title: genomic DNA from whole blood 493

value: B


title: genomic DNA from whole blood 502

status: Public on Sep 21 2012

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2, the non_normalized data matrix contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood_control

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: male

tag: age

tag: diseasestatus

value: 1; control

tag: tissue

value: whole blood

value: yes

tag: dataset

tag: plate

value: PLATE F

tag: sentrixbarcode

tag: sentrixposition

value: K

tag: wellid

tag: trackingsheet

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 571

source_name: whole blood_schizophrenia patient

value: 2; schizophrenia patient

value: PLATE E

value: E


title: genomic DNA from whole blood 552

value: female

value: C


title: genomic DNA from whole blood 122

value: F


title: genomic DNA from whole blood 484

value: I


title: genomic DNA from whole blood 431

value: H


title: genomic DNA from whole blood 468

value: G


title: genomic DNA from whole blood 347


title: genomic DNA from whole blood 528

value: D


title: genomic DNA from whole blood 469

value: no

value: L


title: genomic DNA from whole blood 589

value: 1; control

value: whole blood


title: genomic DNA from whole blood 451

value: male

value: yes

value: PLATE F

value: J


title: genomic DNA from whole blood 450

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 530

value: B


title: genomic DNA from whole blood 120

value: female


title: genomic DNA from whole blood 588


title: genomic DNA from whole blood 524


title: genomic DNA from whole blood 501


title: genomic DNA from whole blood 466


title: genomic DNA from whole blood 121

value: A


title: genomic DNA from whole blood 499

value: C


title: genomic DNA from whole blood 523

value: E


title: genomic DNA from whole blood 483

value: F


title: genomic DNA from whole blood 449


title: genomic DNA from whole blood 482


title: genomic DNA from whole blood 326

value: K


title: genomic DNA from whole blood 534

value: 2; schizophrenia patient

value: PLATE E

value: I


title: genomic DNA from whole blood 516

value: G


title: genomic DNA from whole blood 114

value: whole blood

value: H


title: genomic DNA from whole blood 481

value: 1; control

value: yes


title: genomic DNA from whole blood 498

value: PLATE F


title: genomic DNA from whole blood 576

value: D

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 448

value: female

value: J


title: genomic DNA from whole blood 321

value: male


title: genomic DNA from whole blood 113

value: C


title: genomic DNA from whole blood 517

value: L


title: genomic DNA from whole blood 94

value: F


title: genomic DNA from whole blood 93

value: 2; schizophrenia patient

value: A


title: genomic DNA from whole blood 564

value: PLATE E

value: B


title: genomic DNA from whole blood 464

value: whole blood


title: genomic DNA from whole blood 456

value: E


title: genomic DNA from whole blood 308

value: 1; control


title: genomic DNA from whole blood 584

value: yes

value: G


title: genomic DNA from whole blood 620

value: PLATE G

value: K


title: genomic DNA from whole blood 583

value: female

value: PLATE F

value: D

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 465

value: no

value: L


title: genomic DNA from whole blood 447

value: male


title: genomic DNA from whole blood 521


title: genomic DNA from whole blood 119

value: F


title: genomic DNA from whole blood 115

value: A


title: genomic DNA from whole blood 597

value: J


title: genomic DNA from whole blood 624

value: whole blood


title: genomic DNA from whole blood 619

value: 2; schizophrenia patient


title: genomic DNA from whole blood 511

value: 1; control


title: genomic DNA from whole blood 514

value: yes

value: H


title: genomic DNA from whole blood 463

value: G


title: genomic DNA from whole blood 606

value: PLATE G

value: E


title: genomic DNA from whole blood 604


title: genomic DNA from whole blood 459

value: female

value: PLATE F


title: genomic DNA from whole blood 205

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 603

value: C


title: genomic DNA from whole blood 442


title: genomic DNA from whole blood 509

value: D


title: genomic DNA from whole blood 512

value: B


title: genomic DNA from whole blood 592

value: male

value: L


title: genomic DNA from whole blood 617

value: no

value: I


title: genomic DNA from whole blood 441

value: whole blood


title: genomic DNA from whole blood 618

value: 2; schizophrenia patient


title: genomic DNA from whole blood 478

value: 1; control

value: yes


title: genomic DNA from whole blood 491

value: K


title: genomic DNA from whole blood 111

value: F


title: genomic DNA from whole blood 593

value: A


title: genomic DNA from whole blood 198

value: female


title: genomic DNA from whole blood 458

value: PLATE F

value: G


title: genomic DNA from whole blood 580

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 124


title: genomic DNA from whole blood 591


title: genomic DNA from whole blood 434


title: genomic DNA from whole blood 504

value: H


title: genomic DNA from whole blood 556

value: J


title: genomic DNA from whole blood 474

value: male

value: D


title: genomic DNA from whole blood 538

value: E


title: genomic DNA from whole blood 486


title: genomic DNA from whole blood 503

value: C


title: genomic DNA from whole blood 485

value: whole blood


title: genomic DNA from whole blood 432

value: 2; schizophrenia patient

value: PLATE G


title: genomic DNA from whole blood 452

value: 1; control

value: yes

value: B


title: genomic DNA from whole blood 585

value: no

value: PLATE E


title: genomic DNA from whole blood 440

value: F


title: genomic DNA from whole blood 127


title: genomic DNA from whole blood 445


title: genomic DNA from whole blood 430

value: I


title: genomic DNA from whole blood 601

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 118

value: female


title: genomic DNA from whole blood 437


title: genomic DNA from whole blood 548

value: K


title: genomic DNA from whole blood 615

value: A


title: genomic DNA from whole blood 500

value: male

value: G


title: genomic DNA from whole blood 99


title: genomic DNA from whole blood 520

value: L


title: genomic DNA from whole blood 96

value: whole blood


title: genomic DNA from whole blood 433

value: 2; schizophrenia patient


title: genomic DNA from whole blood 519


title: genomic DNA from whole blood 537


title: genomic DNA from whole blood 444

value: PLATE G

value: H


title: genomic DNA from whole blood 616

value: 1; control

value: yes

value: C


title: genomic DNA from whole blood 533

value: PLATE E

value: D


title: genomic DNA from whole blood 567

value: B


title: genomic DNA from whole blood 472

value: J

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 471

value: E


title: genomic DNA from whole blood 488

value: female

value: PLATE F

value: K


title: genomic DNA from whole blood 454

value: no

value: L


title: genomic DNA from whole blood 475

value: male

value: whole blood

value: I


title: genomic DNA from whole blood 436

value: 1; control


title: genomic DNA from whole blood 177

value: H


title: genomic DNA from whole blood 453

value: yes

value: G


title: genomic DNA from whole blood 101

value: F


title: genomic DNA from whole blood 559

value: 2; schizophrenia patient

value: PLATE G


title: genomic DNA from whole blood 590

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 505

value: B


title: genomic DNA from whole blood 97

value: A


title: genomic DNA from whole blood 134

value: female

value: PLATE F

value: C


title: genomic DNA from whole blood 595

value: J


title: genomic DNA from whole blood 594

value: male


title: genomic DNA from whole blood 522

value: whole blood


title: genomic DNA from whole blood 461

value: E


title: genomic DNA from whole blood 557

value: 1; control

value: D


title: genomic DNA from whole blood 560

value: yes

value: PLATE E

value: K


title: genomic DNA from whole blood 460

value: 2; schizophrenia patient


title: genomic DNA from whole blood 107

value: F


title: genomic DNA from whole blood 495

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 596

value: PLATE G

value: L


title: genomic DNA from whole blood 435


title: genomic DNA from whole blood 455

value: A


title: genomic DNA from whole blood 531


title: genomic DNA from whole blood 529

value: G


title: genomic DNA from whole blood 212

value: H


title: genomic DNA from whole blood 494


title: genomic DNA from whole blood 543

value: I


title: genomic DNA from whole blood 586

value: female

value: B


title: genomic DNA from whole blood 109

value: whole blood


title: genomic DNA from whole blood 587

value: male


title: genomic DNA from whole blood 510

value: no


title: genomic DNA from whole blood 573

value: yes


title: genomic DNA from whole blood 168

value: PLATE E

value: C


title: genomic DNA from whole blood 106

value: 2; schizophrenia patient


title: genomic DNA from whole blood 623


title: genomic DNA from whole blood 95


title: genomic DNA from whole blood 132

value: K


title: genomic DNA from whole blood 568

value: E

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 473


title: genomic DNA from whole blood 565


title: genomic DNA from whole blood 540

value: F


title: genomic DNA from whole blood 577


title: genomic DNA from whole blood 566

value: J


title: genomic DNA from whole blood 518

value: D


title: genomic DNA from whole blood 550

value: H


title: genomic DNA from whole blood 622

value: G


title: genomic DNA from whole blood 547


title: genomic DNA from whole blood 549


title: genomic DNA from whole blood 100

value: I


title: genomic DNA from whole blood 539

value: female

value: A


title: genomic DNA from whole blood 546

value: whole blood


title: genomic DNA from whole blood 536

value: male


title: genomic DNA from whole blood 525

value: yes


title: genomic DNA from whole blood 467

value: no

value: PLATE E

value: B


title: genomic DNA from whole blood 569

value: 2; schizophrenia patient


title: genomic DNA from whole blood 116

value: K


title: genomic DNA from whole blood 535

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 579

value: L


title: genomic DNA from whole blood 527


title: genomic DNA from whole blood 551


title: genomic DNA from whole blood 545


title: genomic DNA from whole blood 492

value: J


title: genomic DNA from whole blood 541


title: genomic DNA from whole blood 138


title: genomic DNA from whole blood 446

value: PLATE G


title: genomic DNA from whole blood 103

value: F


title: genomic DNA from whole blood 136

value: C


title: genomic DNA from whole blood 487

value: E


title: genomic DNA from whole blood 480

value: female

value: 1; control

value: PLATE F


title: genomic DNA from whole blood 462

value: whole blood

value: D


title: genomic DNA from whole blood 582

value: yes


title: genomic DNA from whole blood 526

value: male

value: PLATE E

value: G


title: genomic DNA from whole blood 581


title: genomic DNA from whole blood 496


title: genomic DNA from whole blood 72

value: 2; schizophrenia patient

value: PLATE D

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 515

value: J

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 17

value: K


title: genomic DNA from whole blood 513


title: genomic DNA from whole blood 3

value: I


title: genomic DNA from whole blood 570

value: B


title: genomic DNA from whole blood 84

value: L


title: genomic DNA from whole blood 83


title: genomic DNA from whole blood 563


title: genomic DNA from whole blood 102

value: A


title: genomic DNA from whole blood 71

value: E


title: genomic DNA from whole blood 307

value: 1; control

value: whole blood

value: PLATE F


title: genomic DNA from whole blood 125

value: female

value: yes

value: H


title: genomic DNA from whole blood 108

value: male

value: 2; schizophrenia patient

value: D


title: genomic DNA from whole blood 112

value: no


title: genomic DNA from whole blood 479

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 443


title: genomic DNA from whole blood 497


title: genomic DNA from whole blood 50

value: PLATE D

value: F

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 60

value: C


title: genomic DNA from whole blood 27

value: B


title: genomic DNA from whole blood 18

value: K


title: genomic DNA from whole blood 49

value: A


title: genomic DNA from whole blood 75

value: whole blood

value: J


title: genomic DNA from whole blood 87

value: L


title: genomic DNA from whole blood 52

value: yes


title: genomic DNA from whole blood 281

value: female

value: 1; control

value: PLATE B


