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6 protocols using af7001

1

Tissue Microarray Analysis of Lung Adenocarcinoma

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We established a tissue microarray (TMA, 3 mm) consisting of LUAD samples: 14 AIS samples, 18 MIA samples, and 17 IAC samples (Supplementary Table 4). After antigen repair and blocking, the TMA was incubated with specific primary antibodies (EPCAM, Servicebio, GB14078, 1:200; FOXP3, Servicebio, GB11093, 1:200; TPSB2, Novus, NBP2-33551, 1:300; CD79A, Novus, NB100-64347ss, 1:200; CLDN5, Servicebio, GB11290, 1:200; COL1A1, Affinity, AF7001, 1:200; UBE2C, Abcam, ab12290, 1:50; p-SMAD2, Affinity, AF8314, 1:200; SCGB1A1, Servicebio, GB111412, 1:200; PDPN, Affinity, AF3670-SP, 1:200; FCN1, Novus, NBP1-84706, 1:200; GHD, Proteintech, 67538 1:250; PCNA, Servicebio, GB11010, 1:300), incubated with horseradish peroxidase (HRP)-labeled secondary antibodies or fluorophore-labeled secondary antibodies, and finally stained with diaminobenzidine and counterstained with hematoxylin or stained with DAPI. Three independent pathologists distinguished the pathological type for the TMA.
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2

Quantitative Western Blot Analysis of Kidney Proteins

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Kidney tissues or cells were lysed and subsequently sonicated in PBS that contained 1% Triton X-100, 250 mmol/L phenylmethanesulfonyl fluoride, 2 mmol/L EDTA, and 5 mmol/L dithiothrietol (pH7.5). The total protein concentration was then determined by the BCA protein assay reagent kit (GBC, G3422). Thirty milligrams of protein for each sample was denatured in boiling water for 5 min then separated by SDS-PAGE and transferred onto polyvinylidene difluoride (PVDF) membranes. The blots were blocked 1 h with 5% nonfat dry milk in Tris-buffered saline, followed by incubation overnight with rabbit α-smooth muscle actin (α-SMA) antibody (Affinity, AF1032), Collagen IA (Affinity, AF7001), NLRP3 (Abcam, ab214185), Caspase-1 (Affinity, AF4005), APJ (Fitzgerald, 70R-51439), p47phox (Affinity, AF5220) or p22phox (Affinity, DF10099) at 4 °C. For β-actin, the membranes were stripped and reprobed with rabbit anti-β-actin antibody (Affinity, AF7018) or anti-GAPDH antibody (Affinity, AF7021). After being washed with Tris-buffered saline, membranes were incubated with a secondary antibody labeled with horseradish peroxidase-conjugated secondary antibody (Affinity, S0001) and visualized using enhanced chemiluminescence. The intensities of blotted bands were quantified with the software (ImageJ, free download from http://rsbweb.nih.gov/ij/).
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3

Western Blotting Protocol for Protein Analysis

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RIPA buffer (Beyotime Bio., Shanghai, China) was used to prepare cell extracts for immunoblotting. Afterwards, total protein content was determined using a Bio-Rad protein assay kit (Bio-Rad Laboratories, Hercules, CA, USA). Protein samples were electroblotted onto polyvinylidene difluoride (PVDF) membranes. TBST (Tris-buffered saline containing Tween 20) buffer with 5% bovine serum albumin was used to block the membranes. The membranes were blocked at room temperature for 1 h, and then, the corresponding primary antibodies, α-SMA (Affinity Biosciences, Cincinnati, OH, USA; AF1032; 1 : 500), COL1A1 (Affinity Biosciences; AF7001; 1 : 500), TGF-β (Abcam, Cambridge, MA, USA; Ab179695; 1 : 3000), FGFR4 (Affinity Biosciences; DF10316; 1 : 1000), and GAPDH (Cell Signaling Technology, Danvers, MA, USA; #5174; 1 : 2000), in TBST buffer were used to incubate the membranes. The membranes were kept at 4°C overnight. On the next day, the membranes were incubated with secondary antibodies (Beyotime) at room temperature for 1 h. An enhanced chemiluminescence chromogenic substrate (Thermo Fisher Scientific) was used for visualized protein bands.
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4

