Journal: iScience

Article Title: Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East respiratory syndrome coronavirus infection

doi: 10.1016/j.isci.2023.106780

Figure Lengend Snippet: Illumina and non-strand-specific Nanopore sequence analysis of MERS-CoV-infected cells Top: The MERS-CoV genome is depicted as a black line, with annotated proteins shown as blue bars. Transcription regulatory sequences (TRSs) are indicated with dashed lines in the genome schematic and in all panels. (A) Total Illumina reads were aligned to the MERS-CoV genome reference sequence using the RNA aligner in Geneious Prime and were output as a BAM file. Reads were then sorted using Samtools Sort and arranged by coverage using Bedtools GenomeCoverage. Reads are shown plotted according to number of reads (y axis) versus genome position (x axis). (B) Total Illumina reads were first aligned to a minimal leader sequence (MERS-CoV nts 40–60), and reads that aligned to the minimal sequence were then aligned to the MERS-CoV genome reference sequence. Reads were then sorted and plotted as in A. (C) Leader-containing transcripts were amplified from RNA harvested from MERS-CoV-infected cells using the genome-spanning primer walking strategy shown in Figure S2 A, and the transcripts were then sequenced using Oxford Nanopore amplicon sequencing chemistry. Transcripts were aligned to the genome using the RNA aligner in Geneious, with intron discovery turned on. Reads were output and graphed as described for A and B, and junctions are described in detail in Table S1 . All RNAseq studies were performed in duplicate, with the most representative datasets shown.

Article Snippet: • Illumina, Oxford nanopore, and ribosome profiling sequencing data have been deposited at NCBI Sequence Read Archive.

Techniques: Sequencing, Infection, Amplification, Chromosome Walking

Journal: iScience

Article Title: Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East respiratory syndrome coronavirus infection

doi: 10.1016/j.isci.2023.106780

Figure Lengend Snippet: Strand-specific leader-containing transcripts and leader-body junctions produced during MERS-CoV infection Top: The MERS-CoV genome is depicted as a black line, with annotated proteins shown as blue bars. Transcription regulatory sequences (TRSs) are indicated with dashed lines in the genome schematic and in all panels. (A) Strand-specific leader-containing transcripts were amplified from RNA harvested from MERS-CoV-infected cells using the first-strand cDNA production and genome-spanning primer walking strategy shown in Figure S2 B, and the transcripts were then sequenced using Oxford Nanopore amplicon sequencing chemistry. Transcripts were aligned to the genome using the RNA aligner in Geneious, with intron discovery turned on. Reads were output and graphed as described for Figure 1 C. A. Positive-sense reads. (B) Negative-sense reads. (C and D) Leader-body junction usage for plus and minus strands is shown graphed as strength of junction usage (y axis, expressed as percentages of total junctions identified from the novel junction finder algorithm in Geneious) versus genome position (x axis). (C) Positive-sense junctions. Red: Canonical leader-body junction positions. Yellow: Near-canonical leader-body junction positions (within the TRS CS but not exactly at the canonical leader-body junction). Blue: Noncanonical leader-body junction positions. These junctions are described in detail in Table S2 . (D) Negative-sense junctions. Green: Canonical leader-body junction positions. Yellow: Near-canonical leader-body junction positions (within the TRS CS but not exactly at the canonical leader-body junction). Blue: Noncanonical leader-body junction positions. These junctions are described in detail in Table S3 . All RNAseq studies were performed in duplicate, with the most representative datasets shown.

Article Snippet: • Illumina, Oxford nanopore, and ribosome profiling sequencing data have been deposited at NCBI Sequence Read Archive.

Techniques: Produced, Infection, Amplification, Chromosome Walking, Sequencing

Journal: iScience

Article Title: Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East respiratory syndrome coronavirus infection

doi: 10.1016/j.isci.2023.106780

Figure Lengend Snippet:

Article Snippet: • Illumina, Oxford nanopore, and ribosome profiling sequencing data have been deposited at NCBI Sequence Read Archive.

Techniques: Virus, Recombinant, Ligation, Sequencing, Illumina Sequencing, Nanopore Sequencing, Software, Targeted Proteomics, Mass Spectrometry