title: Genomic DNA from umbilical cord blood buffycoat 429

description:
U473
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 429


title: Genomic DNA from umbilical cord blood buffycoat 426

status: Public on Nov 05 2020

type: genomic

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

country: United Kingdom

institute: University of Oxford

description:
U470
Umbilical cord blood sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
R v3.4.2
Beta_for_GEO.txt includes Beta-mixture Quantile (BMIQ) normalized Beta Values.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: umbilical cord blood buffy coat 426

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from cord blood samples using QIAamp Blood DNA mini kit according to standard instructions.

tag: gender

value: Male

tag: tissue

value: Umbilical cord blood buffy coat

tag: maternal gdm status

value: No GDM


title: Genomic DNA from umbilical cord blood buffycoat 428

description:
U472
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 428


title: Genomic DNA from umbilical cord blood buffycoat 431

description:
U475
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 431

value: GDM


title: Genomic DNA from umbilical cord blood buffycoat 425

description:
U469
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 425


title: Genomic DNA from umbilical cord blood buffycoat 443

description:
U487
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 443


title: Genomic DNA from umbilical cord blood buffycoat 424

description:
U468
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 424

value: Female


title: Genomic DNA from umbilical cord blood buffycoat 423

description:
U467
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 423


title: Genomic DNA from umbilical cord blood buffycoat 422

description:
U466
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 422


title: Genomic DNA from umbilical cord blood buffycoat 419

description:
U463
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 419


title: Genomic DNA from umbilical cord blood buffycoat 418

description:
U462
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 418


title: Genomic DNA from umbilical cord blood buffycoat 416

description:
U460
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 416


title: Genomic DNA from umbilical cord blood buffycoat 420

description:
U464
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 420


title: Genomic DNA from umbilical cord blood buffycoat 415

description:
U459
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 415


title: Genomic DNA from umbilical cord blood buffycoat 421

description:
U465
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 421


title: Genomic DNA from umbilical cord blood buffycoat 413

description:
U457
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 413


title: Genomic DNA from umbilical cord blood buffycoat 412

description:
U456
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 412


title: Genomic DNA from umbilical cord blood buffycoat 414

description:
U458
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 414


title: Genomic DNA from umbilical cord blood buffycoat 409

description:
U453
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 409


title: Genomic DNA from umbilical cord blood buffycoat 410

description:
U454
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 410


title: Genomic DNA from umbilical cord blood buffycoat 408

description:
U452
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 408


title: Genomic DNA from umbilical cord blood buffycoat 406

description:
U450
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 406


title: Genomic DNA from umbilical cord blood buffycoat 407

description:
U451
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 407


title: Genomic DNA from umbilical cord blood buffycoat 404

description:
U447
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 404


title: Genomic DNA from umbilical cord blood buffycoat 405

description:
U448
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 405


title: Genomic DNA from umbilical cord blood buffycoat 403

description:
U446
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 403


title: Genomic DNA from umbilical cord blood buffycoat 402

description:
U445
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 402


title: Genomic DNA from umbilical cord blood buffycoat 400

description:
U443
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 400


title: Genomic DNA from umbilical cord blood buffycoat 401

description:
U444
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 401


title: Genomic DNA from umbilical cord blood buffycoat 399

description:
U442
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 399


title: Genomic DNA from umbilical cord blood buffycoat 397

description:
U439
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 397


title: Genomic DNA from umbilical cord blood buffycoat 398

description:
U441
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 398


title: Genomic DNA from umbilical cord blood buffycoat 396

description:
U438
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 396


title: Genomic DNA from umbilical cord blood buffycoat 417

description:
U461
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 417


title: Genomic DNA from umbilical cord blood buffycoat 395

description:
U437
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 395


title: Genomic DNA from umbilical cord blood buffycoat 393

description:
U434
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 393


title: Genomic DNA from umbilical cord blood buffycoat 394

description:
U435
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 394


title: Genomic DNA from umbilical cord blood buffycoat 411

description:
U455
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 411


title: Genomic DNA from umbilical cord blood buffycoat 392

description:
U433
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 392


title: Genomic DNA from umbilical cord blood buffycoat 390

description:
U431
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 390


title: Genomic DNA from umbilical cord blood buffycoat 388

description:
U428
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 388


title: Genomic DNA from umbilical cord blood buffycoat 389

description:
U430
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 389


title: Genomic DNA from umbilical cord blood buffycoat 387

description:
U427
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 387


title: Genomic DNA from umbilical cord blood buffycoat 385

description:
U424
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 385


title: Genomic DNA from umbilical cord blood buffycoat 382

description:
U421
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 382


title: Genomic DNA from umbilical cord blood buffycoat 391

description:
U432
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 391


title: Genomic DNA from umbilical cord blood buffycoat 381

description:
U420
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 381


title: Genomic DNA from umbilical cord blood buffycoat 380

description:
U419
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 380


title: Genomic DNA from umbilical cord blood buffycoat 386

description:
U426
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 386


title: Genomic DNA from umbilical cord blood buffycoat 378

description:
U417
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 378


title: Genomic DNA from umbilical cord blood buffycoat 383

description:
U422
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 383


title: Genomic DNA from umbilical cord blood buffycoat 375

description:
U414
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 375


title: Genomic DNA from umbilical cord blood buffycoat 373

description:
U412
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 373


title: Genomic DNA from umbilical cord blood buffycoat 374

description:
U413
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 374


title: Genomic DNA from umbilical cord blood buffycoat 371

description:
U410
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 371


title: Genomic DNA from umbilical cord blood buffycoat 370

description:
U409
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 370


title: Genomic DNA from umbilical cord blood buffycoat 372

description:
U411
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 372


title: Genomic DNA from umbilical cord blood buffycoat 368

description:
U405
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 368


title: Genomic DNA from umbilical cord blood buffycoat 369

description:
U406
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 369


title: Genomic DNA from umbilical cord blood buffycoat 367

description:
U404
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 367


title: Genomic DNA from umbilical cord blood buffycoat 366

description:
U403
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 366


title: Genomic DNA from umbilical cord blood buffycoat 364

description:
U401
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 364


title: Genomic DNA from umbilical cord blood buffycoat 384

description:
U423
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 384


title: Genomic DNA from umbilical cord blood buffycoat 363

description:
U400
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 363


title: Genomic DNA from umbilical cord blood buffycoat 365

description:
U402
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 365


title: Genomic DNA from umbilical cord blood buffycoat 361

description:
U397
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 361


title: Genomic DNA from umbilical cord blood buffycoat 358

description:
U394
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 358


title: Genomic DNA from umbilical cord blood buffycoat 362

description:
U398
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 362


title: Genomic DNA from umbilical cord blood buffycoat 360

description:
U396
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 360


title: Genomic DNA from umbilical cord blood buffycoat 356

description:
U392
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 356


title: Genomic DNA from umbilical cord blood buffycoat 357

description:
U393
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 357


title: Genomic DNA from umbilical cord blood buffycoat 376

description:
U415
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 376


title: Genomic DNA from umbilical cord blood buffycoat 377

description:
U416
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 377


title: Genomic DNA from umbilical cord blood buffycoat 355

description:
U391
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 355


title: Genomic DNA from umbilical cord blood buffycoat 379

description:
U418
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 379


title: Genomic DNA from umbilical cord blood buffycoat 349

description:
U384
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 349


title: Genomic DNA from umbilical cord blood buffycoat 350

description:
U385
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 350


title: Genomic DNA from umbilical cord blood buffycoat 354

description:
U390
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 354


title: Genomic DNA from umbilical cord blood buffycoat 351

description:
U386
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 351


title: Genomic DNA from umbilical cord blood buffycoat 353

description:
U389
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 353


title: Genomic DNA from umbilical cord blood buffycoat 346

description:
U380
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 346


title: Genomic DNA from umbilical cord blood buffycoat 345

description:
U379
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 345


title: Genomic DNA from umbilical cord blood buffycoat 347

description:
U381
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 347


title: Genomic DNA from umbilical cord blood buffycoat 344

description:
U378
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 344


title: Genomic DNA from umbilical cord blood buffycoat 342

description:
U376
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 342


title: Genomic DNA from umbilical cord blood buffycoat 343

description:
U377
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 343


title: Genomic DNA from umbilical cord blood buffycoat 341

description:
U375
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 341


title: Genomic DNA from umbilical cord blood buffycoat 340

description:
U374
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 340


title: Genomic DNA from umbilical cord blood buffycoat 359

description:
U395
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 359


title: Genomic DNA from umbilical cord blood buffycoat 339

description:
U373
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 339


title: Genomic DNA from umbilical cord blood buffycoat 337

description:
U371
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 337


title: Genomic DNA from umbilical cord blood buffycoat 338

description:
U372
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 338


title: Genomic DNA from umbilical cord blood buffycoat 335

description:
U369
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 335


title: Genomic DNA from umbilical cord blood buffycoat 336

description:
U370
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 336


title: Genomic DNA from umbilical cord blood buffycoat 332

description:
U366
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 332


title: Genomic DNA from umbilical cord blood buffycoat 333

description:
U367
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 333


title: Genomic DNA from umbilical cord blood buffycoat 352

description:
U387
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 352


title: Genomic DNA from umbilical cord blood buffycoat 329

description:
U363
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 329


title: Genomic DNA from umbilical cord blood buffycoat 328

description:
U362
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 328


title: Genomic DNA from umbilical cord blood buffycoat 348

description:
U383
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 348


title: Genomic DNA from umbilical cord blood buffycoat 326

description:
U359
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 326


title: Genomic DNA from umbilical cord blood buffycoat 327

description:
U360
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 327


title: Genomic DNA from umbilical cord blood buffycoat 323

description:
U356
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 323


title: Genomic DNA from umbilical cord blood buffycoat 324

description:
U357
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 324


title: Genomic DNA from umbilical cord blood buffycoat 322

description:
U355
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 322


title: Genomic DNA from umbilical cord blood buffycoat 325

description:
U358
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 325


title: Genomic DNA from umbilical cord blood buffycoat 320

description:
U353
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 320


title: Genomic DNA from umbilical cord blood buffycoat 321

description:
U354
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 321


title: Genomic DNA from umbilical cord blood buffycoat 316

description:
U349
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 316


title: Genomic DNA from umbilical cord blood buffycoat 319

description:
U352
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 319


title: Genomic DNA from umbilical cord blood buffycoat 317

description:
U350
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 317


