Fig. 1: Experimental design and generation of massive-scale datasets.

a Overall design of the study. A fine-scale temporal atlas of the SARS-CoV-2 translatome and transcriptome was constructed for early (0, 1, 2, and 4) and late (12, 16, 24, and 36) hours post infection (hpi) at multiplicity of infection (MOI) of 10 and at 48 hpi (MOI = 0.1) in Calu-3 and Caco-2 cell lines and at 24 hpi (MOI = 0.1) in Vero cell line. The temporal atlas of the human translatome and transcriptome in response to SARS-CoV-2 invasion were also constructed. Ribosome-protected mRNA fragment sequencing (RPF-seq), quantitative profiling of initiating ribosomes sequencing (QTI-seq), mRNA sequencing (mRNA-seq), and small RNA sequencing (sRNA-seq) were performed for each time point. For more details, see “Methods”. b High reproducibility between the replicates of sequenced data. Correlation coefficient (Spearman’s ρ) was calculated by comparing host gene expression levels between replicates. Both x- and y-axes represent log₁₀(RPKM + 1). Representative examples from early and late hpi are displayed. For a full version, see Supplementary Fig. 1b, c. c The number of total mapped reads are shown in log₁₀ scale (top) with the relative fraction of reads mapped to the human and SARS-CoV-2 genomes (bottom). The upward and downward directions of the y-axis indicate the fraction of the reads mapped to the SARS-CoV-2 and human genomes, respectively. d A growth dynamics curve of SARS-CoV-2 in Calu-3 and Vero cell lines after infection. The mean values ±95% confidence intervals are displayed (n = 3 biological independent experiments). e Distribution of mRNA-seq (left), RPF-seq (middle), and QTI-seq (right) reads with respect to the relative position near the start of ORF. For 4 and 36 hpi, the 13th nucleotide position (12-nt offset from the 5′ end) of the reads mapped to human (green) or SARS-CoV-2 (red) was counted for each sequencing data. The relative fraction to the amount of reads mapped to the entire ORF was calculated for each position, and the y-axis represents the average of the relative fractions for ORFs with >50 reads mapped. Open reading frames are depicted as three different colored bars with the darkest bars indicating in frame and the others out of frames.