title: genomic DNA from whole blood 263

value: male


title: genomic DNA from whole blood 6

value: 2; schizophrenia patient

value: I


title: genomic DNA from whole blood 74

value: no

value: PLATE D

value: E


title: genomic DNA from whole blood 222

value: F

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 30

value: B


title: genomic DNA from whole blood 62

value: C


title: genomic DNA from whole blood 51

value: whole blood

value: A


title: genomic DNA from whole blood 255


title: genomic DNA from whole blood 41

value: D


title: genomic DNA from whole blood 63

value: yes

value: H


title: genomic DNA from whole blood 235

value: female

value: 1; control

value: J


title: genomic DNA from whole blood 396

value: PLATE C

value: L


title: genomic DNA from whole blood 229

value: male

value: PLATE B


title: genomic DNA from whole blood 221


title: genomic DNA from whole blood 385


title: genomic DNA from whole blood 227


title: genomic DNA from whole blood 275


title: genomic DNA from whole blood 86

value: 2; schizophrenia patient

value: PLATE D

value: G


title: genomic DNA from whole blood 249

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 234

value: E


title: genomic DNA from whole blood 248

value: whole blood


title: genomic DNA from whole blood 402

value: I


title: genomic DNA from whole blood 380


title: genomic DNA from whole blood 407

value: K


title: genomic DNA from whole blood 384

value: yes


title: genomic DNA from whole blood 378

value: C


title: genomic DNA from whole blood 369

value: F


title: genomic DNA from whole blood 395

value: 1; control


title: genomic DNA from whole blood 32

value: J


title: genomic DNA from whole blood 31


title: genomic DNA from whole blood 424

value: no

value: PLATE C

value: D


title: genomic DNA from whole blood 362

value: male

value: L


title: genomic DNA from whole blood 7

value: 2; schizophrenia patient

value: PLATE D

value: A


title: genomic DNA from whole blood 64

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 8

value: whole blood


title: genomic DNA from whole blood 185

value: female

value: G


title: genomic DNA from whole blood 415

value: yes

value: B


title: genomic DNA from whole blood 42


title: genomic DNA from whole blood 53

value: I


title: genomic DNA from whole blood 367

value: 1; control


title: genomic DNA from whole blood 295


title: genomic DNA from whole blood 76


title: genomic DNA from whole blood 196


title: genomic DNA from whole blood 305

value: K


title: genomic DNA from whole blood 43


title: genomic DNA from whole blood 19

value: C


title: genomic DNA from whole blood 88


title: genomic DNA from whole blood 342

value: PLATE C

value: H


title: genomic DNA from whole blood 230

value: PLATE B


title: genomic DNA from whole blood 20

value: male


title: genomic DNA from whole blood 316


title: genomic DNA from whole blood 332

value: F


title: genomic DNA from whole blood 354

value: J


title: genomic DNA from whole blood 330

value: A


title: genomic DNA from whole blood 351

value: E

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 277

value: female

value: whole blood


title: genomic DNA from whole blood 340

value: yes


title: genomic DNA from whole blood 284

value: L


title: genomic DNA from whole blood 223

value: I


title: genomic DNA from whole blood 283

value: 1; control

value: no

value: G


title: genomic DNA from whole blood 375

value: PLATE C


title: genomic DNA from whole blood 258


title: genomic DNA from whole blood 250

value: D


title: genomic DNA from whole blood 270

value: PLATE B

value: H


title: genomic DNA from whole blood 398

value: male


title: genomic DNA from whole blood 240

value: B


title: genomic DNA from whole blood 373

value: C


title: genomic DNA from whole blood 383

value: J


title: genomic DNA from whole blood 382

value: E

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 420

value: whole blood


title: genomic DNA from whole blood 268

value: yes


title: genomic DNA from whole blood 276

value: female


title: genomic DNA from whole blood 391

value: L


title: genomic DNA from whole blood 405

value: 1; control

value: K


title: genomic DNA from whole blood 257

value: A


title: genomic DNA from whole blood 339

value: PLATE C


title: genomic DNA from whole blood 363


title: genomic DNA from whole blood 166

value: F


title: genomic DNA from whole blood 329

value: no

value: I


title: genomic DNA from whole blood 323

value: male


title: genomic DNA from whole blood 410

value: B


title: genomic DNA from whole blood 322

value: G


title: genomic DNA from whole blood 374

value: J


title: genomic DNA from whole blood 303

value: H


title: genomic DNA from whole blood 390

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 293

value: whole blood


title: genomic DNA from whole blood 302

value: yes

value: C


title: genomic DNA from whole blood 315

value: E


title: genomic DNA from whole blood 359

value: female

value: 1; control

value: D


title: genomic DNA from whole blood 350

value: PLATE C


title: genomic DNA from whole blood 291

value: A


title: genomic DNA from whole blood 90

value: 2; schizophrenia patient

value: PLATE D

value: L


title: genomic DNA from whole blood 89


title: genomic DNA from whole blood 65


title: genomic DNA from whole blood 33

value: male

value: B


title: genomic DNA from whole blood 44

value: no


title: genomic DNA from whole blood 355


title: genomic DNA from whole blood 320


title: genomic DNA from whole blood 306


title: genomic DNA from whole blood 319

value: G


title: genomic DNA from whole blood 333

value: K

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 287

value: whole blood

value: yes

value: F


title: genomic DNA from whole blood 78

value: female

value: J


title: genomic DNA from whole blood 55


title: genomic DNA from whole blood 21


title: genomic DNA from whole blood 77

value: E


title: genomic DNA from whole blood 311

value: 1; control

value: PLATE C


title: genomic DNA from whole blood 66

value: 2; schizophrenia patient

value: H


title: genomic DNA from whole blood 9

value: PLATE D

value: I


title: genomic DNA from whole blood 325

value: male


title: genomic DNA from whole blood 297

value: C


title: genomic DNA from whole blood 349

value: PLATE B

value: L


title: genomic DNA from whole blood 300

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 313

value: whole blood

value: no

value: K


title: genomic DNA from whole blood 343

value: yes


title: genomic DNA from whole blood 54

value: A


title: genomic DNA from whole blood 344

value: female

value: B


title: genomic DNA from whole blood 336


title: genomic DNA from whole blood 286

value: 1; control

value: PLATE C


title: genomic DNA from whole blood 310

value: 2; schizophrenia patient


title: genomic DNA from whole blood 365

value: F


title: genomic DNA from whole blood 309

value: G


title: genomic DNA from whole blood 296

value: male


title: genomic DNA from whole blood 371

value: H


title: genomic DNA from whole blood 324

value: PLATE B

value: D


title: genomic DNA from whole blood 337

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 298

value: whole blood

value: C


title: genomic DNA from whole blood 288


title: genomic DNA from whole blood 388

value: J


title: genomic DNA from whole blood 285

value: yes


title: genomic DNA from whole blood 368


title: genomic DNA from whole blood 314


title: genomic DNA from whole blood 299

value: E


title: genomic DNA from whole blood 414


title: genomic DNA from whole blood 272

value: L


title: genomic DNA from whole blood 266


title: genomic DNA from whole blood 377


title: genomic DNA from whole blood 426

value: B


title: genomic DNA from whole blood 412


title: genomic DNA from whole blood 304


title: genomic DNA from whole blood 251


title: genomic DNA from whole blood 417

value: female


title: genomic DNA from whole blood 149

value: 1; control

value: PLATE A

value: I


title: genomic DNA from whole blood 206


title: genomic DNA from whole blood 419

value: 2; schizophrenia patient


title: genomic DNA from whole blood 318

value: male


title: genomic DNA from whole blood 428


title: genomic DNA from whole blood 334


title: genomic DNA from whole blood 425

value: PLATE C


title: genomic DNA from whole blood 155

value: K


title: genomic DNA from whole blood 423

value: PLATE B


title: genomic DNA from whole blood 188

value: F

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 186

value: whole blood

value: A


title: genomic DNA from whole blood 345

value: yes

value: D


title: genomic DNA from whole blood 217

value: L


title: genomic DNA from whole blood 429


title: genomic DNA from whole blood 197

value: H


title: genomic DNA from whole blood 216

value: female

value: G


title: genomic DNA from whole blood 408

value: 1; control

value: C


title: genomic DNA from whole blood 171

value: PLATE A

value: B


title: genomic DNA from whole blood 195

value: male


title: genomic DNA from whole blood 401

value: 2; schizophrenia patient


title: genomic DNA from whole blood 418

value: PLATE C

value: J


title: genomic DNA from whole blood 204

value: E

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 409

value: whole blood


title: genomic DNA from whole blood 372

value: yes

value: I


title: genomic DNA from whole blood 180

value: D


title: genomic DNA from whole blood 427

source_name: whole blood_bipolar patient

value: 3; bipolar patient

value: no


title: genomic DNA from whole blood 381

value: K


title: genomic DNA from whole blood 386

value: female

value: 1; control


title: genomic DNA from whole blood 404

value: F


title: genomic DNA from whole blood 397


title: genomic DNA from whole blood 341

value: PLATE B

value: B


title: genomic DNA from whole blood 68

value: male

value: 2; schizophrenia patient

value: PLATE D

value: C


title: genomic DNA from whole blood 416

value: PLATE C

value: E

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 403

value: whole blood

value: yes

value: A


title: genomic DNA from whole blood 47

value: D


title: genomic DNA from whole blood 92

value: L


title: genomic DNA from whole blood 24

value: female

value: K


title: genomic DNA from whole blood 58

value: F


title: genomic DNA from whole blood 57


title: genomic DNA from whole blood 69

value: H


title: genomic DNA from whole blood 23


title: genomic DNA from whole blood 12

value: I


title: genomic DNA from whole blood 80


title: genomic DNA from whole blood 46

value: male


title: genomic DNA from whole blood 81

value: 2; schizophrenia patient

value: J


title: genomic DNA from whole blood 67

value: PLATE D


title: genomic DNA from whole blood 35


title: genomic DNA from whole blood 91

value: G


title: genomic DNA from whole blood 34

value: E


title: genomic DNA from whole blood 98

value: no

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 36

value: whole blood

value: yes

value: B


title: genomic DNA from whole blood 11


title: genomic DNA from whole blood 10

value: A


title: genomic DNA from whole blood 22

value: female

value: C


title: genomic DNA from whole blood 422

value: 1; control

value: PLATE C

value: L


title: genomic DNA from whole blood 45


title: genomic DNA from whole blood 79

value: male


title: genomic DNA from whole blood 56

value: 2; schizophrenia patient

value: I


title: genomic DNA from whole blood 413

value: J


title: genomic DNA from whole blood 376

value: K


title: genomic DNA from whole blood 366


title: genomic DNA from whole blood 411

value: E


title: genomic DNA from whole blood 400

value: F


title: genomic DNA from whole blood 399

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 393

value: whole blood

value: D


title: genomic DNA from whole blood 389

value: yes

value: PLATE B

value: H


title: genomic DNA from whole blood 370

value: B


title: genomic DNA from whole blood 353

value: C


title: genomic DNA from whole blood 364


title: genomic DNA from whole blood 421

value: 1; control

value: PLATE C

value: G


title: genomic DNA from whole blood 387

value: female

value: 2; schizophrenia patient


title: genomic DNA from whole blood 274

value: male

value: no

value: J


title: genomic DNA from whole blood 352

value: A


title: genomic DNA from whole blood 175

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 123

value: whole blood


title: genomic DNA from whole blood 361

value: I


title: genomic DNA from whole blood 406

value: yes


title: genomic DNA from whole blood 392

value: PLATE B


title: genomic DNA from whole blood 226

value: K


title: genomic DNA from whole blood 379

value: D


title: genomic DNA from whole blood 254

value: F