title: Genomic DNA from umbilical cord blood buffycoat 318

description:
U351
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 318


title: Genomic DNA from umbilical cord blood buffycoat 314

description:
U347
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 314


title: Genomic DNA from umbilical cord blood buffycoat 312

description:
U345
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 312


title: Genomic DNA from umbilical cord blood buffycoat 330

description:
U364
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 330


title: Genomic DNA from umbilical cord blood buffycoat 311

description:
U344
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 311


title: Genomic DNA from umbilical cord blood buffycoat 334

description:
U368
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 334


title: Genomic DNA from umbilical cord blood buffycoat 315

description:
U348
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 315


title: Genomic DNA from umbilical cord blood buffycoat 310

description:
U343
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 310


title: Genomic DNA from umbilical cord blood buffycoat 331

description:
U365
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 331


title: Genomic DNA from umbilical cord blood buffycoat 309

description:
U342
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 309


title: Genomic DNA from umbilical cord blood buffycoat 308

description:
U341
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 308


title: Genomic DNA from umbilical cord blood buffycoat 313

description:
U346
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 313


title: Genomic DNA from umbilical cord blood buffycoat 307

description:
U340
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 307


title: Genomic DNA from umbilical cord blood buffycoat 306

description:
U339
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 306


title: Genomic DNA from umbilical cord blood buffycoat 303

description:
U336
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 303


title: Genomic DNA from umbilical cord blood buffycoat 305

description:
U338_rep1
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 305


title: Genomic DNA from umbilical cord blood buffycoat 302

description:
U335
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 302


title: Genomic DNA from umbilical cord blood buffycoat 304

description:
U337
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 304


title: Genomic DNA from umbilical cord blood buffycoat 300

description:
U333
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 300


title: Genomic DNA from umbilical cord blood buffycoat 298

description:
U331
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 298


title: Genomic DNA from umbilical cord blood buffycoat 301

description:
U334
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 301


title: Genomic DNA from umbilical cord blood buffycoat 296

description:
U328
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 296


title: Genomic DNA from umbilical cord blood buffycoat 294

description:
U326
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 294


title: Genomic DNA from umbilical cord blood buffycoat 291

description:
U323
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 291


title: Genomic DNA from umbilical cord blood buffycoat 293

description:
U325
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 293


title: Genomic DNA from umbilical cord blood buffycoat 288

description:
U320
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 288


title: Genomic DNA from umbilical cord blood buffycoat 289

description:
U321
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 289


title: Genomic DNA from umbilical cord blood buffycoat 286

description:
U318
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 286


title: Genomic DNA from umbilical cord blood buffycoat 287

description:
U319
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 287


title: Genomic DNA from umbilical cord blood buffycoat 285

description:
U316
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 285


title: Genomic DNA from umbilical cord blood buffycoat 284

description:
U315
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 284


title: Genomic DNA from umbilical cord blood buffycoat 282

description:
U312
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 282


title: Genomic DNA from umbilical cord blood buffycoat 277

description:
U305
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 277


title: Genomic DNA from umbilical cord blood buffycoat 283

description:
U314
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 283


title: Genomic DNA from umbilical cord blood buffycoat 278

description:
U307
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 278


title: Genomic DNA from umbilical cord blood buffycoat 276

description:
U304
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 276


title: Genomic DNA from umbilical cord blood buffycoat 280

description:
U309
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 280


title: Genomic DNA from umbilical cord blood buffycoat 279

description:
U308
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 279


title: Genomic DNA from umbilical cord blood buffycoat 281

description:
U311
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 281


title: Genomic DNA from umbilical cord blood buffycoat 274

description:
U302
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 274


title: Genomic DNA from umbilical cord blood buffycoat 299

description:
U332
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 299


title: Genomic DNA from umbilical cord blood buffycoat 275

description:
U303
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 275


title: Genomic DNA from umbilical cord blood buffycoat 297

description:
U330
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 297


title: Genomic DNA from umbilical cord blood buffycoat 272

description:
U300
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 272


title: Genomic DNA from umbilical cord blood buffycoat 295

description:
U327
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 295


title: Genomic DNA from umbilical cord blood buffycoat 271

description:
U299
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 271


title: Genomic DNA from umbilical cord blood buffycoat 270

description:
U298
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 270


title: Genomic DNA from umbilical cord blood buffycoat 273

description:
U301
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 273


title: Genomic DNA from umbilical cord blood buffycoat 269

description:
U297
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 269


title: Genomic DNA from umbilical cord blood buffycoat 268

description:
U295
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 268


title: Genomic DNA from umbilical cord blood buffycoat 267

description:
U294
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 267


title: Genomic DNA from umbilical cord blood buffycoat 290

description:
U322
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 290


title: Genomic DNA from umbilical cord blood buffycoat 265

description:
U292
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 265


title: Genomic DNA from umbilical cord blood buffycoat 292

description:
U324
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 292


title: Genomic DNA from umbilical cord blood buffycoat 266

description:
U293
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 266


title: Genomic DNA from umbilical cord blood buffycoat 264

description:
U291
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 264


title: Genomic DNA from umbilical cord blood buffycoat 262

description:
U289
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 262


title: Genomic DNA from umbilical cord blood buffycoat 263

description:
U290
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 263


title: Genomic DNA from umbilical cord blood buffycoat 261

description:
U288
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 261


title: Genomic DNA from umbilical cord blood buffycoat 259

description:
U285
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 259


title: Genomic DNA from umbilical cord blood buffycoat 257

description:
U278
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 257


title: Genomic DNA from umbilical cord blood buffycoat 258

description:
U284
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 258


title: Genomic DNA from umbilical cord blood buffycoat 260

description:
U287
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 260


title: Genomic DNA from umbilical cord blood buffycoat 253

description:
U274
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 253


title: Genomic DNA from umbilical cord blood buffycoat 255

description:
U276
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 255


title: Genomic DNA from umbilical cord blood buffycoat 254

description:
U275
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 254


title: Genomic DNA from umbilical cord blood buffycoat 251

description:
U272_rep2
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 251


title: Genomic DNA from umbilical cord blood buffycoat 250

description:
U271
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 250


title: WT5

type: SRA

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

country: USA

institute: UT Southwestern Medical Center

description: Ascl1-WT tumors

library_source: transcriptomic

data_processing:
Reads were mapped to mm10 assembly using tophat
Transcripts quantificationwas done by featurecounts and differential expression was estimated using DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: Count matrix

molecule: total RNA

organism: Mus musculus

source_name: glioma brain tumor

extract_protocol:
RNA was isolated using commercially available kits
Library preparation was done by the UTSW Next Generation Sequencing Core

treatment_protocol: A single dose of tamoxifen (62.5 mg/K g of bodyweight) was administered intraperitoneally (IP) to pregnant females at E14.5. Tumors were isolated from the brains of symptomatic mice between 2-4 months of age.

tag: cell type

value: gliomas

tag: genotype


title: WT4

description: Ascl1-WT tumors


title: WT3

description: Ascl1-WT tumors


title: WT1

description: Ascl1-WT tumors


title: Genomic DNA from umbilical cord blood buffycoat 249

description:
U270
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 249


title: Genomic DNA from umbilical cord blood buffycoat 248

description:
U269
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 248


title: Genomic DNA from umbilical cord blood buffycoat 252

description:
U273
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 252


title: WT2

description: Ascl1-WT tumors


title: Genomic DNA from umbilical cord blood buffycoat 247

description:
U268
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 247


title: CKO5

description: Ascl1-CKO tumors


title: WT mESC - RNA-seq rep2

city: Clayton

first: Monika

last: Mohenska

state: VIC

address: 15 Innovation Walk

country: Australia

institute: Monash University

data_processing:
TINC-seq data processing:    Raw FASTQ files were quality trimmed with Trimmomatic v0.36, parameters SE -phred 33 SLIDINGWINDOW:3:15 MINLEN:36. FASTQ files were then mapped to a GENCODE’s GRCm38 with default parameters. Following this, sambamba was used to convert the mapped .sam files into .bam files. The .bam files which were then sorted and indexed with sambamba using default parameters. Unlike conventional DNA-pull down techniques such as ChIP or genome wide sequencing experiments, TINC-seq targets a very small fraction of the genome (in theory only one region). Due to the low input fraction and the fact that mostly similar sequences should be pulled down, the method is prone to more noise than experiments which include a vast proportion of the genome. For this reason reads were then quality filtered for blacklisted regions as well as repeat masker regions. Peak calling was then performed with macs2 v2.1.1.20160309 on pooled (by macs2) TALE1 or TALE2 replicates over the input, with the --no-model parameter, reads of MAPQ>10 were considered, and a FDR cut-off of 0.01 was applied. HOMER’s (v3.2) mergePeaks function was applied to calculated overlapping peaks with the parameter -d given. Motif enrichment analysis was performed on peaks called for each TALE sample with meme v5.0.1. The bedtools2 v2.25.0, function getfasta was used to convert the enriched peak regions of each TALE into fasta files. These were then utilised for the motif enrichment analysis with the parameters -dna -revcomp -minw 8 -maxw18.
ChIP-seq data processing:    Data was first quality trimmed with Trimmomatic v0.36 (Bolger, Lohse, and Usadel 2014) with the parameters SE (single-end) or PE (paired-end) -phred 33 SLIDINGWINDOW:3:15 MINLEN:36. FASTtQ files were then mapped to a customized GENCODE’s GRCm38, which included the RCOR2-HA, and mCherry ORF sequences (Rcor2 (C-3xHA-tag; VectorBuilder), mCherry (ORF:IRES:mCherry:T2A:puromycin)) with Bowtie2 v2.3.4.1, with default mapping parameters. Sambamba was used to convert mapped .sam files into .bam files, then sort and index them with default parameters. Reads were then quality filtered for blacklisted regions, and reads with MAPQ>10 were retained using samtools v1.8 and GNU parallel. This was followed by peak calls macs2 v2.1.1.20160309, using the parameters --keep-dup 1 -g 1.87e9. Biological replicates of samples and negative controls were pooled with  macs2, and then using HOMER’s mergePeak function, peaks within 700bp of their peak centre were merged. HOMER’s mergePeak function was then used to determine all variations of co-occupancy between RCOR2 and published (OCT4, SOX2, NANOG, LSD1, NuRD complex, REST/CoREST complex and ESC enhancers) data sets using the parameter -d dist, followed by genomic annotation of all regions using HOMER’s annotatePeaks.pl function (default parameters). This provided the final RCOR2 ChIP-seq peak set.
ATAC-seq data processing:    Data was first quality trimmed with Trimmomatic v0.36, with the parameters PE -phred 33 SLIDINGWINDOW:3:15 MINLEN:36. FASTQ files were then mapped to GENCODE’s GRCm38 with Bowtie2 v2.3.4.1, with default mapping parameters. Sambamba was used to convert mapped .sam files into .bam files, and then sort and index them with default parameters. Reads were then quality filtered for blacklisted regions, and reads with MAPQ>10 were retained using samtools v1.8 and GNU parallel. No peak calling was required for the study.
RNA-seq data processing:    Raw RNA-seq reads in the form of FASTQ format were demultiplexed with sabre using parameters pe -c -u -m 1 -l 8 -n -a 1, for the multiplexing indexes. Trimmomatic v0.36 was ised for quality trimming, with the parameters SE -phred 33 SLIDINGWINDOW:3:15 MINLEN:36. FASTQ files were then mapped to a customized GENCODE’s GRCm38, which included the RCOR2-HA, and mCherry ORF sequences (Rcor2 (C-3xHA-tag; VectorBuilder), mCherry (ORF:IRES:mCherry:T2A:puromycin)), with STAR v2.5.2b, using the parameters --outSAMattributes All --alignIntronMax 1000000 --alignEndsType EndToEnd, samples were sorted with Sambamba, and default parameters. Read counts were then generated with Subread’s featureCount function, using default parameters.
bigWig files were generated using deeptools2. Library size normalised (CPM) BigWig files were generated for all samples with parameters -bs 1 --minMappingQuality 10 --exactsScaling --ignoreDuplicates. For TINC-seq and ChIP-seq samples, the step was followed by generation of mean BigWig samples between the replicates and removal of the input sample (TINC-seq) or negative control (ChIP-seq). The parameters used were --scaleFactors 1:1 -bs 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig; raw counts

