Table 5 Comparison of the four protocols for quantity and quality of extracted RNA for only samples that produced biologically-useful RNA (RIN ≥ 1.4) in ten year old FFPE samples. Case success is defined for each protocol as the percentage of samples where at least one of three RNA extraction attempts provided a RIN ≥ 1.4.
Ten year old samples: | Protocol 1 | Protocol 2 | Protocol 3 | Protocol 4 | |
|---|---|---|---|---|---|
FFPE tissue input | 80 μm | 10 μm | 20 μm | 50 μm | |
Successful extractions | 26/42 (62%) | 26/42 (62%) | 35/42 (83%) | 30/42 (71%) | |
Case success | 12/14 (86%) | 14/14 (100%) | 13/14 (93%) | 13/14 (93%) | |
RNA (pg/μl) | Minimum value | 1,236 | 1,650 | 1,314 | 9,864 |
Maximum value | 73,861 | 165,588 | 137,594 | 314,693 | |
Mean | 17,754 | 51,985 | 30,160 | 107,042 | |
Median | 13,692 | 31,104 | 20,229 | 86,682 | |
Minimum RIN of 1.4 | Minimum value | 1.4 | 1.5 | 1.9 | 1.8 |
Maximum value | 2.5 | 5.2 | 4.4 | 6.1 | |
Mean | 2.0 | 2.5 | 2.3 | 2.4 | |
Median | 2.1 | 2.3 | 2.3 | 2.2 |