title: genomic DNA from whole blood 262

value: 1; control

value: H


title: genomic DNA from whole blood 253


title: genomic DNA from whole blood 273

value: E


title: genomic DNA from whole blood 360

value: G


title: genomic DNA from whole blood 280

value: L


title: genomic DNA from whole blood 394

value: female

value: 2; schizophrenia patient


title: genomic DNA from whole blood 261

value: C


title: genomic DNA from whole blood 358


title: genomic DNA from whole blood 40

value: male

value: PLATE D


title: genomic DNA from whole blood 220

value: whole blood

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 29

value: yes

value: J


title: genomic DNA from whole blood 15


title: genomic DNA from whole blood 245

value: no

value: PLATE B


title: genomic DNA from whole blood 279


title: genomic DNA from whole blood 61

value: K


title: genomic DNA from whole blood 14


title: genomic DNA from whole blood 39


title: genomic DNA from whole blood 233

value: 1; control

value: B


title: genomic DNA from whole blood 117

value: I


title: genomic DNA from whole blood 176

value: PLATE A


title: genomic DNA from whole blood 187

value: L


title: genomic DNA from whole blood 5

value: F


title: genomic DNA from whole blood 28

value: female

value: 2; schizophrenia patient

value: E


title: genomic DNA from whole blood 85

value: male

value: PLATE D

value: D


title: genomic DNA from whole blood 161

value: whole blood

value: yes

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 169


title: genomic DNA from whole blood 170

value: H


title: genomic DNA from whole blood 73


title: genomic DNA from whole blood 159


title: genomic DNA from whole blood 167


title: genomic DNA from whole blood 4

value: A


title: genomic DNA from whole blood 144

value: no


title: genomic DNA from whole blood 128

value: C


title: genomic DNA from whole blood 157

value: G


title: genomic DNA from whole blood 148

value: PLATE A


title: genomic DNA from whole blood 331


title: genomic DNA from whole blood 130


title: genomic DNA from whole blood 162

value: B


title: genomic DNA from whole blood 131

value: I


title: genomic DNA from whole blood 135

value: female


title: genomic DNA from whole blood 317

value: 2; schizophrenia patient


title: genomic DNA from whole blood 137


title: genomic DNA from whole blood 264


title: genomic DNA from whole blood 265

value: K


title: genomic DNA from whole blood 140

value: male

value: J


title: genomic DNA from whole blood 129

value: E


title: genomic DNA from whole blood 289

value: whole blood


title: genomic DNA from whole blood 294

value: yes

value: L


title: genomic DNA from whole blood 247

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 133


title: genomic DNA from whole blood 282

value: F


title: genomic DNA from whole blood 139

value: H


title: genomic DNA from whole blood 292


title: genomic DNA from whole blood 259


title: genomic DNA from whole blood 142


title: genomic DNA from whole blood 256

value: no


title: genomic DNA from whole blood 267


title: genomic DNA from whole blood 269

value: D


title: genomic DNA from whole blood 301

value: 1; control

value: PLATE C


title: genomic DNA from whole blood 126

value: PLATE A

value: A


title: genomic DNA from whole blood 357


title: genomic DNA from whole blood 338


title: genomic DNA from whole blood 348

value: female


title: genomic DNA from whole blood 346


title: genomic DNA from whole blood 328


title: genomic DNA from whole blood 356

value: G


title: genomic DNA from whole blood 246

value: male

value: 2; schizophrenia patient


title: genomic DNA from whole blood 242

value: PLATE B


title: genomic DNA from whole blood 225

value: whole blood


title: genomic DNA from whole blood 252

value: yes

value: I


title: genomic DNA from whole blood 241

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 335

value: C


title: genomic DNA from whole blood 327


title: genomic DNA from whole blood 290


title: genomic DNA from whole blood 232

value: J


title: HepG2-slug on Matrigel (HSM) rep1

type: RNA

city: Tianjin

first: baocun

last: sun

address: Qixiangtai Road No.22, Heping District

country: China

institute: Tianjin Medical University

description: HepG2-slug on Matrigel

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche-NimbleGen MS200, following their standard operating protocol.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

source_name: HepG2-slug cells on Matrigel

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Cells grow in DMEM+10%FBS at 37℃ 5% CO2 incubator.

extract_protocol: Total RNA was extracted using TRIzol following the manufactory’s instruction.

treatment_protocol: HepG2 and hepG2-slug in regular culture; hepG2-slug on Matrigel.

tag: treatment

value: slug overexpression in Matrigel

tag: cell line


title: genomic DNA from whole blood 231

value: E


title: genomic DNA from whole blood 213

value: 1; control

value: D


title: genomic DNA from whole blood 312

value: PLATE C

value: B


title: genomic DNA from whole blood 219

value: F


title: genomic DNA from whole blood 224

value: female


title: genomic DNA from whole blood 260

value: male

value: K


title: HepG2-slug in regular culture (HSR) rep1

description: HepG2-slug in regular culture

source_name: HepG2-slug cells in regular culture

value: slug overexpression in regular culture


title: HepG2-control in regular culture (HCR) rep1

description: HepG2 in regular culture

source_name: HepG2 cells in regular culture

value: control in regular culture


title: genomic DNA from whole blood 218

value: whole blood

value: yes

value: PLATE B

value: A


title: genomic DNA from whole blood 278

value: HYB-XSTAIN 1-4


title: Control – Parthenote 6 day old Embryos Replicate 4

city: Valencia

first: M. Desemparats

last: Saenz-de-Juano

state: Valencia

address: Camino de Vera s/n

department: Animal Science

country: Spain

institute: Universidad Politécnica Valencia

description: Sample 4

hyb_protocol: Hibridization was done using Agilent Gene Expression Hybridization Kit, following manufacturer's instructions. After 17 hours at 65ºC,  hybridised slides were washed sequential.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 10.10.1.1).

data_processing: Agilent Feature Extraction Software (v 10.10.1.1) was used for background correction and LOWESS normalization.

organism: Oryctolagus cuniculus

source_name: Parthenote 6 day old Embryos

label_protocol: Total RNA (150 ng) was labelled using QuickAmp Labelling Kit (Agilent Technologies) following manufacturer's instructions. Excess dye was removed with the RNAeasy Mini Kit (QIAGEN) and dye incorporation and concentration were determined using the microarray setting on the Nanodrop 1000.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Recovered oocytes were submitted to two sets 1 h apart of two DC electrical pulses of 3.2 kv/cm for 20 µs at 1 sec apart in an activation medium (0.3 M mannitol supplemented with 100 µM MgSO4 and 100 µM CaCl2), followed by 1h exposure in TCM199 medium supplemented with 5 µg/µL of cycloheximide and 2mM of 6-DMAP.

tag: strain

value: New Zealand White Rabbit

value: blastocyst

value: 6 days

value: parthenote

source_name: Control 6 day old Embryos

value: untreated


title: Cell Line SBC-5

city: Cologne

first: Felix

last: Dietlein

state: NRW

address: Weyertal 115b

department: Department of Translational Genomics

country: Germany

institute: University of Cologne

description: hybridized to 6.0 SNP arrays

hyb_protocol: according to the manufacturer's instructions DNA was hybridized to Affymetrix SNP Arrays 6.0

scan_protocol: arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: CEL files, TXT and SEG files. SEG Files were created from CEL files by  SNPFileCreator (Genepattern, Broad Institute). SEG files (.seg) list loci and associated numeric copy number values as tab delimited text files. The first row contains column headings. Next, copy numbers were determined by using IGV 2.1 Software (Genepattern, Broad Institute). IGV reads the first four columns as track name, chromosome, start location, and end location and the last column as the numeric value for that locus. The numeric copy number value was then determined as the inferred copy number from IGV 2.1 for each sample separately.

label: biotin

source_name: Small Cell Lung Cancer

label_protocol: as per manufacturer

growth_protocol: Cell lines were grown according to standard conditions (RPMI and HITES Medium supplemented with 10% FCS).

extract_protocol: Genomic DNA was extracted from cell lines using the Gentra PureGene kit (Qiagen) following manufacturer’s instructions and quantified using PicoGreen.

treatment_protocol: Cells were not treated before DNA extraction

tag: cell type

value: Small Cell Lung Cancer


title: Cell Line SBC-9

description: hybridized to 6.0 SNP arrays


title: genomic DNA from whole blood 271

value: 1; control

value: B


title: Cell Line SBC-1

description: hybridized to 6.0 SNP arrays


title: Control – Parthenote 6 day old Embryos Replicate 3

description: Sample 3


title: Cell Line SBC-7

description: hybridized to 6.0 SNP arrays


title: Cell Line SBC-4

description: hybridized to 6.0 SNP arrays


title: Cell Line SBC-6

description: hybridized to 6.0 SNP arrays


title: Cell Line GLC-36

description: hybridized to 6.0 SNP arrays


title: Cell Line H735

description: hybridized to 6.0 SNP arrays


title: genomic DNA from whole blood 59

value: male

value: 2; schizophrenia patient

value: PLATE D


title: genomic DNA from whole blood 48

value: I


title: genomic DNA from whole blood 2

value: whole blood

value: F


title: Cell Line GLC-2

description: hybridized to 6.0 SNP arrays


title: genomic DNA from whole blood 37

value: female

value: yes

value: G


title: genomic DNA from whole blood 70

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 38

value: L


title: genomic DNA from whole blood 26

value: J


title: Cell Line N417

description: hybridized to 6.0 SNP arrays


title: Cell Line H2198

description: hybridized to 6.0 SNP arrays


title: Cell Line H1876

description: hybridized to 6.0 SNP arrays


title: Cell Line GLC-1

description: hybridized to 6.0 SNP arrays


title: Cell Line H1341

description: hybridized to 6.0 SNP arrays


title: genomic DNA from whole blood 152

value: no

value: PLATE A

value: K


title: Cell Line GLC-8

description: hybridized to 6.0 SNP arrays

value: Small Cell Lung Cancer


title: Control – Parthenote 6 day old Embryos Replicate 2

description: Sample 2

value: New Zealand White Rabbit

value: blastocyst

value: 6 days

value: parthenote

value: untreated


title: genomic DNA from whole blood 16

value: male

value: 2; schizophrenia patient

value: whole blood

value: PLATE D

value: H


title: genomic DNA from whole blood 1

value: yes

value: A

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 13

value: C


title: Cell Line SW1271

description: hybridized to 6.0 SNP arrays


title: genomic DNA from whole blood 82

value: D


title: Control – Parthenote 6 day old Embryos Replicate 1

description: Sample 1


title: genomic DNA from whole blood 210

value: female

value: 1; control

value: PLATE A

value: L


title: genomic DNA from whole blood 145

value: no

value: I


title: genomic DNA from whole blood 202

value: J


title: Cell Line H1688

description: hybridized to 6.0 SNP arrays

value: Small Cell Lung Cancer


title: Cell Line H1836

description: hybridized to 6.0 SNP arrays


title: genomic DNA from whole blood 192

value: male


title: Cell Line H187

description: hybridized to 6.0 SNP arrays


title: Cell Line H146

description: hybridized to 6.0 SNP arrays


title: Cell Line H69AR

description: hybridized to 6.0 SNP arrays


title: Cell Line H841

description: hybridized to 6.0 SNP arrays


title: Cell Line H196

description: hybridized to 6.0 SNP arrays


title: Cell Line H211

description: hybridized to 6.0 SNP arrays


title: genomic DNA from whole blood 183

value: whole blood

value: F


title: genomic DNA from whole blood 209

value: G


title: genomic DNA from whole blood 163

value: yes

value: B


title: genomic DNA from whole blood 182

value: A

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 201

value: E


title: genomic DNA from whole blood 181


title: genomic DNA from whole blood 174

value: female

value: D


title: genomic DNA from whole blood 190

value: 1; control

value: PLATE A

value: C


title: genomic DNA from whole blood 160


title: genomic DNA from whole blood 151

value: H


title: genomic DNA from whole blood 173

value: L


title: 6th fraction of Ho series slicing

city: Wako-shi

first: Yuko

last: Okamura-Oho

state: Saitama

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized using per chip: normalize to 50th percentile.

