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185 protocols using ab76003

1

Immunohistochemical Analysis of Tissue Samples

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The tissue is fixed in formalin and embedded in paraffin, and then cut into thin slices. The sections were deparaffinized with xylene and hydrated with ethanol, and then the antigen was recovered by pressure cooking. At room temperature, the sections were sliced with TNC primary antibody (ab108930, Abcam, Cambridge, MA), MMP9 (Abcam, ab76003, 1:1000 dilution), MMP2 (Abcam, ab92536, 1:1000 dilution) and CD31 (ab134168, Abcam), incubated for 60 min and then incubated with IgG H&L (HRP; 1:200 dilution, Abcam, Cambridge, UK). Then, the sections were stained with chromogen and counterstained with hematoxylin. The score is based on the intensity of staining (0 means no staining, 1 means weak staining, 2 means moderate staining, and 3 means strong staining). The product of the two levels was calculated as the final expression score.
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2

Thymoquinone-Induced Apoptosis and Autophagy

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Thymoquinone (TQ) was product of MCE (CAS: 490-91-5). Hoechst 33342 (B2261) was bought from Sigma-Aldrich. Cell counting kit‐8 (CCK‐8) was product of Selleck Chemicals (US). N-Acetyl-L-cysteine (NAC) and Z‐VAD‐FMK (ZVF) were obtained from Beyotime Biotechnology (Shanghai, China). The Apoptosis Detection Kit #556547 was purchased from BD (San Jose, CA). Antibodies against Bax (ab32503), Bcl‐2 (ab182858), LC3B (ab192890), Beclin-1 (ab207612), ATG7 (ab133528), MMP2 (ab92536), MMP9 (ab76003) and PD-L1 (ab213524) were bought from Abcam (San Francisco, CA). Antibody against vimentin (V6389) was purchased from Sigma-Aldrich (US). Antibodies against β‐actin (20536‐1‐AP) and Bcl-xl (10783-1-AP) were obtained from Proteintech (Chicago, IL). Antibodies against cleaved caspase 3 (9664), cleaved poly (ADP‐ribose) polymerase (PARP) (5625), E-cadherin (3195), N-cadherin (13116), and SQSTM1/p62 (8025) were obtained from CST company (NJ, US).
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3

Protein Expression Analysis Protocol

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The cell lysates were collected, and 30 mg protein of each sample was separated using 10% SDS-PAGE. The protein was then electrotransferred onto Polyvinylidene Fluoride (PVDF) membrane (Millipore, Boston, MA, USA). The PVDF membrane was sealed in 10% skimmed milk. Then the membrane was incubated with primary antibodies, including anti-TNC (Abcam, ab108930, 1:1000 dilution), anti-GAPDH (Abcam, ab181602, 1:10,000 dilution), and anti-ERK (Abcam, ab184699, 1:1000 dilution)), anti-p-ERK (Abcam, ab201015, 1:1000 dilution), anti-MMP9 (Abcam, ab76003, 1:1000 dilution), anti-MMP2 (Abcam, ab92536, 1:1000 dilution), anti-E-cadherin (Abcam, ab1416, 1:1000 dilution), anti-N-cadherin (Abcam, ab18203, 1:1000 dilution), anti-vimentin (Abcam, ab92547, 1:1000 dilution), anti-snail (Abcam, ab216347, 1:1000 dilution), anti-clumping (Abcam, ab27568, 1:1000 dilution) and anti-TWIST1 (Abcam, ab50887, 1:1000 dilution) overnight. Then the membrane and horseradish peroxidase-conjugated secondary antibody (Abcam AB6721, 1:10,000 dilution) were incubated for 2 h at room temperature. Chemiluminescence detection reagent (Millipore, Boston, MA, USA) was used to visualize protein bands.
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4

