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123 protocols using β actin

1

WK2-16 Compound Characterization in Cells

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The compound (E)-N-hydroxy-4-methoxy-2-(biphenyl-4-yl)cinnamide (WK2-16) was provided by Professor Wei-Jan Huang [56 (link)]. Dimethyl sulfoxide (DMSO), LPS and SRB were purchased from Sigma-Aldrich (St. Louis, MO, USA). The Iba1 antibody was obtained from Millipore (Temecula, CA). The GFAP antibody was purchased from ProSci Inc. (Poway, CA, USA). 4′,6′-Diamidino-2-phenylindole (DAPI) was obtained from AAT Bioquest, Inc. (Sunnyvale, CA, USA). HIGHDEF® IHC Fluoromount was purchased from Enzo Life Sciences (Farmingdale, NY, USA). β-actin, p-p65, p38, and mouse/rabbit IgG antibodies (DyLight 488) were purchased from GeneTex (Irvine, CA, USA). The acetyl-SMC3 antibody was obtained from MBL international (Woburn, MA, USA). The SMC antibody was purchased from Abcam (Cambridge, MA, USA). The COX-2 and p65 antibodies were purchased from Novus Biologicals (Littleton, CO, USA). The iNOS antibody was purchased from Santa Cruz (Dallas, TX, USA). The p-STAT-1, p-STAT-3, p-Akt, Akt, p-ERK, ERK, p-p38 antibodies were purchased from Cell Signaling (Beverly, MA, USA). The horseradish peroxidase (HRP)-conjugated anti-rabbit/mouse secondary antibodies were purchased from Jackson ImmunoResearch (West Grove, PA, USA).
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2

Immunoblotting Analysis of Protein Expression

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After transfection treatment, the protein expression of USP43 and β-actin was detected by immunoblotting; Primary antibody was incubated overnight at 4 °C; We used the gel imaging system to analyse the band density and compare it with the internal control. Primary antibodies included: USP43(GeneTex, Irvine, CA, USA), βactin(GeneTex), E-cadherin (Cell Signalling Technology, Danvers, MA, USA), Vimentin(Cell Signalling Technology).
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3

Protein Expression Analysis in Xenografts

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Western blotting was performed to analyse protein expression. The antibodies used were specific for EIF4A3 (1:1000; Abcam) and RhoU (1:500; Origene). GAPDH (1:6000, GeneTex) and β-actin (1:3000, GeneTex) were used as the controls. Protein bands were visualized using an enhanced chemiluminescence (ECL) chromogenic substrate (Beyotime, Shanghai, China) and assessed by Image-Lab analysis software (San Leandro, CA, USA).
Paraffin-block tissues of subcutaneous xenografts in mice were stained with haematoxylin and eosin (HE) and IHC, and subsequently evaluated by a pathologist blindly.
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4

Protein Kinase Inhibitor Assay

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Antibodies against PKC-α, JNK, VCAM-1, CD11b, and β-actin were purchased from GeneTex (Hsinchu, Taiwan). Antibodies against p-PKCα and p-JNK were purchased from Cell Signaling Technology (Danvers, MA, USA). 2′,7′-Bis(2-carboxyethyl)-5(6)-carboxyfluorescein tetrakis(acetoxymethyl) ester (BCECF-AM) and GF109203X, Gö6976 and SP600125 inhibitors were obtained from Sigma-Aldrich (St. Louis, MO, USA).
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5

Membrane Protein Extraction and Western Blotting

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Membrane proteins were extracted from LS174T cells using an s compartmental protein extraction kit (Chemicon Inc, Temecula, CA, USA). After the various treatments, LS174T cells were lysed with RIPA lysis buffer supplemented with protease and inhibitor for 30 min on ice followed by centrifugation at 4 °C. The amount of protein was measured by BCA assay (Thermo Fisher Scientific, Waltham, MA, USA) and an equal amount of protein lysates was electrophoresed on an 8–15% polyacrylamide gel at 100 volts for 2 h. The proteins were transferred to a polyvinylidene difluoride (PVDF) membrane (0.2 µm pore size) through wet blotting at 250 mAmp for 2 h (in cold room) (Biorad, Billerica, MA, USA). Blocking was performed using 5% BSA in 1x PBS-T (1X PBS 0.1% TWEEN-20) for 1 h at RT, and then the membrane was incubated with primary antibodies at 4 °C overnight. After that, a washing process was performed four times with 1x PBS-T, and the samples were incubated with secondary antibody HRP–goat–anti-rabbit/mouse (1:10,000) for 1 h at RT. Then, membranes were washed with 1X PBS-T and developed using a Femto chemiluminescent substrate (Thermo Scientific, Waltham, MA, USA) and the image analysis was carried out using ImageJ software. Antibodies for Western blotting, including GPX4 (GTX54095, 1:1000), β actin (GTX109639, 1:5000), were purchased from GeneTex, Irvine, CA, USA.
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6

