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Table 1 Comparison of the four RNA extraction protocols in ten year old samples, by quantity of extracted RNA (in pg/μl) and RNA quality (by RNA integrity number, RIN). NM = not measurable.

From: RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies

Sample

Parameter

Protocol 1

Protocol 2

Protocol 3

Protocol 4

  

Test 1

Test 2

Test 3

Test 1

Test 2

Test 3

Test 1

Test 2

Test 3

Test 1

Test 2

Test 3

1

RNA

91,464

73,861

29,225

32,507

110,621

47,418

21,078

53,731

77,500

231,085

301,416

258,839

 

RIN

NM

2.3

2.0

3.5

3.2

NM

2.2

NM

2.1

NM

2

NM

2

RNA

27,124

4,836

17,711

165,588

63,934

159,656

38,415

43,935

17,635

144,770

110,373

187,249

 

RIN

1.7

1.1

2.0

2.1

NM

2.1

2.2

2.4

1.9

2.0

2.3

2.2

3

RNA

1,236

1,278

6,012

11,050

5,570

7,671

1,416

1,314

18,106

30,239

40,763

105,048

 

RIN

2.3

1.0

2.2

2.3

NM

2.3

2.4

2.5

2.6

1.8

2.2

5.5

4

RNA

5,103

31,145

18,353

71,598

25,791

18,397

34,381

20,229

8,557

122,541

90,564

86,324

 

RIN

NM

2.3

NM

2.2

2.9

NM

2.3

2.2

2.1

NM

NM

NM

5

RNA

5,146

2,893

7,262

43,901

5,140

8,624

29,711

14,415

11,391

68,768

72,550

76,048

 

RIN

1.7

1.1

2.4

NM

2.3

2.3

NM

2.4

2.3

2.2

2.2

6.1

6

RNA

11,416

4,282

975

99,045

27,804

30,150

18,686

14,128

31,289

23,427

84,711

98,565

 

RIN

NM

1.0

1.0

2.2

2.7

NM

2.4

2.4

2.1

NM

2.2

NM

7

RNA

160,254

6,878

7,584

98,598

56,896

39,390

16,501

48,935

6,070

62,394

196,847

150,394

 

RIN

NM

1.0

1.1

2.2

2.5

2.2

1.2

1.0

1.1

2.6

2.2

2.2

8

RNA

65,752

2,088

9,915

66,706

28,998

18,004

46,519

12,300

31,952

12,900

87,934

85,429

 

RIN

1.2

1.8

2.1

3.2

NM

NM

2.4

2.4

2.2

NM

2.2

1.9

9

RNA

15,123

15,579

20,517

32,962

21,034

265,694

137,594

65,451

46,768

101,909

132,994

95,334

 

RIN

1.5

1.1

2.2

5.2

NM

NM

2.2

2.1

2.1

NM

2.3

2.1

10

RNA

31,042

36,583

12,392

68,465

26,950

25,458

35,551

74,122

11,543

35,885

76,333

42,892

 

RIN

2.2

2.3

2.1

NM

2.3

2.3

3.6

4.4

2.2

NM

2.3

1.9

11

RNA

19,588

14,991

11,954

30,333

26,505

18,184

34,319

39,265

12,859

39,093

56,516

17,502

 

RIN

2.2

1.4

2.1

NM

2.3

2.4

2.5

NM

1.9

2.2

2.2

2.1

12

RNA

5,883

3,042

10,918

29,701

106,627

35,362

67,125

28,579

12,037

188,026

314,693

91,516

 

RIN

2

1

NM

1.5

2.1

NM

2.3

2.4

2.3

2.1

2.1

2.1

13

RNA

30,578

36,224

3,943

45,229

74,659

5,371

21,065

11,367

6,659

111,666

190,653

33,443

 

RIN

2.2

2.3

1.8

NM

2.1

NM

2.2

2.3

2.1

2.1

2

NM

14

RNA

3,099

4,057

4,915

22,218

1,650

12,581

9,518

4,916

17,807

9,864

7,790

39,253

 

RIN

2.3

2.5

1.9

2.4

2.3

NM

2.2

NM

2.3

2.3

NM

2.1

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BMC Molecular Biology

ISSN: 1471-2199

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