ena-STUDY-UNIVERSITY OF SZEGED-18-03-2018-08:02:29:236-2016
Dynamic characterization of the Autographa californica multiple nucleopolyhedrovirus transcriptome
In this study Poly(A) selected RNA was isolated from Autographa californica multiple nucleopolyhedrovirus (AcMNPV) infected Sf9 (Spodoptera frugiperda) cell lines 0,1, 2, 4, 6, 16, 24, 48 and 72 hours post infection, reverse transcribed to double-stranded cDNA and barcoded. The cDNA was sequenced using a Oxford Nanopore Technologies' MinIon sequencer. We demultiplexed the reads by barcode using Albacore.  We mapped all of the reads to the reference sequence KM677940 and to the host genome. Reads from separate time points were merged into one file, where each sample was tagged as a Read Group. The sequenced reads were attributed to previously annotated transcripts to characterize the changes in the viral transcriptome. We used relative expression values to classify each transcript into kinetic groups (E - early, L - late, VL - very late). Using long-read sequencing we managed to differentiate between transcript isoforms and we also characterized the kinetics of novel transcripts.
In this study Poly(A) selected RNA was isolated from Autographa californica multiple nucleopolyhedrovirus (AcMNPV) infected Sf9 (Spodoptera frugiperda) cell lines 0,1, 2, 4, 6, 16, 24, 48 and 72 hours post infection, reverse transcribed to double-stranded cDNA and barcoded. The cDNA was sequenced using a Oxford Nanopore Technologies' MinIon sequencer. We demultiplexed the reads by barcode using Albacore.  We mapped all of the reads to the reference sequence KM677940 and to the host genome. Reads from separate time points were merged into one file, where each sample was tagged as a Read Group. The sequenced reads were attributed to previously annotated transcripts to characterize the changes in the viral transcriptome. We used relative expression values to classify each transcript into kinetic groups (E - early, L - late, VL - very late). Using long-read sequencing we managed to differentiate between transcript isoforms and we also characterized the kinetics of novel transcripts.