source_name: WT mESC - RNA-seq

growth_protocol: ESCs were cultured in gelatin coated dishes at 37°C, 5%  CO2 in ESC media (KnockOutTM DMEM (Life Technologies) containing 15% Fetal Bovine Serum (Thermo Scientific), GlutaMAX Supplement, MEM Non-Essential Amino Acids Solution , Penicillin-Streptomycin, 0.1% (v/v) 2-Mercaptoethanol, 1000 U/mL Leukemia Inhibitory Factor, and 2i (1mM PD0325901 (StemMACS) and 3mM CHIR99021 (StemMACS)).

extract_protocol:
RNA was extracted from approximately 1 x 10^6 cells with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA was eluted from the columns with 50 μL RNase-free water and quantified using a Nanodrop.
Library preparation was performed as previously described in, using unique indexes for each sample (ESCs TAAGGCGA and CGTACTAG, Rcor2 KO AGGCAGAA and TCCTGAGC) for multiplexing. Paired end sequencing was performed using 19 bp forward (used for de-multiplexing) and 72 bp reverse reads, with an Illumina NextSeq550 sequencing machine.

tag: strain background

value: WT

value: embryonic stem cells (ESCs)


title: Non-smoker, exoRNA_batch2_biological rep 4

type: RNA

city: Rochester

first: Irfan

last: Rahman

state: NY

address: 601 elmwood ave

department: Environmental Medicine

institute: University of Rochester Medical Center

description: Exosomal RNA

hyb_protocol: Following labelling, single-stranded cDNA(25ng/µl) was mixed hybridized  and loaded onto the GeneChip Cartridge array provided with the kit and incubated for 16 hrs at 45 degree Celsius and 60 rpm rotation in GeneChip™ Hybridization Oven.

scan_protocol: GeneChips were scanned using the GeneChip™ Scanner 3000 System .

data_processing: The data files obtained after the scan were analyzed using the Transcriptome Analysis Console (TAC 4.0.1) Software using the Data flow worksheet as provided by Affymetrix.  The expression data was normalized and log2 transformed expression values of lncRNAs were plotted using R.

label: biotin

source_name: Exosomal RNA isolated from the plasma of non-smoker

label_protocol: Biotinylated cRNA were prepared according to the standard protocol provided with the GeneChip WT Pico kit(Cat# 902622 and 902623, Applied Biosystems, Foster city, CA) from approximately 6 ug ss-cDNA (Publication Number: MAN0017893).

extract_protocol: Norgen Biotek (Cat# 57400; Ontario, Canada) kit was employed to isolate exosomes from human plasma.Thereafter, total RNA from exosomes was isolated using Exosomal RNA isolation kit (Norgen Bioteck Corporation, Cat# 58000).

tag: smoking status

value: Non-smoker

tag: sample type

value: plasma-derived exosomes


title: Genomic DNA from umbilical cord blood buffycoat 246

description:
U267
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 246


title: CKO4

description: Ascl1-CKO tumors


title: RCOR2 KO mESC - RNA-seq rep2

source_name: RCOR2 KO mESC - RNA-seq

value: RCOR2 KO


title: Waterpipe user, exoRNA_batch2_biological rep 4

description: Exosomal RNA

source_name: Exosomal RNA isolated from the plasma of WP user

value: Waterpipe user


title: Non-smoker, exoRNA_batch2_biological rep 6

description: Exosomal RNA


title: Genomic DNA from umbilical cord blood buffycoat 256

description:
U277
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 256


title: Cigarette Smoker, exoRNA_batch2_biological rep 6

description: Exosomal RNA

source_name: Exosomal RNA isolated from the plasma of smoker

value: Cigarette Smoker


title: E-cig Vaper, exoRNA_batch2_biological rep 5

description: Exosomal RNA

source_name: Exosomal RNA isolated from the plasma of E-cig vaper

value: E-cig Vaper


title: E-cig Vaper, exoRNA_batch2_biological rep 6

description: Exosomal RNA


title: E-cig Vaper, exoRNA_batch2_biological rep 4

description: Exosomal RNA


title: Genomic DNA from umbilical cord blood buffycoat 245

description:
U266
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 245


title: Dual Smoker, exoRNA_batch2_biological rep 6

description: Exosomal RNA

source_name: Exosomal RNA isolated from the plasma of dual smoker

value: Dual Smoker


title: RCOR2 KO mESC - RNA-seq rep1


title: Cigarette Smoker, exoRNA_batch2_biological rep 5

description: Exosomal RNA


title: Dual Smoker, exoRNA_batch2_biological rep 2

description: Exosomal RNA


title: Waterpipe user, exoRNA_batch2_biological rep 6

description: Exosomal RNA


title: Non-smoker, exoRNA_batch2_biological rep 5

description: Exosomal RNA


title: Waterpipe user, exoRNA_batch2_biological rep 5

description: Exosomal RNA


title: Dual Smoker, exoRNA_batch2_biological rep 3

description: Exosomal RNA


title: Cigarette Smoker, exoRNA_batch2_biological rep 4

description: Exosomal RNA


title: Dual Smoker, exoRNA_batch2_biological rep 4

description: Exosomal RNA


title: CKO2

description: Ascl1-CKO tumors


title: Dual Smoker, exoRNA_batch2_biological rep 5

description: Exosomal RNA


title: Genomic DNA from umbilical cord blood buffycoat 240

description:
U261_rep1
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 240


title: CKO1

description: Ascl1-CKO tumors


title: Genomic DNA from umbilical cord blood buffycoat 243

description:
U264
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 243


title: WT mESCs - ATAC-seq

library_source: genomic

source_name: WT mESCs - ATAC-seq

extract_protocol:
50,000 FACS isolated cells were collected at 500 x g for 5 min at 4 degrees celsius and then washed in 50 ml of cold PBS. Cells were collected at 500 x g for 5 min at 4_x0004_C and the cell pellets were resuspended in 50 ml of cold ATAC lysis buffer (10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 10 mMTris pH 7.4) by pipetting slowly up and down. The samples were spun down immediately at 500 x g for 10 min at 4 degrees celsius  and the supernatants were removed by carefully pipetting away from the pellets. For the transposition reaction, 22.5 ml of UltraPure Distilled Water (Life Technologies, Cat#10977-015), 25 ml of Tagment DNA Buffer (Illumina, Cat#15027866) and 2.5 ml of Tagment DNA Enzyme 1 (Illumina, Cat#15027865) were combined and added to each pellet. The samples were then incubated at 37 degrees celsius for 30 min followed by immediate purification using a MinElute Reaction Cleanup Kit (QIAGEN, Cat#28204) according to the manufacturer’s specification, except for the final elution volume, which was 11 ml. The PCR was set up in a 50 ml reaction volume using 11 ml of transposed DNA, 25 ml of the NEBNext High-Fidelity 2x PCR Master Mix (Cat#M0541S) and 1.25 mM of the ATACseq oligos published previously (Buenrostro et al., 2013). PCR parameters were: 72 degrees celsius for 5 min, 98 degrees celsius for 30 s and 9 cycles of 98 degrees celsius for 10 s, 63 degrees celsius for 30 s and 72 degrees celsius for 1 min. Libraries were purified using a QIAGEN MinElute PCR purification kit (QIAGEN, Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880) according to the manufacturer’s recommendations.
For the library construction, library fragments ranging from 150-600bp were enriched and libraries were sequenced in 2x75 cycle paired-end read format, with a total of 150.8 million reads, on a NextSeq550 High output v2.5 Illumina machine.


title: WT mESCs - RCOR2 ChIP-seq negative control rep1

extract_protocol:
Approximately 30 x 10^6 cells were used per ChIP. The samples were pre-cleared with 100 μL of Pierce Control Agarose Resin (Thermo Fisher Scientific) for 1 h  at 4 °C and immunoprecipitations were performed with 30 μL of Pierce Anti-HA Agarose (Thermo Fisher Scientific) per sample rotating overnight at 4 °C.
Libraries were prepared using the ThruPLEX DNA-seq 12S kit (Rubicon Genomics, Cat#R400429). After limited PCR amplification, libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880), according to the manufacturer’s recommendations. 75 bp single read sequencing was performed on an Illumina NextSeq500.

