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5 protocols using ribozero kits

1

Total RNA Purification and RNA-seq Library Preparation

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Total RNA was prepared as previously described with minor modifications (Hillier et al. 2009 (link)). Ribosomal subtraction was performed using Ribozero kits (Epicentre) according to the manufacturer's instructions. cDNA was generated, and RNA-seq libraries were prepared as previously described with minor modifications (Hillier et al. 2009 (link)). See Supplemental Methods for details.
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2

RNA-seq analysis of CD133+ and CD133- cells

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RNA was isolated from CD133+ and CD133- cells and RNA-seq was done using Washington University ICTS Core Services. Briefly, ribosomal RNA was removed by a hybridization method using Ribo-ZERO kits (EpiCentre). mRNA was then fragmented and reverse transcribed to yield double stranded cDNA. cDNA was blunt ended, had an A base added to the 3’ ends and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-2500 using single reads extending 50 bases.
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3

Exosomal miRNA Profiling of Fasting Plasma

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The EDTA anticoagulation tube was used to draw 10 mL of peripheral venous blood in the morning of the next morning after fasting. The plasma was separated by high‐speed centrifugation and stored at −80°C in the refrigerator. At the same time, western blotting was used to detect the concentration of marker proteins on the surface of exosomes, so as to identify the extracted exosomes. Total RNAs were isolated from the exosomes in nine patients using the Trizol method, and the concentration and mass of the samples were determined using the Agilent 2100 Bioanalyzer, rRNAs were depleted using the Epicenter Ribo‐Zero kits, and then following the fragmentation of RNAs, first‐strand cDNAs were further synthesized from these RNAs via reverse transcription, a RNA gene library was constructed using PCR technique, and miRNAs were isolated and purified by high‐resolution polyacrylamide gel electrophoresis (PEAG) to form a miRNA library, which was then sequenced using the Illumina‐HiSeq4000 Sequencing Platform.
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4

Total RNA Extraction and Sequencing

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Total RNA extraction was performed with miRvana kit (Ambion). RNA quantity and quality were verified by Nanodrop (Thermo Scientific) and capillary electrophoresis (Bioanalyzer, Agilent) respectively. RNAs (3.5 μg) were rRNA depleted using either Ribominus (Life Techologies) or Ribozero kits (Epicentre). Barcoded libraries were prepared for each sample using SOLiD total RNA-Seq kit (Life Techologies) and following the manufacturer's instructions. Library profiles and concentration were verified with Bioanalyzer and Qubit (Life Technologies) before equimolar pooling of the libraries.
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5

Viral RNA Extraction and Sequencing

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Total viral RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. Viral RNA quality was examined using NanoDrop 2000 (ThermoFisher Scientific, Waltham, MA) and Agilent 2100 bioanalyzer (ThermoFisher Scientific, CA, USA). Residual ribosomal RNA was depleted using Ribo-Zero kits (Epicentre, Madison, WI). Libraries were constructed using a TruSeq total RNA library preparation kit (Illumina), and paired-end (250–300 bp) sequencing was performed on the Hiseq-PE150 platform (Illumina, Sandiego, CA). Additionally, RNA-seq data of thirty-nine grasshoppers collected worldwide were retrieved from the National Center for Biotechnology Information (NCBI) database (Supplementary Table S1). Sequencing reads were quality trimmed using Trimmomatic (Bolger, Lohse, and Usadel 2014 ) and de novo assembled using the Trinity version 2.8.6 with minimum contig length set at 200 nt (Grabherr et al. 2011 ).
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