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22 protocols using anti fto

1

Quantitative Protein Analysis in Cell Lines

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Total proteins were harvested from tissue and cell lines lysates using M-PER protein extraction reagent (Thermo Fisher, USA) respectively supplemented with proteinase and phosphatase inhibitors (Sigma, USA) according to standard protocol. Protein concentrations were determined using the BCA method followed by standard western immunoblotting of proteins using different primary antibodies: Anti-METTL3 (#195352, abcam, USA), Anti-METTL14 (#HPA038002, Sigma, USA), Anti-FTO (#ab124892, abcam, USA), Anti-P21 (#ab109199, abcam, USA), Anti-Phospho-AKT (#9271, Cell Signaling, USA), Anti-AKT (#9272, Cell Signaling, USA), Anti-Phospho ATM (#4526, Cell Signaling, USA), Anti-ATM (#2873, Cell Signaling, USA), Anti-Phospho-IR/IGF1R (#3021, Cell Signaling, USA), Anti-IGF1Rβ (#9750, Cell Signaling, USA), Anti-IRβ (#3025, Cell Signaling, USA), Anti-PDX1 (#5579, Cell Signaling, USA), Anti-Pan-Calcineurin A (#2614, Cell Signaling, USA), Anti-SHP-2 (#3397, Cell Signaling, USA), Anti-β-Actin (#4970, Cell Signaling, USA), Anti-αTubulin (#7291, abcam, USA). (Please see Reporting Summary for further details on antibodies used). The blots were developed using chemiluminescent substrate ECL (ThermoFisher, USA) and quantified using Image studio Lite Ver. 5.2 software (LICOR, USA).
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2

Western Blot Analysis of RNA Methylation Regulators

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Mouse cerebellum and cerebral cortex were dissected as described above and triturated in RIPA buffer supplemented with protease and phosphatase inhibitors; 60–80 µg of tissue lysates were subjected to SDS-PAGE and western blot analysis. Primary antibodies used in our analysis are as follows: anti-METTL3 (Abnova, H00056339-B01P), anti-METTL14 (Atlas Antibodies, HPA038002), anti-ALKBH5 (Sigma, HPA007196), anti-WTAP (Santa Cruz, sc-55438), anti-FTO (Abcam, ab92821) and beta-ACTIN (Santa Cruz, sc-47778). Secondary antibodies used are as follows: peroxidase-conjugated AffiniPure Goat Anti-Rabbit IgG (H + L) (XiYA Biology, Beijing, FZ-4201), peroxidase-conjugated AffiniPure Goat Anti-Mouse IgG (H + L) (XiYA Biology, Beijing, FZ-4202) and peroxidase-conjugated AffiniPure Rabbit Anti-Goat IgG (H + L) (XiYA Biology, Beijing, FZ-4203).
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3

Western Blot Analysis of Protein Expression

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Whole-cell extracts were extracted by directly lysing the cells with 1× radioimmunoprecipitation assay buffer (Beyotime) with 1 mM PMSF (Beyotime) added immediately before use. Samples were boiled by adding 6× SDS sample buffer for 10 min at 100 °C and resolved using SDS-polyacrylamide gel electrophoresis. The proteins were probed with the following antibodies: monoclonal anti-GFP (1:2000 dilution; Thermo Fisher Scientific), anti-βACTIN (1:2000 dilution; Thermo Fisher Scientific), and anti-METTL3 (1:1000 dilution; Abcam), and anti-FTO (1:2000 dilution; Abcam). Immunodetection was performed using horseradish peroxidase–conjugated Affinipure goat anti-mouse IgG (H + L) (1:5000 dilution; catalog no.: SA0 001-1; Proteintech) or horseradish peroxidase–conjugated Affinipure goat anti-Rabbit IgG (H + L) (1:5000 dilution; catalog no.: SA00001-2; Proteintech) and ECL prime substrate (Bio-Rad) according to the manufacturer's instructions.
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4

Quantification of FTO Protein in EC

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Immunohistochemistry was used to determine the FTO expression level in EC tissue samples. The methods followed have been described in detail in a paper published by our research group [17 (link)]. Anti-FTO (1:500, Abcam) was used as the primary antibody. The slices were then imaged using a professional microscope (P-MIDI, 3D HISTECH, Hungary).
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5

Immunohistochemical analysis of Ki-67 and FTO

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IHC analysis of Ki-67 levels was conducted on paraffin slides of mouse liver and metastatic lung tumor tissues using anti-Ki-67 antibodies (Abcam, Cambridge, UK) and anti-FTO (#ab126605, Abcam). The detailed description of IHC was conducted as previously reported [5 (link)].
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6

Quantitative Analysis of Protein Expression by Western Blot

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Quantitative analysis on the change of protein expressions was conducted by western blot analysis according to the previous reports.35 (link), 36 (link) After transfection and induction, the cells were harvested for western blotting analysis. The cells were incubated by radioimmunoprecipitation assay (RIPA) lysis buffer (Beyotime, China) at 4°C for 30 min to extract total proteins. Then, approximately 60 μg of total cell lysates was separated by SDS-PAGE and transferred to a polyvinylidene fluoride (PVDF) membrane (Millipore, USA). The membranes were blocked with 5% non-fat milk for 2 h and immunoblotted overnight at 4°C with anti-FTO (Abcam, UK) or anti-β-actin (ZSGB-BIO, China). Membranes were then incubated with secondary antibodies for 1 h at room temperature in a dark room. The blotted bands were visualized using Image Studio software (Alias, USA).
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7

