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7 protocols using recombinant ribonuclease inhibitor

1

RNA Reverse Transcription Protocol

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Total RNA was reverse transcribed in a 20 μl reaction containing 1 μg of total RNA template, 50 U MMLV reverse transcriptase (Invitrogen, Carlsbad, CA, USA), 40 U recombinant ribonuclease inhibitor (Invitrogen) and 5 μM oligo-dT primers. Reverse transcription took place at 37 °C for 60 min, while enzyme inactivation performed at 70 °C for 15 min.
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2

Polyadenylation and Reverse Transcription of RNA

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Prior to reverse transcription, polyadenylation of 1 μg of total RNA at the 3′-end was carried out using 800 μM ATP and 1 U of E. coli poly (A) polymerase (New England Biolabs, Inc., Ipswich, MA, USA), in a 10 μL reaction incubated at 37 °C for 60 min. Polymerase inactivation was accomplished at 65 °C for 15 min. Subsequently, first-strand cDNA was synthesized with 50 U MMLV reverse transcriptase (Invitrogen, Carlsbad, CA, USA), 40 U recombinant ribonuclease inhibitor (Invitrogen) and 0.25 μM oligo (dT) adapt-er 5′-GCGAGCACAGAATTAATACGACTCACTATAGGTTTTTTTTTTTTVN-3′ (V = G, A, C and N = G, A, T, C), in a 20 μL reaction at 37 °C for 60 min. Finally, MMLV was inactivated at 70 °C for 15 min.
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3

Extraction and Reverse Transcription of Total RNA

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Total RNA was extracted using TRI-Reagent (Molecular Research Center, Inc., Cincinnati, OH, USA) according to the manufacturer’s instructions. The concentration and purity of the extracted RNA were evaluated spectrophotometrically, while the integrity of the extracted RNA was assessed using agarose gel electrophoresis.
Next, 1.0 μg of total RNA was reverse-transcribed in a 20 μL reaction containing 5 μM oligo-dT primer, 50 U MMLV reverse transcriptase (Invitrogen, Carlsbad, CA, USA), 40 U recombinant ribonuclease inhibitor (Invitrogen) and 0.5 mM dNTPs mix (Invitrogen) at 37 °C for 60 min. Enzyme heat inactivation was performed at 70 °C for 15 min.
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4

Polysome Profiling of IAA-Treated C. elegans

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L3 larvae grown on regular NGM plates were transferred to NGM plates with and without 1 mM IAA for 24 hours at 20°C. Animals were liquid nitrogen flash frozen in polysome lysis buffer [74 (link)] and ground in liquid nitrogen (with mortar and pestle). The frozen worm powder was thawed on ice and solubilized in polysome lysis buffer that was supplemented with 1 mM DTT, 100 μg/ml cycloheximide, 40 U/100 μl recombinant ribonuclease inhibitor (Invitrogen), 2 U/100 μl DNase (Invitrogen). Lysates were loaded onto 10% to 50% sucrose gradients and spun for 2.5 hours at 40,000 rpm using SW 40 Ti rotor in an ultracentrifugation system (Beckman Coulter). RNA from monosome and polysome peaks was isolated using a density fractionation system (Brandel). The data were used for the analysis in S2C, S2D and S2E Fig.
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5

Quantification of APP mRNA in Astrocytes

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Total RNA from cultured astrocytes was extracted using an RNeasy mini kit (Qiagen). RNA was quantified using a NanoDrop One (Thermo Fisher Scientific) and retro-transcribed using oligo (dT)20 Primer (Thermo Fisher Scientific), M-MLV Reverse Transcriptase (Promega), Recombinant ribonuclease inhibitor (Invitrogen), and dNTPs (TOYOBO). The cDNA was then subjected to PCR with Taq (Takara), dNTPs (TOYOBO), and primers: for APP, 5′-GGATGCGGAGTTCGGACATG-3′ and 5′-GAAACTCGTCTCAGTCTTG-3′ and for GAPDH, 5′-GGCAAGTTCAATGGCACAGT-3′ and 5′CTCAGATGACCGCAGAAGTGGT-3’. PCR products were separated by electrophoresis on an agarose gel and stained with GelRed Nucleic Acid Stain (Biotium) for visualization. The intensity of bands was measured using Image J. The expression level of APP mRNA was normalized to the level of GAPDH.
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6

Reverse Transcription and qRT-PCR Assay

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Complementary DNA (cDNA) was reverse transcribed from total RNA using SuperScript III, RNaseOUT, Recombinant Ribonuclease Inhibitor, Random Primers and Oligo(dT)12-18 Primer (Thermo Fisher Scientific). Quantitative reverse transcriptase (qRT)-PCR was performed using the TaqMan Probe method. All primers and probe sets were designed by the Universal Probe Library Assay Design Center. All primers were synthesized by GeneNet, and all probes were purchased from Roche Diagnostics. The qRT-PCR assay was performed as previously described (Ishimoto et al., 2017) . Primer and probe sequences for each Custom TaqMan Gene Expression Assay are listed in Table S2.
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7

Quantifying Gene Expression Using RT-qPCR

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RNA was extracted from cultured cells using the RNeasy Mini Kit (#74,106, Qiagen, Hilden, Germany) according to the protocol recommended by the manufacturer. Complementary DNA (cDNA) was reverse transcribed from total RNA using SuperScript III, RNaseOUT, Recombinant Ribonuclease Inhibitor, Random Primers and Oligo(dT)12-18 Primer (Thermo Fisher Scientific, Tokyo, Japan). Quantitative reverse transcriptase (qRT)-PCR was performed using the TaqMan probe method. mRNA expression was measured by qRT-PCR using the TaqMan probe (Roche Diagnostics, Basel, Switzerland), and the value for each gene was normalized to that for β-actin. mRNA expression was measured by qRT-PCR using the TaqMan probe (Roche Diagnostics, Basel, Switzerland), and the value for each gene was normalized to that for β-actin. All qRT-PCR experiments were performed using a LightCycler 480 System II (Roche Diagnostics). All qRT-PCR data are shown as the mean ± standard error of the mean. The MUC20 forward primer sequence was 5'-AGT GGG CAA AAC AAC TTC CTT-3′; the MUC20 reverse primer sequence was 5′-GCT TCC GAG GGG CTG TAG -3′ (Universal Probe Library Probes: 38#). The β-actin forward primer sequence was 5′-ATT GGC AAT GAG CGGTT-3′, and the β-actin reverse primer sequence was 5′-CGT GGA TGC CAC AGG ACT -3′ (Universal Probe Library Probes: #11).
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