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9 protocols using igf2bp2

1

Western Blot Analysis of Breast Cancer Proteins

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Total proteins from human breast cancer cells were extracted using RIPA buffer (P0013C, Beyotime, China) containing 1% phosphatase inhibitor, 1% PMSF and 0.1% protease inhibitor. Total proteins were separated using 10% sodium dodecyl sulfate‐polyacrylamidegel electrophoresis (SDS‐PAGE) and transferred to PVDF (polyvinylidene fluoride) membranes (Millipore, USA). The membranes were placed in Tris‐buffered saline containing 0.1% Tween 20 (TBST) and 5% bovine serum albumin (BSA) for 2 h before the primary antibody was placed and left overnight at 4 °C. The primary antibody stock solution used was shown below. IGF2BP2 (1:1000, Abcam, UK, ab128175), GAPDH (1:1000, Beyotime, China, AF1186), CDK6 (1:1000, Protein‐tech, China, 14052‐1‐AP), EIF4A1 (1:500, Abcam, UK, ab31217), TET1 (1:1000, Affinity, USA, DF6428), TET2 (1:1000, Affinity, USA, DF12089), TET3 (1:1000, Affinity, USA, DF13335), CDK4 (1:1000, Protein‐tech, China, 11026‐1‐AP), CCND1 (1:1000, Protein‐tech, China, 26939‐1‐AP), pRb (1:500, Affinity, USA, AF0030). PVDF membranes were washed three times with TBST and incubated with secondary antibody (1:5000, Cell Signaling Technology, USA, 7074P2) for 2 h at room temperature. Immobilob Western Chemiluminescent HRP Substrate (Millipore, USA) was used to detect the expression level of the target protein.
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2

Protein Expression Analysis Protocol

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Total protein was obtained from cell samples with the RIPA buffer (Beyotime, China) supplemented with protease inhibitor cocktail tablet (Roche, Switzerland). Western blot was carried out with rabbit antibodies targeting IGF2BP2 (1:5000, Abcam, UK), cyclinD1 (1:1000, Abways, china), AKT (1:1000, Abways, china), p-AKT (1:1000, Abways, china), and GAPDH (1:5000, ZENbio, China) antibodies. HRP-conjugated IgG (1:5000, Beyotime, China) was utilized as secondary antibodies. The ECL-Plus reagent (Millipore, USA) was utilized for development. GAPDH was used for normalization.
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3

Exosome and Liver Tissue Protein Analysis

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Exosome, cell, and liver tissue protein concentrations were measured with the Bradford assay. Proteins were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and then transferred to polyvinylidine difluoride (PVDF) membranes. Membranes were incubated with primary antibodies at 4°C overnight in a buffer containing 5% skim milk, and then with a horseradish peroxidase (HRP)-conjugated secondary antibody at 37°C for 2 h. For exosome validation, primary antibodies against TSG101 (1:1000), CD9 (1:1000), MHC-1 (1:1000), and Cytochrome C (1:1000) were purchased from Abcam (Cambridge, UK). For cell migration and invasion assays, primary antibodies against CXCR4(1:500) and MMP-9 (1:500) were purchased from Boster (Wuhan, China). For liver pre-metastatic niche formation assays, primary antibodies against CD11b (1:1000), S100A8(1:1000), and S100A9 (1:1000) were purchased from Santa Cruz (CA, USA). For MS-identified candidates, primary antibodies against FRA2 (1:1000), IGF2BP2 (1:1000), and S100A11 (1:1000) were purchased from Abcam (Cambridge, UK). Selenium binding protein 1(SBP1, 1:500), CKAP4 (1:500), and aldolase C (ALDOC,1:500) were purchased from Bioss(Beijing, China). Protein-band densities were analyzed quantitatively using ImageJ software (NIH, USA).
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4

