Table 1. Effects of degradation on differential expression.
| Comparison | No 3TC | 3TC; N = 
|
Shared |
| RIN 10 vs. RIN 8 | 4377 (36%) | 4344 (36%) | 4133 |
| RIN 10 vs. RIN 6 | 6827 (56%) | 6841 (56%) | 6501 |
| RIN 10 vs. RIN 4 | 6886 (56%) | 6897 (57%) | 6551 |
| RIN 10 vs. RIN 2 | 6664 (54%) | 6795 (56%) | 6319 |
RIN 10 vs. RM
|
3943 (33%) | 3778 (32%) | 3651 |
| RIN 8 vs. RIN 6 | 109 (1%) | 125 (1%) | 99 |
| RIN 8 vs. RIN 4 | 1500 (12%) | 1583 (13%) | 1396 |
| RIN 8 vs. RIN 2 | 2663 (22%) | 2955 (24%) | 2498 |
| RIN 6 vs. RIN 4 | 270 (2%) | 310 (3%) | 256 |
| RIN 6 vs. RIN 2 | 2382 (19%) | 2661 (22%) | 2214 |
| RIN 4 vs. RIN 2 | 561 (5%) | 764 (6%) | 510 |
Control
|
10484 (76%) | 10263 (75%) | 10097 |
RM = The RiboMinus group (RIN 2–6).
Control = Two different cell lines (U2-OS and U251) from high quality RNA [20].
Number of DEGs without 3TC method and with 3TC (isoform filtering only, no length restriction). The first column shows the comparison, the second column shows the number of DEGs without 3TC, the third column shows the number of DEGs with isoform filtering and the forth column shows the number of DEGs that are shared between the two methods. The percentage in parenthesis is the percentage of the total number of genes that are labeled as expressed. See also Figure S4.