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19 protocols using wnt5a b

1

Protein Expression Analysis by SDS-PAGE

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Equal amount of protein was separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to polyvinylidene difluoride (PVDF) membranes. Bovine serum albumin (5%) or skimmed milk was performed to block membranes. Primary antibodies include Fzd2 and CD44 (1:5,000; Abcam); interleukin-6 (IL-6), Stat3, p-Stat3 (Tyr705), non-phospho β-catenin, E-cadherin, vimentin, Slug, Wnt5a/b, Yes-associated protein 1 (Yap1), TGF-β1, Smad3, and ABCG2 (1:1,000; Cell Signaling Technology, Boston, MA, USA); Wnt3, Col1a1, and Col6a1 (1:1,000; Abcam); Zeb1 (1:500; Sigma-Aldrich, St. Louis, MO, USA); and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (1:500; Proteintech, Chicago, IL, USA) were incubated with the membranes overnight. SuperSignal Chemiluminescent Substrates (Thermo Fisher Scientific) and imaging systems were used to analyze the results.
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2

Quantifying Wnt Pathway Proteins

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Total protein was isolated from CS-1 and SW1353 cells with 1 × RIPA lysis buffer (Upstate Biotechnology, Charlottesville, VA) supplemented with complete protease inhibitor cocktail tablets (Roche Applied Science, IN, USA). Protein concentrations were examined by Protein Assay Reagents (Bio-Rad, Hercules, USA). Equal amounts of denatured proteins were separated by NuPAGE® 4–12% Bis-Tris Gel (Life Technologies) and transferred onto a nitrocellulose membrane (Bio-Rad). After blocking in 5% non-fat milk for two hours, the membranes were incubated with specific primary antibodies WIF1 (Cell Signaling Technology, catalog number: 5652, 1:1000 dilution), Wnt5a/b (Cell Signaling Technology, catalog number: 2530, 1:1000 dilution), LRP6 (Cell Signaling Technology, catalog number: 3395, 1:1000 dilution), Dvl2 (Cell Signaling Technology, catalog number: 3224, 1:1000 dilution), and β-Actin (Sigma-Aldrich, dilution 1:2000) at 4 °C overnight. The membranes were further probed with respective secondary antibodies (LI-COR Biosciences, NE, USA), and scanned by Odyssey® CLx equipment (LI-COR Biosciences, NE, USA) to detect the bands and the density.
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3

Bone Morphogenetic Pathway Signaling Assay

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The Human Phospho-Kinase Array Kit and recombinant human BMP-2/ BMP-9 were purchased from R&D Systems (Minneapolis, MN, USA). The primary antibodies against anti-human Phospho-p53 (Ser6, 9, 15, 46, 392, and Thr81), Wnt5a/b, LRP6, Phospho-LRP6, Dvl2, Dvl3, Axin1, GSK3β, Phospho-GSK3β, PI3K, Phospho-PI3K, AKT, Phospho-AKT, MDM2, and β-actin were purchased from Cell Signaling Technology (Danvers, MA, USA). The iScript cDNA Synthesis Kit was purchased from Bio-Rad Laboratories, Inc. (Hercules, CA, USA). All primers and probes (RUNX2 #Hs00231692_m1; ALPL #Hs010291444_m1; BGLAP #Hs01587814_g1; NOG #Hs00271352_s1; GAPDH #Hs99999905-m1) were purchased from Applied Biosystems, Inc. (Bedford, MA, USA). Moreover, the TaqMan MicroRNA Reverse Transcription Kit and TaqMan Universal Master mix were from Applied Biosystems, Inc.
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4

Signaling Pathway Antibody Analysis

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Cell Signaling Technology antibodies used: Wnt5a/b (#2530), Snail (#3879), Slug (#9585), ZEB1 (#3396), LKB1 (#3047), P-ACC S79 (#3661), Total ACC (#4190), Axin2 (#2151), MARK2 (#9118), MARK3 (#9311), AMPKalpha (#2532), P-ULK1 S555 (#5869), Nuak1 (#4458), SIK2 (#6919), GST (#2622), myc-tag (#2272), P-Src family Y416 (#2113), Src (#2109), P-Paxillin Y118 (#2541), Pathscan I for P-ERK1/2 and P-Akt S473 (#5301), Total ERK1/2 (#4695), P-S6K (#9234), HA-tag (#3724), P-MEK1/2 (#9154), P-p90RSK S380 (#11989), P-FAK Y925 (#3284). Epitomics antibodies used: Phospho-FAK Y397 (#2211-1), Phospho-FAK Y576/577 (#2183-1), Total FAK1 (#2146-1), Zyxin (#3586-1). BD Transduction Labs antibodies used: Paxillin (P13520). Sigma antibodies used: Actin (A5441), Flag polyclonal (F7425). Protein Tech antibodies used: MARK1 (21552-1-AP), MARK2 (15492-1-AP). Millipore antibodies used: ZEB2 (ABT332), MARK4 (07-699). Abcam antibodies used Twist (ab50887), IRSp53 (ab15697). CLASP2 antibody was from Santa Cruz Biotechnology (sc-98440). DIXDC1 total antibody was from R&D Systems (AF5599). Phospho-DIXDC1 S592 was developed in collaboration with Antony Wood at Cell Signaling Technologies (CST, Danvers, MA).
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5

Quantitative Protein Expression Analysis

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Primary antibodies N-cadherin, E-cadherin, Vimentin, β-catenin, p-GSK3β (S9), Dvl-2, Wnt5a/b, Notch1, CD44, p-Akt (ser473), Snail, and actin were purchased from Cell Signaling Technology (CST; Danvers, MA). CD44, CD133, and CD24 antibodies were purchased from Biolegend (BioLegend, Inc., San Diego, USA). Secondary Alexa 488-conjugated antibody and HRP conjugated antibody were purchased from CST.
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6

