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262 protocols using ab2413

1

3D Spheroid Extracellular Matrix Analysis

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After 6 days of culturing, the 3D spheroids were harvested, embedded into HistoPrep tissue embedding media (Thermo Fisher Scientific, San Jose, CA, USA), and frozen at −20 °C. Then, the frozen blocks were cut into 10 μm sections, fixed in a mixture of acetone and methanol (1:1) for 15 min and air-dried at room temperature. To identify the desired ECM proteins, the slides were washed with TBS-T (1x) and kept in blocking solution for 1 h at room temperature. Then, samples were incubated with primary antibodies for 3 h at room temperature. The following primary antibodies were used in the experiments: rabbit monoclonal anti-fibronectin primary antibodies (ab2413, Abcam), rabbit polyclonal anti-type I collagen antibodies (ab34710, Abcam), and rabbit polyclonal anti-laminin antibodies (ab11575, Abcam). After incubation with primary antibodies, the samples were washed with TBS-T and incubated with goat anti-rabbit IgG labeled with Alexa Fluor 488 (ab150077, Abcam) for 1 h at room temperature. Nuclear DNA was stained with DAPI for 10 min before the samples were covered with a cover glass. The images of spheroid sections were obtained using an inverted AxioVert.A1 microscope (Zeiss, Oberkochen, Germany) equipped with a ×20/0.6 objective lens.
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2

Immunohistochemical Analysis of ECM Proteins

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IHC was used to analyze the expression ofα-SMA, LN, FN, Type I and III collagen in cells. The primary antibody as follows were used in the present study: Anti-alpha smooth muscle Actin antibody (Abcam, USA, ab5694), Anti-Low-density lipoprotein receptor-related protein 10 antibody (Abcam, USA, Ab111288), Anti-Collagen I antibody (Abcam, USA, Ab34710), Anti-Collagen III antibody (Abcam, USA, Ab7778), Anti-Fibronectin antibody (Abcam, USA, Ab2413), Anti-Laminin antibody (Abcam, USA, Ab128053). The secondary antibody labeled with fluorochrome diluted in 10% NGS (Alexa Fluor 488-labeled Goat Anti-Rabbit IgG (H+L) (Biyuntian Biotechnology Co., Ltd., Shanghai, China) was used. All of the images were obtained by an Eclipse TE2000-S electron fluorescence microscope (Nikon, Japan) and analyzed by Image J software as described previously (Vayrynen et al., 2012 (link)).
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3

Fibronectin Immunofluorescence Imaging in HeLa Cells

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HeLa cells were seeded and monitored by QPM for 24 h, as described in the previous section. The mineral oil was gently removed by aspiration. Cells were then permeabilized with the permeabilization buffer (76 (link)) and fixed with 4% paraformaldehyde (RT 157-8; Electron Microscopy Sciences). After blocking with 2% BSA for 1 h, cells were incubated with or without the anti-fibronectin primary antibody (1:100, ab2413; Abcam) overnight at 4 °C then incubated with the goat anti-rabbit IgG (H+L) secondary antibody Alexa Fluor 568 (1:1,000, A-11011; Thermo Fisher Scientific) for 1 h at room temperature. Finally, cells were stained with 250 ng/mL Alexa Fluor 647 NHS ester (A20006; Thermo Fisher Scientific) and 2 µM DAPI (4, 6- diamidino-2- phenylindole) (D8417; Sigma-Aldrich) for 1 h at room temperature and imaged by the ORCA-ER camera (Hamamatsu) at 10× magnification.
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4