tag: antibody


title: Genomic DNA from umbilical cord blood buffycoat 242

description:
U263
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 242


title: Genomic DNA from umbilical cord blood buffycoat 239

description:
U260
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 239


title: WT mESCs - TINC-seq Input

data_processing:
library strategy: TALE-mediated Isolation of Nuclear Chromatin (TINC)-seq
TINC-seq data processing:    Raw FASTQ files were quality trimmed with Trimmomatic v0.36, parameters SE -phred 33 SLIDINGWINDOW:3:15 MINLEN:36. FASTQ files were then mapped to a GENCODE’s GRCm38 with default parameters. Following this, sambamba was used to convert the mapped .sam files into .bam files. The .bam files which were then sorted and indexed with sambamba using default parameters. Unlike conventional DNA-pull down techniques such as ChIP or genome wide sequencing experiments, TINC-seq targets a very small fraction of the genome (in theory only one region). Due to the low input fraction and the fact that mostly similar sequences should be pulled down, the method is prone to more noise than experiments which include a vast proportion of the genome. For this reason reads were then quality filtered for blacklisted regions as well as repeat masker regions. Peak calling was then performed with macs2 v2.1.1.20160309 on pooled (by macs2) TALE1 or TALE2 replicates over the input, with the --no-model parameter, reads of MAPQ>10 were considered, and a FDR cut-off of 0.01 was applied. HOMER’s (v3.2) mergePeaks function was applied to calculated overlapping peaks with the parameter -d given. Motif enrichment analysis was performed on peaks called for each TALE sample with meme v5.0.1. The bedtools2 v2.25.0, function getfasta was used to convert the enriched peak regions of each TALE into fasta files. These were then utilised for the motif enrichment analysis with the parameters -dna -revcomp -minw 8 -maxw18.
ChIP-seq data processing:    Data was first quality trimmed with Trimmomatic v0.36 (Bolger, Lohse, and Usadel 2014) with the parameters SE (single-end) or PE (paired-end) -phred 33 SLIDINGWINDOW:3:15 MINLEN:36. FASTtQ files were then mapped to a customized GENCODE’s GRCm38, which included the RCOR2-HA, and mCherry ORF sequences (Rcor2 (C-3xHA-tag; VectorBuilder), mCherry (ORF:IRES:mCherry:T2A:puromycin)) with Bowtie2 v2.3.4.1, with default mapping parameters. Sambamba was used to convert mapped .sam files into .bam files, then sort and index them with default parameters. Reads were then quality filtered for blacklisted regions, and reads with MAPQ>10 were retained using samtools v1.8 and GNU parallel. This was followed by peak calls macs2 v2.1.1.20160309, using the parameters --keep-dup 1 -g 1.87e9. Biological replicates of samples and negative controls were pooled with  macs2, and then using HOMER’s mergePeak function, peaks within 700bp of their peak centre were merged. HOMER’s mergePeak function was then used to determine all variations of co-occupancy between RCOR2 and published (OCT4, SOX2, NANOG, LSD1, NuRD complex, REST/CoREST complex and ESC enhancers) data sets using the parameter -d dist, followed by genomic annotation of all regions using HOMER’s annotatePeaks.pl function (default parameters). This provided the final RCOR2 ChIP-seq peak set.
ATAC-seq data processing:    Data was first quality trimmed with Trimmomatic v0.36, with the parameters PE -phred 33 SLIDINGWINDOW:3:15 MINLEN:36. FASTQ files were then mapped to GENCODE’s GRCm38 with Bowtie2 v2.3.4.1, with default mapping parameters. Sambamba was used to convert mapped .sam files into .bam files, and then sort and index them with default parameters. Reads were then quality filtered for blacklisted regions, and reads with MAPQ>10 were retained using samtools v1.8 and GNU parallel. No peak calling was required for the study.
RNA-seq data processing:    Raw RNA-seq reads in the form of FASTQ format were demultiplexed with sabre using parameters pe -c -u -m 1 -l 8 -n -a 1, for the multiplexing indexes. Trimmomatic v0.36 was ised for quality trimming, with the parameters SE -phred 33 SLIDINGWINDOW:3:15 MINLEN:36. FASTQ files were then mapped to a customized GENCODE’s GRCm38, which included the RCOR2-HA, and mCherry ORF sequences (Rcor2 (C-3xHA-tag; VectorBuilder), mCherry (ORF:IRES:mCherry:T2A:puromycin)), with STAR v2.5.2b, using the parameters --outSAMattributes All --alignIntronMax 1000000 --alignEndsType EndToEnd, samples were sorted with Sambamba, and default parameters. Read counts were then generated with Subread’s featureCount function, using default parameters.
bigWig files were generated using deeptools2. Library size normalised (CPM) BigWig files were generated for all samples with parameters -bs 1 --minMappingQuality 10 --exactsScaling --ignoreDuplicates. For TINC-seq and ChIP-seq samples, the step was followed by generation of mean BigWig samples between the replicates and removal of the input sample (TINC-seq) or negative control (ChIP-seq). The parameters used were --scaleFactors 1:1 -bs 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig; raw counts

source_name: WT mESCs - TINC-seq Input

extract_protocol:
Approximately 1 x 10^9 cells were fixed with formaldehyde and nuclei and chromatin were isolated to remove non-chromatin-associated proteins. The chromatin was then resuspended in ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8) containing protease inhibitor cocktail (Sigma Cat#P3840) at 1g of chromatin per 3.2mL of buffer and sonicated on a Bioruptor NextGen device (Diagenode) to shear the chromatin to an average fragment size of 200 - 500 bp. The samples were then diluted 1:5 with ChIP dilution buffer (165 mM NaCl, 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris pH 8.0) containing protease inhibitor cocktail and 0.05% input was put aside on ice. Additionally, 0.05% of the sample was used to determine the DNA concentration to ensure the same amount of chromatin was used for TALE and control samples in the TINC assay. To do so, cross-linking was reversed for 15 min at 100°C, then the sample was purified using a QIAquick PCR Purification Kit (Qiagen) and DNA concentration determined using the Qubit dsDNA HS Assay Kit and Qubit 2.0 Fluorometer (Thermo Fisher Scientific). The samples were then precleared with 1 mL of settled Control Agarose Resin (Pierce Cat#26150) for 1h at 4°C.  TALE-immunoprecipitations were performed with 1 mL of settled Anti-HA Agarose Resin (Pierce 26182) overnight at 4°C. Samples were then washed twice for 10 min at 4°C with dilution buffer containing protease inhibitor cocktail, followed by two washes for 10 min at 4 °C with low salt buffer (150 mM NaCl, 0.5% Na deoxycholate, 0.1% SDS, 1% NP-40, 1 mM EDTA, 50 mM Tris pH 8) containing protease inhibitor cocktail, two washes for 10 min at 4°C with high salt buffer (500 mM NaCl, 0.5% Na deoxycholate, 0.1% SDS, 1% Nonidet P-40, 1 mM EDTA, 50mM Tris pH 8) and a final 5 min wash at 4 °C with TE buffer (0.25 mM EDTA, 10mM Tris pH 8). The volume was 100 mL for each wash step. For elution, the samples were resuspended in 2 mL of 3M NaSCN and incubated rotating for 5 min at room temperature. The eluted samples were removed and the elution step was repeated three times. All four elutions were pooled and concentrated using 3 KDa cut-off concentrators (Amicon Ultra, Cat#UFC800308 and Cat#UFC500308) to 50 μL. During concentration, the samples were diluted 1:20 with PBS to dilute the NaSCN. 1 μL per sample was then removed and processed along with the input sample for DNA purification.
Libraries were prepared using the ThruPLEX DNA-seq 12S kit (Rubicon Genomics, Cat#R400429). After limited PCR amplification, libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880), according to the manufacturer’s recommendations. TINC-seq samples 75 bp single reads were sequenced on a NextSeq550 High output mode and v2 chemistry.

value: TALE expressing

value: Input


title: Genomic DNA from umbilical cord blood buffycoat 238

description:
U259
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 238

value: Male


title: Genomic DNA from umbilical cord blood buffycoat 237

description:
U258
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 237

value: Umbilical cord blood buffy coat


title: WT mESCs - TINC-seq Nanog locus TALE 2 rep2

source_name: WT mESCs - TINC-seq Nanog locus TALE 2

value: Anti-HA Agarose Resin (Pierce 26182)


title: WT mESCs - RCOR2 ChIP-seq rep1

source_name: WT mESCs - RCOR2 ChIP-seq

value: RCOR2-HA expressing

value: Pierce Anti-HA Agarose (Thermo Fisher Scientific)


title: Genomic DNA from umbilical cord blood buffycoat 241

description:
U262
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 241

value: No GDM


title: WT mESCs - TINC-seq Nanog locus TALE 1 rep2

source_name: WT mESCs - TINC-seq Nanog locus TALE 1


title: WT mESCs - TINC-seq Nanog locus TALE 2 rep1


title: Genomic DNA from umbilical cord blood buffycoat 236

description:
U257
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 236

value: Female


title: CKO3

description: Ascl1-CKO tumors

source_name: glioma brain tumor

value: gliomas


title: Genomic DNA from umbilical cord blood buffycoat 235

description:
U256
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 235


title: Genomic DNA from umbilical cord blood buffycoat 234

description:
U255
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 234

value: GDM


title: WT mESCs - TINC-seq Nanog locus TALE 1 rep1

value: embryonic stem cells (ESCs)


title: Genomic DNA from umbilical cord blood buffycoat 244

description:
U265
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 244


title: Dual Smoker, exoRNA_batch2_biological rep 1

description: Exosomal RNA

source_name: Exosomal RNA isolated from the plasma of dual smoker

value: plasma-derived exosomes


title: WT mESC - RNA-seq rep1

source_name: WT mESC - RNA-seq

value: WT


title: Genomic DNA from umbilical cord blood buffycoat 233

description:
U254
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 233


title: Genomic DNA from umbilical cord blood buffycoat 232

description:
U253
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 232


title: LVS_pigR_pF

city: Boston

first: Simon

middle: L

last: Dove

state: MA

address: 300 Longwood Ave

department: Division of Infectious Diseases

institute: Boston Children's Hospital and Harvard Medical School

description: rRNA-depleted RNA

data_processing:
Sequenced reads were trimmed for adaptor sequences and mapped to the LVS genome using bowtie2 v. 2.2.6 with parameters -N 1 -L 28 -i S,1,2.00 -D 20
Sam files were converted to bam files using samtools, bam files were converted to bedgraph files using bedtools, and bedgraph files were converted to bigwig using bedGraphToBigWig
HTSeq-count was used to determine how many reads mapped to each gene using the NC_007880 F. tularensis LVS gene annotation
Differential expression analysis was performed with DESeq2
Genome_build: NC_007880.1
Supplementary_files_format_and_content: bigwig files were generated from alignment files as indicated above and represent read count per base pair

