title: buccal swab 703

source_name: buccal swab 703


title: buccal swab 702

status: Public on May 14 2025

type: genomic

city: Singapore

first: Dennis

last: Wang

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina protocol for Illumina Infinium Human Methylation EPICarray

scan_protocol: Standard Illumina protocol

data_processing:
R/RStudio
The filtered and normalized (preprocessNoob) average Betas use in this study are represented in the Sample Data table

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: buccal swab 702

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from buccal swab samples using IsoHelix DNA Extreme Kit/Qiasymphony SP following the standard protocol

tag: tissue

value: buccal swab

tag: age(month)


title: buccal swab 719

source_name: buccal swab 719


title: buccal swab 692

source_name: buccal swab 692


title: buccal swab 691

source_name: buccal swab 691


title: buccal swab 714

source_name: buccal swab 714


title: buccal swab 684

source_name: buccal swab 684


title: buccal swab 698

source_name: buccal swab 698


title: buccal swab 699

source_name: buccal swab 699


title: buccal swab 697

source_name: buccal swab 697


title: buccal swab 690

source_name: buccal swab 690


title: buccal swab 689

source_name: buccal swab 689


title: buccal swab 688

source_name: buccal swab 688


title: buccal swab 681

source_name: buccal swab 681


title: buccal swab 680

source_name: buccal swab 680


title: buccal swab 694

source_name: buccal swab 694


title: buccal swab 676

source_name: buccal swab 676


title: buccal swab 687

source_name: buccal swab 687


title: buccal swab 686

source_name: buccal swab 686


title: buccal swab 673

source_name: buccal swab 673


title: buccal swab 674

source_name: buccal swab 674


title: buccal swab 685

source_name: buccal swab 685


title: buccal swab 670

source_name: buccal swab 670


title: buccal swab 683

source_name: buccal swab 683


title: buccal swab 682

source_name: buccal swab 682


title: buccal swab 701

source_name: buccal swab 701


title: buccal swab 668

source_name: buccal swab 668


title: buccal swab 695

source_name: buccal swab 695


title: buccal swab 679

source_name: buccal swab 679


title: buccal swab 663

source_name: buccal swab 663


title: buccal swab 662

source_name: buccal swab 662


title: buccal swab 678

source_name: buccal swab 678


title: buccal swab 677

source_name: buccal swab 677


title: buccal swab 675

source_name: buccal swab 675


title: buccal swab 671

source_name: buccal swab 671


title: buccal swab 672

source_name: buccal swab 672


title: buccal swab 656

source_name: buccal swab 656


title: buccal swab 658

source_name: buccal swab 658


title: buccal swab 667

source_name: buccal swab 667


title: buccal swab 655

source_name: buccal swab 655


title: buccal swab 666

source_name: buccal swab 666


title: buccal swab 654

source_name: buccal swab 654


title: buccal swab 665

source_name: buccal swab 665


title: buccal swab 652

source_name: buccal swab 652


title: buccal swab 669

source_name: buccal swab 669


title: buccal swab 649

source_name: buccal swab 649


title: buccal swab 651

source_name: buccal swab 651


title: buccal swab 647

source_name: buccal swab 647


title: buccal swab 664

source_name: buccal swab 664


title: buccal swab 646

source_name: buccal swab 646


title: buccal swab 660

source_name: buccal swab 660


title: buccal swab 661

source_name: buccal swab 661


title: buccal swab 643

source_name: buccal swab 643


title: buccal swab 657

source_name: buccal swab 657


title: buccal swab 659

source_name: buccal swab 659


title: buccal swab 653

source_name: buccal swab 653


title: buccal swab 642

source_name: buccal swab 642


title: buccal swab 650

source_name: buccal swab 650


title: buccal swab 636

source_name: buccal swab 636


title: buccal swab 635

source_name: buccal swab 635


title: buccal swab 645

source_name: buccal swab 645


title: buccal swab 648

source_name: buccal swab 648


title: buccal swab 644

source_name: buccal swab 644


title: buccal swab 629

source_name: buccal swab 629


title: buccal swab 639

source_name: buccal swab 639


title: buccal swab 626

source_name: buccal swab 626


title: buccal swab 637

source_name: buccal swab 637


title: buccal swab 634

source_name: buccal swab 634


title: buccal swab 624

source_name: buccal swab 624


title: buccal swab 632

source_name: buccal swab 632


title: buccal swab 625

source_name: buccal swab 625


title: buccal swab 638

source_name: buccal swab 638


title: buccal swab 621

source_name: buccal swab 621


title: buccal swab 620

source_name: buccal swab 620


title: buccal swab 633

source_name: buccal swab 633


title: buccal swab 640

source_name: buccal swab 640


title: buccal swab 627

source_name: buccal swab 627


title: buccal swab 641

source_name: buccal swab 641


title: buccal swab 618

source_name: buccal swab 618


title: buccal swab 619

source_name: buccal swab 619


title: buccal swab 617

source_name: buccal swab 617


title: buccal swab 616

source_name: buccal swab 616


title: buccal swab 631

source_name: buccal swab 631


title: buccal swab 623

source_name: buccal swab 623


title: buccal swab 615

source_name: buccal swab 615


title: buccal swab 628

source_name: buccal swab 628


title: buccal swab 613

source_name: buccal swab 613


title: buccal swab 630

source_name: buccal swab 630


title: buccal swab 610

source_name: buccal swab 610


title: buccal swab 609

source_name: buccal swab 609


title: buccal swab 608

source_name: buccal swab 608


title: buccal swab 612

source_name: buccal swab 612


title: buccal swab 607

source_name: buccal swab 607


title: buccal swab 605

source_name: buccal swab 605


title: buccal swab 606

source_name: buccal swab 606


title: buccal swab 604

source_name: buccal swab 604


title: buccal swab 622

source_name: buccal swab 622


title: buccal swab 602

source_name: buccal swab 602


title: buccal swab 600

source_name: buccal swab 600


title: buccal swab 601

source_name: buccal swab 601


title: buccal swab 599

source_name: buccal swab 599


title: buccal swab 597

source_name: buccal swab 597


title: buccal swab 598

source_name: buccal swab 598


title: buccal swab 593

source_name: buccal swab 593


title: buccal swab 595

source_name: buccal swab 595


title: buccal swab 594

source_name: buccal swab 594


title: buccal swab 591

source_name: buccal swab 591


title: buccal swab 592

source_name: buccal swab 592


title: buccal swab 614

source_name: buccal swab 614


title: buccal swab 588

source_name: buccal swab 588


title: buccal swab 590

source_name: buccal swab 590


title: buccal swab 587

source_name: buccal swab 587


title: buccal swab 589

source_name: buccal swab 589


title: buccal swab 611

source_name: buccal swab 611


title: buccal swab 586

source_name: buccal swab 586


title: buccal swab 585

source_name: buccal swab 585


title: buccal swab 584

source_name: buccal swab 584


title: buccal swab 583

source_name: buccal swab 583


title: buccal swab 582

source_name: buccal swab 582


title: buccal swab 577

source_name: buccal swab 577


title: buccal swab 581

source_name: buccal swab 581


title: buccal swab 578

source_name: buccal swab 578


title: buccal swab 580

source_name: buccal swab 580


