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9 protocols using ab5694

1

Immunofluorescence Analysis of Cell Markers

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Cells seeded on a glass coverslip were washed three times in warm PBS prior to fixation in 4% paraformaldehyde (PFA, 10 min, room temperature). Cells were subsequently permeabilized with 0.5% Triton-X-100 (10 min, room temperature), quenched with 3%H2O2 (30 min, room temperature), blocked with a protein block (Dako, 30 min, room temperature) and incubated overnight with primary antibodies (ACTA2 1:200, Abcam #ab5694; cleaved-caspase 3 1:200, Cell Signalling #9661; Ki67 1:500, Thermo Fisher, A7L6 HSPG2 1:300 (mAb targeting domain IV of mouse HSPG2, Merck Millipore; CCN1 1:1000 (anti-HSPG2 antibody, developed by the Whitelock laboratory) and t-RFP 1:100, Evrogen #AB233). Subsequently, secondary antibodies (Envision) coupled to HRP were applied and detection was performed with DAB.
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2

Fibroblast Immunofluorescence Analysis of Tenascin-C

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Fibroblasts seeded on 8-well Lab-Tek II chamber glass slides (Nalgene Nunc International) were incubated in serum-free DMEM with or without tenascin-C (2 μg/ml) for 72 hours. Cells were then fixed, permeabilized, and incubated with antibodies against ASMA (Abcam, 1:500, ab5694), type I collagen (Southern Biotechnology, 1:100, 1310-01), RP105 (Abcam, 1:100, ab184956), and MD1 (Santa Cruz, 1:50, sc-390613), followed by Alexa Fluor–labeled secondary antibodies (Invitrogen) as described previously (18 (link)). For tissue immunofluorescence analyses, paraffin-embedded skin sections were incubated with ASMA (Abcam, 1:100, ab5694), p-p65 (Cell Signaling Technology, 1:100, 3033), Fn-EDA (Abcam, 1:100, ab6328), tenascin-C (Abcam, 1:100, ab108930), RP105 (Abcam, 1:100, ab184956), and MD1 (Santa Cruz, 1:50, sc-390613), followed by appropriate secondary antibodies. Nuclei were detected using DAPI. Slides were mounted, and immunofluorescence and immunohistochemistry were evaluated under Nikon A1R laser scanning confocal microscope in a blinded manner. Negative controls stained without primary antibodies were used to confirm immunostaining specificity.
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3

Immunohistochemical Characterization of Liver Tissue

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Liver tissue sections were stained for α-SMA, Abcam (ab5694) (Cambridge, UK), SPARC, Cell Signaling Technology (D10F10) (Danvers, USA), COL-1A, Abcam (ab90395) (Cambridge, UK), pan-Cytokeratin, Ventana Medical Systems (AE1/AE3/PCK26) (Tucson, Arizona, USA) and PCNA, Cell Signaling Technology (PC10) (Danvers, USA).
Formalin-fixed and paraffin-embedded tissue sections were deparaffinized in xylene and graded alcohols, hydrated, and washed in phosphate buffered saline (PBS). After an antigen retrieval in a sodium citrate buffer (pH 6) in a microwave oven, the endogenous peroxidase was blocked by 0.3% H2O2 for 15 min. Sections were incubated overnight at 4°C with primary antibody (1 : 100) and as a secondary antibody; a horseradish peroxidase (HRP) SuperPicTure Polymer detection kit was used (Invitrogen). As a chromogen substrate for HRP, either DAB or ACE (Dako) was used. A matched isotype control was used as a control for nonspecific background staining, and a routine standard staining showing a normal histology of liver sections from respective groups was performed with hematoxylin/eosin and Masson's Trichrome, respectively. The proliferative index was assessed by counting the number of PCNA-positive cells at ×200 magnification in five randomly chosen fields per slide in three animals, one at 0, one at 3, and one at 6 weeks after PHx.
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4

Immunohistochemical Analysis of Renal Markers

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The deparaffinized and rehydrated sections (3 μm) of paraffin-embedded renal cortices were subjected to heat-mediated antigen retrieval and incubated with 3% H2O2 for 10 mins. Sections were then incubated overnight at 4°C with primary antibodies against proliferating cell nuclear antigen (PCNA) (Wanleibio, wl02208, 1:200), phosphor-nuclear factor-κB p65 (p-NF-κB) (Wanleibio, wl02169, 1:100), podocin (Abcam, ab181143, 1:500), fibronectin (Proteintech, 15613-1-AP, 1:200), α-SMA (Abcam, ab5694, 1:50), NLRP3 (Cell Signaling Technology, 15101, 1:200), caspase-1 (Abcam, ab1872, 1:25) or IL-1β (Cell Signaling Technology, 12242, 1:100). For PCNA, p-NF-κB and podocin, the percentage of a positively stained area over the whole glomerular area was calculated. For other antibodies, the micrographs were quantified blindly using Image-Pro Plus 6.0 software and were expressed as the ratio of integrated optical density to the whole area. Each renal section was counted for at least 10 images.
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5