organism: Francisella tularensis

source_name: Bacterial cells grown OD600 0.3 - 0.4

growth_protocol: On cystine heart agar plates, large patches were made from single colonies. Individual patches were scraped up and resuspsended in supplemented Mueller-Hinton broth. Cultures were grown with aeration at 37°C until OD600 reached 0.3 - 0.4

extract_protocol:
Total RNA was extracted using Direct-zol Minprep kit (Zymo Research) and rRNA was depleted using the Ribo-Zero Magnetic Bead kit (Epicentre)
Sequencing libraries were generated using KAPA stranded RNA-Seq libary preparation kit (Kapa Biosystems) following manufacturer's instructions

value: delta-pigR with pF plasmid

tag: strain

value: LVS


title: LVS_mglA_pF

description: rRNA-depleted RNA

value: delta-mglA with pF plasmid


title: liragutide 2

city: Akita

first: Takehiro

last: Sato

state: Akita

address: Hondo 1-1-1

department: Endocrinology, Diabetes, and Geriatric Medicine

country: Japan

institute: Akita University

hyb_protocol: Following fragmentation, 600 ng of cRNA were hybridized for 17 hr at 65C in a rotating Agilent hybridization oven. GeneChips were washed by Agilent's washer Buffer.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x80k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (GE1_107_Sep09 Protocol).

source_name: lung

label_protocol: Cy-3 cRNA were prepared according to the protocol recommended by Agilent from 100 ug total RNA (low Input Quick Amp Labeling ver 6.5, May 2005).

extract_protocol: Total RNA was extracted from frozen middle lobes of right lung using RNeasy Mini kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Liraglutide(200 μg per kg body weight/0.2ml) or saline (0.2ml) are subcutaneously injected to each mice.

value: lung

tag: age

value: 9 week

value: male

tag: treatment


title: vehicle 3

value: saline (0.2ml)


title: Left ventricle E2 rep2

city: Berlin

first: Georgios

last: Kararigas

address: Hessische Str. 3-4

country: Germany

institute: Charite University Hospital

description: Left ventricle E2 rep2

hyb_protocol: Biotinylated cRNA was prepared and hybridized according to the standard Affymetrix processing protocol.

scan_protocol: The array was scanned in a GeneChip Scanner 3000.

data_processing: The data were normalized and transformed using R version 2.14.2, the Bioconductor package 'vsn' and the vsnrma algorithm with all defualt values, i.e. library('vsn') vsnrmadata = vsnrma(object = data).

source_name: Left ventricle E2

growth_protocol: The mice were kept on a 12-hour light, 12-hour dark cycle in temperature-controlled rooms with water ad libitum.

extract_protocol: Total RNA was isolated using the RNeasy Fibrous Tissue Mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Left ventricles were snap frozen in liquid nitrogen and stored at -80°C until further analysis.

value: left ventricle


title: liragutide 1

value: Liraglutide(200 μg per kg body weight/0.2ml)


title: vehicle 2


title: liragutide 3


title: Genomic DNA from umbilical cord blood buffycoat 231

description:
U252
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 231

value: Male

value: Umbilical cord blood buffy coat


title: Waterpipe user, exoRNA_batch1_biological rep 2

description: Exosomal RNA

source_name: Exosomal RNA isolated from the plasma of WP user

value: Waterpipe user


title: Left ventricle E2 rep1

description: Left ventricle E2 rep1

label_protocol: Biotinylated cRNA was prepared and hybridized according to the standard Affymetrix processing protocol.


title: Genomic DNA from umbilical cord blood buffycoat 230

description:
U251
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 230

value: Female


title: Scerevisiae_Ctrl_rep2

city: Frederick

first: Girma

middle: Moges

last: Woldemichael

state: Maryland

institute: National Cancer Institute-Frederick

hyb_protocol: Arrays were incubated overnight and then stained and scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix). Please see Jo et al., 2009, PMID: 19635755

data_processing: Raw TAG4 array data were log2 transformed, corrected for signal saturation as previously described (Pierce et al., 2006), and corrected for mean chip background using robust location and scale estimators for log2-transformed intensities of null features (total of 18,000 equally distributed on the array). Please see Jo et al., 2009, PMID: 19635755

organism: Saccharomyces cerevisiae

source_name: Pooled Saccharomyces cerevisiae heterozygous and homozygous deletion mutants treated with DMSO

label_protocol: The strain-specific barcodes in the DNA were amplified by PCR using a set of biotinylated primers. Please see Jo et al., 2009, PMID: 19635755

extract_protocol: Heterozygous and homozygous deletion mutant samples were combined and 3OD600 unit of cells were collected and genomic DNA was extracted using YeaStar Genomic DNA kit (Zymo Research, #D2002)

tag: agent

value: Control treatment


title: Scerevisiae_mithramycin_rep2

scan_protocol: Arrays were incubated overnight and then stained and scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix). Please see Jo et al., 2009, PMID: 19635755

source_name: Pooled Saccharomyces cerevisiae heterozygous and homozygous deletion mutants treated with 2.7 mM Mithramycin A

value: Mithramycin treatment


title: Cigarette Smoker, exoRNA_batch1_biological rep 3

description: Exosomal RNA

source_name: Exosomal RNA isolated from the plasma of smoker

value: Cigarette Smoker

value: plasma-derived exosomes


title: vehicle 1


title: 24h_3

city: Xinyang

first: Qingsong

last: Liu

state: Henan

address: No. 237, Nanhu road

country: China

institute: Xinyang Normal University

data_processing:
For transcriptome data, raw Illumina data of fastq format were first processed using in-house perl scripts. After removing reads containing adaptors, reads containing poly-N and low-quality reads from raw data, we obtained the clean data. The Q20, Q30, GC (guanine-cytosine)-content and sequence duplication level of the clean data were calculated. The clean reads were aligned to the reference genome IRGSP-1.0 (https://rapdb.dna.affrc.go.jp)using HISAT2 tools (version 2.09)
Feature Counts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. Gene expression levels were estimated using fragments per kilobase of transcript per million mapped reads (FPKM) based on the length of the gene and reads count mapped to this gene. Differentially expressed genes analysis was performed using the DESeq2 R package.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each sample.

organism: Oryza sativa

source_name: rice plant leaves

extract_protocol:
Total RNA from rice leaves samples was isolated using TRIzol Reagent (Life Technologies, Grand Island, NY, USA) following to the manufacturer’s instructions.
Libraries were prepared using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA USA) according to the manufacturer’s instructions.

treatment_protocol: A soft brush was used to place one 3rd-instar C. medinalis on the second leaf from the top. The larvae were starved for 2 h before experiments and confined within a small Parafilm bag. For the time-course bioassays, the larvae were transferred to rice leaves for the final 1, 6, 12, or 24 h of the experiment (Figure S1). Control rice plants were placed in the same type of Parafilm bags as in the herbivory treatment but without placement of insects. All leaf materials were harvested at the same time. The samples were immediately frozen in liquid nitrogen and stored at -80 °C for further use. Five leaf tissues collected from five independent plants within the same treatments were merged as one sample (i.e., biological replicate).

value: rice plant leaves

value: five weeks

tag: time point


title: 24h_4


title: Genomic DNA from umbilical cord blood buffycoat 229

description:
U250
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 229

value: GDM


title: 24h_2


title: Waterpipe user, exoRNA_batch1_biological rep 3

description: Exosomal RNA


title: 24h_1


title: NAA15+/K336* iPS cardiomyocytes

first: Jon

last: Seidman

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Libraries were sequenced (Illumina HiSeq 2000 or Illumina HiSeq 2500, 50-base paired-end reads).
All data was combined into a single fastq file
Reads were aligned to the hg19 reference genome using STAR.
Mitochondrial and duplicate reads were discarded using Samtools and PicardÕs MarkDuplicates, respectively
The aligned reads were quantitated by Feature counts and counts were normalized.
Genome_build: hg19
Supplementary_files_format_and_content: matrix table with RPKM values and read counts for each gene

source_name: cardiomyocytes derived from Induced pluripotent stem cells

growth_protocol: Induced pluripotent stem cells (iPSCs) were routinely generated by re-plating 6 non-adherent cell line cultures (typically 5 x 106 cells) on a matrigel coated plate in MTESR medium (Stemcell Technologies)

extract_protocol:
RNA was purified from iPSCs using Trizol (Life Technologies) methods. Purified poly-A RNA that had gone through two rounds of oligo-dT selection was converted into cDNA for construction of libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3 undifferentiated IPS samples were differentiated into cardiomyocytes using published cardiac differentiation protocols  (Mummery et al. 2012, Lian et al. 2012)

value: heterozygous

value: untreated


title: Scerevisiae_Ctrl_rep1

growth_protocol: Please see Jo et al., 2009, PMID: 19635755


title: NAA15+/G348* iPS cardiomyocytes


title: Genomic DNA from umbilical cord blood buffycoat 227

description:
U248
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 227

value: No GDM


title: Left ventricle plac rep3

description: Left ventricle plac rep3

source_name: Left ventricle plac

value: Plac


title: Non-smoker, exoRNA_batch1_biological rep 3

description: Exosomal RNA

source_name: Exosomal RNA isolated from the plasma of non-smoker

value: Non-smoker


title: Genomic DNA from umbilical cord blood buffycoat 228

description:
U249
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 228


title: Left ventricle plac rep2

description: Left ventricle plac rep2

value: left ventricle


title: Cigarette Smoker, exoRNA_batch1_biological rep 2

description: Exosomal RNA


title: Genomic DNA from umbilical cord blood buffycoat 226

description:
U247
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 226


title: E-cig Vaper, exoRNA_batch1_biological rep 2

description: Exosomal RNA

source_name: Exosomal RNA isolated from the plasma of E-cig vaper

value: E-cig Vaper


title: 12h_4


title: Left ventricle E2 rep3

description: Left ventricle E2 rep3


title: 12h_3


title: Wildtype iPS cardiomyocytes_R2

value: wildtype


title: Genomic DNA from umbilical cord blood buffycoat 225

description:
U246_rep2
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 225

value: Umbilical cord blood buffy coat


title: INPUT Raw rep3 [ChIP-seq_H3K27ac]

city: London

first: Anastasios

last: Karadimitris

address: Hammersmith Campus, Du Cane Road

department: Department of Immunology and Inflammation

institute: Imperial College London

data_processing:
Quality check using FastQC.
Reads alignment using bowtie2.
Peak calling using MACS2.
Subsampling.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Peaks files (broadpeak format).

