Table 1. Comparison of differentially expressed lncRNA and protein coding genes in response to Fp infection.
| Comparison | Day, genetic line and infection status | No. differentially expressed protein-coding genesa | No. differentially expressed lncRNAs |
|---|---|---|---|
| Infected vs PBS | Day 1 R-line (Fp) vs. R-line (PBS) | 515 | 57 |
| Day 5 R-line (Fp) vs. R-line (PBS) | 428 | 36 | |
| Day 1 C-line (Fp) vs. C-line (PBS) | 20 | 0 | |
| Day 5 C-line (Fp) vs. C-line (PBS) | 2201 | 54 | |
| Day 1 S-line (Fp) vs. S-line (PBS) | 1663 | 125 | |
| Day 5 S-line (Fp) vs. S-line (PBS) | 2225 | 196 | |
| Genetic lines (PBS) | Day 1 R-line (PBS) vs. S-line (PBS) | 76 | 24 |
| Day 1 R-line (PBS) vs. C-line (PBS) | 3 | 2 | |
| Day 1 S-line (PBS) vs. C-line (PBS) | 28 | 6 | |
| Day 5 R-line (PBS) vs. S-line (PBS) | 45 | 22 | |
| Day 5 R-line (PBS) vs. C-line (PBS) | 246 | 28 | |
| Day 5 S-line (PBS) vs. C-line (PBS) | 61 | 25 | |
| Genetic lines (Fp) | Day 1 R-line (Fp) vs. S-line (Fp) | 150 | 15 |
| Day 5 R-line (Fp) vs. S-line (Fp) | 1016 | 83 | |
| Day 1 R-line (Fp) vs. C-line (Fp) | 28 | 12 | |
| Day 5 R-line (Fp) vs. C-line (Fp) | 159 | 21 | |
| Day 1 S-line (Fp) vs. C-line (Fp) | 37 | 13 | |
| Day 5 S-line (Fp) vs. C-line (Fp) | 1758 | 5 | |
| Time points | Day 5 vs. Day 1 R-line (PBS) | 1286 | 26 |
| Day 5 vs. Day 1 C-line (PBS) | 294 | 36 | |
| Day 5 vs. Day 1 S-line (PBS) | 376 | 14 | |
| Day 5 vs. Day 1 R-line (Fp) | 334 | 22 | |
| Day 5 vs. Day 1 C-line (Fp) | 2469 | 70 | |
| Day 5 vs. Day 1 S-line (Fp) | 2434 | 45 |
Four different comparisons were made to quantify the differentially expressed transcripts: infected vs. non-infected, one genetic line vs. another without infection, one genetic line vs. another post infection, and day 1 vs. day 5 of infection. Differential expression was considered at fold change ±2 and FDR-corrected p < 0.05. Number of differentially expressed protein coding genes and lncRNAs showed positive correlation (R2 = 0.40, P = 0.0011).
aData are from9.