Table 1

Summary of miRNA reads and library information.

Library

# of reads analyzed

# of miRNA reads

% miRNA reads

# of detected pre-miRNAs

# of detected miRNAs

# of detected miRNAs at opposite arm

Description


SRX018957

8,057,617

7,025,801

87.19%

381

475

42

Normal

SRX018958

11,234,315

10,241,350

91.16%

439

555

62

Normal

SRX018959

10,035,888

9,229,254

91.96%

424

535

65

Normal

SRX018960

8,493,004

7,424,150

87.41%

400

486

39

HBV(+)

SRX018961

8,214,755

7,290,360

88.75%

507

609

82

Severe HBV(+)

SRX018962

7,413,793

5,767,890

77.80%

417

519

48

HBV(+) distal

SRX018963

8,214,714

6,623,536

80.63%

418

529

51

HBV(+) adjacent

SRX018964

8,042,722

6,668,203

82.91%

426

540

44

HBV(+) side

SRX018965

7,859,049

6,332,172

80.57%

472

598

64

HBV(+) HCC

SRX018966

10,640,841

8,683,683

81.61%

467

596

60

HBV(+) adjacent

SRX018967

10,979,156

9,790,644

89.17%

465

584

64

HBV(+) HCC

SRX018968

5,686,232

3,663,927

64.44%

443

556

58

HCV(+) adjacent

SRX018969

9,224,742

4,754,658

51.54%

430

521

68

HCV(+) HCC

SRX018970

8,967,260

7,618,011

84.95%

407

519

56

HBV(-) HCV(-) adjacent

SRX018971

9,102,563

7,259,865

79.76%

546

682

112

HBV(-) HCV(-) HCC


We mapped the sequence reads back to human pre-miRNAs, quantifying the expression levels of pre-miRNAs, mature miRNAs and isomiRs. According to miRBase 16, 730 out of the 1,048 human pre-miRNAs encode only one mature miRNA at one arm, either 5p or 3p arm. With the improvement on NGS's sequencing depth, we also detected the opposite-arm mature miRNAs at the pre-miRNAs originally annotated to encode only one miRNA. HBV, HCV and HCC are abbreviations of hepatitis B virus, hepatitis C virus and hepatocellular carcinoma, respectively. Distal, adjacent and side mean that the sites at which the tissues were sampled were >10cm, 2-5cm and 0-2cm far from the HCC sites.

Li et al. BMC Systems Biology 2012 6(Suppl 2):S14   doi:10.1186/1752-0509-6-S2-S14

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