source_name: Bone marrow

growth_protocol: Treated and untreated cells were cultured using DMEM medium. 10e7 cells per ChIP were cross-linked with 1% formaldehyde for 15min. The ChIP protocol was the same as for ChIP-qPCR until the elution.

extract_protocol:
The ChIP DNA was purified with AMPure beads (Beckman).
ChIP and input DNA libraries were prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB) following manufacturer’s protocols. The quantity was determined using the Qubit High Sensitivity DNA kit (Life Technologies) and library size was determined using the Bioanalyser High Sensitivity DNA kit (Agilent). Libraries were quantified using the Universal Library Quantification Kit for Illumina (Kapa Biosystems) and run on AB StepOne Plus Real-Time PCR (Applied Biosystems). Libraries were diluted to 2nM and sequenced at the MRC Imperial facility using the Illumina HiSeq 2500 platform to obtain single-end 50bp reads.

treatment_protocol: Replicates were treated with RANKL, RANKL/I-BET, or I-BET for 4 hours.

tag: cell line

value: Monocyte-derived cell line

value: Untreated

tag: chip antibody


title: INPUT RANKL rep2 [ChIP-seq_H3K27ac]

value: RANKL

value: 4 hours


title: INPUT RI rep2 [ChIP-seq_H3K27ac]

value: RANKL+Ibet


title: INPUT IBET rep3 [ChIP-seq_H3K27ac]

value: Ibet only


title: Left ventricle plac rep1

description: Left ventricle plac rep1


title: INPUT RI rep3 [ChIP-seq_H3K27ac]


title: INPUT RANKL rep3 [ChIP-seq_H3K27ac]


title: Wildtype iPS cardiomyocytes_R3


title: Wildtype iPS cardiomyocytes_R1


title: 12h_2

value: rice plant leaves

value: five weeks


title: INPUT Raw rep2 [ChIP-seq_H3K27ac]


title: E-cig Vaper, exoRNA_batch1_biological rep 1

description: Exosomal RNA

value: plasma-derived exosomes


title: Coculture DMSO

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Library strategy: scRNA-seq
Libraries were sequenced by Illumina HiSeq2500 Sequencing System.
fastq files were generated using Cellranger mkfastq (v2.1.1 ). The raw reads were mapped to human reference genome (hg38) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: endothelial + tumor cells

extract_protocol:
Cultures of PaTu-8902 (375,000 cells) and HUVECs (200,000 cells), alone or as co-cultures (PaTu-8902 cells onto HUVEC monolayers), previously exposed to either 1.0 µM niclosamide or DMSO were isolated after 8 hours. For the generation of single-cell GEMs, 5200 suspended cells were loaded on a Chromium Single Cell Instrument (10x Genomics) per sample.
Library was generated by Chromium™ Single Cell 3’ Library Construction (10x Genomics).

value: endothelial + tumor cells

tag: drug treatment

value: DMSO

tag: culture method

value: coculture


title: 12h_1

tag: tissue


title: Monoculture DMSO

value: monoculture


title: Waterpipe user, exoRNA_batch1_biological rep 1

description: Exosomal RNA

source_name: Exosomal RNA isolated from the plasma of WP user

value: Waterpipe user


title: Genomic DNA from umbilical cord blood buffycoat 223

description:
U244
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 223

tag: gender

value: Female

tag: maternal gdm status

value: GDM


title: Non-smoker, exoRNA_batch1_biological rep 2

description: Exosomal RNA

value: Non-smoker


title: NAA15+/R276W (RC10) iPS cells

source_name: Induced pluripotent stem cells

tag: genotype

value: heterozygous

value: untreated


title: INPUT RI rep1 [ChIP-seq_H3K27ac]

tag: cell type

value: Monocyte-derived cell line


title: E-cig Vaper, exoRNA_batch1_biological rep 3

description: Exosomal RNA

tag: smoking status

value: E-cig Vaper


title: 6h_4


title: Genomic DNA from umbilical cord blood buffycoat 222

description:
U241
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 222

value: Umbilical cord blood buffy coat


title: NAA15+/R276W (RB12) iPS cells


title: Genomic DNA from umbilical cord blood buffycoat 224

description:
U245_rep1
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 224

value: Male

value: No GDM


title: Cigarette Smoker, exoRNA_batch1_biological rep 1

description: Exosomal RNA

source_name: Exosomal RNA isolated from the plasma of smoker

value: Cigarette Smoker

tag: sample type


title: Scerevisiae_mithramycin_rep1

source_name: Pooled Saccharomyces cerevisiae heterozygous and homozygous deletion mutants treated with 2.7 mM Mithramycin A

treatment_protocol: Please see Jo et al., 2009, PMID: 19635755

value: Mithramycin treatment


title: Coculture niclosamide

value: endothelial + tumor cells

value: niclosamide


title: Genomic DNA from umbilical cord blood buffycoat 220

description:
U239
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 220


title: INPUT Raw rep1 [ChIP-seq_H3K27ac]

value: Untreated


title: INPUT RANKL rep1 [ChIP-seq_H3K27ac]

value: RANKL

value: 4 hours


title: NAA15+/G348* _R2 iPS cells


title: 6h_2

source_name: rice plant leaves

value: rice plant leaves

value: five weeks


title: 6h_1


title: 6h_3


title: NAA15+/G348* _R1 iPS cells


title: RI rep3 [ChIP-seq_H3K27ac]

value: RANKL+Ibet


title: Genomic DNA from umbilical cord blood buffycoat 219

description:
U238
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 219

value: Female

value: GDM


title: IBET rep3 [ChIP-seq_H3K27ac]

value: Monocyte-derived cell line

value: Ibet only


title: Genomic DNA from umbilical cord blood buffycoat 218

description:
U237
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 218

value: Umbilical cord blood buffy coat


title: NAA15+/K336* _R2 iPS cells

value: heterozygous

value: untreated


title: NAA15+/K336* _R1 iPS cells


title: 1h_3


title: 1h_4


title: NAA15L314*/L314* _R2 iPS cells

value: homozygous


title: Genomic DNA from umbilical cord blood buffycoat 217

description:
U236
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 217

value: No GDM


title: 1h_2


title: Raw rep3 [ChIP-seq_H3K27ac]


title: Genomic DNA from umbilical cord blood buffycoat 216

description:
U235
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 216

value: Male


title: NAA15L314*/L314* _R1 iPS cells


title: Genomic DNA from umbilical cord blood buffycoat 221

description:
U240
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 221


title: 1h_1


title: Non-smoker, exoRNA_batch1_biological rep 1

description: Exosomal RNA

source_name: Exosomal RNA isolated from the plasma of non-smoker

value: Non-smoker

value: plasma-derived exosomes


title: 0h_3


title: 0h_4


title: NAA15K336*/G348* _R2 iPS cells


title: Genomic DNA from umbilical cord blood buffycoat 213

description:
U232
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 213


title: Genomic DNA from umbilical cord blood buffycoat 214

description:
U233
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 214


title: RI rep2 [ChIP-seq_H3K27ac]

source_name: Bone marrow


title: Raw rep2 [ChIP-seq_H3K27ac]

value: Untreated


title: NAA15K336*/G348* _R1 iPS cells


title: RANKL rep3 [ChIP-seq_H3K27ac]

value: RANKL

value: 4 hours


title: Genomic DNA from umbilical cord blood buffycoat 215

description:
U234
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 215


title: Wildtype_R3 iPS cells

source_name: Induced pluripotent stem cells

value: wildtype


title: RI rep1 [ChIP-seq_H3K27ac]

value: RANKL+Ibet


title: Wildtype_R2 iPS cells


title: Genomic DNA from umbilical cord blood buffycoat 212

description:
U231
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 212


title: RANKL rep1 [ChIP-seq_H3K27ac]


title: 0h_2

value: rice plant leaves

value: five weeks


title: 0h_1


title: LVS_pF

description: rRNA-depleted RNA

source_name: Bacterial cells grown OD600 0.3 - 0.4

value: wild-type with pF plasmid

value: LVS


title: Genomic DNA from umbilical cord blood buffycoat 211

description:
U230
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 211

value: Female

value: Umbilical cord blood buffy coat


title: Genomic DNA from umbilical cord blood buffycoat 210

description:
U228
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 210


title: Wildtype_R1 iPS cells

value: untreated


title: Raw rep1 [ChIP-seq_H3K27ac]

value: Monocyte-derived cell line


title: INPUT RI [ChIP-seq_BRD]

data_processing:
Quality check using FastQC.
Reads alignment using bowtie2 (2.3.4.1 64bit).
Subsampling based on the same INPUT file for BRD2, BRD3 and BRD4 samples.
Peak calling using MACS2 (VERSION 2.1.1.20160309) for subsamples.
MSPC used for filtering peaks, and then the peaks/tracks files were merged from subsamples.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Pileup track files (bigwig format) for merged subsamples.
Supplementary_files_format_and_content: Peak files (bed format) for merged subsamples.


title: NC-5 LncRNA

city: zhenjiang

first: xiangmei

last: ding

address: No. 8 of Power Road

institute: The Affiliated People’s Hospital of Jiangsu University

data_processing:
Use Ribo-Zero rRNA Removal Kits (Illumina, USA) to remove rRNAs from total RNA. Use TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) to preprocess RNA to construct a sequencing library. A BioAnalyzer 2100 instrument (Agilent Technologies, USA) was used for library quality control and quantification. According to the Illumina sequencing instructions, the 10 pM library was denatured into single-stranded DNA molecules, captured on an Illumina flowcell, amplified into clusters in situ, and performed 150 cycles in the paired-end mode (PE mode) on the Illumina HiSeq sequencer Sequencing.
Use Q30 for quality control, use cutadapt[1] software (v1.9.3) to remove connectors, remove low-quality reads, and obtain high-quality reads.
Use hisat2 software (v2.0.4) to compare high-quality reads to the human reference genome (UCSC HG19). Then, under the guidance of the gtf gene annotation file, use the cuffdiff software (v2.2.1, part of the cufflinks software suite) to obtain the FPKM (Fragments per kilobase of exon per million fragments mapped) value of the transcript level LncRNA as the expression profile of the LncRNA, And calculate the fold change and p-value between two/group samples to screen for differential expression of LncRNA and mRNA.