organism: Mus musculus

source_name: 5 micron x 200 horizontal a little oblique slices (1 mm width) of the brain, set 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were grown in pathogen-free conditions.

extract_protocol: RNA was prepared using the Mag-max-96 for Microarrays Total RNA Isolation Kit (Ambion) following the manufacturer's recommendations of the spin column protocol.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: brain

value: 8 weeks

tag: section type

value: horizontal oblique plane

tag: mouse id


title: 1st fraction of Ho series slicing

value: male


title: 4th fraction of Ho series slicing


title: 2nd fraction of Ho series slicing


title: genomic DNA from whole blood 172

value: whole blood

value: G


title: genomic DNA from whole blood 156

value: yes


title: 3rd fraction of Ho series slicing


title: 5th fraction of Ho series slicing


title: genomic DNA from whole blood 208


title: 7th fraction of Ho series slicing


title: 6th fraction of H series slicing

source_name: 5 micron x 200 horizontal slices (1 mm width) of the brain, set 1

value: horizontal plane


title: genomic DNA from whole blood 143

value: no

value: F

value: HYB-XSTAIN 1-4


title: 4th fraction of H series slicing


title: 5th fraction of H series slicing


title: genomic DNA from whole blood 194

value: K


title: genomic DNA from whole blood 179

value: female

value: 1; control


title: genomic DNA from whole blood 141

value: PLATE A

value: A


title: 1st fraction of H series slicing


title: genomic DNA from whole blood 150

value: C


title: genomic DNA from whole blood 165

value: J


title: genomic DNA from whole blood 184

value: I


title: genomic DNA from whole blood 199

value: B


title: 2nd fraction of H series slicing

value: brain

value: male

value: 8 weeks


title: 16th fraction of Co series slicing

source_name: 5 micron x 200 coronal a little oblique slices (1 mm width) of the brain, set 2

value: coronal oblique plane


title: genomic DNA from whole blood 154

value: whole blood

value: yes

value: H


title: 3rd fraction of H series slicing

value: horizontal plane


title: genomic DNA from whole blood 178

value: no

value: G

value: HYB-XSTAIN 1-4


title: 15th fraction of Co series slicing


title: genomic DNA from whole blood 147

value: female

value: 1; control

value: PLATE A

value: F


title: 13th fraction of Co series slicing


title: 10th fraction of Co series slicing


title: genomic DNA from whole blood 203


title: genomic DNA from whole blood 164

value: E


title: genomic DNA from whole blood 146

value: A


title: genomic DNA from whole blood 215

value: D


title: 14th fraction of Co series slicing

value: brain

value: male


title: genomic DNA from whole blood 153

value: C


title: 11th fraction of Co series slicing

value: 8 weeks

value: coronal oblique plane


title: 12th fraction of Co series slicing


title: genomic DNA from whole blood 243

value: 2; schizophrenia patient

value: whole blood

value: yes

value: J


title: genomic DNA from whole blood 244

value: L

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 228

value: K


title: 5th fraction of Co series slicing


title: HepG2-control in regular culture (HCR) + anti-slug

description: Comparison of HCR, HSR, HSM

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 80 ul of hybridization buffer (3×SSC, 0.2%SDS, 5×Denhart’s, 25% formamide). Arrays were hybridized in CapitalBio hybridization stations for 16-18 h at 42℃, and then washed in 42℃ 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC.

scan_protocol: Arrays were scanned on LuxScan 10KA (CapitalBio corporation).

data_processing: Analyzed by LuxScan 3.0 analyze software.

source_name: Slug ChIP DNA from HepG2 cells in regular culture

label_protocol: 1 µg ChIP DNA was directly labeled by DSL technology in CapitalBio corporation

extract_protocol: 1x10E8 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and washed in 10 ml of lysis buffer (10 mM Tris-HCl pH7.5, 10mM NaCl, 3mM MgCl2, 0.5% IGEPAL, 1mM PMSF) for three times at 4℃. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a sonicator. The chromatin solution was then incubated overnight with an anti-slug antibody at 4℃. After incubation with protein A beads for 2h at 4℃, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4℃; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40), LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55℃for 2 h followed by the addition of proteinase K to 500 µg/ml and overnight incubation at 65℃. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

value: control in regular culture

tag: antibody

value: slug

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog #

tag: antibody lot #

source_name: Input DNA from HCR

value: input


title: 6th fraction of Co series slicing

tag: tissue

tag: gender

tag: age


title: genomic DNA from whole blood 25

tag: diseasestatus

tag: dataset

tag: plate

value: PLATE D

tag: sentrixbarcode

value: E


title: 8th fraction of Co series slicing

value: brain

value: male


title: HepG2-slug on Matrigel (HSM) + anti-slup

description: Comparison of HCR, HSR, HSM

source_name: Slug ChIP DNA from HepG2-slug cells on Matrigel

growth_protocol: DMEM+10%FBS on Matrigel

treatment_protocol: DMEM+10%FBS on Matrigel

tag: treatment

value: slug overexpression in Matrigel

source_name: Input DNA from HSM


title: genomic DNA from whole blood 214

value: PLATE A

tag: sentrixposition

value: I

tag: wellid

tag: trackingsheet


title: 7th fraction of Co series slicing

tag: strain

value: 8 weeks

tag: section type

value: coronal oblique plane


title: 4th fraction of Co series slicing

tag: mouse id


title: genomic DNA from whole blood 211

value: 2; schizophrenia patient

value: whole blood

value: yes

value: G


title: HepG2-slug in regular culture (HSR) + anti-slug

description: Comparison of HCR, HSR, HSM

source_name: Slug ChIP DNA from HepG2-slug cells in regular culture

value: slug overexpression in regular culture

tag: antibody

tag: cell line

tag: antibody manufacturer

source_name: Input DNA from HSR


title: 2nd fraction of Co series slicing

tag: tissue


title: 3rd fraction of Co series slicing

tag: gender


title: genomic DNA from whole blood 239

source_name: whole blood_schizophrenia patient

tag: age

value: H

value: HYB-XSTAIN 1-4


title: genomic DNA from whole blood 238

tag: diseasestatus

value: F


title: 9th fraction of Co series slicing


title: 13th fraction of C series slicing

source_name: 5 micron x 200 coronal slices (1 mm width) of the brain, set 1

value: coronal plane


title: genomic DNA from whole blood 237

tag: dataset

value: D


title: 12th fraction of C series slicing

value: brain


title: genomic DNA from whole blood 207

value: male

tag: plate

value: E


title: 1st fraction of Co series slicing


title: 9th fraction of C series slicing


title: genomic DNA from whole blood 189

source_name: whole blood_control

value: female

value: 1; control

value: PLATE A

tag: sentrixbarcode

value: K


title: genomic DNA from whole blood 200

value: 2; schizophrenia patient

value: C


title: 7th fraction of C series slicing

value: 8 weeks


title: Memory B cell (day 40), rep2

city: Yokohama

first: Kaji

last: Tomohiro

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

department: Research center for allergy and immunology

description: Mice were immunized with NP-CG/alum.  On day 40 postimmunization, splenocytes were negatively selected with MACS system using biotinylated Abs against IgM, IgD, CD5, Gr1, NK1.1, DX5, TER119, F4/80, CD3 and CD90, followed by sorted NIP-binding B220+IgG1+CD38+PNA- fraction as memory B cells.

hyb_protocol: Affymetrix standard procedures

scan_protocol: Using a microarray scanner as manufacture's instruction (Affymetrix)

data_processing: GCRMA

source_name: IgG1 memory B cells (day40)

label_protocol: Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2

extract_protocol: Total RNAs were extracted using TRIZOL reagent.

value: spleen

value: 8 to 10 weeks old when immunized with NP-CGG/alum


title: Germinal center B cell (day 40), rep2

description: Mice were immunized with NP-CG/alum.  On day 40 postimmunization, splenocytes were negatively selected with MACS system using biotinylated Abs against IgM, IgD, CD5, Gr1, NK1.1, DX5, TER119, F4/80, CD3 and CD90, followed by sorted NIP-binding B220+IgG1+CD38dullPNA+ fraction as germinal center B cells.

source_name: IgG1 germinal center B cells (day40)


title: Follicular B cell,anti-IgM+CD40 stimulation, 6h, rep2

description: Sorted follicular B cells were stimulated with 10 μg/ml anti-mouse IgM F(ab’)2 and 2 μg/ml rat anti-mouse CD40 mAb for 6h.

source_name: Splenic follicular B cell stimulated with anti-IgM and CD40 for 6h

value: 8 to 10 weeks


title: 11th fraction of C series slicing


title: Follicular B cell,anti-IgM+CD40 stimulation, 6h, rep3


title: 8th fraction of C series slicing


title: Germinal center B cell (day 40), rep3


title: 10th fraction of C series slicing


title: 5th fraction of C series slicing


title: Memory B cell (day 40), rep1


title: RootD6h_1

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: Biological replicate 1 of 2.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.probe file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Oryza sativa Japonica Group

source_name: Root after 6 hours of stress treatment

growth_protocol: Non-transgenic rice seeds (Oriza sativa L. japonica cultivar Nakdong) were germinated on MS0 (Murashi and Skoog) agar media (0.25% phytagel) and incubated in a growth chamber (28oC, 2 days in dark followed by 1 day in light). Seedlings were then transferred into soil and grown in a greenhouse (16-hr-light/ 8-hr-dark cycle).

extract_protocol: Total RNAs were extracted using TriReagent (Molecular Research Center, Inc.).

treatment_protocol: For drought stress, 14-day-old seedlings were removed from soil and maintained in fresh water for 1 day, all water attached to the plant was removed by tissue, and seedlings were dried in a 32oC-chamber under continuous fluorescent light of 150 μmol.m-2.s-1. A humidity of 50% was maintained during stress treatment.The roots were covered by a tissue layer and an aluminum foil layer on the outmost. After 0, 0.5, 2, 6, 12 h, leaves and roots were collected separately.

