Table 1.
Experimental design and RNA-Seq mapping results.
| ID | Virus | hpi | Age | Total Reads | Cleaned Reads | Mapped to Rabbit Genome * | Mapped to GI Genome ^ | RT-qPCR (Copies/mg Tissue) |
|---|---|---|---|---|---|---|---|---|
| A130 | cont | N/A ** | A | 36,608,811 | 33,019,057 | 30,372,424 (92.0%) | 0 (0.00%) | 55 |
| A440 | cont | 12 | A | 31,544,539 | 29,690,688 | 27,851,164 (93.8%) | 0 (0.00%) | 0 |
| A445 | cont | 12 | A | 33,024,742 | 30,839,504 | 28,557,666 (92.6%) | 0 (0.00%) | 0 |
| K11 | cont | 12 | K | 30,376,750 | 28,436,074 | 26,697,303 (93.9%) | 0 (0.00%) | 0 |
| K2 | cont | 12 | K | 26,466,336 | 24,621,221 | 23,121,670 (93.9%) | 0 (0.00%) | 0 |
| K9 | cont | 12 | K | 38,879,760 | 35,838,449 | 33,677,252 (94.0%) | 0 (0.00%) | 0 |
| A446 | cont | 24 | A | 26,875,056 | 25,190,314 | 23,565,537 (93.5%) | 0 (0.00%) | 0 |
| A447 | cont | 24 | A | 30,801,403 | 28,647,130 | 26,648,792 (93.0%) | 0 (0.00%) | 0 |
| K12 | cont | 24 | K | 21,522,682 | 19,510,404 | 18,264,437 (93.6%) | 0 (0.00%) | 0 |
| K14 | cont | 24 | K | 32,273,375 | 30,146,422 | 28,183,027 (93.5%) | 0 (0.00%) | 0 |
| K3 | cont | 24 | K | 34,270,680 | 31,856,522 | 29,771,558 (93.5%) | 0 (0.00%) | 0 |
| A444 | GI.1 | 12 | A | 41,554,574 | 38,521,840 | 35,819,416 (93.0%) | 0 (0.00%) | 94 |
| A451 | GI.1 | 12 | A | 34,269,029 | 31,413,217 | 29,237,190 (93.1%) | 0 (0.00%) | 28 |
| A452 | GI.1 | 12 | A | 30,744,544 | 28,741,202 | 26,469,612 (92.1%) | 0 (0.00%) | 0 |
| K1 | GI.1 | 12 | K | 35,648,932 | 33,188,895 | 31,053,518 (93.6%) | 0 (0.00%) | 0 |
| K13 | GI.1 | 12 | K | 28,834,630 | 26,852,299 | 25,283,903 (94.2%) | 0 (0.00%) | 0 |
| K5 | GI.1 | 12 | K | 32,247,351 | 30,065,559 | 28,089,931 (93.4%) | 0 (0.00%) | 0 |
| K7 | GI.1 | 12 | K | 34,983,905 | 32,474,265 | 30,104,239 (92.7%) | 0 (0.00%) | 85 |
| A443 | GI.1 | 24 | A | 32,025,317 | 29,266,843 | 27,437,173 (93.7%) | 4321 (0.01%) | 1,359,870 |
| A448 | GI.1 | 24 | A | 41,956,002 | 38,817,349 | 35,919,297 (92.5%) | 817 (0.00%) | 213,792 |
| A449 | GI.1 | 24 | A | 32,829,766 | 29,594,927 | 27,422,586 (92.7%) | 352 (0.00%) | 83,234 |
| A450 | GI.1 | 24 | A | 39,743,588 | 37,093,310 | 34,584,907 (93.2%) | 5 (0.00%) | 1205 |
| K10 | GI.1 | 24 | K | 26,707,074 | 24,485,698 | 22,779,842 (93.0%) | 2 (0.00%) | 307 |
| K4 | GI.1 | 24 | K | 35,102,440 | 32,387,798 | 30,179,957 (93.2%) | 49 (0.00%) | 18,929 |
| K6 | GI.1 | 24 | K | 30,314,748 | 27,870,816 | 25,865,930 (92.8%) | 19 (0.00%) | 6405 |
| K8 | GI.1 | 24 | K | 30,187,241 | 28,311,539 | 26,206,586 (92.6%) | 5 (0.00%) | 1490 |
| K379 | GI.2 | 12 | K | 32,179,571 | 30,150,297 | 28,485,814 (94.5%) | 0 (0.00%) | 81 |
| K380 | GI.2 | 12 | K | 30,937,894 | 29,113,196 | 27,110,731 (93.1%) | 0 (0.00%) | 66 |
| K381 | GI.2 | 12 | K | 24,208,541 | 22,521,030 | 20,774,527 (92.2%) | 0 (0.00%) | 0 |
| K375 | GI.2 | 24 | K | 31,299,465 | 29,544,132 | 27,913,303 (94.5%) | 26,558 (0.09%) | 20,966,939 |
| K376 | GI.2 | 24 | K | 30,626,983 | 28,656,602 | 26,667,507 (93.1%) | 1410 (0.00%) | 3,634,306 |
| K377 | GI.2 | 24 | K | 35,624,017 | 33,340,447 | 31,470,468 (94.4%) | 1947 (0.00%) | 323,906 |
| K378 | GI.2 | 24 | K | 26,510,091 | 24,505,534 | 22,803,925 (93.1%) | 22,528 (0.09%) | 4,857,896 |
* rabbit genome is OryCun2.0 (http://www.ensembl.org/Oryctolagus_cuniculus). ^ GI.1 is GenBank#KF594473, and GI.2 is GenBank #KT280060. ** A130 was an additional negative control animal that was not part of the infection experiment. A = adult, k = kitten, cont = noninfected control, hpi = hours post infection.