source_name: peripheral blood mononuclear cells

extract_protocol:
Human PBMCs were isolated by density-gradient centrifugation over Ficoll-Hypaque solution (Tianjin Haoyang Biological Technology Co., Tianjin, China) according to the manufacturer’s instructions and stored at -80 °C   until use for miRNA sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Healthy

value: Adult

tag: Sex

value: Blood

value: peripheral blood mononuclear cells


title: pSP RNA Rep 1 (expt2)

city: Roscoff

first: J. Mark

last: Cock

address: Place Georges Teissier

country: France

institute: Station Biologique de Roscoff

description:
Corresponding replicate: ADPH-119
ADPH-118
featureCounts_output_rmdup_batch2.txt
RNA-seq_GA_SP_TPM_and_RAW_counts_rmdup_featureCounts.xlsx

data_processing:
Illumina base calling
Sequence quality was evaluated with FASTQC and poor quality sequence removed with Flexcat (Dodt M, Roehr JT, Ahmed R, Dieterich C. 2012. FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology 1: 895–905). For the RNA-seq, reads that were shorter than 50 nucleotides after trimming were removed. For ChIP-seq, reads that were shorter than 22 nucleotides after trimming were removed.
ChIP-seq Illumina reads were mapped onto the Ectocarpus genome using Bowtie (v2.2.5; Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013).
Peaks corresponding to regions enriched in PTMs were identified using the MACS2 (version 2.1.1) callpeak module (minimum FDR of 0.01) and refined with the MACS2 bdgpeakcall and bdgbroadcall modules (Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, et al. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biology 9: R137). Colocalised peaks corresponding to regions enriched in several PTMs were detected using MACS2 outputs in BedTools multiinter (Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, Oxford, England 26: 841–842).
Trimmed RNA-seq reads were mapped to the Ectocarpus reference genome using Tophat2 (Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36).
Mapped RNA-seq data was processed using featureCounts (Liao Y, Smyth GK, Shi W, 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics (Oxford, England) 30: 923–930) to obtain counts of numbers of reads mapped to exons. Expression values were represented as TPM.
Differential expression was detected using the DESeq2 package (Bioconductor; Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550) using an adjusted p‐value cut‐off of 0.05 and a minimal fold‐change of 2.
Genome_build: Ectocarpus sp. Ec32 genome v2 2018 (https://bioinformatics.psb.ugent.be/orcae/overview/EctsiV2)
Supplementary_files_format_and_content: bigWig files were generated from bam files, which were merges of the two replicates, normalised with SES with the signal subtracted from the input using deeptools (v3.2.0; Fidel R, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. 2016. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research 44:W160-W165). Peak calling files, based on the bigWig files, are in either narrowPeak (bed9) or GAPPEDPEAK (bed12+3) format.

organism: Ectocarpus sp. Ec32

source_name: partheno-sporophyte

growth_protocol: Cultures were grown in 140 mm round Petri dishes in natural sea water with 0.01% Provasoli enrichment at 13°C with a 12h/12h day/night cycle and 20 (µmol photons).m-2.s-1 irradiance.

extract_protocol: For ChIP-seq, Ectocarpus tissue was fixed for five minutes in seawater containing 2% formaldehyde and the formaldehyde eliminated by rapid filtering followed by incubation in PBS containing 400 mM glycine. Nuclei were isolated by grinding in liquid nitrogen and in a Tenbroeck Potter in nuclei isolation buffer (0.1% triton X-100, 125 mM sorbitol, 20 mM ptassium citrate, 30 mM MgCl2, 5 mM EDTA, 5 mM β-mercaptoethanol 55 mM HEPES at pH 7.5 with complete ultra protease inhibitors), filtering through Miracloth and then washing the precipitated nuclei in nuclei isolation buffer with and then without triton X-100. Chromatin was fragmented by sonicating the purified nuclei in nuclei lysis buffer (10 mM EDTA, 1% SDS, 50 mM Tris-HCl at pH 8 with complete ultra protease inhibitors) in a Covaris M220 Focused-ultrasonicator (duty 25%, peak power 75, cycles/burst 200, duration 900 sec at 6°C). The chromatin was incubated with an anti-histone PTM antibody overnight at 4°C and the immunoprecipitation carried out using Dynabeads protein A and Dynabeads protein G. Following immunoprecipitation and washing, a reverse cross-linking step was carried out by incubating for at least six hours at 65°C in 5 M Na Cl and the samples were then digested with Proteinase K and RNAse A. The purified DNA was then prepared for Illumina sequencing. For MNase digestion, nuclei were prepared using the same procedure as that used for ChIP samples except that the isolation buffer did not contain EDTA. Each sample of nuclei was digested with 400 agarose gel units of MNase for 10 min at 37°C in MNase reaction buffer (5 mM CaCl2, 60 mM KCl, 0.5 mM DTT, 15 mM NaCl, 125 mM sorbitol, 50 mM Tris-HCl pH 7.5). Following lysis of the nuclei, reverse cross-linking and digestion with Proteinase K and RNAse A, 120-210 bp fragments were excised from a 2% agarose gel and sequenced on a HiSeq 4000 platform. using the same procedure as that used for ChIP samples except that the isolation buffer did not contain EDTA. Each sample of nuclei was digested with 400 agarose gel units of MNase for 10 min at 37°C in MNase reaction buffer (5 mM CaCl2, 60 mM KCl, 0.5 mM DTT, 15 mM NaCl, 125 mM sorbitol, 50 mM Tris-HCl pH 7.5). Following lysis of the nuclei, reverse cross-linking and digestion with Proteinase K and RNAse A, 120-210 bp fragments were excised from a 2% agarose gel and sequenced on a HiSeq 4000 platform. For RNA-seq, RNA was extracted from the same duplicate sporophyte and gametophyte cultures as were used for the ChIP-seq analysis using the Qiagen RNeasy plant mini kit with an on-column Deoxyribonuclease I treatment. RNA quality and concentration was then analysed on 1.5% agarose gel stained with ethidium bromide and a NanoDrop ND-1000 spectrophotometer (NanoDrop products, Wilmington, DE, USA).

treatment_protocol: No treatment

value: male

value: whole organism

tag: Stage

value: mature, 4 weeks old

tag: phenotype

value: wild type

tag: generation

value: partheno-sporophyte

tag: sample code


title: NC-4 LncRNA

tag: age


title: INPUT IBET [ChIP-seq_BRD]

tag: cell line

tag: treatment

value: Ibet only

tag: time point

value: 4 hours

tag: chip antibody


title: Genomic DNA from umbilical cord blood buffycoat 208

description:
U226
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 208

extract_protocol: Genomic DNA was extracted and purified from cord blood samples using QIAamp Blood DNA mini kit according to standard instructions.

tag: gender

tag: tissue

value: No GDM


title: NC-3 LncRNA


title: Genomic DNA from umbilical cord blood buffycoat 207

description:
U224
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 207

value: Male

tag: maternal gdm status


title: SP MNase Rep2 (expt2)

description:
Corresponding replicate: ADPH-82
ADPH-83.bed
SP.nucleosomes.120-200bp.RPKM.rmdup.bw


title: INPUT RANKL [ChIP-seq_BRD]

tag: cell type

value: RANKL


title: SP MNase Rep1 (expt2)

description:
Corresponding replicate: ADPH-83
ADPH-82.bed
SP.nucleosomes.120-200bp.RPKM.rmdup.bw


title: NC-2 LncRNA

value: Female


title: NC-1 LncRNA


title: HT-5 LncRNA

value: Hashimoto's Thyroiditis


title: Genomic DNA from umbilical cord blood buffycoat 205

description:
U222
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 205

value: Umbilical cord blood buffy coat


title: HT-4 LncRNA


title: Genomic DNA from umbilical cord blood buffycoat 204

description:
U221
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 204


title: SP H3K27me3 Rep2 (expt2)

description:
Corresponding replicate: ADPH-94
SP_H3K27me3.bw

value: Tri-Methyl-Histone H3 (K27) (C36B11) Rabbit mAb, CST, 9733S, Lot No 14


title: SP H2AZ Rep2 (expt2)

description:
Corresponding replicate: ADPH-114
SP_H2AZ.bw

value: Anti-Histone H2A.Z antibody - ChIP Grade, Abcam, ab97966, received 09/04/18


title: SP H2AZ Rep1 (expt2)

description:
Corresponding replicate: ADPH-115
SP_H2AZ.bw


title: BRD4 RI [ChIP-seq_BRD]

value: Monocyte-derived cell line

value: RANKL+Ibet


title: BRD4 IBET [ChIP-seq_BRD]


title: HT-3 LncRNA

value: Adult

value: Blood

value: peripheral blood mononuclear cells


title: Genomic DNA from umbilical cord blood buffycoat 203

description:
U220
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 203

value: GDM


title: BRD4 RANKL [ChIP-seq_BRD]


title: SP H3K27me3 Rep1 (expt2)

description:
Corresponding replicate: ADPH-96
SP_H3K27me3.bw

value: male

value: whole organism

value: mature, 4 weeks old

value: wild type

value: partheno-sporophyte


title: HT-2 LncRNA


title: SP H4K20me3 Rep2 (expt2)

description:
Corresponding replicate: ADPH-102
SP_H4K20me3.bw
SP_H4K20me3_c35.0_C30.00_l200_g50_G800_broad.bed12.GAPPEDPEAK

value: Tri-Methyl-Histone H4 (Lys20) (D84D2) Rabbit mAb, CST, 5737S, Lot No 1


title: Genomic DNA from umbilical cord blood buffycoat 209

description:
U227
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 209

value: Male

value: No GDM


title: pSP RNA Rep 2 (expt2)

description:
Corresponding replicate: ADPH-118
ADPH-119
featureCounts_output_rmdup_batch2.txt
RNA-seq_GA_SP_TPM_and_RAW_counts_rmdup_featureCounts.xlsx


title: Genomic DNA from umbilical cord blood buffycoat 206

description:
U223
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 206

value: Umbilical cord blood buffy coat


title: BRD4 Raw [ChIP-seq_BRD]

value: Untreated


title: RANKL rep2 [ChIP-seq_H3K27ac]

