Table 1 RNAseq statistics for I. ricinus IRE/CTVM20 cells, uninfected at 0 hpi, or infected with LIV or TBEV at 168 hpi (upper panel), and differential gene expression statistics at 168 hpi following infection with LIV or TBEV at 0 hpi, compared to uninfected cells at 0 hpi (lower panel)
Parameter | Uninfected 0 hpi (replicate 1/replicate 2) | LIV 168 hpi (replicate 1/replicate 2) | TBEV 168 hpi (replicate 1/replicate 2) |
|---|---|---|---|
Total reads | 11,976,631/10,334,781 | 16,075,150/13,693,034 | 13,339,640/18,910,604 |
Aligned reads | 11,976,631/10,334,781 | 16,075,150/13,693,034 | 13,339,640/18,910,604 |
PF_reads | 11,976,631/10,334,781 | 16,075,150/13,693,034 | 13,339,640/18,910,604 |
PF_aligned reads | 11,976,631/10,334,781 | 16,075,150/13,693,034 | 13,339,640/18,910,604 |
PF_HQ_aligned reads | 3,878,432/3,760,670 | 4,956,000/3,983,347 | 4,775,958/6,552,021 |
Mean read length | 119/119 | 119/119 | 119/119 |
PF_HQ_error rate | 0.76256/0.76193 | 0.763221/0.764392 | 0.766099/0.765034 |
PF_indel rate | 0.000667/0.000668 | 0.0007/0.000667 | 0.000629/0.000636 |
Total genes annotated | na | 20,861 | 20,861 |
Total DE genes | na | 613 (2.96%) | 409 (1.98%) |
Upregulated DE genes | na | 402 (65.6%) | 252 (61.6%) |
Downregulated DE genes | na | 211 (34.4%) | 157 (38.4%) |