Western Blot Analysis of Protein Targets

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Total proteins from cells and tissues were extracted by the RIPA lysate. Protein quantification was conducted with a BCA protein quantification kit. An appropriate amount of protein sample was denatured at 100°C for 3–5 min and then subjected to protein electrophoresis using 10% SDS-PAGE for 1 h. the samples were transferred to PVDF membranes. The membranes were blocked in Tris Buffered Saline with Tween 20 blocking solution containing 5% skim milk powder at room temperature for 2 h. The membranes were washed three times with TBST and incubated overnight at 4°C using primary antibodies against MMP-2, MMP-9, p-PI3K, PI3K, p-AKT, AKT, and GAPDH (ab92536, ab76003, ab278545, ab140307, ab192623, ab8805, ab8245; all from Abcam, Shanghai, China). The next day, the horseradish peroxidase-labeled goat anti-rabbit secondary antibody IgG (ab96899) and goat anti-mouse secondary antibody IgG (ab96879) dilution buffer were added, and membranes were incubated with these secondary antibodies at room temperature for 2 h. The enhanced chemiluminescence reagent was added dropwise, and the membranes were imaged by the gel imaging system. The gray value of each band was analyzed by the ImageJ software. The results were expressed as the ratio of the gray value of the target protein to GAPDH, the internal reference protein.
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5

Immunohistochemical Analysis of ECM Proteins

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For immunohistochemical analyses, the sections were exposed overnight at 4°C to antibodies against E-cadherin (rabbit monoclonal; 1 : 200; ab76319; Abcam), COL I (rabbit monoclonal; 1 : 200; ab270993; Abcam, Cambridge, UK), MMP-9 (rabbit monoclonal; 1 : 200; ab76003; Abcam), TIMP-1 (rabbit polyclonal; 1 : 200; Abcam), α-SMA (mouse monoclonal; 1 : 200; ab7817; Abcam), or fibronectin (rabbit monoclonal; 1 : 200; ab199056; Abcam), followed by incubation with secondary horseradish peroxidase-conjugated goat anti-rabbit IgG antibody (1 : 500; 115-035-003; Jackson ImmunoResearch, Ely, UK).
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6

Protein Expression Analysis in Tissue Homogenate

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PBS was used to wash fresh tissue which was grounded into a homogenate, and then RIPA buffer was used to lyse them to obtain total protein. Protein concentrations were determined by the BCA assay (Solarbio, PC0020, China). Samples (30 μg protein) were resolved on 8% SDS-PAGE gel and transferred to PVDF at 4°C. Membranes were blocked in fat-free milk combined with TBST for 1 hour at 25°C and immunoblotted with the appropriate diluted primary antibody KIF20A (Abcam, ab104118, UK; 1 : 1000 dilution for Western blot and 1 : 200 dilution for IHC-P), PCNA (Abcam, ab92552, UK; 1 : 1000 dilution for Western blot), Ki67 (Abcam, ab16667, UK; 1 : 1000 dilution for Western blot), MMP2 (Abcam, ab37150, UK; 1 : 500 dilution for Western blot), MMP9 (Abcam, ab76003, UK; 1 : 5000 dilution for Western blot), and GAPDH (SunGene Biotech, KM9002, China; 1 : 5000 dilution for Western blot) at 4°C overnight. Then, membranes were washed 10 minutes three times and incubated with the secondary antibody for 1 hour at 25°C. Finally, the blots were visualized by Imager.
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7

Western Blot Analysis of Protein Biomarkers

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Proteins were electrophoresed on SDS-PAGE gels and transferred onto PVDF membranes. Membranes were blocked with 5% non-fat skim milk and then incubated 4°C overnight with the following primary antibodies: rabbit anti-MMP2 (ab37150, Abcam, 1μg/ml ), rabbit anti-MMP9 (ab76003, Abcam, 1μg/ml ), rabbit anti-C/EBPβ (ab32358, Abcam, 1μg/ml ), rabbit anti-SMAD3 (A7536, Abclonal, 1μg/ml ), rabbit anti-p-SMAD3 (Ser423/425, #9520, CST, 1μg/ml ), rabbit anti-ERK (A11186, Abclonal, 1μg/ml ), rabbit anti-p-ERK (AP0472, Abclonal 1μg/ml ), rabbit anti-PARP (#9532S, CST, 1μg/ml), rabbit anti-cleaved caspase3 (Asp175) (#9664S, CST, 1μg/ml), rabbit anti-IGFBP5 (A13858, Abclonal, 1μg/ml ), rabbit anti-p53 (ab26, Abcam, 1μg/ml ), mouse anti-PUMA: (sc-377015, Santa Cruz, 5μg/ml ), or rabbit anti-β-actin (bs-0061R, Bioss, 0.5μg/ml ). PVDF membranes were washed and then incubated with the corresponding horseradish peroxidase-conjugated secondary antibody (DingGuo, Beijing). Protein bands were developed using Chemiluminescence ECL Plus-Western Blotting detection reagents (Bio-Rad). The intensities of protein bands were quantified with Gel-Pro analyzer software with P-actin served as an internal control prior to statistical analyses.
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8

