Table 1 Details of sample metadata and RNA-seq analysis
From: Neural transcriptomic signature of chronic wasting disease in white-tailed deer
Sample Metadata | Sequencing | Post Quality Control | White-Tailed Deer Reference Mapping | Bovine Reference Mapping | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample ID | CWD Status | Technical replicate | RIN | Batch | reads (M) | reads (M) | reads (%) | Unique alignments | Assigned to genes | Unique alignments | Assigned to genes | ||||
(M) | (%) | (M) | (%) | (M) | (%) | (M) | (%) | ||||||||
1256-1c | + | No | 8.9 | 1 | 56.2 | 51.8 | 92.1 | 48.6 | 93.9 | 38.8 | 73.4 | 38.2 | 73.8 | 30.4 | 73.0 |
1258-1 h | – | No | 8 | 1 | 55.9 | 51.6 | 92.4 | 48.4 | 93.7 | 38.3 | 72.6 | 37.7 | 73.0 | 30.0 | 72.7 |
1285-1c | + | No | 7.8 | 1 | 53.4 | 49.4 | 92.6 | 46.2 | 93.5 | 36.0 | 71.3 | 35.4 | 71.6 | 28.1 | 72.3 |
1295-1c | + | No | 7.7 | 1 | 50.3 | 46.6 | 92.5 | 43.6 | 93.7 | 34.1 | 72.1 | 33.6 | 72.3 | 26.8 | 72.7 |
324,593-1 h | – | No | 7.8 | 1 | 40.6 | 37.5 | 92.4 | 35.2 | 93.8 | 27.6 | 72.1 | 27.2 | 72.5 | 21.8 | 73.3 |
324,600-1 h | – | No | 7.9 | 1 | 57.8 | 53.4 | 92.4 | 50.0 | 93.7 | 39.0 | 71.7 | 38.4 | 71.9 | 30.9 | 73.5 |
NBSK10-1 h | – | No | 7.2 | 1 | 49.4 | 45.7 | 92.5 | 42.7 | 93.5 | 33.0 | 70.9 | 32.6 | 71.3 | 25.7 | 72.0 |
NBSK23–1 s | preclinical | No | 7.4 | 1 | 43.1 | 39.7 | 92.1 | 37.1 | 93.5 | 28.4 | 69.9 | 28.1 | 70.6 | 22.0 | 71.6 |
1285-2c | + | Yes | 7.8 | 2 | 33.0 | 22.2 | 67.3 | 20.5 | 92.6 | 15.6 | 68.3 | 15.0 | 67.7 | 11.7 | 69.9 |
1295-2c | + | Yes | 7.7 | 2 | 47.3 | 33.2 | 70.2 | 30.8 | 92.9 | 24.2 | 71.2 | 23.3 | 70.2 | 18.2 | 70.7 |
324,601-2 h | – | No | 7.3 | 2 | 44.0 | 31.6 | 71.8 | 29.1 | 92.3 | 22.0 | 67.7 | 21.4 | 67.6 | 16.9 | 71.3 |
NBSK1-2 h | – | No | 7.4 | 2 | 46.9 | 34.7 | 74.0 | 32.2 | 92.9 | 25.1 | 70.7 | 24.3 | 70.2 | 19.2 | 71.4 |
NBSK11-2 h | – | No | 8.2 | 2 | 41.7 | 29.8 | 71.5 | 27.8 | 93.0 | 21.9 | 71.5 | 21.2 | 70.9 | 16.7 | 71.6 |
NBSK23–2 s | preclinical | Yes | 7.4 | 2 | 38.3 | 26.9 | 70.3 | 24.9 | 92.7 | 19.0 | 68.9 | 18.5 | 68.8 | 14.4 | 70.4 |
NBSK27-2 h | – | No | NA | 2 | 40.3 | 29.5 | 73.2 | 27.3 | 92.6 | 21.3 | 70.7 | 20.7 | 70.3 | 16.3 | 70.9 |