Quantification of MMP-1 and COL1A1 Levels

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The expression of MMP-1 and Collagen1A1 (COL1A1) was verified by Western blot (Gupta et al., 2014b). The skin tissues were grounded, then the supernatant was carefully absorbed after centrifugation at 4 °C at 4360.2xg for 30 min. The concentration of protein was evaluated by a BCA kit (Thermo Fisher Scientific, USA). 50μL of protein was separated in 10% SDS-PAGE gel and transferred onto a PVDF membrane. After transfer, the membranes were blocked with 5% skimmed milk powder-TBST. Anti-MMP1 (Proteintech, 10371-2-AP, 1:1000 dilution), Anti-Collagen I (Affinity, AF7001, 1:1000 dilution), and GAPDH (Abcam, ab9485, 1:2500 dilution) as an internal control protein, followed by the secondary antibody was applied to the membrane for 1.5 h at 20 °C. ECL detection was used to expose the protein, and the images were taken at a WSE-6100 LuminoGraph (ATTO, Tokyo, Japan). The amount of target protein was calculated by gray scanning with ImageJ version 1.50 (National Institutes of Health, USA).
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5

Fibroblast Protein Expression Analysis

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To detect the protein expression after BMSC-CM treatment, fibroblasts (3 × 106 cells) were seeded in 100 mm dishes in triplicate. Whole proteins (three from serum-free DMEM/F12-treated cells and the other three from BMSC-CM-treated cells) were extracted and their concentrations were determined using a bicinchoninic acid (BCA) protein assay kit (Thermo Fisher Scientific, USA). The whole proteins from each sample were separated on 10% SDS-PAGE gels and blotted onto polyvinylidene difluoride (PVDF) membranes (Millipore, IPVH00010, USA). After blocking with 5% BSA, the membranes were incubated overnight at 4° C with antibodies against GAPDH (1:1000, Affinity Biosciences, AF7021, USA), collagen I (1:1000, Affinity Biosciences, AF7001, USA), collagen III (1:1000, Abcam, ab7778, USA), MMP1 (1:1000, ABclonal, A1191, USA), and MMP2 (1:1000, Proteintech, 10373-2-AP, USA). After washing thrice with TBST, the membranes were incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies. The protein bands were detected by chemiluminescence. The intensity of protein bands was measured using Image-J.
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6

Paraffin-Embedded Tissue Preparation and Immunofluorescence

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The tissue samples were processed as follows: they were initially fixed in 4% paraformaldehyde for 24 h, then embedded in paraffin, and subsequently sectioned into 5-μm thick slices. For hard tissues, extensive decalcification was conducted using 14% EDTA solution (pH 7.4) for four weeks before embedding.
Hematoxylin-Eosin (H&E) and Masson staining were conducted on all serial sections. For immunofluorescence, sections or cells were incubated with primary antibodies, including ETV2 (ab181847, 1:500, Abcam), CD90 (105,201, 1:100, Biolegend), pERK1/2 (YP1055, 1:100, ImmunoWay), HIF-1α (BF8002, AF1009, 1:100, Affinity), PHD2 (DF6285, 1:100, Affinity), CD31 (AF6191, 1:100, Affinity), OPN (NB110-89062, 1:100, Novus), and Collagen I (AF7001, 1:100, Abcam) overnight at 4 °C. Subsequently, secondary antibodies, including FITC-Conjugated Goat anti-mouse IgG (HA1003, 1:200, HUABIO), Alexa Fluor 594 Anti-rabbit IgG (8889, 1:500, Cell Signaling Technology), Alexa Fluor 488 Anti-rabbit IgG (4412, 1:500, Cell Signaling Technology), and FITC-conjugated goat anti-rabbit IgG (SA00003-11, 1:100, Proteintech), were applied for 1 h. Nuclei were labeled with DAPI (Beyotime) for 5 min and images were captured using a fluorescence microscope (Leica).
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