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


Ribeiro-Silva et al. BMC Molecular Biology 2007 8:118   doi:10.1186/1471-2199-8-118

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