SRX18050290 MERS_Nano_Pos SRP404925 bp0 Cell-based RNA was reverse transcribed to cDNA and amplified for leader-containing transcripts using a primer-walking strategy. Amplicons were then sequenced SRS15556678 MERS-CoV_Nanopore_Pos MERS_Nano_Pos RNA-Seq VIRAL RNA other MinION SRX18050291 MERS_Nano_Neg SRP404925 bp0 Cell-based RNA was reverse transcribed to cDNA and amplified for leader-containing transcripts using a primer-walking strategy. Amplicons were then sequenced SRS15556679 MERS-CoV_Nanopore_Neg MERS_Nano_Neg RNA-Seq VIRAL RNA other MinION SRX18050292 MERS_RiboP6h SRP404925 bp0 Cell-based RNA was harvested using a RiboProfile Kit and then subjected to nuclease digestion. Protected RNAs were then extracted and sequenced. SRS15556680 MERS-CoV_6h_RiboProt MERS_RiboP6h RNA-Seq VIRAL RNA other Illumina HiSeq 2500 SRX18050293 MERS_RiboP16h SRP404925 bp0 Cell-based RNA was harvested using a RiboProfile Kit and then subjected to nuclease digestion. Protected RNAs were then extracted and sequenced. SRS15556681 MERS-CoV_16h_RiboProt MERS_RiboP16h RNA-Seq VIRAL RNA other Illumina HiSeq 2500 SRX18050294 MERS_RiboT6h SRP404925 bp0 Cell-based RNA was harvested using a RiboProfile Kit and then subjected to nuclease digestion. Protected RNAs were then extracted and sequenced. SRS15556682 MERS-CoV_6h_RiboTotal MERS_RiboT6h RNA-Seq VIRAL RNA other Illumina HiSeq 2500 SRX18050295 MERS_RiboT16h SRP404925 bp0 Cell-based RNA was harvested using a RiboProfile Kit and then subjected to nuclease digestion. Protected RNAs were then extracted and sequenced. SRS15556683 MERS-CoV_16h_RiboTotal MERS_RiboT16h RNA-Seq VIRAL RNA other Illumina HiSeq 2500