Western Blot Analysis of Signaling Proteins

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Cells for western blotting were cultured in RPMI 1640 medium with 10% FBS for 24 h. Protein expression was detected with rabbit antibodies: p62/IMP2, β-catenin, Wnt3a, Wnt 5a/b, GSK3β, Snail, N-cadherin, and GAPDH (Cell Signaling Technology, Danvers, MA, USA); and mouse antibodies: E-cadherin (Cell Signaling Technology, Danvers, MA, USA). Primary antibodies were detected with goat anti-mouse IgG (HPR conjugate) or anti-rabbit IgG (HPR conjugate). The membranes were finally scanned by Invitrogen iBright Imaging System (Thermo Fisher Scientific, Waltham, MA, USA).
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7

Immunoblotting Analysis of Cell Signaling Proteins

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Cells were harvested and lysed in RIPA buffer and the concentration was determined by Coomassie Plus Protein Assay (Thermo Scientific, Catlog#1856210). Whole cell protein extracts were resolved on SDS-PAGE, and proteins were transferred into nitrocellulose membranes. After blocking in 5% milk in PBS+0.1% Tween-20 for 1 hour at room temperature, targeted proteins were detected by incubating with primary antibodies at 4 °C overnight. AR 441, 1:1000 dilution (Santa Cruz Biotechnology, Santa Cruz, CA. Catelog#22616); Wnt5a/b, 1:1000 dilution (Cell Signaling Technology, Catalog # 2530s); FZD2 (R&D, Catalog# MAB1307–050); Tubulin 1:5000 dilution from Sigma-Aldrich (Catalog#T5168), GAPDH (. Tubulin or GAPDH was used as loading control. Following secondary antibody incubation, immunoreactive proteins were visualized by applying Immobilon Crescendo Western HRP substrate (Millipore, Catalog#WBLUR0500).
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8

β-catenin and GPC5 Expression Analysis

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As previous described, the expression alteration of β-catenin and GPC5 was both detected by Immunofluorescence [12 (link)] and western blot [6 (link)]. The β-catenin was labelled with fluorescein isothiocyanate (FITC) and the GPC5 was labeled with tetramethyl rhodamine isothiocyanate (TRITC). WNT/β-catenin signaling pathway-related proteins (wnt3a, wnt5a/b, cyclinD1, MMP2, MMP7, MMP9, E-cadherin, β-catenin) and internal control proteins (LaminB, β-actin, Gapdh) antibodies were purchased from Cell Signaling Technology, Inc. (Beverly, MA, USA). Protein density on scanned western blots was analyzed using Image J 1.44 software, and we performed semi-quantitative analysis for the results of the western blot analysis.
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9

Molecular Signaling Pathways in Metabolic Regulation

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VAT and/or liver lysates were probed for MCP-1, matrix metalloproteinase-12 (MMP12), phospho-P42/44 mitogen-activated protein kinase (MAPK), total- P42/44 MAPK, CCAAT/enhancer binding protein α (C/EBPα), peroxisome proliferator-activated receptor gamma (PPARγ), dishevelled segment polarity protein 3 (DVL3), Axin1, wingless-type MMTV integration site family, member 3A (Wnt3A) and Wnt5A/B. The antibodies for these proteins were obtained from Cell Signaling Tech. The lysates were also probed for anti-cluster of differentiation 68 (CD68, Abcam), glyceraldehyde 3-phosphate dehydrogenase (GAPDH, Millipore), and fatty acid binding protein 4 (FABP4) and plasminogen activator inhibitor-1 (PAI1) from Santa Cruz Biotech.
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10

Immunoblotting Workflow for Protein Analysis

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Immunoblotting was performed as described (38 (link)). Briefly, proteins were extracted from cultured cells or homogenized frozen tumor bits using a TissueRuptor (Qiagen, Cat No./ID: 9002755) on ice using RIPA buffer. Protein extraction from 3D/organoid cultures started with digestion of the Matrigel matrix using Cell Recovery Solution (DLW354253, Sigma) for 1 hour on ice. After digestion with Cell Recovery Solution, cells were centrifuged and RIPA buffer was added into the pellets for protein extraction. Antibodies against the following proteins (and clone or catalogue number) were from Cell Signaling: ROR1 (D6T8C), ROR2 (D3B6F), Non-phospho (Active) β-Catenin (Ser45) (D2U8Y), LEF1 (C12A5), Wnt5a/b (C27E8), Dvl2 (30D2), Axl (C89E7), Integrin β2 (D4N5Z), IGFBP3 (D1U9C), YAP/TAZ (D24E4), Phospho-YAP (Ser127) (D9W2I), MST1 (#3682), MST2 (#3952), MOB1 (E1N9D), Phospho-MOB1 (Thr35) (D2F10), LATS1 (C66B5), Phospho-LATS1 (Ser909) (#9157), SAV1 (D6M6X), Phospho-MST1 (Thr183)/MST2 (Thr180) (E7U1D), Merlin (D3S3W), Lamin B2 (D8P3U), Survivin (71G4B7), Phospho-Merlin (Ser518) (D5A4I), Tubulin (#2148). Additional antibodies were against Kif26B (Proteintech, 17422–1-AP), β-Actin (Santa Cruz), GAPDH (Abcam Ab-9485), and Vinculin (Sigma V9131). The primary antibodies were incubated overnight. Gels shown are representative of at least three independent experiments.
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