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3 protocols using oligo dt 18 primers

1

Quantifying Gene Expression in Drosophila

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Total RNA was extracted from 10–20 third-instar larvae or adult flies grown on the food indicated using TrizolTM (Life Technologies, Carlsbad, CA, USA) [84 ]. Total RNA (1 µg) was DNase-treated using the DNA-free Kit (Ambion, Foster City, CA, USA) with inactivation buffer (DNA-free DNA Removal Kit, Invitrogen, Carlsbad, CA, USA). cDNAs were generated using oligo (dT) 18 primers (Eurofins, Luxembourg), dNTPs (ThermoFisher, Waltham, MA, USA), and Moloney Murine Leukemia Virus Reverse Transcriptase (M-MLV RT) (Fisher, Waltham, MA, USA). After amplification, the samples were treated with RNAse H (New England BioLabs, Ipswich, MA, USA). The cDNA was diluted in RNase/DNase-free water (ThermoFisher) (1:16), and qRT-PCR experiments were performed using ThermoScientific Absolute qPCR Mix, SYBR Green, ROX (Fisher) in an Applied Biosystems StepOnePlus System. Triplicate samples were used in all the experiments including linearizations and melt curves. All the experiments were performed at least three independent times (separate biological samples), as indicated in the figure legends. The results were normalized to the transcript levels of Drosophila melanogaster ribosomal protein L32 (RpL32). The following primers were used: MIOX exon 2-3 forward GACACCACCGATCCTCTAAAGG and reverse GGAAGGCGTGGATGATGT, RpL32 forward CCAGCATACAGGCCCAAGAT and reverse GCACTCTGTTGTCGATACCC.
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2

Quantitative Analysis of mRNA Expression

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Northern blot analysis of β-globin mRNA was performed as previously described (30 (link)), using digoxygenin-labeled antisense probes and alkaline phosphatase-coupled anti-digoxygenin antibody (Roche). Blots were developed with the LAS 3000 imaging system (Fujifilm) using CSPD reagent (Roche). For RT-qPCR 500 ng of total RNA was reverse-transcribed using oligo(dT)18 primers (Eurofins) and RevertAid Reverse Transcriptase (Thermo Fisher Scientific). qPCRs were carried out as described (13 (link)), using TaqMan assays (Life Technologies, assay-ID Hs00230071_m1 for NFKBIZ mRNA, Hs00174131_m1 for IL6 mRNA, Hs99999905_m1 for GAPDH mRNA, Hs00262018_m1 for NFKBID mRNA, Hs00153283_m1 for NFKBIA mRNA and custom-made assays for rabbit β-globin and firefly luciferase mRNAs) or SybrGreen-based detection (Life Technologies) for mRNAs using primers as follows: GFP: sense 5′-TGCAGTGCTTCAGCCGCTAC-3′, antisense 5′-TCGCCCTCGAACTTCACCTC-3′; Renilla luciferase: sense 5′-CGTCGTGCCTCACATCGAGC-3′, antisense 5′-GCTCGAACCAAGCGGTGAGG-3′; MCPIP1: sense 5′-GGCTGGACAGAGGGAGGATT-3′, antisense 5′-TGACCCACTGAGGCAGACAG-3′; in vitro-transcribed CrPV IRES RNA: sense 5′-GCCTAATACGACTCACTATAGGGTTTAGTGAACCGTGGATC-3′, antisense 5′-GGCGGATCCTGTATCTTGAAATGTAGCAGGTAAA-3′; in vitro-transcribed TSE RNA: sense 5′-TTGGAGCCTGGCTAGCAACA-3′, antisense 5′-TTGCCAATATAAGGCAAATGGTCT-3′.
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3

RNA Extraction and qRT-PCR for Gene Expression

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Total RNA was extracted from 10–20 third instar larvae or adult flies grown on the food indicated using Trizol™ (Life Technologies) (Green and Sambrook, 2012 ). Total RNA (1 µg) was DNase treated using the DNA-free Kit (Ambion) and inactivation buffer (DNA-free DNA Removal Kit, Invitrogen). cDNAs were generated using oligo (dT) 18 primers (Eurofins), dNTPs (ThermoFisher Scientific), and Moloney Murine Leukemia Virus Reverse Transcriptase (M-MLV RT) (Fisher). After amplification the samples were treated with RNAse H (New England BioLabs). The cDNA was diluted in RNase/DNase free water (ThermoFisher Scientific) (1:16) and for qRT-PCR experiments using ThermoFisher Scientific Absolute qPCR Mix, SYBER Green, ROX (Fisher) in an Applied Biosystems StepOnePlus System. Triplicate samples were used in all the experiments including linearizations and melt curves. All the experiments were performed at least three independent times (separate biological samples) as indicated in the figure legends. The results were normalized to the transcript levels of ribosomal protein 32 (RpL32). The following primers were used: Inos exon 1-2 forward GAAAGTGCAGGTGGACGATG and reverse GTCAGCGTGGATCCGTTGT, RpL32 forward CCAGCATACAGGCCCAAGAT and reverse GCACTCTGTTGTCGATACCCT.
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