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Fig. 2 | Genome Biology

Fig. 2

From: Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection

Fig. 2

Dual RNA-seq generates high-quality datasets suitable for probing host–pathogen transcriptomes. a On average, there are 70 million reads per library: 42 % of the reads aligned to the human genome and 58 % to the S. pneumoniae D39 genome. b In order to simplify downstream analysis, we excluded three gene fractions: unexpressed genes, i.e., those without counts in any libraries; genes that were differentially expressed at 0 mpi (p < 0.05) between ∆cps2E and wild-type (wt) libraries; and genes with no statistical significance (p > 0.05) and fold changes (FC) < 2 in all comparisons. After exclusion, the epithelial working libraries contained 4337 genes (7 % of all human genes) while the pneumococcal working libraries contained 860 genes (41 % of all pneumococcal genes). c Gene expression in epithelial working libraries was normalized, centered, and clustered. The left panel shows epithelial genes in response to the encapsulated strain while the right panel shows the epithelial response to ∆cps2E S. pneumoniae at different time points. Clear clusters of co-expressed epithelial genes can be observed in the heat map. Blue indicates relatively lower expression while red indicates a higher value. d Pneumococcal expression: the left panel shows the wild-type pneumococcal response to epithelial cells, while the right panel shows the response of the ∆cps2E strain

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