title: buccal swab 579

source_name: buccal swab 579


title: buccal swab 603

source_name: buccal swab 603


title: buccal swab 576

source_name: buccal swab 576


title: buccal swab 596

source_name: buccal swab 596


title: buccal swab 573

source_name: buccal swab 573


title: buccal swab 572

source_name: buccal swab 572


title: buccal swab 568

source_name: buccal swab 568


title: buccal swab 570

source_name: buccal swab 570


title: buccal swab 569

source_name: buccal swab 569


title: buccal swab 566

source_name: buccal swab 566


title: buccal swab 575

source_name: buccal swab 575


title: buccal swab 571

source_name: buccal swab 571


title: buccal swab 564

source_name: buccal swab 564


title: buccal swab 565

source_name: buccal swab 565


title: buccal swab 563

source_name: buccal swab 563


title: buccal swab 561

source_name: buccal swab 561


title: buccal swab 562

source_name: buccal swab 562


title: buccal swab 560

source_name: buccal swab 560


title: buccal swab 567

source_name: buccal swab 567


title: buccal swab 559

source_name: buccal swab 559


title: buccal swab 557

source_name: buccal swab 557


title: buccal swab 558

source_name: buccal swab 558


title: buccal swab 556

source_name: buccal swab 556


title: buccal swab 555

source_name: buccal swab 555


title: buccal swab 554

source_name: buccal swab 554


title: buccal swab 553

source_name: buccal swab 553


title: buccal swab 552

source_name: buccal swab 552


title: buccal swab 548

source_name: buccal swab 548


title: buccal swab 549

source_name: buccal swab 549


title: buccal swab 551

source_name: buccal swab 551


title: buccal swab 574

source_name: buccal swab 574


title: buccal swab 550

source_name: buccal swab 550


title: buccal swab 546

source_name: buccal swab 546


title: buccal swab 545

source_name: buccal swab 545


title: buccal swab 544

source_name: buccal swab 544


title: buccal swab 540

source_name: buccal swab 540


title: buccal swab 547

source_name: buccal swab 547


title: buccal swab 542

source_name: buccal swab 542


title: buccal swab 539

source_name: buccal swab 539


title: buccal swab 535

source_name: buccal swab 535


title: buccal swab 534

source_name: buccal swab 534


title: buccal swab 533

source_name: buccal swab 533


title: buccal swab 543

source_name: buccal swab 543


title: buccal swab 537

source_name: buccal swab 537


title: buccal swab 541

source_name: buccal swab 541


title: buccal swab 531

source_name: buccal swab 531


title: buccal swab 536

source_name: buccal swab 536


title: buccal swab 538

source_name: buccal swab 538


title: buccal swab 532

source_name: buccal swab 532


title: buccal swab 530

source_name: buccal swab 530


title: buccal swab 528

source_name: buccal swab 528


title: buccal swab 529

source_name: buccal swab 529


title: buccal swab 527

source_name: buccal swab 527


title: buccal swab 524

source_name: buccal swab 524


title: buccal swab 523

source_name: buccal swab 523


title: buccal swab 521

source_name: buccal swab 521


title: buccal swab 519

source_name: buccal swab 519


title: buccal swab 522

source_name: buccal swab 522


title: buccal swab 520

source_name: buccal swab 520


title: buccal swab 517

source_name: buccal swab 517


title: buccal swab 516

source_name: buccal swab 516


title: buccal swab 515

source_name: buccal swab 515


title: buccal swab 513

source_name: buccal swab 513


title: buccal swab 512

source_name: buccal swab 512


title: buccal swab 511

source_name: buccal swab 511


title: buccal swab 509

source_name: buccal swab 509


title: buccal swab 507

source_name: buccal swab 507


title: buccal swab 510

source_name: buccal swab 510


title: buccal swab 506

source_name: buccal swab 506


title: buccal swab 508

source_name: buccal swab 508


title: buccal swab 504

source_name: buccal swab 504


title: buccal swab 502

source_name: buccal swab 502


title: buccal swab 500

source_name: buccal swab 500


title: buccal swab 505

source_name: buccal swab 505


title: buccal swab 501

source_name: buccal swab 501


title: buccal swab 498

source_name: buccal swab 498


title: buccal swab 503

source_name: buccal swab 503


title: buccal swab 526

source_name: buccal swab 526


title: buccal swab 499

source_name: buccal swab 499


title: buccal swab 525

source_name: buccal swab 525


title: buccal swab 497

source_name: buccal swab 497


title: buccal swab 495

source_name: buccal swab 495


title: buccal swab 518

source_name: buccal swab 518


title: buccal swab 496

source_name: buccal swab 496


title: buccal swab 494

source_name: buccal swab 494


title: buccal swab 493

source_name: buccal swab 493


title: buccal swab 514

source_name: buccal swab 514


title: buccal swab 491

source_name: buccal swab 491


title: buccal swab 490

source_name: buccal swab 490


title: buccal swab 492

source_name: buccal swab 492


title: buccal swab 487

source_name: buccal swab 487


title: buccal swab 486

source_name: buccal swab 486


title: buccal swab 485

source_name: buccal swab 485


title: buccal swab 484

source_name: buccal swab 484


title: buccal swab 483

source_name: buccal swab 483


title: buccal swab 481

source_name: buccal swab 481


title: buccal swab 480

source_name: buccal swab 480


title: buccal swab 482

source_name: buccal swab 482


title: buccal swab 479

source_name: buccal swab 479


title: buccal swab 475

source_name: buccal swab 475


title: buccal swab 478

source_name: buccal swab 478


title: buccal swab 477

source_name: buccal swab 477


title: buccal swab 476

source_name: buccal swab 476


title: buccal swab 489

source_name: buccal swab 489


title: buccal swab 467

source_name: buccal swab 467


title: buccal swab 464

source_name: buccal swab 464


title: buccal swab 473

source_name: buccal swab 473


title: buccal swab 488

source_name: buccal swab 488


title: buccal swab 463

source_name: buccal swab 463


title: buccal swab 471

source_name: buccal swab 471


title: buccal swab 468

source_name: buccal swab 468


title: buccal swab 470

source_name: buccal swab 470


title: buccal swab 465

source_name: buccal swab 465


title: buccal swab 460

source_name: buccal swab 460


title: buccal swab 474

source_name: buccal swab 474


title: buccal swab 472

source_name: buccal swab 472


title: buccal swab 461

source_name: buccal swab 461


title: buccal swab 459

source_name: buccal swab 459


title: buccal swab 457

source_name: buccal swab 457


title: buccal swab 454

source_name: buccal swab 454


title: buccal swab 456

source_name: buccal swab 456


title: buccal swab 453

source_name: buccal swab 453


title: buccal swab 455

source_name: buccal swab 455


title: buccal swab 451

source_name: buccal swab 451


title: buccal swab 452

source_name: buccal swab 452


title: buccal swab 449

source_name: buccal swab 449


title: buccal swab 448

source_name: buccal swab 448


title: buccal swab 447

source_name: buccal swab 447


title: buccal swab 469

source_name: buccal swab 469


title: buccal swab 466

source_name: buccal swab 466


title: buccal swab 446

source_name: buccal swab 446


title: buccal swab 462

source_name: buccal swab 462


title: buccal swab 445

source_name: buccal swab 445


title: buccal swab 441

source_name: buccal swab 441


title: buccal swab 444

