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Table 1 Summary statistics of PARE and smRNA libraries

From: Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops

  

Trimmed

Genome Matched

cDNA Matched

Condition

ID#

Distincta

Totalb

Distinctc

Totald

Distincte

Totalf

Brachypodium PARE

 Root Bio#1

BDI20

2,273,863

10,551,854

1,600,582

9,263,616

1,576,585

7,451,753

 Leaf Bio#1

BDI21

1,226,270

13,696,309

682,819

12,251,858

658,393

9,549,413

 Stem Bio#1

BDI23

3,499,449

16,005,365

1,416,469

12,416,968

1,350,442

11,930,438

 Panicle Bio#1

BDI25

4,256,035

28,940,535

3,415,326

26,535,542

3,355,513

23,614,486

 Root Bio#2

BDI381

14,892,253

71,328,838

10,909,520

64,296,408

10,072,279

62,003,648

 Leaf Bio#2

BDI288

15,673,931

93,529,302

8,204,778

80,615,543

7,675,634

75,965,360

 Stem Bio#2

BDI289

20,330,230

106,942,289

11,417,928

93,078,760

10,527,104

85,961,342

 Panicle Bio#2

BDI287

13,605,701

70,071,025

10,619,657

64,290,369

10,165,770

53,396,674

 Control Bio#1

BDI283

18,739,274

116,856,674

8,033,068

99,574,648

7,475,766

94,337,424

 Control Bio#2

BDI490b

11,609,931

57,136,919

9,220,303

51,975,771

8,871,646

44,558,561

 Cold Bio#1

BDI507

14,094,807

71,335,970

10,300,680

63,667,922

9,476,866

60,202,779

 Cold Bio#2

BDI542

5,954,379

26,243,974

4,873,635

23,735,487

4,626,612

23,513,295

 Drought Bio#1

BDI284

16,895,332

110,043,868

8,551,529

94,797,698

7,833,753

70,824,614

 Drought Bio#2

BDI514

6,549,245

30,377,458

4,954,837

27,533,267

4,509,215

21,352,193

 Heat Bio#1

BDI491

9,064,716

36,739,900

7,008,303

32,960,526

6,557,997

24,894,799

 Heat Bio#2

BDI544

12,502,104

71,856,374

10,147,454

65,621,210

9,309,732

64,252,301

 Submergence Bio#1

BDI508

19,248,274

143,926,223

13,013,551

129,521,309

12,049,556

117,577,209

 Submergence Bio#2

BDI493

11,085,014

47,501,130

8,186,439

42,683,558

7,802,211

38,304,004

Sorghum PARE

 Root Bio#1

SBI617

7,408,495

47,925,541

4,667,519

40,934,942

4,158,647

33,879,769

 Root Bio#2

SBI620

7,471,715

37,774,801

4,059,238

30,725,474

3,799,122

13,074,749

 Leaf Bio#1

SBI619

10,557,426

57,604,765

3,881,705

41,917,126

3,274,739

36,707,076

 Leaf Bio#2

SBI615

6,473,759

40,090,222

4,233,698

34,957,079

3,841,772

29,383,910

 Panicle Bio#1

SBI616

6,872,817

34,611,413

3,981,997

24,631,577

3,158,582

19,666,227

 Panicle Bio#2

SBI618

12,386,838

49,631,535

8,261,402

41,607,791

7,172,569

36,467,170

 Control for Cold Bio#1

SBI517

3,256,249

39,956,679

2,092,580

35,409,035

1,743,771

31,035,771

 Control for Cold Bio#2

SBI519

3,885,061

39,822,428

2,579,391

35,514,462

2,183,104

31,347,460

 Cold Bio#1

SBI518

3,197,687

47,188,888

2,294,992

44,114,986

1,957,618

30,508,940

 Cold Bio#2

SBI520

3,420,185

36,488,885

2,324,259

33,101,913

1,795,310

22,262,865

Switchgrass PARE

 Leaf Bio#1

SWI352

18,119,798

66,514,735

7,302,551

29,289,132

6,684,352

27,261,224

 Leaf Bio#2

SWI498

22,300,993

114,883,981

16,237,561

100,834,434

13,901,137

91,031,475

 Stem Bio#1

SWI353

20,252,951

94,311,170

5,644,700

24,757,380

5,276,609

21,054,163

 Stem Bio#2

SWI500

5,712,914

18,900,653

4,315,446

16,340,546

3,600,582

14,307,880

 Panicle Bio#1

SWI382

23,916,903

96,013,301

15,181,789

80,968,945

13,320,327

76,420,288

 Panicle Bio#2

SWI499

3,052,670

7,845,043

2,448,779

6,885,542

2,140,816

6,234,349

 Control for Cold Bio#1

SWI521

10,188,795

62,673,164

7,125,183

55,462,967

6,454,159

50,607,577

 Control for Cold Bio#2

SWI523

7,480,243

42,889,534

4,344,702

33,834,492

3,456,913

29,312,647

 Cold Bio#1

SWI522

8,657,953

50,614,176

4,996,684

39,012,357

3,302,826

28,359,863

 Cold Bio#2

SWI524

6,617,641

42,861,290

4,203,457

36,211,923

2,949,417

24,326,833

Switchgrass smRNA

 Control for Cold

SWI560

5,575,102

33,117,391

4,036,929

29,240,850

NA

NA

 Cold

SWI559

10,477,573

74,342,226

7,231,085

64,406,974

NA

NA

 Control for Drought

SWI551

6,099,269

34,328,102

4,490,488

30,101,667

NA

NA

 Drought

SWI552

5,288,223

34,223,739

3,807,420

30,123,899

NA

NA

 Re-water

SWI553

5,202,390

30,490,652

3,728,694

26,891,552

NA

NA

 Leaf

SWI561

1,021,704

5,310,089

764,472

4,710,729

NA

NA

 Stem

SWI534

774,658

5,081,224

575,800

4,428,676

NA

NA

 Panicle

SWI562

1,798,117

3,221,179

1,472,871

2,807,413

NA

NA

  1. aThe number of unique sequences found in a library after trimming. bThe total number of sequences found in a library after trimming. cThe number of unique sequences that match the genome at least once. dThe total number of sequences that match the genome at least once. eThe number of unique sequences that match the sense strand of the transcriptome at least once. fThe total number of sequences that match the sense strand of the transcriptome at least once