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5 protocols using hpa020352

1

Far-Western Blotting of eIF3 Complex

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Far-Western blotting was performed by referring to a published literature51 (link) with minor modifications. The eIF3 protein complex (30 μg) in rabbit reticulocytes (P1318, BioVision) was separated by a 10% SDS-PAGE and transferred to PVDF membrane. An equal amount of BSA was also loaded as a negative control. The gel was first stained with coomassie blue to ensure the proteins had been successfully transferred and then washed by wash buffer (5% ethanol and 10% acetic acid in ddH2O) to remove the dye. Afterward, the proteins on the membrane were denatured and renatured in AC buffer (100 mM NaCl, 20 mM Tris-HCl pH 7.6, 0.5 mM EDTA, 10% glycerol, 0.1% Tween-20, 2% non-fat milk and 1 mM DTT) by gradually reducing the guanidine-HCl concentration. After blocking the membrane with 5% non-fat milk in 1 × PBST buffer at RT for 1 h, the membrane was incubated with 1 μg/ml recombinant METTL16 protein (81085, Active Motif) at 4°C overnight. After that, the membrane was washed with 1 × PBST buffer to remove the unbound protein and incubated with anti-METTL16 antibody (1:1000, HPA020352, Millipore Sigma) in the PBST buffer containing 3% milk at RT for 1h. Finally, the HRP conjugated goat anti-rabbit secondary antibody (1:5000, ab6721, Abcam) was incubated for another 1h and chemiluminescent detection was performed.
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2

Immunohistochemical Analysis of METTL16, eIF3a, and eIF3b

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The mice were euthanized by CO2 inhalation and portions of the indicated organs or tumors were employed to paraffin embedding and H&E staining. IHC staining was performed according to standard protocols. Briefly, the samples were deparaffinized, rehydrated through an ethanol series followed by antigen retrieval with sodium citrate or tris–EDTA buffer according to antibody manufacturer’s instruction. Sections were blocked with 10% FBS in PBS for 60 min at room temperature and were incubated with 3% H2O2 in methanol for 10 min at room temperature to block endogenous peroxidase and then incubated with anti-METTL16 (1:250, HPA020352, Millipore Sigma), anti-eIF3a antibody (1:200; ab86146, Abcam) or anti-eIF3b antibody (1:200; sc-137214, Santa Cruz Biotechnology). IHC staining was performed with horseradish peroxidase (HRP) conjugates using DAB (550,880, Biosciences) detection. All the slides were captured by a Widefield Zeiss Observer 7 microscope.
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3

Immunofluorescence staining of RNA methylation proteins

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The cells were seeded onto the sterile slides and placed in the 6 well plates with the cell density of 1 × 105 cells per well. After incubation for 24h, the cells were gently rinsed by phosphate-buffered saline (PBS) 3 times followed by fixed with 4% paraformaldehyde for 15min. Then, the cells were washed with PBS three times followed by permeabilized by 0.1% Triton X-100 in PBS for 15 min. To block the nonspecific binding, the cells were incubated with 2% bovine serum albumin (BSA) in PBS for 1h. The cells were subsequently incubated with primary antibodies against METTL16 (1:100, HPA020352, Sigma-Aldrich), METTL3 (1:100, ab195352, Abcam), METTL 14 (1:100, HPA038002, Sigma-Aldrich) and SC35 (1:500, ab11826, Abcam) overnight at 4°C, respectively. After washing with PBS three times, the corresponding fluorescence-labeled secondary antibodies (1:200, goat anti-rabbit IgG(H+L) Alexa Fluor 555: 4413S, Cell Signaling Technology; 1:200, goat anti-mouse IgG(H+L) Alexa Fluor 488: 4408S, Cell Signaling Technology) were applied to stain the cells and kept incubating for 1h. The nuclei were counterstained by mounting the cells in DAPI (F6057, Sigma-Aldrich). The immunofluorescent signals were photographed by a confocal laser scanning microscope (CLSM) (Carl Zeiss LSM 880).
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Proximity Ligation Assay for Protein Interactions

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HepG2 cells were seeded on an 8-well chamber slide (154534, Thermo Fisher Scientific). After three washes with PBS, the cells were fixed with 4% paraformaldehyde for 15 min at room temperature. Then, the cells were incubated with 1 × Permeabilization Buffer (00-8333-56, Thermo Fisher Scientific) for 15 min, followed by blocked with Duolink block solution for 1 h at room temperature and incubated overnight at 4 °C with the following antibodies: (1) mouse anti-Flag (F3165, Sigma-Aldrich) and rabbit anti-eIF3a (ab86146, Abcam); (2) rabbit anti-METTL16 (HPA020352, Sigma-Aldrich) and mouse anti-eIF3b (sc-137214, Santa Cruz Biotechnology). The next day, cells were washed twice with a large volume of PBS and incubated in PLA probes (DUO92002 and DUO92004, Sigma-Aldrich) for 1 h at 37 °C. Then, the cells were washed with 1 × Duolink for two times In Situ Wash Buffer A (DUO82049, Sigma-Aldrich) and incubated with ligation mix at 37 °C for 30 min. Subsequently, the cells were washed with 1 × Duolink In situ Wash Buffer A twice and incubated with amplification mix (DUO92008, Sigma-Aldrich) at 37 °C for 100 min. Finally, the cells were washed twice with 1 × Duolink in situ wash buffer B, washed once with 0.01 × Buffer B and mounted with Duolink in situ mounting medium with DAPI (DUO82040, Sigma-Aldrich). The pictures were captured under LSM 880 confocal microscope (Zeiss, Germany).
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5

Visualizing METTL Enzymes and m6A RNA in Embryonic Hearts

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Cryo-sections (10 µm) of whole embryonic hearts (at stage e15) were stained with primary antibody: anti-METTL3 (A8370; AB Clonal); anti-METTL14 (A8530; AB Clonal); anti-METTL16 (HPA 020352; Sigma-Aldrich); anti-α-actinin (A7811; Sigma-Aldrich); anti-N6-methyladenosine (202111; Synaptic System), to visualize the distribution pattern of METTLs or m6A in RNAs. For image acquisition, we used the tile-scanning mode and the following objective: HCX PL APO lambda blue 20.0 × 0.7 IMM UV (Leica Microsystems) or HCX PL APO, 63×, NA = 1.4. Scanning was performed at a resolution of 1024 × 1024 pixels, 200 Hz, and for image reconstruction, we used the auto-stitched tile-scanning mode involving the smooth-scanning mode with a slow/fine speed accuracy (set in the Leica LAS AF software connected to the Leica SP5 microscope).
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