source_name: buccal swab 444


title: buccal swab 440

source_name: buccal swab 440


title: buccal swab 434

source_name: buccal swab 434


title: buccal swab 437

source_name: buccal swab 437


title: buccal swab 439

source_name: buccal swab 439


title: buccal swab 458

source_name: buccal swab 458


title: buccal swab 435

source_name: buccal swab 435


title: buccal swab 443

source_name: buccal swab 443


title: buccal swab 432

source_name: buccal swab 432


title: buccal swab 442

source_name: buccal swab 442


title: buccal swab 436

source_name: buccal swab 436


title: buccal swab 438

source_name: buccal swab 438


title: buccal swab 430

source_name: buccal swab 430


title: buccal swab 433

source_name: buccal swab 433


title: buccal swab 429

source_name: buccal swab 429


title: buccal swab 427

source_name: buccal swab 427


title: buccal swab 431

source_name: buccal swab 431


title: buccal swab 425

source_name: buccal swab 425


title: buccal swab 450

source_name: buccal swab 450


title: buccal swab 424

source_name: buccal swab 424


title: buccal swab 426

source_name: buccal swab 426


title: buccal swab 423

source_name: buccal swab 423


title: buccal swab 422

source_name: buccal swab 422


title: buccal swab 420

source_name: buccal swab 420


title: buccal swab 421

source_name: buccal swab 421


title: buccal swab 419

source_name: buccal swab 419


title: buccal swab 417

source_name: buccal swab 417


title: buccal swab 418

source_name: buccal swab 418


title: buccal swab 416

source_name: buccal swab 416


title: buccal swab 415

source_name: buccal swab 415


title: buccal swab 411

source_name: buccal swab 411


title: buccal swab 409

source_name: buccal swab 409


title: buccal swab 412

source_name: buccal swab 412


title: buccal swab 413

source_name: buccal swab 413


title: buccal swab 407

source_name: buccal swab 407


title: buccal swab 405

source_name: buccal swab 405


title: buccal swab 406

source_name: buccal swab 406


title: buccal swab 410

source_name: buccal swab 410


title: buccal swab 399

source_name: buccal swab 399


title: buccal swab 403

source_name: buccal swab 403


title: buccal swab 402

source_name: buccal swab 402


title: buccal swab 400

source_name: buccal swab 400


title: buccal swab 404

source_name: buccal swab 404


title: buccal swab 397

source_name: buccal swab 397


title: buccal swab 396

source_name: buccal swab 396


title: buccal swab 428

source_name: buccal swab 428


title: buccal swab 401

source_name: buccal swab 401


title: buccal swab 393

source_name: buccal swab 393


title: buccal swab 394

source_name: buccal swab 394


title: buccal swab 392

source_name: buccal swab 392


title: buccal swab 391

source_name: buccal swab 391


title: buccal swab 389

source_name: buccal swab 389


title: buccal swab 408

source_name: buccal swab 408


title: buccal swab 414

source_name: buccal swab 414


title: buccal swab 387

source_name: buccal swab 387


title: buccal swab 379

source_name: buccal swab 379


title: buccal swab 390

source_name: buccal swab 390


title: buccal swab 386

source_name: buccal swab 386


title: buccal swab 388

source_name: buccal swab 388


title: buccal swab 398

source_name: buccal swab 398


title: buccal swab 385

source_name: buccal swab 385


title: buccal swab 372

source_name: buccal swab 372


title: buccal swab 381

source_name: buccal swab 381


title: buccal swab 376

source_name: buccal swab 376


title: buccal swab 382

source_name: buccal swab 382


title: buccal swab 378

source_name: buccal swab 378


title: buccal swab 370

source_name: buccal swab 370


title: buccal swab 369

source_name: buccal swab 369


title: buccal swab 373

source_name: buccal swab 373


title: buccal swab 371

source_name: buccal swab 371


title: buccal swab 395

source_name: buccal swab 395


title: buccal swab 380

source_name: buccal swab 380


title: buccal swab 375

source_name: buccal swab 375


title: buccal swab 367

source_name: buccal swab 367


title: buccal swab 366

source_name: buccal swab 366


title: buccal swab 364

source_name: buccal swab 364


title: buccal swab 384

source_name: buccal swab 384


title: buccal swab 363

source_name: buccal swab 363


title: buccal swab 365

source_name: buccal swab 365


title: buccal swab 383

source_name: buccal swab 383


title: buccal swab 362

source_name: buccal swab 362


title: buccal swab 361

source_name: buccal swab 361


title: buccal swab 377

source_name: buccal swab 377


title: buccal swab 358

source_name: buccal swab 358


title: buccal swab 360

source_name: buccal swab 360


title: buccal swab 374

source_name: buccal swab 374


title: buccal swab 356

source_name: buccal swab 356


title: buccal swab 359

source_name: buccal swab 359


title: buccal swab 357

source_name: buccal swab 357


title: buccal swab 354

source_name: buccal swab 354


title: buccal swab 353

source_name: buccal swab 353


title: buccal swab 351

source_name: buccal swab 351


title: buccal swab 350

source_name: buccal swab 350


title: buccal swab 352

source_name: buccal swab 352


title: buccal swab 349

source_name: buccal swab 349


title: buccal swab 368

source_name: buccal swab 368


title: buccal swab 346

source_name: buccal swab 346


title: buccal swab 347

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source_name: buccal swab 27


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source_name: buccal swab 26


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source_name: buccal swab 20


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source_name: buccal swab 25


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source_name: buccal swab 43


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source_name: buccal swab 19


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source_name: buccal swab 22


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source_name: buccal swab 42


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source_name: buccal swab 18


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source_name: buccal swab 15


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source_name: buccal swab 16


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source_name: buccal swab 13


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source_name: buccal swab 12


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source_name: buccal swab 11


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source_name: buccal swab 36


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source_name: buccal swab 10


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source_name: buccal swab 14


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source_name: buccal swab 9


title: buccal swab 8

source_name: buccal swab 8


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source_name: buccal swab 7


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source_name: buccal swab 6


title: buccal swab 5

source_name: buccal swab 5


title: buccal swab 4

source_name: buccal swab 4


title: buccal swab 3

source_name: buccal swab 3


title: buccal swab 23

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title: buccal swab 1

source_name: buccal swab 1


title: buccal swab 2

source_name: buccal swab 2


title: Rat 47 [GRC369-47_S11]

