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11 protocols using nedd4l

1

Lung Fibroblast Cell Culture Protocol

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Human lung fibroblast cell lines (Mrc5 and IMR90) were purchased from ATCC (Manassas, VA). Human primary lung fibroblasts (HLF) and lung myofibroblasts (IPF-LF) from adult normal human subjects and IPF patients were obtained from the Center for Organ Recovery and Education and Lung Transplantation at the University of Pittsburgh. The study was approved by the institutional Review Board at the University of Pittsburgh (STUDY18100070). Cells were cultured in Eagle’s Minimum Essential Medium (EMEM) containing 10% fetal bovine serum (FBS) in 5% CO2 cell culture incubator. V5 antibody, mammalian expressional plasmid pcDNA3.1/His-V5-topo, and Escherichia coli Top10 competent cells were purchased from Life technologies (Grand Island, NY). Nedd4L, TβRII, collagen I, ubiquitin, smurf1, Smad4, p-Smad2/3, and Smad2/3 antibodies were purchased from Cell Signaling (Danvers, MA). Fibronectin (FN), alpha-smooth muscle actin (α-SMA), E2F4 antibodies, immobilized protein A/G beads, and control IgG were purchased from Santa Cruz Biotechnology (Santa Cruz, CA). HLM006474, bleomycin, and β-actin antibody were purchased from Sigma (St. Louis, MO). Human recombinant TGF-β1 was purchased from R&D systems (Minneapolis, MN). All materials used in the experiments are the highest grade commercially available.
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2

Western Blot and Immunoprecipitation Analysis

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Western blot and immunoprecipitation analysis were performed as described previously [13 (link)]. The antibodies for GAPDH (sc-47724; 1 : 1000), p62 (sc-101542; 1 : 1000), anti-LC3 (sc-398822; 1 : 1000), and individual secondary antibodies were purchased from Santa Cruz (Santa Cruz Biotechnology, Santa Cruz, CA). The antibodies for ATG5 (#12994; 1 : 1000), ATG13 (#13468; 1 : 1000), ULK1 (#8054; 1 : 1000), and NEDD4L (#4013; 1 : 1000) were all obtained from Cell Signaling Technology (Cell Signaling Technology Inc., Beverly, USA).
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3

SNAP-LGR5 and SNAP-FZD5 Colocalization

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HEK293T cells were grown on laminin‐coated glass coverslips. Cells were co‐transfected with 100 ng SNAP‐LGR5 or SNAP‐FZD5 and 150 ng myc‐NEDD4, HA‐NEDD4‐CS, myc‐NEDD4L, HA‐NEDD4L‐CA or pcDNA4 as a control with Fugene according to the manufacturer's instructions. After 24 h of transfection, cells were labelled with 1 μM SNAP‐Surface Alexa 488 (NEB) for 15 min at 4°C to block endocytosis. Cells were then immediately washed with fresh RPMI media and fixed in 4% paraformaldehyde. Cells were incubated with primary antibodies NEDD4 (Santa Cruz) or NEDD4L (Cell Signaling) for 1 h at RT followed by a secondary antibody conjugated to Alexa‐568 (Invitrogen) and DAPI (Sigma) in 2% BSA‐PBS (Roche). Cells were mounted in Prolong Diamond (Life technologies) and imaged using a DeltaVision Core system.
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4

Multimodal Protein Analysis Protocol

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β‐catenin (610154, BD), caspase‐3 (9661L, Cell Signalling), Cyclin D1 (2978S, Cell Signalling), DVL2 (10B5) (sc‐8026, Santa Cruz), GAPDH (sc‐47724, Santa Cruz), Flag (F3165, SIGMA), HA (Y‐11) (sc‐7392, Santa Cruz), LGR4 (C‐12) (sc‐390630, Santa Cruz), Lysozyme (A0099, Dako), c‐Myc (9E10) (sc‐40, Santa Cruz), NEDD4 (sc‐25508, Santa Cruz), NEDD4L (4013S, Cell Signalling), SNAP (P9310S, NEB), Sox9 (AB5335, Millipore) and V5 (ab27671) were used in immunohistochemistry, immunoprecipitations or Western blot analysis.
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5