Immunofluorescent Staining of Key Proteins

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Immunofluorescent staining was performed using primary antibodies targeting EGR1 (1:100 dilution; ThermoFisher, PA5-83115), MFGE8 (1:100 dilution; ThermoFisher, PA5-82036), MMP1 (1:100 dilution; Abcam, ab52631), α-smooth muscle actin (1:200 dilution; Abcam, ab5694), YAP (1:100 dilution; CellSignaling, 14074 S), and Perilipin-1 (1:100 dilution; Abcam, ab172907). The percentage of fluorescent area was quantified using custom a MATLAB image processing code written by the authors and previously published26 (link). All histology and immunofluorescent images shown are representative images of multiple experiments.
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6

Immunofluorescence and H&E Analysis of MPDOs

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For immunofluorescence and H&E analysis, MPDOs in collagen gel were embedded in OCT and sectioned into 25 μm, followed by fixation with 4% paraformaldehyde for 30 min. MPDOs in Matrigel were analyzed using whole mount staining without sectioning for subsequent staining. The following primary antibodies were used: anti-α-SMA (Abcam, ab5694, 1:200), anti-vimentin (Cell Signaling Technology, 5741S, 1:200), anti-ICAM-1 (Proteintech, 10020-1-AP, 1:200), anti-HMB-45 (Abcam, ab733, 1:200), anti-CD45 (CST, 13917S, 1:200), anti-CD3e (Proteintech, 60181-1-Ig, 1:200), anti-CD8a (Abcam, ab4055, 1:200), anti-CD14 (Proteintech, 17000-1-AP, 1:200), anti-CD11b (Novus Biologicals, NB110-89474, 1:200) and anti-PD-L1 (CST, 13684S, 1:200). The primary antibodies were incubated overnight at 4 °C and followed by secondary antibodies incubated with Alexa Fluor 488 (1:500 dilutions; CST), Alexa Fluor 555 (1:500 dilutions; CST) and Alexa Fluor 647 (1:500 dilutions; Invitrogen)-conjugated secondary antibodies for 1 h at room temperature. Nuclei were stained with DAPI (1:1000 dilutions; Invitrogen) for 15 min, and images were captured using a Zeiss LSM 710 Confocal microscopy.
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7

Protein Expression Profiling in Cells and Liver

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Cells and liver tissues were lysed with RIPA buffer (ATTO Corporation, Tokyo, Japan) and quantified using a BCA protein assay kit (Thermo Fisher Scientific, Waltham, MA, USA). Proteins were separated by SDS-PAGE and transferred to a polyvinylidene difluoride membrane. The membrane was incubated with 5% skim milk for blocking, and then washed with Tris-buffered saline, 0.1% Tween 20 (TBST). The membrane was incubated with primary antibodies against α-SMA (Abcam, ab5694), p-NFκB (Cell Signaling, 3033S), NFκB (Santa Cruz, sc-372), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) (Santa Cruz, sc-25778) overnight at 4 °C. Specific bands were visualized by a Chemi-luminescent Image Analyzer (ImageQuantTM LAS 4000, Fujifilm, Tokyo, Japan) and analyzed by Image J software.
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8

Protein Extraction and Western Blot Analysis

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Flash frozen livers were homogenized using TissueLyser (Qiagen) in RIPA buffer containing protease inhibitors (Thermoscientific Pierce complete protease and phosphatase inhibitors (ThermoFisher, A32963 and 78420), 1 tablet/10 ml RIPA buffer). Bradford protein quantification was performed (Biorad, 5000006) for liver lysates. LX2 cells were directly collected in 2x Laemmli buffer (Biorad, 1610737). 50 μg liver protein or 10μL of LX2 lysate were analyzed by SDS-PAGE and immunoblotting with antibodies to hNTRK3 (Biotechne, AF373), mNTRK3 (Biotechne AF1404), αSMA (Abcam, ab5694), pERK (Cell Signaling, 4370S) and CALNEXIN (Abcam, ab75801).
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9

Immunohistochemical Analysis of Lung Tissues

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Isolated lungs were fixed in 4% paraformaldehyde in PBS for 30 minutes at 4°C. Lungs were washed four times for 15 minutes with PBST (0.1% Triton X-100 in PBS) and then blocked with 5% goat serum and 0.1% BSA for one hour. Samples were then incubated with primary antibodies against αSMA (Sigma a5228, 1:400 or Abcam ab5694, 1:200), E-cadherin (Cell Signaling 3195, 1:200 or Invitrogen 13–1900, 1:200), fibronectin (Invitrogen PA5-29578, 1:200), Lef1 (Cell Signaling 2230, 1:200), Ki67 (Abcam a15580, 1:200), pMLC2 (Cell Signaling 3671, 1:200), RFP (Abcam ab62341, 1:400), Sox9 (Sigma AB5535, 1:1000), or Tbx3 (Invitrogen 42–4800, 1:200), followed by incubation with Alexa Fluor-conjugated secondary antibodies (1:400; Thermo Fisher Scientific A11007, A21244, A11012, A21240 and A11006) or Alexa Fluor-conjugated phalloidin (1:400, Thermo Fisher Scientific A12380 or A12379) and then counterstained with Hoechst (1:1000). Lungs were dehydrated in a methanol or isopropanol (for phalloidin-stained samples) series and cleared with Murray’s clear (1:2 ratio of benzyl alcohol to benzyl benzoate). Samples were imaged using a spinning disk confocal (BioVision X-Light V2) fitted to an inverted microscope.
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