type: SRA

city: Research Triangle Park

first: Colette

last: Miller

state: NC

address: 109 TW Alexander

country: USA

institute: U.S. Environmental Protection Agency

library_source: transcriptomic

data_processing:
Partek Flow NGS analysis software (Build 11.0.24.0102) was used to demultiplex data, trim adapters, and remove low quality bases.
Reads were mapped to the rat genome (rn6) using Bowtie 1.0.0. The following annotation models were used for rat: mature miRNAs from miRbase v22, tRNAs from GtRNAdb (RGSC 6.0), and PIWI-interacting RNAs (piRNAs) from piRBase v3.0. Then, a final alignment was performed using Ensembl release 108 to detect additional small RNAs including fragments.
An FDR ≤ 0.05 was implemented to identify differentially expressed genes (DEGs).
Assembly: rn6
Supplementary files format and content: tab-delimited text file contains normalized values for each sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Cauda sperm

extract_protocol:
The frozen sperm pellet was homogenized in the mirVana Lysis Buffer (ThermoFisher Scientific) in Lysing Matrix D tubes (MP Biomedical) on a Percellys 24 Tissue Homogenizer, followed by a 5-minute incubation at 65◦C. Extraction was continued as described in the mirVana protocol. The concentration of isolated small RNAs (< 200 nucleotides) was determined using Qubit and the quality was assessed using RNA 6000 Nano chips on an Agilent 2100 Bioanalyzer. All samples had RNA integrity number between 2 – 4.
Library preparation was performed using the CleanTag Small RNA Library Prep Kit (TriLink Biotechnologies). The pooled library concentrations were determined using the Qubit dsDNA High Sensitivity Assay and quality was assessed using the High Sensitivity DNA kit on the Agilent 2100 Bioanalyzer. Sequencing was performed using the NextSeq 500/550 High Output Kit v2.5 on a NextSeq 500 system set to single end reads at 75 cycles.

treatment_protocol: A subset of rats was exposed to episodic exposures which included 3 exposures on the first week and 2 exposures on the second. Exposures occurred for 4 hours from 0700-1100 in Rochester-style Hinners chambers. Ozone was generated via a silent arc discharge generator (OREC) and transferred to the chambers using a mass flow controller. Control rats were exposed to filtered air. Temperature and humidity in each chamber were controlled throughout the final exposure and remained between 21 – 23C and 41 – 43%, respectively. he average ozone concentration for each chamber was 0.000 ± 0.000 ppm, 0.401 ± 0.001 ppm, and 0.798 ± 0.001 ppm.

value: Cauda sperm

tag: Sex

value: male

tag: treatment

value: 0.8 ppm ozone


title: Rat 46 [GRC369-46_S12]


title: Rat 44 [GRC369-44_S3]


title: Rat 42 [GRC369-42_S5]


title: Rat 41 [GRC369-41_S5]


title: Rat 43 [GRC369-43_S9]


title: Rat 32 [GRC369-32_S12]

value: 0.4 ppm ozone


title: Rat 31 [GRC369-31_S10]


title: Rat 48 [GRC369-48_S1]


title: Rat 27 [GRC369-27_S7]


title: Rat 26 [GRC369-26_S11]


title: Rat 28 [GRC369-28_S4]


title: Rat 30 [GRC369-30_S9]


title: Rat 14 [GRC369-14_S8]

value: Air


title: Rat 16 [GRC369-16_S3]


title: Rat 25 [GRC369-25_S2]


title: Rat 15 [GRC369-15_S8]


title: Rat 11 [GRC369-11_S7]


title: Rat 29 [GRC369-29_S6]


title: 5_RNA_CD8T_cells

city: Boston

first: Or-Yam

middle: GENERAL

last: Revach

state: MA

address: 55 fruit street

institute: MGH

description:
Library name: Sample 1
melanoma CD8+ TILs expression data

library_source: transcriptomic single cell

data_processing:
We received the sequences, mapped the reads against the GRCh38 human reference genome, and quantified the read counts using Cell Ranger pipeline version 3.1.0 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Processed CD8+ T cells expression data

source_name: melanoma tumor

extract_protocol:
We enzymatically digested and dissociated fresh tumor samples according to tissue dissociation kit protocols using the gentleMACS™ Dissociator (Miltenyi). Dissociated tissues were filtered, centrifuged, and the isolated cells were resuspended in 0.1% BSA in PBS.
Briefly, 5000-6000 cells were profiled per sample using the Chromium Single Cell 3’ RNA reagent kit v3 according to the 10X Genomics protocol. The generated cDNA libraries were indexed, pooled, and sequenced in batches.

value: melanoma tumor

tag: cell line

value: CD8+ T cells


title: Rat 12 [GRC369-12_S1]


title: Rat 13 [GRC369-13_S6]


title: Patient 2 remission DNA library

city: Portland

first: Theodore

middle: Paul

last: Braun

state: OR

address: 3181 SW Sam Jackson Park Road

department: Knight Cancer Institute

institute: OHSU

description: Library name: 24-00175_DNA

library_source: genomic

data_processing:
Mission Bio Tapestry Pipeline
Assembly: HG38
Supplementary files format and content: .h5 files containing per cell DNA and protein matrices

source_name: Bone marrow

extract_protocol: Mission Bio DNA plus protein seq

value: Bone marrow


title: Patient 1 diagnosis Protein library

description: Library name: 20-00148_Protein

library_source: other

molecule: protein


title: Patient 2 diagnosis DNA library

description: Library name: 24-00127_DNA


title: Patient 2 diagnosis Protein library

description: Library name: 24-00127_Protein


title: Patient 2 remission Protein library

description: Library name: 24-00175_Protein


title: Patient 1 diagnosis DNA library

description: Library name: 20-00148_DNA


title: Rat 45 [GRC369-45_S10]


title: 4DNEX8YC3ET9, H. sapiens - K562, condition2 - conditionAI - anti-Lamin B1, B1 T1

last: DCIC

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description:
TSA-seq in K562 (H. sapiens), condition2 - conditionAI - anti-Lamin B1, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX8YC3ET9/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSHJ517WZ/, Results include counts in BigWig (.bw) format.
4DNEX8YC3ET9

