RNA-seq of SINV-infected Drosophila melanogaster cells; CMC treatment
RNA was extracted from SINV-infected cells immediately after collection using TRIzol. RNA was treated with a 5' exonuclease terminator to deplete ribosomal RNA. RNA was treated with CMC or no CMC and then treated with a base. Libraries were prepared as described in Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA by Schwartz et al. 2014. The libraries were analyzed by Agilent 4200 TapeStation, and pooled. Libraries were sequenced on Illumina NextSeq 2000 or NextSeq 1000 with paired end reads. The demultiplexing of the reads was performed using bcl2fastq, version 2.20.0.