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5 protocols using protease k

1

Immunoprecipitation of AGO2-miRISC Complex

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For RIP, Dynabeads Protein G (Thermo Fisher Scientific) were coated with control IgG (Santa Cruz Biotechnology) or AGO2 antibodies (Sigma-Aldrich, St. Louis, MO). Cytoplasmic lysates were prepared using a protein extraction buffer (PEB) containing protease/phosphatase inhibitors and RNaseOUT inhibitor (Invitrogen). Equal amounts of lysates were incubated with antibody-coated Dynabeads at 4°C for 4 h. After washing several times with PEB buffer, the AGO2-IP materials were treated with DNase I (Ambion, Austin, TX) and Protease K (Bioneer). Proteins were denatured with acid phenol (Ambion), and RNA was precipitated with absolute ethanol overnight at −20°C. The target mRNA level in the miRISC was determined by qRT-PCR.
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2

RNA Immunoprecipitation (RIP) Assay

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The RIP assay was performed using Dynabeads® Protein G (Thermo Fisher Scientific) as described in a previous report [20 (link)]. Briefly, the beads were coated with IgG or the indicated antibody (Ago2 antibody, Sigma, St. Louis, MO, USA or HuR antibody, Santa Cruz Biotechnology, Dallas, TX, USA). After equal amounts of PEB lysate were incubated with antibody-coated Dynabeads for 4 h, the beads were washed several times with NT2 buffer (Supplementary Table 4). Following treatment with DNase I (Ambion) and protease K (Bioneer), RNA was isolated by precipitation with absolute ethanol. The level of mRNA in RIP was quantified by RT-qPCR.
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3

hnRNP K and Ago2 Immunoprecipitation Protocol

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For RNP-IP, Dynabeads® Protein G (Thermo Fisher Scientific, Rockford, IL, USA) were coated with control IgG (Santa Cruz Biotechnologies, Santa Cruz, CA, USA) or hnRNP K antibody (Abcam, Cambridge, UK). For Ago2 IP, beads were coated with an Ago2 antibody (Sigma, St. Louis, MO, USA). Cytoplasmic lysates were prepared using PEB lysis buffer containing a protease inhibitor, a phosphatase inhibitor, and RNaseOUT (Invitrogen, Carlsbad, CA, USA). Equal amounts of lysates were incubated with antibody-coated Dynabeads for 4 hours at 4°C. hnRNP K-IP materials were washed several times with PEB buffer and treated with DNase I (Ambion, Austin, TX, USA) and protease K (Bioneer, Daejeon, South Korea). The RNA was isolated with acid phenol (Ambion) and precipitated with absolute ethanol overnight at −20°C. The mRNA expression level was determined by RT-qPCR, as described above.
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4

Ago2-Mediated RNA-Induced Silencing Complex Analysis

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For RNP-IP, the Dynabeads® Protein G (Thermo Fisher Scientific, Rockford, IL, USA) were coated with control IgG (Santa Cruz Biotechnologies, Santa Cruz, CA, USA) or Ago2 antibody (Sigma, St. Louis, MO, USA). Cytoplasmic lysates were prepared using the protein extraction buffer (PEB) containing protease/phosphatase inhibitors and RNaseOUT (Invitrogen, Carlsbad, CA, USA). Equal amounts of lysates were incubated with antibody-coated Dynabeads for 4 h at 4 °C. After washing several times with PEB buffer, the Ago2-IP materials were treated with DNase I (Ambion, Austin, TX, USA) and protease K (Bioneer, Daejeon, South Korea). Proteins were denatured with acid phenol (Ambion) and RNAs were precipitated with absolute ethanol overnight at −20 °C. The level of mRNA in Ago2-mediated RNA-induced silencing complex (RISC) was determined by RT-qPCR as described above.19 (link)
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5

Characterization of Bioactive Scaffold Materials

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The cross-section morphology of the scaffolds was observed using scanning electron microscopy (SEM; GENESIS-1000, Emcraft, Gwangju, Korea). The thermal property of the scaffolds was analyzed by a thermal gravimetric analyzer (TGA 4000, PerkinElmer, Waltham, MA, USA). To assess the neutralization capacity of the scaffolds, the mass and pH changes were measured in 500 μL phosphate-buffered saline (PBS) solution (pH 7.4) with 20 µg/mL protease K (Bioneer, Daejeon, Korea) for 14 days. The inorganic compositions of the scaffold were measured using inductively coupled plasma-optical emission spectroscopy (ICP-OES, Optima 8000, PerkinElmer, Waltham, MA, USA). The water contact angle (WCA) was analyzed using the sessile drop method at room temperature to evaluate the hydrophilicity and hydrophobicity of the scaffolds.
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