Table 1 Summary of RNA-seq experimental scenarios
Scenario | Number of | Number of | Total reads | Total cost | ≈ depth per | Number of | Pool size | RNA |
|---|---|---|---|---|---|---|---|---|
|  | RNA | libraries | counts |  | library ×106 | libraries |  | pooling |
|  | samples |  | ×106 |  | (min – max) | per group |  |  |
a Scenarios based on the Zhang neuroblastoma samples | ||||||||
A0 (reference) | 80 | 80 | 1600 | € 21,800.00 | 20 (11.2–30.0) | 40 | - | No |
A1 | 40 | 40 | 800 | € 10,800.00 | 20 (11.2–29.7) | 20 | - | No |
A2 | 40 | 40 | 400 | € 7,800.00 | 10 (4.9–13.1) | 20 | - | No |
A3 | 80 | 80 | 800 | € 15,600.00 | 10 (5.0–13.5) | 40 | - | No |
A4 | 80 | 80 | 400 | € 12,600.00 | 5 (2.5–6.7) | 40 | - | No |
B1 | 80 | 40 | 800 | € 11,600.00 | 20 (11.8–28.3) | 20 | 2 | Yes |
B2 | 40 | 20 | 400 | € 5,800.00 | 20 (13.4–28.7) | 10 | 2 | Yes |
B3 | 80 | 40 | 400 | € 8,600.00 | 10 (5.3–12.7) | 20 | 2 | Yes |
B4 | 40 | 20 | 200 | € 4,300.00 | 10 (6.0–12.9) | 10 | 2 | Yes |
C1 | 80 | 20 | 400 | € 6,600.00 | 20 (15.00–27.8) | 10 | 4 | Yes |
C2 | 40 | 10 | 200 | € 3,300.00 | 20 (14.7–26.0) | 5 | 4 | Yes |
C3 | 80 | 20 | 200 | € 5,100.00 | 10 (6.7–12.5) | 10 | 4 | Yes |
C4 | 40 | 10 | 100 | € 2,550.00 | 10 (6.6–11.7) | 5 | 4 | Yes |
b Scenarios based on the NGP neuroblastoma cell lines | ||||||||
A0 (reference) | 18 | 18 | 270 | € 4,185.00 | 15 (14.3–19.3) | 9 | - | No |
A | 6 | 6 | 90 | € 1,395.00 | 15 (15.0–17.7) | 3 | - | No |
B | 12 | 6 | 90 | € 1,515.00 | 15 (14.9–17.6) | 3 | 2 | Yes |
C | 18 | 6 | 90 | € 1,635.00 | 15 (15.3–17.9) | 3 | 3 | Yes |