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6 protocols using nucleospin mirna

1

Small RNA Detection by Northern Blotting

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Total RNAs or smaller RNAs (shorter than 200 nucleotides) from human cells were purified with the Isogen-II (Nippon Gene, Japan) or NucleoSpin miRNA (Takara, Japan) reagent, according to the manufacturer's protocol. The RNAs (2.5–10 μg) were separated by 10% (v/v) polyacrylamide gel electrophoresis under denaturing conditions, and blotted onto a Hybond-N+ membrane (GE Healthcare, Japan) using a Trans-Blot SD semi-dry Electrophoretic Transfer Cell (Bio-Rad, Japan), according to the manufacturer's protocol. Hybridization was performed overnight at 55°C in PerfectHyb Hybridization solution (Toyobo, Japan), using 5΄-32P-labeled oligo DNA probes. The membrane was washed three times in 2 × standard saline citrate (SSC) and 0.1% (w/v) SDS at 55°C for 20 min. The DNA sequences used as specific probes are shown in Supplementary Table S1.
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2

Halo-Tagged Protein Interactome Isolation

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293 T cells constitutively expressing the Halo tag, Halo-UBAP2L or Halo-G3BP1 were lysed in lysis buffer (25 mM Tris-HCl (pH 7.6), 150 mM NaCl, and 0.1% NP-40) supplemented with a phosphatase inhibitor cocktail (Nacalai Tesque, Inc., Japan), protease inhibitor (Promega), 1.5 mM DTT, and RNase inhibitor (Takara) for 10 min on ice and treated with DNaseI(Takara) for 10 min at room temperature. The lysates were centrifuged at 15,000 rpm for 10 min and the supernatants were incubated with Halo Resin (Promega) for 12 h. The resin beads were washed with wash buffer (25 mM Tris-HCl (pH 7.6), 150 mM NaCl, and 0.005% NP-40) five times, and suspended in ML buffer (NucleoSpin miRNA: Takara) to isolate large and small RNAs.
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3

Quantifying miRNA Expression in Tissues

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Total RNA was isolated from cultured cells using NucleoSpin miRNA (TaKaRa, Otsu, Japan). RNA concentration and purity were assessed by UV spectrophotometry. RNA integrity was checked by formaldehyde gel electrophoresis. Total RNA from normal epithelial tissues from colon and pancreas were human colon total RNA and human pancreas total RNA (TaKaRa). To assess the expression levels of MIR143-3p, we conducted qRT-PCR using TaqMan miRNA assays (Applied Biosystems) and the Thunderbird Probe qPCR Mix (Toyobo, Osaka, Japan) according to the manufacturer’s protocol. RNU6B was used as an internal control. Relative expression levels were calculated using the ΔΔCt method.
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4

Mouse BSM Tissue Total RNA Isolation

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Total RNA of the mouse BSM tissue was isolated from an aliquot of the tissue
using NucleoSpin™ miRNA (TaKaRa Bio, Inc., Shiga, Japan) according to the
manufacturer’s instruction. cDNAs were prepared from the total RNA by using
PrimeScriptTM RT reagent Kit (TaKaRa) according to the
manufacturer’s instruction.
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5

Quantitative RNA Expression Analysis in HeLa Cells

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RNA was extracted from HeLa cells using the RNeasy Mini kit (Qiagen, Hilden, Germany), and cDNA was generated using PrimeScript reverse transcriptase (Takara). Small RNA was extracted from RIP assay using NucleoSpin miRNA (Takara), and cDNA was generated using miRCURY LNA™ Universal RT microRNA PCR Universal cDNA synthesis KitII (EXIQON, Copenhagen, Denmark). PCR was performed using the SYBR® Premix Ex Taq™ II (Takara) (for mRNA) or miRCURY LNA™ Universal RT microRNA PCR ExiLENT SYBR® Green master mix (EXIQON) (for small RNA). The relative RNA expression levels were normalized to GAPDH or miRCURY LNA UniRT PCR Control primer mix UniSp6 (203954, EXIQON). The sequences of primers used to amplify each gene were: 5′-AGGTGGAGGAGTGGGTGTCGCTGTT-3′ and 5′-CCGGGAAACTGTGGCGTGATGG-3′ (GAPDH); 5′-CAGCATCCACAGTGCAGATC-3′and 5′-GCACCTCAGAGAAGCAATGC-3′(NOP56); 5′-TGGCAGCTATGTGTCTTGGA-3′and 5′-TGCCAGCCATACCATTCTCT-3′(NOP58); 5′-TGCTCTGATGAAATCACTAA-3′and 5′-AATCAGACAGGAGTAGTCTT-3′(SNORD49A); miRCURY LNA UniRT PCR Reference primer mix SNORD44 (203902, EXIQON).
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6

RNA Extraction and RT-PCR Protocol

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Total RNAs of hBSMCs and mouse BSM tissues were extracted using NucleoSpin™ miRNA (TaKaRa Bio, Inc., Shiga, Japan) according to the manufacturer’s instruction. cDNAs were prepared from the total RNA by using PrimeScript™ RT reagent Kit (TaKaRa) according to the manufacturer’s instructions. cDNA samples were subjected to PCR with Quick Taq™ HS DyeMix (TOYOBO Co., Ltd., Osaka, Japan) in a final volume of 10 µL. The PCR primer sets used are shown in Table 1 (for human) and Table 2 (for mouse), which was designed from published database, BLAST. The thermal cycle profile used was (1) denaturing for 30 s at 94 °C, (2) annealing primers for 30 s at 60 °C, (3) extending the primers for 1 min at 68 °C, and the reaction was run for 40 cycles. The PCR products were subjected to electrophoresis on 2% agarose gel and visualized by ethidium bromide staining.
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