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6 protocols using hybond n membrane

1

Quantification of m6A Levels in mRNAs

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Total RNAs were harvested from pericytes or retinal vessels using the Trizol reagent. mRNAs were enriched using the Dynabeads mRNA Direct Purification Kit. RNA quantity was monitored by the NanoDrop ND-1000 Spectrophotometer (Agilent, USA). mRNAs were denatured by heating at 95°C for 5 min and then chilled on the ice. Then, mRNAs were blotted onto Hybond N+ membranes (FFN13, Beyotime, China). UV crosslinking of RNAs to the membranes were conducted in an Ultraviolet Crosslinker. The membranes were blocked with 5% defatted milk for 1 h at room temperature. The membranes were incubated with m6A-specific antibody (1:1000, 202003, Synaptic Systems) at 4°C overnight. After three washes with 1 × PBST, the membranes were incubated in HRP-conjugated goat anti-rabbit IgG secondary antibody (1:2500, sc-2030, Santa Cruz) for 1 h at room temperature with gentle shaking. Finally, the membranes were washed again three times in 1 × PBST. The signals were detected by the SuperSignal West Dura Extended Duration Substrate (34075, Thermo Fisher Scientific). Quantified m6A levels were normalized to the amount of the loaded mRNAs.
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2

RNA Quantification and m5C Detection

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Total RNA was extracted using TRIzol reagent (Invitrogen) according to the standard manufacturer's protocol and then quantified and diluted in 10 mM Tris‐EDTA buffer. The indicated amounts of RNA samples were loaded onto Hybond‐N + membranes (FFN10, Beyotime, China). The membrane was crosslinked at 254 nm UV for 60 s after a short drying process, blocked with 5% milk for 1.5 h at RT and incubated with an anti‐m5C antibody (ab214727, Abcam, USA) at 4°C overnight. After three washes with TBST (Thermo Fisher Scientific, USA), the membranes were incubated with HRP‐conjugated anti‐rabbit IgG (SA00001‐2, Proteintech) for 1.5 h at RT and then visualized using an enhanced chemiluminescence kit (WBKLS0100, Thermo Fisher Scientific) and a detection instrument (Tanon Science, Shanghai, China).
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3

Biotinylated miR-543 Probe Enrichment

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Biotinylated-miR-543 probe and biotinylated NC (Bio-NC) probe were generated by Guangzhou RiboBio Co., Ltd. The RNA pull-down was performed as previously described (28 (link)). To produce probe-coated beads, miR-543 (Guangzhou RiboBio Co., Ltd.) was incubated with C-1 magnetic beads (Thermo Fisher Scientific, Inc.) for 2 h at 25°C. The cell lysates were then harvested and treated with the 50 pmol miR-543 probe or Bio-NC probe overnight at 4°C. After washing with wash/binding buffer, the RNA complexes adsorbed in the beads were collected and used to conduct RT-qPCR assay and northern blot analysis. For northern blot analysis, 30 µg RNAs were separated in a 1% agarose-formaldehyde gel and transferred to Hybond-N+ membrane (Beyotime Institute of Biotechnology). Then, the membranes were hybridized with digoxin-labeled DNA oligonucleotides specific to circ-FOXO3 (Guangzhou RiboBio Co., Ltd.) at 37°C. The membranes were exposed to phosphorimager screens and analyzed using Image Lab V3.0 software (Bio-Rad Laboratories, Inc.).
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4

N6-methyladenosine RNA Detection

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Total RNAs were extracted by using TRIzol reagent (Invitrogen, USA) and then extracted and purified by an mRNA purification kit (TOYOBO, Japan) according to the manufacturer's protocol. The extracted mRNAs were directly spotted onto a Hybond-N+ membrane (Beyotime, Shanghai, China) and then UV-crosslinked to the Hybond-N+ membrane by a Stratalinker 2400 UV crosslinker (UVP, CA, USA). The membrane was washed with Tris-buffered saline with Tween 20 (TBST) for three time to remove unbound mRNAs and then blocked with 5% fat-free dry milk for 1 h at room temperature. Next, the membrane was incubated with N6-mA antibody (1:500, Synaptic Systems, Germany) at 4℃ overnight followed by HRP-conjugated anti-rabbit IgG (1:500, Synaptic Systems, Germany) for 1 h at room temperature. Finally, the membrane was mixed with Thermo ECL Signal Western Blotting Detection Reagent (Thermo Fisher Scientific, Waltham, USA) and analyzed with Image Studio software (LI-COR Biosciences, USA).
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5

m6A RNA Quantification Protocol

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The mRNA concentration obtained from the total cellular RNA was determined using a NanoDrop 2000 instrument, and the mRNA was diluted to various concentrations with RNase‐free water. Serially diluted mRNA sample were denatured at 95 °C for 3 min and chilled on ice. The nucleic acid was transferred onto a Hybond‐N+ membrane (Beyotime Biotechnology, China) through a spotter and then 2400 UV cross‐linked to the membrane. After washing, the membrane was incubated with m6A antibody in 5% nonfat milk at 4°C overnight. The following day, an additional incubation of 1 h was conducted with HRP‐conjugated secondary antibodies (ZSGB‐BIO, China) and measured with ECL reagents (BIO‐RAD, USA). Methylene blue in 0.3 m sodium acetate staining was used as a loading control.
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6

Quantifying m6A RNA Methylation in PDA Tumors

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Total RNA isolated from four PDA patients tumors specimens and adjacent nontumor tissues was extracted using RNAiso Plus (Takara, Japan, #9019) and diluted into a gradient concentration of 500 ng/μl, 250 ng/μl, and 125 ng/μl. Samples (500 ng, 250 ng, or 125 ng) that degenerated under 70°C for 2 min were deposited on an Hybond-N+ membrane (Beyotime, China, #FFN10). Then, the membrane was crosslinked by ultraviolet rays for 2 min and stained with 0.02% methylene blue (Sigma-Aldrich, USA, # M9140-25G) and washed with 75% ethanol for 30 min. The membrane was incubated with primary m6A antibody (1:5,000, Synaptic System, #202003) overnight at 4°C. Dot blots were visualized by autoradiography imager G: Box Chemi XT4 System (Syngene, Cambridge, United Kingdom) after incubation with secondary antibody (CST, USA, #7074S).
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