tag: cultivar

value: Nakdong

value: root

tag: treatment

value: drought stress

tag: treatment duration

value: 6 hrs


title: Memory B cell (day 40), rep3


title: genomic DNA from whole blood 236

value: whole blood

value: yes

tag: sentrixposition

value: B

tag: wellid

tag: trackingsheet

value: HYB-XSTAIN 1-4


title: Germinal center B cell (day 40), rep1

tag: strain

value: female


title: HCC70 fip EZH2, replicate 1

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Faculty of Medicine, Ein kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

description:
BP15
HCC70 cells stably infected with EZH2 cDNA vector.

hyb_protocol: 2ug ss cDNA in 80 ul were hybridized to a Human Gene 1.0 ST array using Affymetrix hybridization kit materials for 17 hours at 45° at 60rpm. Post-hybridization washes were done with Affymetrix wash solutions on the FS450 station using the FS450_0007 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was quantified using Affymetrix Expression Console, applying the RMA method.

label: Biotin

source_name: HCC70 breast cancer cell line, EZH2 cDNA vector

label_protocol: 200ng Total RNA were used. cDNA samples were generated and labeled using the Affymetrix WT-cDNA synthesis and labeling kit.

growth_protocol: Cells were grown under standard conditions as specified by the ATCC. 24 hours prior to RNA extraction, cells were seeded at equal confluence.

extract_protocol: Total RNA was extracted using the RNeasy Mini Plus kit (Qiagen).

treatment_protocol: Infected cells were exposed to viral supernatants of the specified vector in the presence of 6μg/ml polybrene. 48 hours post infection, cells were placed under 1μg/ml puromycin selection.

tag: cell type

value: breast cancer cells

value: EZH2 cDNA


title: RootD12h_1

description: Biological replicate 1 of 2.

source_name: Root after 12 hours of stress treatment

value: 12 hrs


title: Plasma cell (day 7), rep3

description: Mice were immunized with NP-CG/alum.  On day 7 postimmunization, splenocytes were negatively selected with MACS system using biotinylated Abs against IgM, IgD, CD5, Gr1, NK1.1, DX5, TER119, F4/80, CD3 and CD90, followed by sorted NIP-binding B220+IgG1lowCD138+Igλ+ fraction as plasma cells

source_name: Plasma cells (day7)


title: HCC70 fip EZH2, replicate 2

description:
BP16
HCC70 cells stably infected with EZH2 cDNA vector.

tag: cell line


title: 6th fraction of C series slicing

value: brain

value: male

tag: section type

value: coronal plane

tag: mouse id


title: RootD6h_2

description: Biological replicate 2 of 2.

tag: tissue


title: 4th fraction of C series slicing

tag: gender

tag: age

value: 8 weeks


title: HCC70 plKO Puro, replicate 2

description:
BP14
HCC70 cells stably infected with empty vector.

source_name: HCC70 breast cancer cell line, empty vector

value: empty vector


title: HCC70 plKO Puro, replicate 1

description:
BP13
HCC70 cells stably infected with empty vector.


title: RootD2h_1

description: Biological replicate 1 of 2.

source_name: Root after 2 hours of stress treatment

value: Nakdong

value: 2 hrs


title: HCC70 shEED, replicate 2

description:
BP12
HCC70 cells stably infected with shRNA targeting EED.

source_name: HCC70 breast cancer cell line, shRNA targeting EED

value: shEED


title: Plasma cell (day 7), rep2

value: spleen

value: 8 to 10 weeks old when immunized with NP-CGG/alum


title: RootD2h_2

description: Biological replicate 2 of 2.

value: root

value: drought stress


title: Plasma cell (day 7), rep1


title: 2nd fraction of C series slicing


title: Follicular B cell,anti-IgM+CD40 stimulation, 6h, rep1

value: 8 to 10 weeks


title: HCC70 shEED, replicate 1

description:
BP11
HCC70 cells stably infected with shRNA targeting EED.


title: Germinal center B cell (day 7), rep2

description: Mice were immunized with NP-CG/alum.  On day 7 postimmunization, splenocytes were negatively selected with MACS system using biotinylated Abs against IgM, IgD, CD5, Gr1, NK1.1, DX5, TER119, F4/80, CD3 and CD90, followed by sorted NIP-binding B220+IgG1+CD38dullPNA+ fraction as germinal center B cells.

source_name: IgG1 germinal center B cells (day7)

value: female


title: genomic DNA from whole blood 193

tag: diseasestatus

value: 2; schizophrenia patient

value: whole blood

value: yes

tag: dataset

value: PLATE A

value: A

value: HYB-XSTAIN 1-4


title: RootD0h_1

description: Biological replicate 1 of 2.

source_name: Root at the onset of stress treatment

value: onset


title: Germinal center B cell (day 7), rep3


title: 10th fraction of So series slicing

source_name: 5 micron x 200 sagittal a little oblique slices (1 mm width) of the brain, set 2

value: brain

value: male

value: 8 weeks

value: sagittal oblique plane


title: Memory B cell (day 7), rep3

description: Mice were immunized with NP-CG/alum.  On day 7 postimmunization, splenocytes were negatively selected with MACS system using biotinylated Abs against IgM, IgD, CD5, Gr1, NK1.1, DX5, TER119, F4/80, CD3 and CD90, followed by sorted NIP-binding B220+IgG1+CD38+PNA- fraction as memory B cells.

source_name: IgG1 memory B cells (day7)

value: spleen


title: RootD0h_2

description: Biological replicate 2 of 2.

value: Nakdong


title: 9th fraction of So series slicing


title: Germinal center B cell (day 7), rep1

value: 8 to 10 weeks old when immunized with NP-CGG/alum


title: 3rd fraction of C series slicing

value: coronal plane


title: 1st fraction of C series slicing


title: RootD0.5h_1

description: Biological replicate 1 of 2.

source_name: Root after 30 minutes of stress treatment

value: root

value: drought stress

value: 30 min


title: MDA-MB-468 shEZH2, replicate 2

description:
BP08
MDA468 cells stably infected with shRNA targeting EZH2.

source_name: MDA-MB-468 breast cancer cell line, shRNA targeting EZH2

value: breast cancer cells


title: HCC70 shCont, replicate 1b

description:
BP09
HCC70 cells stably infected with scrambled shRNA sequence.

source_name: HCC70 breast cancer cell line, scrambled shRNA

value: scrambled shRNA


title: LeafD12h_2

description: Biological replicate 2 of 2.

source_name: Leaf after 12 hours of stress treatment

value: leaf

value: 12 hrs


title: LeafD12h_1

description: Biological replicate 1 of 2.


title: HCC70 shCont, replicate 2b

description:
BP10
HCC70 cells stably infected with scrambled shRNA sequence.


title: RootD0.5h_2

description: Biological replicate 2 of 2.


title: Memory B cell (day 7), rep2

value: female


title: Memory B cell (day 7), rep1


title: MDA-MB-468 shCont, replicate 2

description:
BP06
MDA468 cells stably infected with scrambled shRNA sequence.

source_name: MDA-MB-468 breast cancer cell line, scrambled shRNA


title: HCC70 shEZH2, replicate 2

description:
BP04
HCC70 cells stably infected with shRNA targeting EZH2.

source_name: HCC70 breast cancer cell line, shRNA targeting EZH2


title: MDA-MB-468 shCont, replicate 1

description:
BP05
MDA468 cells stably infected with scrambled shRNA sequence.


title: MDA-MB-468 shEZH2, replicate 1

description:
BP07
MDA468 cells stably infected with shRNA targeting EZH2.


title: Marginal zone B cell, rep3

description: Cells were negatively selected with MACS system using biotynilated Abs against CD5, CD11b, CD95, CD138, CD43, Gr-1, TER119, F4/80, CD3 and CD90, followed by sorted B220+AA4.1-CD21highCD23low fraction as marginal zone B cells.

source_name: Splenic marginal zone B cells

value: 8 to 10 weeks


title: LeafD6h_2

description: Biological replicate 2 of 2.

source_name: Leaf after 6 hours of stress treatment

value: 6 hrs


title: LeafD6h_1

description: Biological replicate 1 of 2.


title: RootD12h_2

description: Biological replicate 2 of 2.

source_name: Root after 12 hours of stress treatment


title: 7th fraction of So series slicing

value: brain

value: male


title: LeafD2h_2

description: Biological replicate 2 of 2.

source_name: Leaf after 2 hours of stress treatment

value: 2 hrs


title: 8th fraction of So series slicing

value: 8 weeks

value: sagittal oblique plane


title: Marginal zone B cell, rep2

value: spleen


title: 6th fraction of So series slicing


title: HCC70 shEZH2, replicate 1

description:
BP03
HCC70 cells stably infected with shRNA targeting EZH2.


title: LeafD2h_1

description: Biological replicate 1 of 2.

value: Nakdong


title: 4th fraction of So series slicing


title: Follicular B cell, rep1

description: Cells were negatively selected with MACS system using biotynilated Abs against CD5, CD11b, CD95, CD138, CD43, Gr-1, TER119, F4/80, CD3 and CD90, followed by sorted B220+AA4.1-CD21intCD23+ fraction as follicular B cells.

source_name: Splenic follicular B cell


title: LeafD0.5h_2

description: Biological replicate 2 of 2.

source_name: Leaf after 30 minutes of stress treatment


title: Follicular B cell, rep2


title: HCC70 shCont, replicate 1a

description:
BP01
HCC70 cells stably infected with scrambled shRNA sequence.


title: 5th fraction of So series slicing


title: 2nd fraction of So series slicing


title: 10th fraction of S series slicing

source_name: 5 micron x 200 sagittal slices (1 mm width) of the brain, set 2

value: sagittal plane


title: 3rd fraction of So series slicing


title: LeafD0h_1

description: Biological replicate 1 of 2.

source_name: Leaf at the onset of stress treatment

value: drought stress

value: onset


title: 1st fraction of So series slicing


title: Marginal zone B cell, rep1


title: HCC70 shCont, replicate 2a

description:
BP02
HCC70 cells stably infected with scrambled shRNA sequence.

value: breast cancer cells


title: Donor 5, GM (Cy3) vs. GM+Super-4 (Cy5)

city: Stanford

first: Remi

middle: J

last: Creusot

address: 269 Campus Dr, CCSR 2240

department: Medicine

institute: Stanford University

description: Donor 5

hyb_protocol: As per the Agilent standard protocol.

scan_protocol: Data were scanned at the Stanford Human Immune Monitoring Core.

data_processing: Data were extracted and normalized using Feature Extraction software (Agilent).

source_name: primary CD14+ monocytes, GM-CSF + Super-4

label_protocol: RNA was labelled using the Two-Color Low Input Quick Amp Labeling kit from Agilent.

growth_protocol: Monocytes were isolated from PBMCs using the RosetteSep Human Monocytes Enrichment Kit followed by CD14-positive selection by MACS.

extract_protocol: Cells were washed in PBS and then lysed in Trizol. Total mRNA was isolated using a combined Trizol and RNeasy Micro kit protocol.

treatment_protocol: Monocytes were cultured for 6 hours in the presence of select cytokines as described for each sample.

value: primary CD14+ monocytes

value: GM-CSF + Super-4

tag: donor

source_name: Primary CD14+ monocytes, GM-CSF

value: GM-CSF


title: 8th fraction of S series slicing

source_name: 5 micron x 200 sagittal slices (1 mm width) of the brain, set 1


title: Marginal Zone B cell from mb1-cre(+/-)Bcl6(flox/flox), rep2

data_processing: Follicular B cells and Marginal zone B cells were separately processed with GCRMA.