value: RANKL

value: 4 hours


title: Genomic DNA from umbilical cord blood buffycoat 201

description:
U218
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 201

value: Female


title: HT-1 LncRNA

value: Hashimoto's Thyroiditis

value: Adult


title: BRD3 IBET [ChIP-seq_BRD]

source_name: Bone marrow

value: Monocyte-derived cell line

value: Ibet only


title: Genomic DNA from umbilical cord blood buffycoat 200

description:
U217
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 200


title: SP H3K79me2 Rep2 (expt2)

description:
Corresponding replicate: ADPH-100
SP_H3K79me2.bw
SP_H3K79me2_c40.0_C30.00_l200_g50_G800_broad.bed12.GAPPEDPEAK

value: male

value: Di-Methyl-Histone H3 (Lys79) (D15E8) XP Rabbit mAb, CST, 5427S, Lot No 4


title: Input NN3

city: Beijing

first: Yanan

last: Wang

state: China

address: No. 1 Shuai Fu Yuan Street

institute: Peking Union Medical College Hospital

data_processing:
Briefly, Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC HG19)  by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Genome_build: hg19
Supplementary_files_format_and_content: peak

source_name: skin tissue

extract_protocol:
RNA extraction protocol
Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library  Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.
MeRIP-seq

value: epidermis and dermis

tag: condition

value: healthy control skin samples


title: BRD3 RANKL [ChIP-seq_BRD]


title: SP H3K79me2 Rep1 (expt2)

description:
Corresponding replicate: ADPH-101
SP_H3K79me2.bw
SP_H3K79me2_c40.0_C30.00_l200_g50_G800_broad.bed12.GAPPEDPEAK

value: whole organism

value: mature, 4 weeks old

value: wild type

value: partheno-sporophyte


title: Genomic DNA from umbilical cord blood buffycoat 199

description:
U216
Umbilical cord blood sample

data_processing:
R v3.4.2
Beta_for_GEO.txt includes Beta-mixture Quantile (BMIQ) normalized Beta Values.

source_name: umbilical cord blood buffy coat 199

value: Umbilical cord blood buffy coat

value: GDM


title: Input NN4


title: BRD3 Raw [ChIP-seq_BRD]

value: Untreated


title: Genomic DNA from umbilical cord blood buffycoat 197

description:
U214
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 197

value: No GDM


title: Genomic DNA from umbilical cord blood buffycoat 198

description:
U215
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 198

value: Female


title: BRD2 RI [ChIP-seq_BRD]

value: RANKL+Ibet

value: 4 hours


title: Genomic DNA from umbilical cord blood buffycoat 202

description:
U219
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 202

value: Male


title: Input NN2


title: SP H3K36me3 Rep2 (expt2)

description:
Corresponding replicate: ADPH-97
SP_H3K36me3.bw
SP_H3K36me3_c50.0_C45.00_l200_g50_G800_broad.bed12.GAPPEDPEAK

value: Tri-Methyl-Histone H3 (Lys36) (D5A7) XP Rabbit mAb, CST, 4909S, Lot No 2


title: SP H3K14ac Rep2 (expt2)

description:
Corresponding replicate: ADPH-108
SP_H3K14ac.bw
SP_H3K14ac_c10.0_l200_g50_peaks.narrowPeak

value: male

value: Acetyl-Histone H3 (Lys14) (D4B9) Rabbit mAb, CST, 7627S, Lot No 0001


title: BRD2 RANKL [ChIP-seq_BRD]

value: Monocyte-derived cell line

value: RANKL


title: SP H3K36me3 Rep1 (expt2)

description:
Corresponding replicate: ADPH-98
SP_H3K36me3.bw
SP_H3K36me3_c50.0_C45.00_l200_g50_G800_broad.bed12.GAPPEDPEAK

value: whole organism


title: Genomic DNA from umbilical cord blood buffycoat 196

description:
U213
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 196


title: BRD3 RI [ChIP-seq_BRD]


title: SP H4K20me3 Rep1 (expt2)

description:
Corresponding replicate: ADPH-104
SP_H4K20me3.bw
SP_H4K20me3_c35.0_C30.00_l200_g50_G800_broad.bed12.GAPPEDPEAK

source_name: partheno-sporophyte

value: mature, 4 weeks old

value: Tri-Methyl-Histone H4 (Lys20) (D84D2) Rabbit mAb, CST, 5737S, Lot No 1


title: Input PP3

value: epidermis and dermis

value: involved psoriatic skin


title: Genomic DNA from umbilical cord blood buffycoat 195

description:
U212
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 195

value: Umbilical cord blood buffy coat

value: GDM


title: BRD2 Raw [ChIP-seq_BRD]

value: Untreated


title: Input PP2


title: SP H3K4me2 Rep2 (expt2)

description:
Corresponding replicate: ADPH-103
SP_H3K4me2.bw
SP_H3K4me2_c13.0_l200_g50_peaks.narrowPeak

value: wild type

value: partheno-sporophyte

value: Di-Methyl-Histone H3 (Lys4) (C64G9) Rabbit mAb, CST, 9725S, Lot No 9


title: SP H3K14ac Rep1 (expt2)

description:
Corresponding replicate: ADPH-109
SP_H3K14ac.bw
SP_H3K14ac_c10.0_l200_g50_peaks.narrowPeak


title: INPUT RI [ChIP-seq_MYC_MAX]

data_processing:
Quality check using FastQC.
Reads alignment using bowtie2 (2.3.4.1 64bit).
Subsampling based on the same INPUT file for MYC and MAX samples.
Peak calling using MACS2 (VERSION 2.1.1.20160309) for subsamples.
MSPC used for filtering peaks, and then the peaks/tracks files were merged from subsamples.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Pileup track files (bigwig format) for merged subsamples.
Supplementary_files_format_and_content: Peak files (bed format) for merged subsamples.

value: RANKL+Ibet

value: 4 hours


title: Input NN1

value: healthy control skin samples


title: SP H3K4me2 Rep1 (expt2)

description:
Corresponding replicate: ADPH-107
SP_H3K4me2.bw
SP_H3K4me2_c13.0_l200_g50_peaks.narrowPeak

value: male


title: Genomic DNA from umbilical cord blood buffycoat 194

description:
U211
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 194

value: Male

value: No GDM


title: Genomic DNA from umbilical cord blood buffycoat 192

description:
U209
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 192


title: INPUT IBET [ChIP-seq_MYC_MAX]

value: Monocyte-derived cell line

value: Ibet only


title: SP Input Rep2 (expt2)

description: Corresponding replicate: ADPH-111

value: whole organism

value: mature, 4 weeks old


title: Genomic DNA from umbilical cord blood buffycoat 193

description:
U210
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 193


title: SP Input Rep1 (expt2)

description: Corresponding replicate: ADPH-112


title: Input PP1

value: epidermis and dermis

value: involved psoriatic skin


title: BRD2 IBET [ChIP-seq_BRD]


title: INPUT RANKL [ChIP-seq_MYC_MAX]

value: RANKL


title: Genomic DNA from umbilical cord blood buffycoat 190

description:
U207
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 190

value: Female

value: Umbilical cord blood buffy coat


title: Genomic DNA from umbilical cord blood buffycoat 191

description:
U208
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 191


title: INPUT Raw [ChIP-seq_MYC_MAX]

value: Untreated


title: MAX RI [ChIP-seq_MYC_MAX]

value: Max


title: Genomic DNA from umbilical cord blood buffycoat 189

description:
U206
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 189


title: GA RNA Rep 2 (expt2)

description:
Corresponding replicate: ADPH-116
ADPH-117
featureCounts_output_rmdup_batch2.txt
RNA-seq_GA_SP_TPM_and_RAW_counts_rmdup_featureCounts.xlsx

source_name: gametophyte

value: wild type

value: gametophyte


title: MAX IBET [ChIP-seq_MYC_MAX]

source_name: Bone marrow

value: 4 hours


title: Input PN1

value: uninvolved psoriatic skin


title: Input PN2


title: Input PN3


title: NN4

value: healthy control skin samples


title: Genomic DNA from umbilical cord blood buffycoat 188

description:
U205
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 188

value: No GDM


title: Input PN4

source_name: skin tissue


title: Genomic DNA from umbilical cord blood buffycoat 187

description:
U204
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 187


title: Input PP4


title: MAX RANKL [ChIP-seq_MYC_MAX]

value: Monocyte-derived cell line


title: Genomic DNA from umbilical cord blood buffycoat 186

description:
U203
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 186

value: GDM


title: NN2


title: MAX Raw [ChIP-seq_MYC_MAX]


title: INPUT Raw [ChIP-seq_BRD]


title: Genomic DNA from umbilical cord blood buffycoat 185

description:
U202
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 185

value: Male


title: NN1


title: GA H2AZ Rep1 (expt2)

description:
Corresponding replicate: ADPH-113
GA_H2AZ.bw

value: male

value: whole organism

value: mature, 4 weeks old

value: Anti-Histone H2A.Z antibody - ChIP Grade, Abcam, ab97966, received 09/04/18


title: PP4

value: epidermis and dermis

value: involved psoriatic skin


title: Genomic DNA from umbilical cord blood buffycoat 184

description:
U201
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 184

value: Female

value: Umbilical cord blood buffy coat


title: MYC IBET [ChIP-seq_MYC_MAX]

value: Ibet only

value: Myc


title: GA MNase Rep2 (expt2)

description:
Corresponding replicate: ADPH-80
ADPH-81.bed
GA.nucleosomes.120_200bp.RPKM.rmdup.bw

value: wild type

value: gametophyte


title: PP3


title: GA RNA Rep 1 (expt2)

description:
Corresponding replicate: ADPH-117
ADPH-116
featureCounts_output_rmdup_batch2.txt
RNA-seq_GA_SP_TPM_and_RAW_counts_rmdup_featureCounts.xlsx


title: PP2


title: MYC Raw [ChIP-seq_MYC_MAX]

value: Untreated


title: Genomic DNA from umbilical cord blood buffycoat 183

description:
U200
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 183


title: Genomic DNA from umbilical cord blood buffycoat 182

description:
U199
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 182

value: No GDM


title: GA MNase Rep1 (expt2)

description:
Corresponding replicate: ADPH-81
ADPH-80.bed
GA.nucleosomes.120_200bp.RPKM.rmdup.bw


title: NN3

value: healthy control skin samples