data_processing:
For detecting SON TSA-seq Type I and Type II peaks, the SON TSA-seq score (25 kb bins) first was smoothed using locally weighted regression (LOESS). Next, a local maximum filter with window size (w) was applied, which recorded the maximum SON TSA-seq score within this window for each genomic locus. Then the data after the maximum filter were subtracted from the original smoothed data. Peaks were retained only if they showed a reduction in value, which indicates true local peaks. A parameter optimization procedure was conducted in order to maximize the peak agreement between two SON TSA-seq replicates. As a result, a smoothing factor (span=0.005) and a window size (w=50) were selected. To distinguish local peaks into Type I and Type II, we overlapped them with Hi-C subcompartments (Rao et. al, 2014). Genomic loci overlapping A1 subcompartments were classified as Type I peaks, while those overlapping A2/B1 were designated as Type II peaks.
Assembly: GRCh38
Supplementary files format and content: Counts in BigWig (.bw) format

extract_protocol:
H1, HCT116, and HFF cells were cultured according to standard operation protocols established by the NIH 4D Nucleome Consortium (https://www.4dnucleome.org/cell-lines.html). K562 cells were cultured according to the ENCODE Consortium protocol (http://genome.ucsc.edu/ENCODE/protocols/cell/human/K562_protocol.pdf).
SON and MKI67IP TSA-Seq was performed using Condition E (labeling with 1:300 tyramide biotin, 50% sucrose and 0.0015% hydrogen peroxide) (Zhang et al., 2020) with the following minor modification: 150ul of Dynabeads M-270 streptavidin (Invitrogen, catalog no. 65306) was used to purify the biotinylated DNA. For LMNB1 TSA-Seq, Condition A2 (Zhang et al., 2020) (labeling with 1:10000 tyramide biotin, 50% sucrose, 0.0015% hydrogen peroxide and reaction time 20 min at RT) was used.

tag: cell type

value: immortalized cell line

tag: genotype


title: 4DNEXM48NI2B, H. sapiens - K562, input - condition2 - conditionE - anti-SON, B1 T1

description:
TSA-seq in K562 (H. sapiens), input - condition2 - conditionE - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXM48NI2B/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSSMMI95I/
4DNEXM48NI2B


title: 4DNEX6SVEFSH, H. sapiens - HFFc6, input - condition2 - conditionE -  anti-MKI67IP, B1 T1

description:
TSA-seq in HFFc6 (H. sapiens), input - condition2 - conditionE -  anti-MKI67IP, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX6SVEFSH/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS74TFUQ1/
4DNEX6SVEFSH


title: 4DNEXJMBFUE3, H. sapiens - K562, condition2 - conditionE - anti-MKI67IP, B1 T1

description:
TSA-seq in K562 (H. sapiens), condition2 - conditionE - anti-MKI67IP, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXJMBFUE3/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSSMMI95I/, Results include counts in BigWig (.bw) format.
4DNEXJMBFUE3

value: condition2 - conditionE - anti-MKI67IP


title: 4DNEXQYVJALC, H. sapiens - K562, condition2 - conditionE - anti-MKI67IP, B2 T1

description:
TSA-seq in K562 (H. sapiens), condition2 - conditionE - anti-MKI67IP, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXQYVJALC/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSDNILMUO/, Results include counts in BigWig (.bw) format.
4DNEXQYVJALC


title: 4DNEXHV9WRTG, H. sapiens - HFFc6, input - condition2 - conditionE -  anti-MKI67IP, B2 T1

description:
TSA-seq in HFFc6 (H. sapiens), input - condition2 - conditionE -  anti-MKI67IP, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXHV9WRTG/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS56GW121/
4DNEXHV9WRTG


title: 4DNEXSCYT6S8, H. sapiens - K562, input - condition2 - conditionE -  anti-MKI67IP, B1 T1

description:
TSA-seq in K562 (H. sapiens), input - condition2 - conditionE -  anti-MKI67IP, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXSCYT6S8/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSSMMI95I/
4DNEXSCYT6S8


title: 4DNEX9KJSTC2, H. sapiens - HFFc6, condition2 - conditionE - anti-MKI67IP, B1 T1

description:
TSA-seq in HFFc6 (H. sapiens), condition2 - conditionE - anti-MKI67IP, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX9KJSTC2/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS74TFUQ1/, Results include counts in BigWig (.bw) format.
4DNEX9KJSTC2


title: 4DNEXBS7EC7G, H. sapiens - HFFc6, condition2 - conditionE - anti-MKI67IP, B2 T1

description:
TSA-seq in HFFc6 (H. sapiens), condition2 - conditionE - anti-MKI67IP, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXBS7EC7G/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS56GW121/, Results include counts in BigWig (.bw) format.
4DNEXBS7EC7G


title: 4DNEX6F94KL9, H. sapiens - K562, condition2 - conditionE - anti-SON, B1 T1

description:
TSA-seq in K562 (H. sapiens), condition2 - conditionE - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX6F94KL9/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSSMMI95I/, Results include counts in BigWig (.bw) format.
4DNEX6F94KL9

value: condition2 - conditionE - anti-SON


title: 4DNEXZYGCS2T, H. sapiens - K562, input - condition2 - conditionAI - anti-Lamin B1, B1 T1

description:
TSA-seq in K562 (H. sapiens), input - condition2 - conditionAI - anti-Lamin B1, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXZYGCS2T/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSHJ517WZ/
4DNEXZYGCS2T


title: 4DNEXPAOHM58, H. sapiens - K562, input - condition2 - conditionE -  anti-MKI67IP, B2 T1

description:
TSA-seq in K562 (H. sapiens), input - condition2 - conditionE -  anti-MKI67IP, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXPAOHM58/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSDNILMUO/
4DNEXPAOHM58


title: ALT_VZV3

city: Hangzhou

first: xinna

last: wu

address: Yuhangtang Road

country: China

institute: zhejiang university

description: Library name: B3

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo Sapiens Ensembl v107
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Lung

growth_protocol: WI-38 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 100 U/ml of penicillin and streptomycin solution with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

value: fibroblast

value: WT

value: VZV infection, ALT treatment

tag: batch

value: Day 3


title: Rat 10 [GRC369-10_S4]


title: ALT_VZV2

description: Library name: B2


title: Skin, Healthy Control_4

city: Ann Arbor

first: hui

last: shi

address: 5560 Medical Science Research Building-II 1150 W Medical Center Drive

institute: Division of Rheumatology, Department of Internal Medicine, University of Michigan

description:
Library name: Sample 4
10x Genomics

data_processing:
Data processing including quality control, read alignment (hg38), and gene quantification was conducted using the 10x Cell Ranger software.
Assembly: hg38
Supplementary files format and content: matrix files