Subcellular Fractionation and Immunoblotting

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Cells harvested in lysis buffer were resolved using SDS-PAGE and reacted with primary antibodies. A nuclear extraction kit (Panomics) was used for subcellular fractionation. The pS197-N and pan-N antibodies were generated as described previously (Wu et al., 2009 (link)). DDX1, lamin A/C, and β-actin antibodies were purchased from Genetex. The tubulin antibody was purchased from Sigma-Aldrich. Details are provided in the Supplemental Experimental Procedures.
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7

Immunoblot Analysis of Nr1d2 in HSCs

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For immunoblot analysis HSC lysate was resolved by a 4–20% gradient gel, transferred to a PVDF membrane (Bio-rad), and blotted with the appropriate primary antibody, anti-Nr1d2 (Abnova, Taiwan) followed by peroxidase-conjugated secondary antibody (GE Healthcare Life Sciences, Pittsburgh, PA, USA). Protein bands were visualized using enhanced chemiluminescence reagents (Thermo Fisher Scientific) and digitized using a CCD camera (LAS4000 mini; Fuji film, JAPAN). Expression intensity was quantified by Multi Gauge (Fuji). Protein load was verified using β-actin (GeneTex) antibody.
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8

Western Blot Analysis of Hedgehog Pathway

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Eca109 and Eca109R cells were lysed using RIPA lysis buffer (Beyotime Institute of Biotechnology) for 30 min at room temperature. Cells were centrifuged at 12,000 × g for 15 min at 4°C and the supernatant was collected. The BCA Protein Quantitative Assay kit (Servicebio) was used to determine the protein concentration. The samples were denatured by boiling prior to separation (35 µg per lane) using 10% SDS-PAGE followed by transfer to nitrocellulose membranes. Skimmed milk (5%) was used as a blocking agent for 1.5 h at room temperature. Next, the membranes were incubated on a shaker with the primary antibodies against Gli1 (1:2,000; cat. no. NBP2-45872; Novus Biologicals), Shh (1:5,000; cat. no. ab53281; Abcam), Smo (1:200; cat. no. GTX60154; GeneTex, Inc.), Ptch (1:500; cat. no. GTX83771; GeneTex, Inc.) and β-actin (1:5,000; cat. no. GTX629630; GeneTex, Inc.), overnight at 4°C, washed with Tris-buffered saline with 0.05% Tween-20, and incubated with secondary antibodies (1:4,000; cat. nos. 1031-05 and 4050-05; Southern Biotech) for 1 h at 37°C. Bands were detected using enhanced chemiluminescence substrate (Bio-Rad Laboratories, Inc.), and grayscale images were analyzed with ImageJ 15.0 software (National Institutes of Health). This procedure was performed three times.
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9

Oxaliplatin and CTSS Inhibitor Synthesis

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Oxaliplatin was purchased from Sanofi Pharmaceutical Company (NY, USA). The procedure for synthesizing the CTSS inhibitor RJW-58 was described previously 14 (link). The following primary antibodies were purchased: Cathepsin S (Thermo Fisher catalog: #PA5-81369), EBF (Santa Cruz, #sc-137065), ATF-3 (Biossua, #BS-0519R), α-tubulin (Sigma, MO, USA), IRF-1 (Bio-Rad, #VPA00801), CBP (GeneTex, #GTX101249), Iba1 (Abcam, #ab-5076), NeuN (Novus, #NBP2-10491), IL-10 (Abcam, #ab189392), STIM1 (Cell signaling (D88E10), #5668S), CD11b (Abcam, #ab52478), CD45 (BD Biosciences, #553079), STAT3 (BD, #50402), P-STAT3 (Cell signaling, #9145S), NFκB (Cell signaling, #4727S), OR5B3 (Abcam, #ab186624), OR5M3 (LSBio, #LS-C200406), and β-actin (GeneTex, #GTX109639). Horseradish-peroxidase-conjugated secondary antibodies were purchased from GeneTex (#GTX213110, #GTX213111, #GTX224125, and #GTX232040).
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10

Signaling Pathway Protein Analysis

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WISP-3, VEGF-C, ERK, p38, JNK, and β-actin antibodies were obtained from GeneTex (Hsinchu, Taiwan). The phosphorylated forms of ERK, p38, and JNK antibodies were bought from Cell Signaling (Danvers, MA, USA). ERK, p38, JNK, and control ON-TARGETplus siRNAs were purchased from Dharmacon (Lafayette, CO, USA). Taqman® One-Step PCR Master Mix and qPCR primers and probes were bought from Applied Biosystems (Foster City, CA, USA). Recombinant human WISP-3 was acquired from PeproTech (Rocky Hill, NJ, USA). All other chemicals not already mentioned were acquired from Sigma-Aldrich (St. Louis, MO, USA).
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