Western Blot Analysis of Protein Expression

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The cells were harvested and washed 3 times with ice cold PBS and lysed with RIPA buffer (cat. no. 20-188; Sigma-Aldrich; Merck KGaA). The protein was quantified using the BCA kit (Beyotime Institute of Biotechnology), according to the manufacturer's protocol. Equal amounts of protein (40 µg/lane) were separated using 12% SDS-PAGE, then transferred onto a PVF membrane and blocked with 5% skimmed milk for 1 h at room temperature. The membranes were subsequently incubated with the primary antibodies overnight at 4°C, washed with 0.1% TBS-Tween-20, then incubated with the donkey anti mouse/rabbit secondary antibody (1:10,000; cat. no. 5724; KPL, Inc.) for 1 h at room temperature. The target proteins were detected using an ECL (EMD Millipore) kit. The following primary antibodies were used: HOXB-AS3 (1:1,000; cat. no. SBSN250; Genscript), β-actin (cat. no. 3700; 1:1,000; Cell Signaling Technology, Inc.), IGF2BP2 (cat. no. ab109284; 1:1,000; Abcam), and c-Myc (cat. no. ab32072; 1:1,000; Abcam).
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5

Western Blot Analysis of Protein Expression

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Total protein (25 μg) from each sample was separated by 12% SDS-PAGE gel. The protein was transferred onto a PVDF membrane (Millipore, Billerica, MA, USA). The primary antibodies ERK (1:400; Abcam, Cambridge, MA, USA), pERK (1:200; Santa Cruz Biotechnologies, Santa Cruz, CA, USA), PI3K (1:500; Abcam), pPI3K (1:400; Cell Signaling Technology, Danvers, MA, USA), Akt (1:300; Santa Cruz), pAkt (1:200; Cell Signaling Technology), IGF2BP2 (1:400; Abcam), and β-actin (1:1,000; Abcam) were used to incubate with the membrane at 4°C overnight. After incubation with the HRP-conjugated secondary antibody (1:2,000) for 1 h at room temperature, proteins were analyzed with an ECL kit (Millipore) and analyzed with a UV transilluminator (Bio-Rad, Hercules, CA, USA).
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6

Quantification of Recombinant Protein by Western Blot

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A serial dilution of purified recombinant protein was used for western blot to generate the standard curve. The mass of interest protein in a known number of cells was quantitated from the standard curve. Western blot signal intensities were quantified using the ImageJ program. The protein molecular weight was calculated by Protein Molecular Weight Calculator from the following website (http://endmemo.com/bio/promw.php). Purified recombinant RIG-I and IGF2BP2 proteins were from Abcam, and IGF2BP1 and IGF2BP3 proteins were from RayBiotech.
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7

Immunofluorescence and Immunohistochemistry Assays of ccRCC Cells

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To perform an immunofluorescence assay, ccRCC cells were grown on a μ‐Slide 8 Well (iBiDi, Martin Reid, Germany) culture plate and incubated with antibodies specific to IGF2BP2 (Millipore, MA, USA) overnight at 4°C. Further, the cells were stained using DAPI (300 nmol/L) and IgG antibody (Alexa Fluor 488, 1:400). For immunohistochemistry assay, paraffin sections were dewaxed and hydrated, following which they were incubated with the corresponding antibody overnight at 4°C. Subsequently, the sections were stained using haematoxylin and DAB. The antibodies used for immunohistochemical experiments were as follows: Ki67 (1:500, Servicebio, Wuhan, China), SERPINH1 (1:100, SAB, Maryland, USA), IGF2BP2 (1:200, Abcam, Cambridge, UK), SLUG (1:100, SAB, Maryland, USA) and SNAIL (1:200, Bioss, Beijing, China).
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8

RIP Assay for RNA-Binding Proteins

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RIP assay was carried out using the Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore) as the manufacturer’s instructions. Briefly, cell lysates were incubated with magnetic beads coated with normal IgG (Millipore), RBM15 (Abcam), METTL5 (Proteintech), IGF2BP1 (Abcam), IGF2BP2 (Abcam), IGF2BP3 (Abcam), METTL3 (Cell Signaling Technology), WTAP (Abcam), YBX1 (Abcam) or GFP (Abcam). The RNA-protein complexes were washed and purified and then subjected to RNA extraction by TRIzol. The UBA6 mRNA enriched by indicated antibody was determined by qRT-PCR. MS2-RIP was performed as previous study described [22 (link)].
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9

m6A Transcriptome Immunoprecipitation Analysis

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RIP assays were performed by Imprint ® RNA Immunoprecipitation (RIP) Kit (Sigma, USA) as the manufacturer's protocol. The immunoprecipitation antibodies of m 6 A, IGF2BP2 and IGF2BP3 were obtained from Abcam as shown in Table S2. mRNA expression was detected as described before.
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