source_name: skin

extract_protocol:
Generation of single-cell suspensions for scRNA-seq was performed as follows: Skin biopsies were incubated overnight in 0.4% Dispase (Life Technologies) in Hank’s balanced saline solution (Gibco) at 4°C. Epidermis and dermis were separated. Epidermis was digested in 0.25% trypsin-EDTA (Gibco) with deoxyribonuclease I (10 U/ml; Thermo Scientific) for 1 hour at 37°C, quenched with fetal bovine serum (Atlanta Biologicals), and strained through a 70-µm mesh. Dermis was minced, digested in 0.2% collagenase II (Life Technologies) and 0.2% collagenase V (Sigma) in plain medium for 1.5 hours at 37°C, and strained through a 70-µm mesh. Epidermal and dermal cells were combined in 1:1 ratio.
Epidermal and dermal cells were combined in 1:1 ratio, and libraries were constructed by the University of Michigan Advanced Genomics Core on the 10x Chromium system with chemistry v3. Libraries were then sequenced on the Illumina NovaSeq 6000 sequencer to generate 150–base pair paired-end reads.

value: skin

tag: subject status

value: healthy control

value: Epidermal and dermal cells


title: Skin, Healthy Control_3

description:
Library name: Sample 3
10x Genomics


title: Skin, Healthy Control_1

description:
Library name: Sample 1
10x Genomics


title: Skin, APS_2

description:
Library name: Sample 6
10x Genomics

value: APS


title: Skin, APS_3

description:
Library name: Sample 7
10x Genomics


title: Skin, Healthy Control_2

description:
Library name: Sample 2
10x Genomics


title: DMSO_VZV2

description: Library name: D2

value: VZV infection, DMSO treatment


title: DMSO_VZV3

description: Library name: D3


title: ALT_VZV1

description: Library name: B1


title: DMSO_VZV1

description: Library name: D1


title: Skin, APS_1

description:
Library name: Sample 5
10x Genomics


title: Mock1

description: Library name: C1


title: Mock3

description: Library name: C3


title: m4b mut melanoma, biol rep 2

city: Delhi

first: Vivek

middle: T

last: Natarajan

state: Delhi

address: Mathura Road

country: India

institute: CSIR-IGIB

data_processing:
Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads.
The reads were then aligned with zebrafish reference assembly (GRCz11) using STAR.
Featurecounts was used to calculate raw counts from the aligned reads.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file including raw counts for each sample

organism: Danio rerio

extract_protocol:
The cell isolation process involved density gradient centrifugation, followed by RNA extraction using Trizol method.
Illumina standard total RNA prep kit was used for library construction

value: melanoma

value: mgat4b mutant

value: MAZERATI


title: TXNIP_KO_Thaps_3

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

description: Library name: LTR12-R12-EX16.12

data_processing:
Batch correction
removing redundant counts <3
DESEQ2
Assembly: GRCh38
Supplementary files format and content: CP20M_240620_A00154_1531_AHJ273DSXC_LTR.xlsx
Supplementary files format and content: raw counts

molecule: polyA RNA

extract_protocol:
Total RNA
mRNA enrichment

treatment_protocol: Thapsigargin treatment

value: Stem cells

value: KO

value: Thaps


title: TXNIP_KO_DMSO_3

description: Library name: LTR11-R11-EX16.11

value: DMSO


title: Control

data_processing:
Cellranger mkfastq pipeline was used to generate fastq files
The fastq files were then aligned with custom zebrafish reference assembly (GRCz11) using cellranger.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file including barcodes and features, and matrix files

source_name: melanocytes

extract_protocol:
The gfp positive cells are isolated using FACS and 10x Genomics Next GEM 3'reagent kit (Dual Index) was used for bead generation and cDNA synthesis
10x Genomics Next GEM 3'reagent kit (Dual Index) was used for library construction

value: melanocytes

tag: age

value: 36 hpf

value: control

value: No


title: m4b mut


title: TXNIP_WT_Thaps_3

description: Library name: LTR10-R10-EX16.10

value: WT


title: Mock2

description: Library name: C2

value: Lung

value: fibroblast

value: Day 3


title: m4b mut melanoma, biol rep 1

value: skin


title: wild-type melanoma,control, biol rep 2


title: melanophore, biol rep 1

value: melanophore


title: TXNIP_KO_DMSO_2

description: Library name: LTR7-R7-EX16.7


title: TXNIP_KO_Thaps_2

description: Library name: LTR8-R8-EX16.8


title: Hippocampus, Dark phase, Syt7 KO, vehicle, 30min, rep1

city: beijing

first: xinyu

last: She

address: shuangqing road, haidian district

department: school of life sciences

institute: Tsinghua university

description: Library name: Dark-Syt7 KO sample 1

data_processing:
Primary sequencing data, called as raw reads, is subjected to quality control (QC)to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences, QC of alignment is performed to determine if resequencing is needed. The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio. If alignment result passes QC, we will proceed with downstream analysis including gene expression and deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes and so on). Further, we also can perform deep analysis based on DEGs, including Gene Ontology (GO) enrichment analysis, KEGG pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcription factor.
Assembly: ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10
Supplementary files format and content: An Excel spreadsheet includes FPKM values for each sample

organism: Mus musculus

source_name: brain

growth_protocol: Quick-freeze samples immediately after collection and store at –80°C or in liquid nitrogen until RNA isolation.

extract_protocol:
1. Add 1 mL of TRIzol™ Reagent per 50 mg of hippocampual tissue to the sample. 2. Pipet the lysate up and down several times to homogenize. 3. Incubate for 5 minutes to permit complete dissociation of the nucleoproteins complex. 4. Add 0.2 mL of chloroform per 1 mL of TRIzol™ Reagent used for lysis, then securely cap the tube. 5. Incubate on ice for 2–3 minutes. 6. Centrifuge the sample for 30 minutes at 12,000 × g at 4°C. The mixture separates into a lower red phenol-chloroform, and interphase, and a colorless upper aqueous phase. 7. Transfer the aqueous phase containing the RNA to a new tube. 8. Add 0.5 mL of isopropanol to the aqueous phase, per 1 mL of TRIzol™ Reagent used for lysis. 9. Incubate at -80 ℃ for 30 mins. 10. Centrifuge for 30 minutes at 12,000 × g at 4°C. Total RNA precipitate forms a white gel-like pellet at the bottom of the tube. 10. Discard the supernatant with a micropipettor. 11. Resuspend the pellet in 1 mL of 75% ethanol per 1 mL of TRIzol™ Reagent used for lysis. 12. Vortex the sample briefly, then centrifuge for 5 minutes at 7500 × g at 4°C. 13. Discard the supernatant with a micropipettor. 14. Air dry the RNA pellet for 5–10 minutes. 15. Resuspend the pellet in 20–50 µL of RNase-free water.16. Deliver the samples to the company using dry ice.
1)There are two methods to treat total RNA. Oligo(dT)magnetic beads are used to select mRNA with poly A tail, or hybridize the rRNA with DNA probe and digest the DNA / RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at5' end and stickiness 'A'at3'end, then ligate and adaptor with stickiness 'T'at3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6)Perform sequencing on prepared library.