Immunohistochemical Analysis of FTO in Ovarian Tissues

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Immunohistochemistry (IHC) was performed as previously described [36 (link)]. The ovarian tissues of mice were fixed in 4% formaldehyde and paraffin-embedded using standard procedures. First, consecutive 4-µm sections were cut, deparaffinized with xylenes, rehydrated, and retrieved the antigen in sodium citrate solution (pH 6.0) for 20 min. Then the slides were treated with 3% hydrogen peroxide to quench the endogenous peroxidase and blocked with 1% bovine serum albumin for 30 min to block the nonspecific binding. Next, tissue sections were incubated with primary antibody anti-FTO (Abcam, Cambridge, ab126605, USA; 1:150) overnight at 4 ℃. Finally, wash the slides with PBS three times and incubate the slides with HRP-conjugated goat anti-rabbit IgG secondary antibody (1:1000, Santa, Cruze) for another 30 min. Finally, a 3, 3-diaminobenzidine tetrahydrochloride (DAB) (Beyotime, Wuhan, China) substrate kit was applied to detect peroxidase reactivity. According to the manufacturer instructions, we prepared DAB peroxidase substrate in 5 ml ddH2O in a glass vial. Then, drop the DAB substrate on top of the slides and watch the brown staining. Dip slides into ice plus tap water to stop the reaction and rinse under cold tap water for 5 min.
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8

Bone Marrow Stromal Cell Protein Analysis

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BMSCs were lysed using RIPA buffer (Sigma-Aldrich). Following detecting protein concentration, cell lysate was isolated using 10% SDS-PAGE, followed by being transferred on PVDF membranes. After incubating with primary antibodies (anti-BGLAP, anti-COL1A1, anti-RUNX2, anti-OCN, anti-OPN, anti-METTL14, anti-FTO, anti-ALKBH5, anti-WTAP, anti-RBM15, anti-VIRMA, anti-METTL3, anti-SMAD1, and anti-GAPDH, Abcam, Cambridge) at 4 °C overnight, the membranes were incubated with HRP-conjugated secondary antibody (Abcam) at 25 °C for 1 h. Bands were visualized using immobilon ECL ultra western HRP substrate (Sigma-Aldrich). The original bands are shown in the Supplementary material.
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9

Antibody Panel for m6A RNA Modifications

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The antibodies used in this study were: anti-GAPDH (AHP1628, Bio-Rad), anti-FLAG (F1804, Sigma-Aldrich), anti-METTL3 (15073-1-AP, Proteintech Group), anti-METTL14 (HPA038002, Sigma-Aldrich), anti-FTO (ab124892, Abcam), anti-ALKBH5 (HPA007196, Sigma-Aldrich), anti-MDA5 (D74E4, Cell Signaling), anti-RIG-I (D14G6, Cell Signaling), anti-HIV-1 Gag (clone #24–2, the NIH AIDS Reagent Program), anti-IRF3 (124399, Abcam), anti-phospho-IRF3 (Ser396) (4D4G) (4947, Cell Signaling), anti-IRF7 (4920S, Cell Signaling), anti-phospho-IRF7 (Ser471/472) (5184, Cell Signaling) and anti-m6A polyclonal rabbit antibody (202 003, Synaptic Systems). Cells were harvested and lysed in cell lysis buffer (Cell Signaling) supplemented with a protease inhibitor cocktail (Sigma-Aldrich) and a phosphatase inhibitor cocktail (Cell Signaling). Immunoblotting was performed as described [23 (link)]. Detection of GAPDH expression was used as a loading control.
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10

Western Blot Analysis for Protein Expression

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Total proteins were extracted from the cells and tissues using radio immunoprecipitation assay buffer (BIOSS) mixed with phenylmethylsulfonyl fluoride (BIOSS) and quantified using bicinchoninic acid assay (Beyotime Institute of Biotechnology). Protein extractions (30ug per well) were separated using 10% sodium dodecyl sulphate-polyacrylamide gel electrophoresis and transferred onto polyvinylidene fluoride membranes (MilliporeSigma). The membranes were blocked with 5% fat-free dried milk for 1 h at room temperature. After incubation with high-affinity anti-FTO (1:1000, Abcam, USA), anti-STAT3 (1:1000, Cell Signaling Technology, USA), anti- phosphorylation-STAT3 (1:1000, Cell Signaling Technology, USA), anti-Bcl-2 (1:1000, Cell Signaling Technology, USA), anti-c-Myc (1:1000, Abways Technology, China), anti-CyclinD-1 (1:1000, Abways Technology, China), anti-β-actin (1:5 000, Bioss, China), or anti-GAPDH (1:5000, Bioss, China) antibodies at 4°C overnight, the membranes were incubated with the HRP-conjugated secondary antibodies goat anti-rabbit (1:10,000; Boster, China) or goat anti-mouse (1:5000; Boster, China) for 1 h at room temperature. Proteins were detected using BeyoECL chemiluminescence kit (Biyuntian, China) and detected using the Amersham ImageQuant 800 system (Cytiva). The density of bands were measured using ImageJ (v1.51, National Institutes of Health).
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