RhoA Activation Assay and Immunoblotting

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Cycloheximide was purchased from Beyotime Biotechnology (Hangzhou, China). MG132 was purchased from Sigma-Aldrich (USA). Rhodamine phalloidin was purchased from Cytoskeleton (USA). A G-LISA RhoA Activation Assay Biochem Kit was purchased from Cytoskeleton. Antibodies against AAMP (used for western blot [WB]) and RhoA (used for WB and IHC staining) were purchased from Acbam. Antibodies against β-actin, p-ERM, N-cadherin, E-cadherin, Snail, Ubiquitin, NEDD4, NEDD4L, and SMURF2 were obtained from Cell Signal Technology. Antibody against AAMP (used for IHC staining) was obtained from GeneTex. Antibody against RhoA (used for IP) was purchased from Santa Cruz Biotechnology.
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6

Murine Lung Epithelial Cell Culture

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Murine lung epithelial (MLE12) cells (from ATCC) were cultured with HITES medium containing 10% fetal bovine serum (FBS) and antibiotics at 37 °C in 5% CO2. Primary culture of human bronchial cells (HBEpCs) (from Lonza, Baltimore, MD) was conducted using medium supplemented with growth factors provided by Lonza. V5 antibody, mammalian expressional plasmid pcDNA3.1-His-V5-topo, and Escherichia coli Top10 competent cells were from Life technologies (Grand Island, NY). P-p38 MAPK, p38 MAPK, p-IκB, Nedd4L, HA tag, and ubiquitin antibodies were from Cell Signaling (Danvers, MA). LPA1 and LPA2 antibodies were from LifeSpan BioScience, Inc. (Seattle, WA). Cycloheximide (CHX, 3-[2-(3,5-Dimethyl-2-oxocyclohexyl)-2-hydroxyethyl]glutarimide), leupeptin (Acetyl-Leu-Leu-Arg-al), lipopolysaccharide (LPS), β-actin and myc tag antibodies were from Sigma (St. Louis, MO). MG-132 (Z-L-Leu-D-Leu-L-Leu-al) and bafilomycin A1 (C35H58O9) were from EMD Chemicals (Philadelphia, PA). Immunobilized protein A&G beads, control IgG, p-Erk1&2, Erk1&2, and USP11 antibodies were from Santa Cruz Biotechnology (Santa Cruz, CA). All materials in highest grades used in the experiments are commercially available.
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7

Western Blot Analysis of Bladder Proteins

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For western blotting, total protein was extracted from mouse bladders and clinical specimens using RIPA lysis buffer (Beyotime, Shanghai, China), and protein concentrations were measured using a Bio-Rad DC Protein Assay Kit (Bio-Rad, Hercules, CA, USA). Fifty micrograms of protein was then loaded onto SDS-PAGE gels and separated before being transferred to PVDF membranes (Merck Millipore, Darmstadt, Germany). After being blocked with 5% bovine serum albumin dissolved in Tris-buffered saline for 2 h, the membranes were incubated with primary antibodies to the following proteins overnight at 4 °C: IL-6 (GeneTex, San Antonio, TX, USA,GTX110527, 1:1000), TNF-α (GeneTex, GTX110520, 1:1000), HCN1 (Abcam, Cambridge, UK, ab84816, 1:1000), HCN2 (Abcam, ab65704, 1:1000), HCN3 (Abcam, ab84818, 1:1000), HCN4 (Abcam, ab69054, 1:1000), Filamin A (Cell Signaling Technology, Beverly, MA, USA, 4762, 1:1000), NEDD4L (Cell Signaling Technology, 4013, 1:1000), α-tubulin (Beyotime, AT819, 1:1000) and GAPDH (Beyotime, AG019, 1:1000). Horseradish peroxidase-conjugated species-specific secondary antibodies (Zhongshan Co., Beijing, China, ZB-2301, ZB-2305, 1:5000) were used to detect the above primary antibodies. The proteins were visualized using ECL Substrate (Millipore, Billerica, MA, USA) and detected using an Image Quant LAS-4000 BioImaging System (GE Healthcare, Stockholm, Sweden).
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8