Western Blot Analysis of Cell Adhesion and Proliferation Markers

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The radioimmunoprecipitation assay buffer (Thermo Fisher Scientific) was used to isolate the total protein. Following quantification with bicinchoninic acid kit (Thermo Fisher Scientific), 20 μg samples were separated via sodium dodecyl sulfate–polyacrylamide gel electrophoresis and transferred on the polyvinylidene fluoride membrane (Bio-Rad, Hercules, CA, USA). The membranes were blocked in 5% fat-free milk for 1 h and then incubated with primary antibodies (E-cadherin [ab40772, 1:8000; Abcam, Cambridge, UK], intercellular adhesion molecule-1 [ICAM-1] [ab109361, 1:1000; Abcam], vitronectin [ab45139, 1:2000; Abcam], proliferating cell nuclear antigen [PCNA] [ab18197, 1:5000; Abcam], matrix metalloproteinase 9 [MMP9] [ab76003, 1:5000; Abcam], AQP4 [ab81355, 1:300; Abcam], and GAPDH [1:5000; Abcam]) overnight, followed by interacting with secondary antibodies (ab6721, 1:2000; Abcam) for 2 h. Then blots were exposed to enhanced chemiluminescence (Solarbio) and detected via ImageJ v1.8, with GAPDH as a normalized control.
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9

Quantifying Neutrophil, Macrophage, and Inflammatory Markers in Implant and Wound Tissue

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Implant neutrophil and macrophage numbers were determined by staining for Myeloperoxidase (MPO; ab90810, Abcam) and CD68 (ab31630, Abcam) respectively. Cellular localisation of NGAL and MMP-9 in implant inflammatory cells and isolated peripheral blood neutrophils was determined using antiNGAL (M145, SantaCruz) and antiMMP-9 (sc-6840, SantaCruz) antibodies according to standard procedures [19 (link)]. The secondary antibodies (Alexa Fluor 488 or 594, Invitrogen) were used for visualisation and the nuclei were stained with DAPI. Images were captured using an Olympus AX-70-Fluorescence microscope.
The cellular localisation of NGAL (ab41105; Abcam) and MMP-9 (ab76003; Abcam) was examined in skin wound tissue by immunohistochemistry. For quantitation of NGAL, the staining intensity was examined in the epithelial (top), granulation tissue (middle) and inflammatory (basal) zones and scored by two independent observers based on a scale of 0 = no staining above isotype control to 3 = intense staining. The score for each zone was summed and the data was analysed using Chi squared analysis at an intensity cut off at ≥ 6. MMP-9 staining was localised mainly to cells in the granulation tissue layer and the staining intensity in this area was quantified using Image J software.
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10

Antibody Profiling and Activation Analysis

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The following primary antibodies were used: antibodies against Rictor (ab70374), MMP‐2 (ab37150) and MMP‐9 (ab76003) from Abcam (Cambridge, USA); antibodies against phospho‐AKT (S473) (#9721) and phospho‐AKT (T308) (#13038) from Cell Signaling Technology; and antibodies against AKT (AF6259), phospho‐CDK2 (Thr160) (AF3237), phospho‐Histone H3.1 (Ser10) (AF3358) and β‐actin (T0022) from Affinity Biosciences. HRP‐conjugated goat anti‐rabbit IgG and anti‐mouse IgG secondary antibodies were obtained from Santa Cruz (Dallas, TX, USA). Gelatin (G7041) was purchased from Sigma‐Aldrich (St. Louis, MO, USA). MK‐2206, 8‐[4‐(1‐aminocyclobutyl)phenyl]‐9‐phenyl‐1,2,4‐triazolo [3,4‐f] 1, 6naphthyridin‐3(2H)‐one hydrochloride [1:1], was obtained from Selleck (Shanghai, China). 3‐(4,5‐dimethyl‐2‐thiazolyl)‐2,5‐diphenyl‐2‐H‐tetrazolium bromide (MTT) was purchased from Sigma‐Aldrich (St. Louis, MO).
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