value: brain

value: hippocampal neurons

value: glutamatergic pyramidal neurons

value: Syt7 KO

value: RO25, 30min


title: melanophore, biol rep 2


title: TXNIP_WT_DMSO_3

description: Library name: LTR9-R9-EX16.9

value: Stem cells


title: APOE Control group replicate3

type: RNA

city: 泉州

first: 清石

last: 陈

state: 福建省

address: 福建省泉州市鲤城区中山北路34号

institute: 医科大学附属第二医院

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 manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°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 (G2505B) using 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 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: renal tissues

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 RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: We placed mice assigned to receive CIH in a specially designed chamber, which contained oxygen sensors for measuring the concentration of O2 in the chamber. Cages were connected to a gas regulator that controls the infusion of sufficient nitrogen to reduce O2 to 6% for 60 seconds, after which the gas control system allows for a rapid replacement of oxygen leading to a quick restoration of O2 to 21% for another 60 seconds. This 2-minutes CIH cycle was repeated 30 times per h, 8 h/day, for a total duration of 8 weeks.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Tissues from pancreatic tissues and promptly cooled at -80℃ refrigerator.

value: pancreatic

tag: strain

value: BALB/c


title: APOE CIH group replicate1

address: 福建省泉州市鲤城区中山北路34号


title: APOE Control group replicate1

address: 福建省泉州市鲤城区中山北路34号


title: APOE CIH group replicate2

address: 福建省泉州市鲤城区中山北路34号


title: APOE Control group replicate2

address: 福建省泉州市鲤城区中山北路34号


title: APOE CIH group replicate3

address: 福建省泉州市鲤城区中山北路34号


title: Hippocampus, Dark phase, WT, RO25, 30min, rep1

description: Library name: Dark-WT+RO25 sample 1


title: TXNIP_KO_Thaps_1

description: Library name: LTR4-R4-EX16.4

value: KO

value: Thaps


title: Hippocampus, Dark phase, WT, vehicle, 30min, rep3

description: Library name: Dark-WT sample 3

value: vehicle, 30min


title: Hippocampus, Dark phase, WT, vehicle, 30min, rep2

description: Library name: Dark-WT sample 2

value: WT


title: TXNIP_KO_DMSO_1

description: Library name: LTR3-R3-EX16.3

value: DMSO


title: TXNIP_WT_DMSO_1

description: Library name: LTR1-R1-EX16.1


title: Hippocampus, Dark phase, WT, vehicle, 30min, rep1

description: Library name: Dark-WT sample 1


title: Hippocampus, Light phase, Syt7 KO, vehicle, 30min, rep1

description: Library name: Light-Syt7 KO sample 1


title: wild-type melanoma,control, biol rep 1

value: melanoma

value: MAZERATI


title: Hippocampus, Light phase, WT, BMS, 30min, rep3

description: Library name: Light-WT+BMS sample 3

value: BMS, 30min


title: IP_shA5.fastq.gz

city: Hangzhou City

first: Jingyu

last: Hou

state: Zhejiang Province

address: Zhejiang University Student Apartment

institute: Zhejiang University

data_processing:
Illumina bcl2fastq (version 2.0)  for basecalling.
Illumina sequencing reads were treated with fastp (version 0.23.2)  for adaptor removal and quality trimming.
The remaining reads were mapped to  human transcriptome using Hisat2 with default parameters.
SAMtools(version 1.9) were used to select high-quality alignments, remove PCR duplications, and extract the reads mapping of every nucleotide in the transcriptome
Peaks were calling using MACS2. RPKM was calculated using in-house scripts following the definition of RPKM.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each RNA-Seq Sample

extract_protocol:
Total RNA was isolated from cell lines by Trizol(Invitrogen). polyA+ RNA was purified using Dynabeads Oligo(dT)25 (Invitrogen).
RNA fragments  were converted to cDNA. RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq;MeRIP-seq

value: Human embryonic kidney

value: X-ray


title: Hippocampus, Light phase, Syt7 KO, vehicle, 30min, rep2

description: Library name: Light-Syt7 KO sample 2

value: brain

value: hippocampal neurons


title: Input_shA5.fastq.gz


title: TXNIP_WT_Thaps_1

description: Library name: LTR2-R2-EX16.2


title: Hippocampus, Light phase, WT, BMS, 30min, rep2

description: Library name: Light-WT+BMS sample 2

value: glutamatergic pyramidal neurons


title: TXNIP_WT_Thaps_2

description: Library name: LTR6-R6-EX16.6


title: Hippocampus, Light phase, WT, vehicle, 30min, rep3

description: Library name: Light-WT sample 3


title: NK_DC_PCI-15B_Ave_3

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

institute: CLEVELAND CLINIC LERNER COM-CWRU

data_processing:
STAR alignment to Reference Genome
Mapped reads count for each gene to Human GENECODE GTF annotation file with the featureCounts read summarization program
Differential gene expression analysis was performed using DESeq2
Gene Set Enrichment Analysis (GSEA)
Statistical comparison of two sets of data was achieved with student’s t-test. Comparison of multiple sets of data was achieved with one-way or two-way analysis of variance (ANOVA). Error bars reflect SEM from individual experiments. Analysis was performed using GraphPad Prism v10.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file includes raw data counts for each sample
Supplementary files format and content: Tab delimited text file includes FPKM (fragments per kilobase per million) normalized counts data counts for each sample

source_name: PCI-15B and NK cells and Dendritic cells

growth_protocol: PCI-15B cells, PCI-15B+NK cells, PCI-15B+NK+DC cells were incubated in IMDM media with 10% heat inactivated FBS, penicillin-streptomycin in humidified incubator with 5% CO2 and 37 degree celsius

extract_protocol:
RNA was extracted by using Qiagen Rneasy Plus mini kit
Illumina Trueseq stranded mRNA kit was used for library preperations. 200 ng sample input was used to prepare library. Manufacturer instruction was used for library preperation.

treatment_protocol: PCI-15B cells, PCI-15B+NK cells coculture, PCI-15B+NK+DC coculture were treated with no_ab, IgG1-10 microgram per ml, Durvalumab-10 microgram per ml and Avelumab-10 microgram per ml as indicated.