Western Blot Protein Analysis Protocol

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Western blot analyses were performed as described previously [37 (link)]. The protein concentrations of cell or tissue lysates were measured using the Lowry assay. Afterward, 40 μg protein samples were separated using 10% or 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE, according to the molecular weight of the proteins of interest) and then electroblotted onto a nitrocellulose membrane. The membranes were blocked with BlockPRO blocking buffer (BP01-1L; Visual Protein, Taipei, Taiwan), immunoblotted with specific primary antibodies against THBS2 (1:1000, A8561; ABclonal, Woburn, MA, USA), HSP90 (1:500, sc-101494; Santa Cruz Biotechnology), transferrin (1:1000, GTX112729; Gene Tex, Irvine, CA, USA), CD 81 (1:500, GTX101766; Gene Tex), α-SMA (1:1000, bsm-52396R; Bioss Antibodies Inc, Woburn, MA, USA), β-catenin (1:1000, GTX632676; Gene Tex), Fibronetin (1:500, ab2413; Abcam, Cambridge, MA, USA), Vimentin (1:1000, SC-7557; Santa Cruz Biotechnology), and β-actin (1:1000, NB600-501; Novus Biologicals, Centennial, CO, USA), and then detected using horseradish peroxidase-conjugated secondary antibodies. The signals were visualized by chemiluminescence using an enhanced detection kit (ECL, TU-ECL03, TOOLS, Taipei, Taiwan).
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5

Antibody Sources for Protein Analysis

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The primary antibodies against fibronectin (FN, ab2413), type IV collagen (Col-IV, ab6586), quinolinate phosphoribosyltransferase (QPRT, ab171944, for cell Western blotting), nicotinamide mononucleotide adenylyltransferase 1 (NMNAT1, ab45652, for kidney tissue Western blotting and immunofluorescence staining) and nicotinamide riboside kinase 1 (NRK1, ab169548, for cell Western blotting) were purchased from Abcam (Cambridge, MA, USA). Antibodies of anti-vimentin (#5741), anti-α-Tubulin (#3873) and horseradish peroxidase (HRP)-conjugated anti-rabbit IgG (#7074) were obtained from Cell Signaling Technology (Beverly, MA, USA). Antibodies against α-smooth muscle actin (α-SMA, A5228), β-actin (A5441) and QPRT (SAB1410425, for kidney tissue Western blotting and immunofluorescence staining) were from Sigma-Aldrich (St Louis, MO, USA). The anti-NMNAT1 (sc-271557, for cell Western blotting) and anti-NRK1 (sc-398852, for kidney tissue Western blotting and immunofluorescence staining) were from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Antibodies against nicotinic acid phosphoribosyltransferase 1 (NAPRT1, 13549-1-AP), nicotinamide phosphoribosyltransferase (NAMPT, 11776-1-AP), glyceraldehyde-3-phosphate dehydrogenase (GAPDH, 60004-1-IG) and HRP-conjugated anti-mouse IgG (SA00001-1) were purchased from Proteintech Group (Wuhan, China).
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6

Fibroblast Characterization via Immunofluorescence

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For the characterization of primary fibroblasts isolated from patients, cells were seeded in glass coverslips. The following day, cells were fixed with 4% paraformaldehyde for 10 min at room temperature, permeabilized with 0.125% Triton X‐100 for 10 min and blocked with 4% BSA for 1 h. Primary antibodies against Fibronectin (ab2413, 1 : 100; Abcam, Cambridge, UK) and Vimentin (sc‐6260, 1 : 50; Santa Cruz, CA, USA) were incubated overnight in a humidified chamber at 4 ºC. Coverslips were washed three times with PBS containing 0.1% Tween‐20 and incubated for 1 h at room temperature with the respective secondary antibody (1 : 400; Abcam). Finally, coverslips were again washed and mounted in ProLong Diamond Antifade mounting media containing 4′,6‐diamidino‐2‐phenylindole (DAPI; Thermo Fisher Scientific, Waltham, MA, USA). Samples were imaged with Zeiss Cell Observer inverted microscope and processed using imagej (NIH).
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7