label_protocol: GeneChip 3'IVT Express Kit

value: female

tag: genotype

value: 10 weeks


title: Donor 4, GM (Cy3) vs. GM+KFR (Cy5)

description: Donor 4

source_name: primary CD14+ monocytes, GM-CSF + KFR

tag: treatment

value: GM-CSF + KFR


title: Follicular B cell, rep3

value: 8 to 10 weeks


title: Donor 5, GM (Cy3) vs. GM+KFR (Cy5)

description: Donor 5


title: 9th fraction of S series slicing

value: brain

value: male


title: LeafD0h_2

description: Biological replicate 2 of 2.

tag: cultivar

value: leaf

tag: treatment duration


title: Donor 5, GM (Cy3) vs. GM+IL-4 (Cy5)

description: Donor 5

source_name: primary CD14+ monocytes, GM-CSF + IL-4

value: GM-CSF + IL-4


title: Marginal Zone B cell from mb1-cre(+/-)Bcl6(flox/flox), rep1


title: 7th fraction of S series slicing

value: 8 weeks


title: LeafD0.5h_1

description: Biological replicate 1 of 2.

value: Nakdong

value: 30 min


title: Marginal Zone B cell from mb1-cre(+/-)Bcl6(+/flox), rep1


title: 6th fraction of S series slicing

value: sagittal plane


title: 5th fraction of S series slicing


title: Marginal Zone B cell from mb1-cre(+/-)Bcl6(+/+), rep2


title: Donor 4, GM (Cy3) vs. GM+IL-4 (Cy5)

description: Donor 4


title: Donor 4, GM (Cy3) vs. GM+Super-4 (Cy5)

description: Donor 4


title: Marginal Zone B cell from mb1-cre(+/-)Bcl6(+/flox), rep2


title: 4th fraction of S series slicing


title: 3rd fraction of S series slicing


title: Follicular B cell from mb1-cre(+/-)Bcl6(flox/flox), rep1


title: Donor 3, GM (Cy3) vs. GM+IL-4 (Cy5)

description: Donor 3


title: eca39adapted

city: Okayama

first: Hidekazu

last: Takahashi

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

institute: Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

description: The cells adaptively grown near WT were inoculated in rich medium

hyb_protocol: Affymetrix standard protocol using the GeneChip Yeast 2.0.

scan_protocol: Affymetrix standard protocol using the GeneChip Scanner 3000 7G.

data_processing: RMA algorithm using the Bioconductor Affy package. The expression values only for the S. pombe probes were finally collected.

organism: Schizosaccharomyces pombe

label_protocol: Biotin labeling using the Affymetrix 3’ IVT Express kit following the standard protocol.

growth_protocol: Culture in liquid YE + 2mM Ile, Leu and Val from OD ~ 0.1 to 1.

extract_protocol: Acid-phenol extraction followed by RNeasy mini (Qiagen).

treatment_protocol: Inoculated from a YE + 2mM Ile, Leu and Val plate or an EMM2-N + 15mM Glu + 2mM Ile, Leu and Val plate near the WT strain.

value: SpHT257-1 (h- eca39∆::kanMX4) adapted

tag: inoculated from


title: 2nd fraction of S series slicing


title: Follicular B cell from mb1-cre(+/-)Bcl6(+/+), rep2


title: eca39

description: The cells (without adaptation) were inoculated into rich medium.

value: SpHT257-1 (h- eca39∆::kanMX4)

value: YE plate


title: Follicular B cell from mb1-cre(+/-)Bcl6(flox/flox), rep2


title: Donor 1, GM (Cy3) vs. GM+IL-4 (Cy5), replicate

description: Donor 1

value: primary CD14+ monocytes


title: Retina-1

city: Fukuoka

first: Keijiro

last: Ishikawa

address: 3-1-1  Maidashi, Higashi-ku

department: Ophthalmology

institute: Kyushu University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw gene expression data were summarized using the Illumina Bead Studio software. Thresholding of the signal values to 1 is done and then normalized the data to 75th percentile and performs baseline transformation to median of all samples.These are performed by Genespring v 11.

source_name: retina

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: To extract the RNAs, fibrous membranes isolated from patients with PVR were homogenized with a Polytron homogenizer in extraction reagent, extracted with chloroform, and the aqueous phase was precipitated in isopropanol.

value: retina


title: Donor 2, GM (Cy3) vs. GM+IL-4 (Cy5)

description: Donor 2

value: GM-CSF


title: WT

description: The cells were inoculated into rich medium

source_name: prototroph


title: Donor 1, GM (Cy3) vs. GM+Super-4 (Cy5)

description: Donor 1

value: GM-CSF + Super-4


title: Follicular B cell from mb1-cre(+/-)Bcl6(+/+), rep1

value: female

value: 10 weeks


title: Donor 2, GM (Cy3) vs. GM+Super-4 (Cy5)

description: Donor 2


title: Donor 1, GM (Cy3) vs. GM+IL-4 (Cy5)

description: Donor 1


title: Donor 1, GM (Cy3) vs. GM+KFR (Cy5)

description: Donor 1

value: GM-CSF + KFR


title: Follicular B cell from mb1-cre(+/-)Bcl6(+/flox), rep1


title: Donor 3, GM (Cy3) vs. GM+Super-4 (Cy5)

description: Donor 3


title: Donor 2, GM (Cy3) vs. GM+KFR (Cy5)

description: Donor 2


title: Retina-2


title: Follicular B cell from mb1-cre(+/-)Bcl6(+/flox), rep2


title: Retina-3


title: PVR-1

source_name: epiretinal membrane

value: fibrous epiretinal membrane


title: PVR-3


title: [delta smelt]-[Hood4 vs Control]-[4]

status: Public on Sep 20 2012

city: Davis

first: Richard

middle: Edward

last: Connon

address: One Shields Avenue

department: Anatomy, Physiology and Cell Biology

institute: University of California at Davis

hyb_protocol: Hybridization was carried out manually, slides were incubated at 42C.

scan_protocol: Slides were scanned using a GenePix 4000B scanner instrument (Axon Instruments, Sunnyvale, Ca, USA)

data_processing: Data analysis: Two color microarray assessments were carried out on quadruplicate treatments, using 5µg of amplified RNA for each pooled control vs exposed sample (total 4 samples). Microarray hybridizations were performed manually in a waterbath at 42C. Slides were scanned using a GenePix 4000B scanner (Axon Instruments). Data was analyzed using LIMMA GUI (Linear model for microarray analysis graphical user interface) (Smyth, 2005), written in the R-programming language available through Bioconductor http://www.Bioconductor.org. Data was normalized within using print-tip Lowess and between arrays applying average intensity quantile (Aquantile) normalization methods with background correction (Smyth, 2005). A linear model fit was computed using the duplicates on the arrays and the least-squares method, with Benjamin Hochberg false discovery rate adjustment

label: Alexa Fluor 555

organism: Hypomesus transpacificus

source_name: Control

label_protocol: Five micrograms of amplified RNA was labeled with Alexa Fluor dyes using Superscript Plus Indirect cDNA Labeling System (Invitrogen, Carlsbad, Ca, USA)

growth_protocol: Juveniles obtained from the Fish Culture Conservation Facility (FCCL) at the University of California at Davis.

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen, Carlsbad, Ca, USA) as per manufacturer's protocol

treatment_protocol: 47-old juveniles were exposed for 7 days to ambient water samples collected from the Sacramento River at the Hood field water station

value: 47-day old

value: whole larvae

label: Alexa Fluor 647

source_name: Hood

value: Pooled mixed age


title: PVR-2


title: [delta smelt]-[Control vs Hood3]-[3]


title: [delta smelt]-[Hood1 vs Control]-[1]


title: GalX deletion mutant A.niger, biological rep2

city: Utrecht

first: miaomiao

last: Zhou

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: centre of fungal biodiversity, Utrecht, KNAW

description: GalX-gal 2

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized to Affymetrix A. niger Genome Gene chips (GPL6758). GeneChips were washed and stained in an automated process.

scan_protocol: GeneChips were scanned.

data_processing: Affymetrix CEL-data files were preprocessed by using the statistical language and environment R (R Development Core Team, 2007) version 2.6.1. The probe intensities were normalized for background by using the robust multiarray average method (Irizarry, 2003) by using only perfect match (PM) probes. Normalization was performed subsequently by using the quantiles algorithm (Bolstad, 2003). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

organism: Aspergillus niger

source_name: ΔgalX mutant_D-galactose_2h

label_protocol: Biotin-labeled antisense cRNA was produced from 2 μg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com).

growth_protocol: The A. niger strains used in this study are N402 (reference, genotype: cspA) and FP-315.1 (galX disruptant, genotype: cspA, 5 ΔkusA::amdS+,  galX::pyrG+). Spore plates contained Complete Medium + 2% glucose. All liquid cultures were grown in Erlenmeyer flasks on a rotary shaker (250 rpm) at 30°C.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) and purified using TRIzol® Plus RNA Purification Kit (Sigma-Aldrich) according to the instructions of the manufacturer.

treatment_protocol: Pre-cultures for DNA and RNA isolation were grown overnight in 1L Erlenmeyer flasks containing 250 ml CM with 2% D-fructose. For microarray analysis, the pre-grown cultures were washed with MM and transferred to 250 ml Erlenmeyer flasks containing 50 ml MM + 25 mM monosaccharide or 1% polysaccharide and were incubated for an additional 2 hours. After incubation, the mycelium was harvested by vacuum filtration, dried between towels and immediately frozen in liquid nitrogen.

tag: strain background

tag: genotype/variation

value: cspA, 5 ΔkusA::amdS+,  galX::pyrG+,  ΔgalX mutant

value: mycelium

tag: incubated in

value: minimal medium with 25 mM D-galactose for 2hr


title: Donor 3, GM (Cy3) vs. GM+KFR (Cy5)

description: Donor 3

tag: cell type


title: Marginal Zone B cell from mb1-cre(+/-)Bcl6(+/+), rep1

source_name: Splenic marginal zone B cells

tag: strain


title: Wild type A.niger, biological rep2

description: Gal 2

source_name: wild type_D-galactose_2h

value: cspA, wild type


title: [delta smelt]-[Control vs Hood2]-[2]


title: GalX deletion mutant A.niger, biological rep1

description: GalX-gal 1


title: HSF1-/- T cells at 37oC replicate #1

city: Lexington

first: Jerold

middle: G

last: Woodward

state: ky

address: 800 Rose St. MS-415

department: Microbiology, Immunology & Molecular Genetics

institute: University of Kentucky

description:
5hr activation with plate bound anti-CD3
Gene expression data from HSF1-/- T cells activated at 37oC for 5h with plate bound anti-CD3.

hyb_protocol: Following fragmentation, 20μg of cRNA were hybridized for 16h at 45C on whole mouse Affymetrix 430-2.0 Mouse Genome Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as a normalization method.   The trimmed mean target intensity of each array was arbitrarily set to 100.  Statistical analysis was performed using two-way ANOVA and SAS software.

source_name: HSF1-/- T cells activated at 37oC

label_protocol: Biotinylated cRNA was prepared by transcribing  2.5 μg of Total RNA according to standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Purified T cells were cultured in RPMI 1640 medium for 5h at 37oC or 40oC and at 5% CO2

extract_protocol: Total RNA from activated T cells were isolated using RNA easy Kit according to manufacturer's protocol. The RNA quantification and quality was performed using a Model 2100 bioanalyzer.

treatment_protocol: T cells were activated with plate bound anti-CD3

value: T cell

tag: genetic background

value: mixed 129Sv.BALB/c background


title: HSF1+/+ T cells at 37oC replicate #2

description:
5hr activation with plate bound anti-CD3
Gene expression data from HSF1+/+ T cells activated at 37oC for 5h with plate bound anti-CD3.

source_name: HSF1+/+ T cells activated at 37oC


title: HSF1+/+ T cells at 37oC replicate #1


title: z-VRPR-fmk Treated OCI-Ly3 - 30 hrs - mAdbID:99972

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 99972

hyb_protocol: Agilent Hybridization Protocol Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: DMSO Treated OCY-Ly3 cells

label_protocol:
Cy3 Labeling Protocol
Other: 2 ug total RNA were labeled with Cy3.

