), proliferating cell nuclear antigen (PCNA) (1: 500, A12427, Abclonal, China), p-MEK1/2 (1: 500, AP0209, Abclonal), MEK1/2 (1: 500, A4868, Abclonal), p-ERK1/2 (1: 500, AF1015, Affinity), ERK1/2 (1: 500, AF6240, Affinity) and GAPDH (1: 10000, 60004-1-Ig, Proteintech, China). Next, the membrane was incubated with goat anti-mouse IgG (1: 3000, SE131, Solarbio) or goat anti-rabbit IgG (1: 3000, SE134, Solarbio) secondary antibody for 40 min at 37 °C. At last, the specific protein bands were visualized with Western ECL Substrate (D1010, Solarbio).
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7

Western Blot Analysis of Fibrosis Markers

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The western blot analysis was conducted according to Taylor et al.’s method20 (link) with a GAPDH monoclonal antibody (1:5,000, Abcam, ab181602) used as an internal control. The primary antibodies used were the TGF-β1 antibody (1:1,000, Affinity, AF1027), Smad3 antibody (1:1,000, Affinity, AF6362), α-SMA antibody (1:1,000, Abcam, ab32575), Col1a1 antibody (1:1,000, Abcam, ab34710), Col1a2 antibody (1:1,000, Abcam, ab34712) and FN antibody (1:1,000, Proteintech, 15613–1-AP), respectively.
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8

Immunohistochemical Analysis of Inflammatory Markers

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The IHC analysis was carried out as follows: Briefly, HNP tissue sections embedded in paraffin were cut into 15 μm sections. These sections were then deparaffinized with environment-friendly de-paraffin liquid (G1128, Servicebio, China) and dehydrated using gradient alcohol. Membrane-breaking solution (G1204, Servicebio, China) was applied according to the protocols. The sections were subsequently incubated with 3% BSA for 25 min to block endogenous peroxidase, followed by overnight incubation at 4°C with primary antibodies against IL-1β (#AF4006, Affinity, China, 1:200), p65 (#AF5006, Affinity, China, 1:200), and TGF-β1 (#AF1027, Affinity, China, 1:200). The next day, sections were incubated with HRP-conjugated Goat Anti-Rabbit IgG H&L (511,203, ZENBIO, China, 1:300) for 1 h, and counterstaining was performed with hematoxylin solution for 5 min. Images of stained sections were acquired using a light microscope (BX43, Olympus, Japan).
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9

Quantification and Profiling of Protein Markers

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The total proteins were extracted using a RIPA assay kit. Total protein was quantified by BCA Protein Assay Kit (Beyotime, China). Subsequently, the proteins were separated via SDS-PAGE and then transferred onto a polyvinylidene fluoride (PVDF) membrane (Pall, USA). The membranes were blocked with the QuickBlock™ Blocking Buffer (P0252; Beyotime Biotechnology) at room temperature for 15 min at room temperature, and blots were then incubated at 4 °C with the following diluted primary rabbit anti-human antibodies: anti-IGF1R (1:3000, K106546P; Solarbio), anti-EGR1 (1:600, D120585; BBI), anti-OBCAL (1:1000, DF8584; Affinity), anti-TGF beta1 (1:1000, AF1027; Affinity), anti-TGF beta2 Ab (1:1000, AF0260; Affinity), anti-Smad2/3 (1:1000, AF6367; Affinity), anti-Smad4 (1:1000, AF5247; Affinity), anti-HIF1A (1:1000, AF1009; Affinity), and anti-beta Actin (1:5000, AF7018; Affinity), followed by horseradish peroxidase (HRP)-labeled goat anti-rabbit immunoglobulin G (IgG) H&L (1:5000; ZB-2301; ZSG-BIO) for 2 h at room temperature. After washing three times in TBST, bands were visualized utilizing BeyoECL Plus Moon (P0018S; Beyotime Biotechnology). The immunoblotting results were analyzed using the Image J software.
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10

Immunohistochemical Analysis of TGF-β1

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Tissue sections with a thickness of 4 μm were baked at 60°C for at least 2 h. Paraffin sections were soaked in fresh xylene, anhydrous ethanol, 95% ethanol and 75% ethanol. After a blocking step, the primary antibody against TGF‐β1 (AF1027, Affinity Biosciences) was added at a 1:100 dilution and incubated overnight at 4°C. After washing, the tissue was incubated at room temperature for 10–15 min in the presence of biotin‐labelled secondary antibody (histochemical secondary antibody kit 19149A01, Beijing Zhongshan Jinqiao Biotechnology Co., LTD.), washed again, and incubated under the same conditions in the presence of horseradish enzyme‐labelled streptomycin working solution. DAB colour rendering solution was finally added, and the tissue was further incubated for 5–8 min. The slices were also stained with hematoxylin staining solution for 20 s at the end of the staining protocol. Imaging of the stained slides was performed using a confocal laser scanning microscope (Leica Microsystems (Shanghai) Co., LTD.) at a magnification of ×800.
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