Western Blot Analysis of Protein Expression

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Cells were lysed with ice-cold RIPA buffer and centrifuged at 13,000 g for 15 min at 4 °C. 20 ug of protein lysate (concentration determined by bicinchoninic acid assay) was run on a 10% SDS-PAGE gel at 120 V for 1.5 h and then transferred to nitrocellulose filter membranes (Millipore, Bedford, MA). After blocking with 5% BSA at room temperature (RT) for 1 h, the membranes were incubated with the following primary antibodies: α-SMA (#19245, 1:1000, Cell Signaling Technology, Danvers, MA), fibronectin (ab2413, 1:1000, Abcam, Cambridge, UK), arginase-1 (Arg1) (16001-1-AP, 1: 5000, Proteintech, Wuhan, China), ornithine δ-aminotransferase (OAT) (A6235, 1:1000, ABclonal Technology, Wuhan, China), PYCR1 (13108-1-AP, 1:4000, Proteintech), proline dehydrogenase (oxidase) 1 (PRODH) (22980-1-AP, 1:2000, Proteintech) and β-actin (20536-1-AP, 1:5000, Proteintech) at 4 °C overnight. The next day, the membranes were incubated with HRP-conjugated goat anti-rabbit IgG(H + L) (SA00001-2, 1:10000, Proteintech) for 1 h at room temperature and then washed three times for 10 min with tris-buffered saline containing 0.1% Tween 20. Quantitative analysis was performed on the immunoreactive bands using ImageJ software.
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8

Cardiac Fibrosis Quantification via Histochemistry

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Hearts were harvested, fixed with 4% paraformaldehyde and then paraffin‐embedded. After that, 5‐mm sections were made. Masson staining were employed to assess cardiac fibrosis along with collagen deposition by a Masson stain kit. The whole‐heart fibrosis (fibrosis area/whole heart area) and left ventricular CVF (collagen area/total observed area in multiple random ×20 magnification visual fields) were computed as the ratio of fibrosis area to the overall or left ventricular assessed area quantified with the ImageJ software (V.1.50, Bethesda, USA). Soaking of the sections in 3% H2O2 was done to stop the endogenous peroxidase activity. Subsequently, the sections were inoculated overnight with anti‐NLRP3 antibody (Novus, NBP2‐12446, USA; 1:200), anti‐α‐SMA (Abcam, ab124964, USA; 1:200) and anti‐Fibronectin (Abcam, ab2413, USA; 1:200) at 4°C for immunohistochemistry. We randomly selected 5 vision fields (×20) for every section with a microscope (Olympus, Tokyo, Japan).
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9

Immunohistochemical Fibronectin Expression Assay

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Protein expression was assayed by immunohistochemistry using the paraffin-embedded sections from the patients. The sections were first deparaffinized by xylene (Shanghai Sangon, Shanghai, China). Then, the sections were incubated with rabbit polyclonal anti-fibronectin antibody (1:500, ab2413; Abcam, Cambridge, MA, USA) at 4°C for 24 h. After washing with TBST buffer (Shanghai Sangon) for three times, the sections were incubated with goat anti-rabbit IgG H&L (HRP, 1:500, ab6721; Abcam) at room temperature for 1 h. Then, protein immunostaining was performed using DAB Plus substrate (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer's instructions. The scoring of the stained tumor cells were divided into five grades: 0 (positive cells <5%), 1 (positive cells between 5 and 25%), 2 (positive cells between 26 and 50%), 3 (positive cells between 51 and 75%), and 4 (positive cells between 75 and 100%). The cells were observed using a light microscope (Axioskop; Zeiss, Germany). We designated grade 1 and 2 as low expression of fibronectin and grade 3 and 4 as high expression of fibronectin for the prognosis analysis.
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10

Cardiac Protein Extraction and Western Blot

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Protein was extracted from cardiac tissue with 1× RIPA buffer containing 0.1% SDS. Protein (20 µg) was subjected to SDS-PAGE and transferred to polyvinylidene fluoride membranes. Primary antibodies for β-MHC (1:1000, #AF7533, Beyotime, Shanghai, China), fibronectin (1:1000, #ab2413, Abcam), and GAPDH (1:10,000, #2118S, CST). The appropriate secondary antibodies conjugated to horseradish peroxidase (HRP) were from Santa Cruz Biotechnology (1:10,000). Membranes were visualized with SuperSignal West Pico Substrate (Pierce Biotechnologies, Rockford, IL, USA) or Immobilon Western HRP Substrate (Millipore, Billerica, MA, USA). Quantification was performed by using ImageJ software.
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