Table 6 Comparison of the four protocols for quantity and quality of extracted RNA for only samples that produced biologically-useful RNA (RIN ≥ 1.4) in recently archived months 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.
Months old samples: | Protocol 1 | Protocol 2 | Protocol 3 | Protocol 4 | |
|---|---|---|---|---|---|
FFPE tissue input | 80 μm | 10 μm | 20 μm | 50 μm | |
Successful extractions | 34/42 (81%) | 34/42 (81%) | 39/42 (93%) | 35/42 (83%) | |
Case success | 14/14 (100%) | 14/14 (100%) | 14/14 (100%) | 14/14 (100%) | |
RNA (pg/μl) | Minimum value | 76 | 152 | 987 | 34 |
Maximum value | 185,703 | 259,012 | 115,194 | 2,209,739 | |
Mean | 24,818 | 64,317 | 26,843 | 180,584 | |
Median | 14,781 | 48,255 | 15,146 | 51,245 | |
Minimum RIN of 1.4 | Minimum value | 1.5 | 1.6 | 1.4 | 1.4 |
Maximum value | 5.1 | 2.7 | 2.6 | 4.9 | |
Mean | 2.3 | 2.1 | 2.3 | 2.3 | |
Median | 2.3 | 2.0 | 2.4 | 2.2 |