Western Blot Analysis of Mitochondrial Proteins

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Total proteins or mitochondrial proteins were isolated, separated and transferred onto polyvinylidene fluoride membranes (Millipore, Boston, USA). The membranes were incubated overnight with primary antibodies. The primary antibodies and their respective dilutions were NEDD4L, p-AMPK, AMPK, DRP-1, and HSP60 (all with a dilution ratio of 1:1000, Cell Signaling Technology, Danvers, USA), CaMKKβ and MFN-2 (1:1000 dilution, Abcam, Cambridge, UK), and phospho-DRP1 (Ser616) (1:1000 dilution, Biorbyt, Cambridge, UK). Following this procedure, the sections were incubated with secondary anti-mouse/rabbit antibodies (Sungene Biotech, Tianjin, China). The protein bands were subsequently visualized using ECL Blotting Detection Reagents (Invigentech, California, USA). The final quantification of these blots was achieved using densitometry via the application of ImageJ software.
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9

Quantitative Protein Analysis by BCA-SDS-PAGE

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For each group of proteins quantified by bicinchoninic acid (BCA), sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was performed at 50 μg/well. After electrophoresis, the cells were transferred to the polyvinylidene fluoride (PVDF) membrane under a constant pressure of 60 V for 180 minutes. The blocking solution was blocked for 1 hour and reacted with the primary antibody overnight at 4 °C. Tris-Buffered Saline Tween-20 (TBST) was washed three times; horseradish peroxidase (HRP)-labeled goat anti-rabbit antibody was reacted at room temperature for 1 h, and TBST was washed 4 times; electrogenerated chemiluminescence (ECL) was added, exposed on X-ray film, film development, fixing, washing with water, drying, storage and photographing. NEDD4L, MEK, ERK, phospho-MEK, phospho-ERK, ERBB3, p62, LC3, ULK1, ACTB (β-actin) antibodies were purchased from Cell Signaling Technology (Denver, Massachusetts, USA). Horseradish peroxidase (HRP) labeled secondary antibody and ECL kit were purchased from Pierce (Thermo Fisher Scientific, Inc.).
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10

Antibodies for Intracellular Signaling Pathways

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Antibodies for phospho‐ERK1/2 (#4370S), phospho‐JNK (#9251S), phospho‐p38 (#4511S), phospho‐p65 (NF‐κB) (#3033 s), ERK1/2 (#4696), JNK (#9251 s), p38 (#8690), NF‐κB p65 (#8242), and NEDD4L (#4013) were from Cell Signaling Technology (Cell Signaling Technology, Beverly, MA). Antibodies for TRAF2 (#5525–1), MEKK3 (#1673–1), and MEKK5 (#1772–1) were from Epitomics (Epitomics, Burlingame, CA). Antibodies for TAK1 (SC‐7967), MEKK2 (SC‐1088), TRAF3 (SC‐949), and TRAF6 (SC‐7221) were obtained from Santa Cruz Biotechnology (Santa Cruz Biotechnology, Santa Cruz, CA). Phospho‐MEKK2 Ser520‐specific antibody was prepared in Abmart (Shanghai, China). Human or mouse IL‐17A/F (human IL‐17, #200–17; Murine IL‐17A, #210–17; human IL‐17F, #200–25; and murine IL‐17F, #210‐17F) were purchased from PeproTech (PeproTech, Rocky Hill, NJ). E1, UBCH5b, and ubiquitin recombinant proteins were gifts from Prof. Zongping Xia (Zhejiang University).
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