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).

tag: tissue

value: blood

tag: cell line

tag: disease state

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: z-VRPR-fmk Treated OCY-Ly3 - 30 hr

label_protocol:
Cy5 Labeling Protocol
Other: 2 ug total RNA were labeled with Cy5.

treatment_protocol:
Treatment type: compound
Agent: z-VRPR-fmk
Treatment dose: 50 mM
Treatment time: 30 hours
In-vitro treatment: Cells were incubated with 50 mM z-VRPR-fmk (Alexis Biochemicals) for 30 hours.


title: HSF1-/- T cells at 40oC replicate #2

description:
5hr activation with plate bound anti-CD3
Gene expression data from HSF1-/- T cells activated at 40oC for 5h with plate bound anti-CD3.

source_name: HSF1-/- T cells activated at 40oC


title: z-VRPR-fmk Treated HBL-1 - 30 hrs - mAdbID:99738

description: mAdb experiment ID: 99738

source_name: DMSO Treated HBL-1 cells

source_name: z-VRPR-fmk Treated HBL-1 - 30 hr


title: HSF1-/- T cells at 40oC replicate #1


title: HSF1+/+ T cells at 40oC replicate #1

description:
5hr activation with plate bound anti-CD3
Gene expression data from HSF1+/+ T cells activated at 40oC for 5h with plate bound anti-CD3.

source_name: HSF1+/+ T cells activated at 40oC


title: Wild type A.niger, biological rep1

description: Gal 1


title: z-VRPR-fmk Treated HBL-1 - 24 hrs - mAdbID:99737

description: mAdb experiment ID: 99737

source_name: z-VRPR-fmk Treated HBL-1 - 24 hr

treatment_protocol:
Treatment type: compound
Agent: z-VRPR-fmk
Treatment dose: 50 mM
Treatment time: 24 hours
In-vitro treatment: Cells were incubated with 50 mM z-VRPR-fmk (Alexis Biochemicals) for 24 hours.


title: HSF1+/+ T cells at 40oC replicate #2


title: z-VRPR-fmk Treated HBL-1 - 12 hrs - mAdbID:99736

description: mAdb experiment ID: 99736

source_name: z-VRPR-fmk Treated HBL-1 - 12 hr

treatment_protocol:
Treatment type: compound
Agent: z-VRPR-fmk
Treatment dose: 50 mM
Treatment time: 12 hours
In-vitro treatment: Cells were incubated with 50 mM z-VRPR-fmk (Alexis Biochemicals) for 12 hours.


title: z-VRPR-fmk Treated OCI-Ly3 - 24 hrs - mAdbID:99971

description: mAdb experiment ID: 99971

source_name: z-VRPR-fmk Treated OCY-Ly3 - 24 hr


title: z-VRPR-fmk Treated OCI-Ly3 - 6 hrs - mAdbID:99969

description: mAdb experiment ID: 99969

source_name: z-VRPR-fmk Treated OCY-Ly3 - 6 hr

treatment_protocol:
Treatment type: compound
Agent: z-VRPR-fmk
Treatment dose: 50 mM
Treatment time: 6 hours
In-vitro treatment: Cells were incubated with 50 mM z-VRPR-fmk (Alexis Biochemicals) for 6 hours.


title: z-VRPR-fmk Treated HBL-1 - 6 hrs - mAdbID:99735

description: mAdb experiment ID: 99735

source_name: z-VRPR-fmk Treated HBL-1 - 6 hr


title: HSF1-/- T cells at 37oC replicate #2


title: z-VRPR-fmk Treated OCI-Ly3 - 12 hrs - mAdbID:99970

description: mAdb experiment ID: 99970

source_name: z-VRPR-fmk Treated OCY-Ly3 - 12 hr


title: 3b_697_N

city: New York

first: Elisa

last: Oricchio

address: 1275 York Avenue

institute: MSKCC

hyb_protocol: Labeling and hybridization was performed according to protocols provided by Agilent.

scan_protocol: Agilent G2565 Microarray Scanner System and Agilent Feature Extraction software (v9.1) was used to generate the data

data_processing: The modified CBS algorithm was used to identify segmental gains and losses along the autosomes1. Change-points were defined as segments, corresponding to p-values < 0.05.

source_name: Lymphonode

growth_protocol: Paraffin or OCT-embedded

extract_protocol: standard phenol-chloroform extraction method

tag: tumor type

value: Follicular Lymphoma

tag: tumor grade

source_name: human genomic DNA (reference)

tag: gender

value: male

tag: ref. source

value: Promega (Cat# G147A)


title: 3b_2181_N

label_protocol: Labeling and hybridization was performed according to protocols provided by Agilent.


title: 3b_2326_P


title: 3a_739_N


title: 3a_2309_P


title: 3a_946_P


title: 3b_1175_P


title: 3a_2162_P


title: 3b_1377_P


title: 3b_1125_P


title: 3b_1530_P


title: 3a_2230_P


title: 3a_2377_P


title: 3a_153_P


title: 3a_1952_P


title: 3a_1444_N


title: 3a_1513_P


title: 2_2386_N


title: 2_2341_P


title: 3a_843_N


title: 2_2394_N


title: 3a_2363_N


title: 2_2348_P


title: 3a_112_P


title: 2_2375_P


title: 3a_1277_P


title: 2_491_P


title: 3a_885_P


title: 3a_1109_P


title: 2_2310_P


title: 2_2279_P


title: 2_2487_N


title: 2_691_N


title: 2_966_P


title: 2_2192_P


title: 2_2215_P


title: 2_2063_P


title: 2_2007_N


title: 2_2116_N


title: DOX.2h.4

city: Gentofte

first: Morten

last: Tonnesen

address: Niels Steensensvej 1

country: Denmark

institute: Hagedorn Research Institute

hyb_protocol: Fifteen micrograms of biotin-labelled cRNA was fragmented and 10 mg were hybridized onto Affymetrix Rat Genome 230 2.0 arrays overnight in the GeneChip Hybridisation oven 6400 using standard procedures, The arrays were washed and stained in a GeneChip Fluidics Station 450.

scan_protocol: Scanning was carried out using the GeneChip Scanner 3000 and image analysis was performed using GeneChip Operating Software.

organism: Rattus norvegicus

source_name: Pdx1 overexpression, harvest after 2h, replica 4

label_protocol: Total RNA was processed following the GeneChip Expression 30-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-labelled cRNA following manufacturer’s specifications.

growth_protocol: Cells were cultured in RPMI 1640 with or without 500 ng/ml doxycycline.

extract_protocol: Isolation of total cellular RNA was performed with cells from a single 10cm diameter dish. The monolayer was rapidly washed twice with phosphate-buffered saline, pH 7.5, and lysed in a guanidinium thiocyanatesolution. The resulting suspension was homogenized by several passes through a 21-gaugeneedle. Phenol extraction of the homogenate and isopropyl alcohol precipitation of RNA were performed. Two additional cycles of suspension in the guanidinium thiocyanate solution and isopropyl alcohol precipitation were carried out.

treatment_protocol: After 24 h, 40 ng/ml IL-1b was added, and cells were harvested at 2h, 4h, 6h, 12h, and 24h, respectively.

value: rat insulinoma INS-1ab cell line with doxycyclin inducible Pdx1 expression

tag: agent

value: 500 ng/ml doxycyclin

value: not added

tag: time point

tag: biological replica


title: 2_1001_P


title: DOX.IL1.2h.4

source_name: Pdx1 overexpression, Il-1b added, harvest after 2h, replica 4


title: 2_1552_P


title: Control.2h.4

source_name: Harvest after 2h, replica 4


title: DOX.IL1.6h.4

source_name: Pdx1 overexpression, Il-1b added, harvest after 6h, replica 4


title: IL1.2h.4

source_name: Il-1b added, harvest after 2h, replica 4

value: 40 ng/m IL-1b


title: Control.24h.4

source_name: Harvest after 24h, replica 4


title: DOX.IL1.12h.4

source_name: Pdx1 overexpression, Il-1b added, harvest after 12h, replica 4


title: DOX.24h.4

source_name: Pdx1 overexpression, harvest after 24h, replica 4


title: DOX.IL1.4h.4

source_name: Pdx1 overexpression, Il-1b added, harvest after 4h, replica 4


title: IL1.12h.4

source_name: Il-1b added, harvest after 12h, replica 4


title: Control.2h.3

source_name: Harvest after 2h, replica 3


title: IL1.24h.4

source_name: Il-1b added, harvest after 24h, replica 4


title: 1_947_P


title: 2_1501_P


title: 1_807_P


title: 1_679_P


title: 1_718_P


title: 1_593_P


title: DOX.24h.3

source_name: Pdx1 overexpression, harvest after 24h, replica 3


title: 1_46_P


title: IL1.6h.4

source_name: Il-1b added, harvest after 6h, replica 4


title: DOX.IL1.4h.3

source_name: Pdx1 overexpression, Il-1b added, harvest after 4h, replica 3


title: IL1.12h.3

source_name: Il-1b added, harvest after 12h, replica 3


title: DOX.IL1.6h.3

source_name: Pdx1 overexpression, Il-1b added, harvest after 6h, replica 3


title: IL1.24h.3

source_name: Il-1b added, harvest after 24h, replica 3


title: IL1.6h.3

source_name: Il-1b added, harvest after 6h, replica 3


title: Control.24h.3

source_name: Harvest after 24h, replica 3


title: DOX.IL1.2h.3

source_name: Pdx1 overexpression, Il-1b added, harvest after 2h, replica 3


title: 2_1278_N

source_name: Lymphonode

source_name: human genomic DNA (reference)


title: IL1.4h.4

source_name: Il-1b added, harvest after 4h, replica 1


title: DOX.IL1.24h.4

source_name: Pdx1 overexpression, Il-1b added, harvest after 24h, replica 4


title: IL1.4h.3

source_name: Il-1b added, harvest after 4h, replica 3


title: IL1.2h.3

source_name: Il-1b added, harvest after 2h, replica 3


title: Control.2h.2

source_name: Harvest after 2h, replica 2


title: DOX.IL1.24h.3

source_name: Pdx1 overexpression, Il-1b added, harvest after 24h, replica 3


title: DOX.24h.2

source_name: Pdx1 overexpression, harvest after 24h, replica 2


title: DOX.2h.3

source_name: Pdx1 overexpression, harvest after 2h, replica 3


title: DOX.IL1.6h.2

source_name: Pdx1 overexpression, Il-1b added, harvest after 6h, replica 2


title: 1_26_P


title: DOX.IL1.4h.2

source_name: Pdx1 overexpression, Il-1b added, harvest after 4h, replica 2


title: 1_449_P


title: 1_2343_P


title: 1_2297_P


title: 1_421_P


title: IL1.24h.2

source_name: Il-1b added, harvest after 24h, replica 2


title: 1_2249_P


title: 1_2182_P


title: DOX.IL1.24h.2

source_name: Pdx1 overexpression, Il-1b added, harvest after 24h, replica 2


title: 1_2196_P


title: IL1.4h.2

source_name: Il-1b added, harvest after 4h, replica 2


title: DOX.IL1.12h.3

source_name: Pdx1 overexpression, Il-1b added, harvest after 12h, replica 3


title: IL1.12h.2

source_name: Il-1b added, harvest after 12h, replica 2


title: DOX.IL1.2h.2

source_name: Pdx1 overexpression, Il-1b added, harvest after 2h, replica 2


title: Control.24h.2

source_name: Harvest after 24h, replica 2


title: PRR5-VP_ZT18_rep2

first: Norihito

last: Nakamichi

address: Suehiro1-7-22, Tsurumi

department: Plant Science Center

description: The expression estimates of CHP file is calculated using the Affymetrix® “Statistical Algorithm” for absolute analysis.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Summarization was performed by RMA using the original CEL files. The expression estimates of CHP file is calculated using the Affymetrix Statistical Algorithm for absolute analysis.

