Table 4 ATAC-seq metadata and quality control statistics

From: An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development

Sample ID

Celltype

Date ATAC was performed

Date of library prep

Read count from sequencer

Read count successfully aligned

Read count after filtering for mapping quality

Read count after removing duplicate reads

Read count after removing mitochondrial reads

Non-Redundant Fraction (NRF)

PBC1

PBC2

Fraction of reads in NFR

NFR/mono-nuc reads

Presence of NFR peak

Presence of Mono-Nuc peak

Raw peaks

IDR peaks

TSS enrichment

Number of reads in universal DHS regions

Number of reads in promoter regions

Number of reads in enhancer regions

Number of reads in called peak regions

H7_hESC_ATAC1

D0 hESC

11/8/2015

13/8/2015

93261696

89445943

63427355

48401487

33057240

0.874173

0.877391

7.963726

0.672145531

4.48815287

OK

OK

348998

72107

5.677532655

7501297

2181218

9420055

7113974

H7_hESC_ATAC2

D0 hESC

11/8/2015

13/8/2015

151825178

145741374

103141220

74914035

46080346

0.784357

0.780965

4.355791

0.594905988

3.111463078

OK

OK

254898

72107

5.417971046

8093722

2271676

10309049

6258218

APS_ATAC3

D1 APS

4/8/2015

13/8/2015

88401812

83952797

60558447

42312884

23641140

0.589525

0.549898

1.940211

0.591169991

3.182374684

OK

OK

345846

59125

6.454679332

5428052

1625595

6652426

5366166

APS_ATAC4

D1 APS

4/8/2015

13/8/2015

66716160

63482035

51529472

44238724

36710784

0.788187

0.778657

4.278458

0.647351136

4.050393391

OK

OK

243565

59125

5.615858894

7885350

2329280

10127389

6313436

MPS_ATAC5

D1 MPS

4/8/2015

13/8/2015

129125340

123708067

86733447

60812283

34369150

0.737118

0.727553

3.416704

0.594271523

3.19534847

OK

OK

359273

57945

6.99517666

8210077

2525384

9790941

8632701

MPS_ATAC6

D1 MPS

4/8/2015

13/8/2015

128802054

122229341

96453862

81570579

66255516

0.823556

0.818931

5.306797

0.678716288

4.711491841

OK

OK

258726

57945

4.580237486

7712954

2117515

10307394

5862319

DLL1pPXm_ATAC7

D2 DLL1+ PXM

6/8/2015

13/8/2015

191702808

183718196

132414659

99511940

66060614

0.870262

0.875024

7.831789

0.6619457

4.286335569

OK

OK

276391

109250

7.628156666

9726101

3070226

11125097

10862818

DLL1pPXm_ATAC8

D2 DLL1+ PXM

6/8/2015

13/8/2015

147291642

140788669

100167093

74377015

48138988

0.876385

0.882327

8.327058

0.648651946

4.078567409

OK

OK

277230

109250

6.923491809

9028293

2770033

10754812

9077103

D2Ltm_ATAC9

D2 LatM

13/8/2015

26/8/2015

95742814

89161027

55998269

38367024

20466238

0.809605

0.81417

5.168049

0.645042836

3.413532025

OK

OK

276175

83109

10.03275293

5519359

1819707

6117321

5451176

D2Ltm_ATAC10

D2 LatM

13/8/2015

26/8/2015

192134220

179733937

113070226

75469447

37284730

0.738965

0.735284

3.560357

0.618695962

3.008369035

OK

OK

271235

83109

9.294310086

9382874

3039301

10769509

9234041

D6Sclrtm_ATAC11

D6 Sclerotome

13/8/2015

26/8/2015

328044572

305242787

181293318

101400785

20559368

0.35659

0.275679

1.094047

0.620269839

3.299242828

OK

OK

253472

100590

17.34139067

6701318

3110272

5575866

9432698

D6Sclrtm_ATAC12

D6 Sclerotome

13/8/2015

26/8/2015

138904558

130498363

77296400

45578855

13471630

0.591614

0.570517

2.065099

0.622210362

3.106016386

OK

OK

273702

100590

22.34978045

5050293

2376784

3803650

7543825

ESMT_ATAC13

D3 Somite

10/8/2015

26/8/2015

97028570

90293961

63339679

50618923

37539350

0.898727

0.903776

10.279185

0.603838363

2.810326908

OK

OK

282813

116312

12.47182107

11055518

4184717

10999339

14172891

ESMT_ATAC14

D3 Somite

10/8/2015

26/8/2015

91342558

84065314

58377777

46807655

34919048

0.90416

0.90955

10.96564

0.63869863

3.207448669

OK

OK

269952

116312

11.90248274

10346635

3811873

10541840

12560254

D3CrdcM_ATAC15

D3 Cardiac

10/8/2015

26/8/2015

191778720

183897391

125066804

80344503

35114474

0.817896

0.842331

6.475016

0.657794431

3.578035603

OK

OK

319458

180380

20.14099152

15988868

5748762

13938902

26578992

D3CrdcM_ATAC16

D3 Cardiac

10/8/2015

26/8/2015

134871886

129649682

87780976

57145039

26151482

0.839505

0.863365

7.520129

0.670442227

3.796855645

OK

OK

286851

180380

19.13967334

11303563

4006843

10070805

16347057

Drmmtm_ATAC19

D5 Dermomytome

12/8/2015

26/8/2015

152978836

144566390

108536158

84652575

60077794

0.79836

0.805027

5.208383

0.701894281

5.092762813

OK

OK

263326

48916

8.862852148

8300267

2617001

10695931

7189919

Drmmtm_ATAC20

D5 Dermomytome

12/8/2015

26/8/2015

71382368

67502665

50296672

40140535

29655914

0.865341

0.871256

7.841101

0.688026099

4.642126486

OK

OK

285309

48916

8.873565459

6769259

2144352

8681073

5847726

Smtmrs_ATAC21

D2.25 Somitomere

6/8/2015

26/8/2015

425477876

407097668

310085861

238535286

165584332

0.791969

0.797997

4.973526

0.730157497

5.929894484

OK

OK

280874

83545

9.602687176

9101861

2824194

11178718

8781283

Smtmrs_ATAC22

D2.25 Somitomere

6/8/2015

26/8/2015

178465724

169037246

129385205

104336662

78489898

0.86589

0.870784

7.749138

0.70693823

4.987984435

OK

OK

277098

83545

9.442978111

9099713

2875813

11146695

9079702

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