organism: Arabidopsis thaliana

source_name: PRR5-VP expressing plants harvested at ZT18 (18 hr after light on)

label_protocol: Total RNA was processed to produce biotinylated cRNA targets according to Affymetrix instructions.

growth_protocol: Plants were grown on MS madium containing 2% sucrose and 0.3% gellan gum, under 12 h light / 12 h dark conditions for 18 days

extract_protocol: Total RNA was isolated by RNeasy (Qiagen, Hilden, Germany) and the RNase-free DNase Set (Qiagen).

value: PRR5-VP expressing

value: whole plant


title: PRR5-VP_ZT12_rep3

source_name: PRR5-VP expressing plants harvested at ZT12 (12 hr after light on)


title: PRR5-VP_ZT18_rep1


title: PRR5-VP_ZT12_rep1


title: IL1.6h.2

source_name: Il-1b added, harvest after 6h, replica 2


title: PRR5-VP_ZT12_rep2


title: PRR5-VP_ZT18_rep3


title: 1_1687_N

source_name: Lymphonode

source_name: human genomic DNA (reference)


title: PRR5-VP_ZT6_rep3

source_name: PRR5-VP expressing plants harvested at ZT6 (6 hr after light on)


title: 1_2106_P


title: 1_1233_N


title: IL1.2h.2

source_name: Il-1b added, harvest after 2h, replica 2


title: IL1.6h.1

source_name: Il-1b added, harvest after 6h, replica 1


title: DOX.2h.2

source_name: Pdx1 overexpression, harvest after 2h, replica 2


title: PRR5-VP_ZT6_rep2


title: 1_1297_P


title: DOX.IL1.12h.2

source_name: Pdx1 overexpression, Il-1b added, harvest after 12h, replica 2


title: 1_1571_P


title: 1_1231_P


title: Wild_ZT18_rep3

source_name: Wild-type plants harvested at ZT18 (18 hr after light on)

value: wild type


title: Wild_ZT12_rep3

source_name: Wild-type plants harvested at ZT12 (12 hr after light on)


title: PRR5-VP_ZT6_rep1


title: Wild_ZT12_rep2


title: DOX.IL1.2h.1

source_name: Pdx1 overexpression, Il-1b added, harvest after 2h, replica 1


title: Wild_ZT18_rep2


title: 1_1597_N


title: Wild_ZT18_rep1


title: Control.24h.1

source_name: Harvest after 24h, replica 1


title: IL1.24h.1

source_name: Il-1b added, harvest after 24h, replica 1


title: Control.2h.1

source_name: Harvest after 2h, replica 1


title: IL1.4h.1

source_name: Il-1b added, harvest after 4h, replica 1


title: Wild_ZT6_rep3

source_name: Wild-type plants harvested at ZT6 (6 hr after light on)


title: IL1.12h.1

source_name: Il-1b added, harvest after 12h, replica 1


title: DOX.IL1.6h.1

source_name: Pdx1 overexpression, Il-1b added, harvest after 6h, replica 1


title: Wild_ZT12_rep1


title: IL1.2h.1

source_name: Il-1b added, harvest after 2h, replica 1


title: DOX.2h.1

source_name: Pdx1 overexpression, harvest after 2h, replica 1


title: Wild_ZT6_rep1


title: DOX.IL1.12h.1

source_name: Pdx1 overexpression, Il-1b added, harvest after 12h, replica 1


title: Wild_ZT6_rep2


title: Control IP/Input #2

first: Zachary

last: Knight

state: NY

address: 1230 York Ave

institute: Rockefeller University

hyb_protocol: Hybridization followed Nugen's recommendation and temperature in their biotin labelling protocol

scan_protocol: The standard DirectHyb Illumina expression array protocol was used.

data_processing: Raw Data was exported using illumina Genomestudio software without normalization. The raw data was transformed in Excel as follows: The ratio IP/Input (the fold-enrichment) was calculated for the Salt and Control samples for replicates #1 and #2.  The replicates were then averaged and the differential fold-enrichment was determined by dividing the average Salt (IP/Input) by the average Control (IP/Input). The log2 of this differential fold-enrichment was then calculated and these values were plotted. These caculations are shown in the Matrix normalized worksheet.

source_name: Control IP #2

label_protocol: RNA was amplified using the Ovation RNA Amplification System V2 and labelled using the Nugen Biotin Labelling Protocol.

growth_protocol: Mice were maintained on a 12h light dark cycle and sacrificed at 12 weeks of age at approximately CT6

extract_protocol: RNA was purified using the RNAeasy Micro kit.

treatment_protocol: Mice were given an injection of vehicle (PBS) or 2M NaCl solution (325 uL), water was removed, and mice were sacrificed 2h later

value: Hypothalamus

tag: ip antibody

value: pS6 244/247 IP [Cell Signaling #2215 lot 10]

source_name: Control Input #2


title: DOX.24h.1

source_name: Pdx1 overexpression, harvest after 24h, replica 1


title: DOX.IL1.24h.1

source_name: Pdx1 overexpression, Il-1b added, harvest after 24h, replica 1


title: Salt IP/Input #2

source_name: Salt IP #2

source_name: Salt Input #2


title: Control IP/Input #1

source_name: Control IP #1

source_name: Control Input #1


title: Salt IP/Input #1

source_name: Salt IP #1

source_name: Salt Input #1


title: heart_BMPER het_replicate 2

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

description: Biological replicate 2 of 4

hyb_protocol: Cy-5 labeled cRNA was co-hybridized to Agilent 014868 Whole Mouse Genome Microarrays with equimolar amounts of Cy-3 labeled WMRR-derived cRNA. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.  After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner and processed using Agilent FeatureExtractor 9.5.1.1.

data_processing: Samples were loess normalized per array. Data files were uploaded into Genespring 11.5.1 using a median value baseline transformation. Entities where at least 50 percent of the samples have flags in Comprimised or Not Detected were filtered and removed. Remaining entities with Compromised or Not Detected flags (maximum 3 samples per entity) were treated as missing and imputed using k nearest neighbors (k = 5).

source_name: Whole Mouse Reference RNA (WMRR)

label_protocol: 500 ng of WMRR or heart RNA labeled with Cy-3 or Cy-5, respectively (Perkin Elmer) and amplified using the Low Input RNA Amplification Kit (Agilent) as described by the manufacturer.

extract_protocol: Total RNA was extracted using the TRIzol method (Invitrogen), followed by an RNA cleanup step and on-column DNA digestion using the Rneasy miniprep kit according manufacturers' instructions

treatment_protocol: Heart ventricle tissues were isolated by dissection from wild-type and BMPER+/- adult mice

tag: developmental stage

value: neonatal

tag: tissue type

value: whole animal

value: mixed 129Sv and C57BL/6

value: adult - 1 y

source_name: RNA purified from heart ventricle, adult, BMPER+/- mouse

value: heart ventricles


title: DOX.IL1.4h.1

source_name: Pdx1 overexpression, Il-1b added, harvest after 4h, replica 1


title: heart_BMPER het_replicate 3

description: Biological replicate 3 of 4


title: heart_BMPER het_replicate 4

description: Biological replicate 4 of 4


title: heart_wild-type_replicate 2

description: Biological replicate 2 of 4

source_name: RNA purified from heart ventricle, adult, wild-type mouse


title: heart_wild-type_replicate 4

description: Biological replicate 4 of 4


title: heart_BMPER het_replicate 1

description: Biological replicate 1 of 4


title: heart_wild-type_replicate 3

description: Biological replicate 3 of 4


title: fhm F Liver recovery DES 10-3

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 μm resolution

data_processing: Microarray image processing and data pre-processing were performed Agilent's Feature Extraction software v 9.5 following the manufacturer’s protocol and recommendations.

organism: Pimephales promelas

source_name: liver from female fish exposed to 10 ng DES/L for 96 h, followed by an additional 96 h in control water

label_protocol: cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling Kit; Agilent, Palo Alto, CA)

growth_protocol: The fish were held at 25+1ºC under a 16:8 L:D photoperiod and were fed frozen adult brine shrimp twice daily (San Francisco Bay Brand, Newark, CA, USA).  Fish used for the experiment were from an on-site culture, and all procedures involving animals conformed to guidelines approved by the local Animal Care and Use Committee.

extract_protocol: Total RNA was isolated from liver tissue with Tri Reagent (Sigma, St. Louis, MO) according to the manufacturer’s protocol. RNA quality was verified using an Agilent 2100 bioanalyzer (Agilent, Palo Alto, CA) and concentration was quantified spectrophotometrically using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE).

treatment_protocol: Fish were exposed to 0, 1, 10, or 100 ng DES/L delivered in a continuous flow (45 ml/min) of sand filtered, UV treated, Lake Superior Water, without the use of carrier solvents for a total of 96 h.  Delivery of DES then ceased and fish were held in a continuous flow (45 ml/min) of control water for an additional 96 h (4 d depuration).

tag: ctid

tag: treatment

value: 10 ng DES/L for 4 days then recovery for another 4 days

tag: tank

tag: Sex

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: time sampled

tag: gsi

tag: liver vtg mrna

tag: liver esr1 mrna

tag: ex vivo e2 (ng/ml/12h)

tag: ex vivo t (ng/ml/12h)

tag: plasma e2 (ng/ml)

tag: plasma vtg

value: liver


title: heart_wild-type_replicate 1

description: Biological replicate 1 of 4

tag: strain


title: fhm F Liver recovery DES 10-4

tag: tissue


title: fhm F Liver recovery DES 1-4

source_name: liver from female fish exposed to 1 ng DES/L for 96 h, followed by an additional 96 h in control water

value: 1.0 ng DES/L for 4 days then recovery for another 4 days


title: fhm F Liver recovery DES 100-1

source_name: liver from female fish exposed to 100 ng DES/L for 96 h, followed by an additional 96 h in control water

value: 100 ng DES/L for 4 days then recovery for another 4 days


title: fhm F Liver recovery CON-4

source_name: liver from female fish exposed to control water for 8d

value: con


title: fhm F Liver recovery CON-2