value: Epithelial cell and immune cells

value: Not applicable

value: Avelumab


title: IP_shCTL.fastq.gz

value: shCTL


title: NK_DC_PCI-15B_Ave_2

value: PCI-15B and NK cells and Dendritic cells


title: Hippocampus, Light phase, WT, BMS, 30min, rep1

description: Library name: Light-WT+BMS sample 1


title: Hippocampus, Light phase, WT, vehicle, 30min, rep2

description: Library name: Light-WT sample 2


title: NK_DC_PCI-15B_Ave_1


title: TXNIP_WT_DMSO_2

description: Library name: LTR5-R5-EX16.5

value: Stem cells


title: Hippocampus, Light phase, WT, vehicle, 30min, rep1

description: Library name: Light-WT sample 1

value: vehicle, 30min


title: NK_DC_PCI-15B_Durv_3

value: Durvalumab


title: Input_shCTL.fastq.gz


title: NK_DC_PCI-15B_Durv_2


title: NK_DC_PCI-15B_Durv_1


title: M2

city: Shanghai

first: Baichao

last: Yu

state: Shanghai

address: NO.130,  Dong'an Road , Xuhui District

institute: Fudan University

data_processing:
The sequencing data were filtered by filtering software SOAPnuke to obtain Clean reads
Clean reads were then aligned to the reference genome sequence using HISAT.
Clean reads were aligned to the reference sequence using Bowtie2.
RSEM was used to calculate the expression levels of genes and transcripts.
Analyses based on gene expression levels, such as principal components, correlation, differential gene screening, and so on, were performed.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: spleen

extract_protocol:
Total RNA was extracted by RNAsimple Total RNA Kit (TIANGEN, China).
RNA libraries were prepared using MGIEasy RNA Library Prep Set Kit following manufacture's protocol

value: spleen

value: B cell


title: M1


title: M3


title: NK_DC_PCI-15B_IgG1_1


title: NK_DC_PCI-15B_IgG1_3


title: NK_DC_PCI-15B_IgG1_2


title: B2

value: anti-CD40 stimulated


title: B1


title: UN3

value: naive


title: B3


title: PCI-15B_No_ab_3

value: Epithelial cell


title: PCI-15B_No_ab_2


title: UN1


title: UN2


title: NK_PCI-15B_No_ab_3

source_name: PCI-15B and NK cells

value: PCI-15B and NK cells


title: NK_PCI-15B_Durva_3


title: NK_PCI-15B_No_ab_1


title: PCI-15B_No_ab_1


title: NK_PCI-15B_Durva_2


title: Panc-shRen_PBS_d2

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: T3.shRen.584-0
10x Genomics

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v4.0.12 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Gene expression reads were aligned to the mouse reference genome version gex-mm10-2020-A, available from the 10X Genomics website.
Assembly: mm10
Supplementary files format and content: Filtered single cell cell/gene matrices in .h5 format generated by cellbender v0.3.0

source_name: Pancreas (pre-malignant)

growth_protocol: Mice were generated by 8-cell or blastocyst injection of KC-shSmad4 or KC-shRen ESCs.

extract_protocol:
Cells were freshly isolated from non-tumor-bearing KC-shRen and KC-shSmad4 pancreata by FACS for mKate2+GFP+DAPI- cells. Sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 700–1,300 cells per μl. The viability of cells was above 80%, as confirmed by 0.2% (w/v) Trypan Blue staining (Countess II).
Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction (Chromium instrument (10X Genomics) user guide manual for 3’ v2).
Around 5,000 cells were targeted for each sample. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles). Single-cell RNA-seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X Genomics) following the user guide manual for 3’ v2.

treatment_protocol: shRNAs were induced by treatment of the resulting mice with doxycycline (625 mg/kg; Envigo) in the chow starting at 5-6 weeks of age. To examine the effects of tissue injury and Smad4 depletion on the premalignant pancreas, 8-week-old KC-shRen and KC-shSmad4 mice were treated with eight-hourly i.p. injections of cerulein (80 μg/kg; Bachem) or PBS for two consecutive days.

value: Pancreas (pre-malignant)

value: shRen

value: Dox+PBS

value: M


title: Panc-shRen_Cerulein_d2

description:
Library name: T4.shRen.584-3
10x Genomics

value: Dox+Cerulein


title: Panc-shSmad4_Cerulein_d2

description:
Library name: T4.shSmad4.587-1
10x Genomics


title: Ela-K

city: Gosselies

first: Denis

middle: LJ

last: Lafontaine

state: Hainaut

address: Av Profs Jeneer & Brachet, 12

institute: Universite libre de Bruxelles

description: Library name: DLRMS00130

data_processing:
RiboMethSeq was conducted as previously described in Marchand et al., NAR 2016 (doi: 10.1093/nar/gkw547). The bioinformatic analysis was performed as follows: Adapter sequences were trimmed from raw reads using Trimmomatic v0.39 with the following parameters: LEADING:30, TRAILING:30, SLIDINGWINDOW:4:15, AVGQUAL:30, and MINLEN:17. Quality control of the raw and trimmed reads was assessed using FastQC (v0.11.9). Alignment to the reference rRNA sequence was done by Bowtie2 (v2.3.5.1), with default parameters. Sorting, indexing and extraction of mapped reads was done using Samtools (v1.15.1), with option -F 4 to exclude the unmapped reads. Subsequent analysis was conducted using R: the quantification of ribosomal RNA (rRNA) 2′-O-Me residues was performed using the RNAmodR.RiboMethSeq package (v1.18.0), the final processed data were exported using the writexl (v1.5.0) package, display output were generated with the Prism software (v10.3.0).
Assembly: The rRNA reference sequences used are: 18S: NR_003278.3; 5.8S: NR_003280.2; and 28S: NR_003279.1
Supplementary files format and content: The processed data used to generate the Fig 4 A & B are in the file "Libert_et_al_Fig4AB.xlsx".

source_name: pancreas

extract_protocol:
Biopsies were obtained from mouse pancreas, incubated in RNALater (Thermo Fisher Scientific) overnight at 4°C, and frozen in liquid nitrogen. Tissue homogenization was performed by grinding the biopsies in liquid nitrogen with a plastic pestle. Total RNA was extracted using the TRI Reagent (Life Technologies) according to the manufacturer’s protocol.
RNA was hydrolyzed in bicarbonate buffer and the reaction was stopped by ethanol precipitation. The resulting fragments were then end-repaired and converted into an Illumina library using the NEB Next Small RNA Library Prepkit (Bioke, E7300S), according to the manufacturer’s protocol.

value: pancreas


title: Ela-K + ceru

description: Library name: DLRMS00131


title: NK_PCI-15B_Ave_2

value: Epithelial cell and immune cells

value: Not applicable

value: Avelumab


title: CLPP knockout, untreated, mBA cells

city: Cologne

first: Aleksandra

last: Trifunovic

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: CECAD research center

description: Library name: Input KO-UT

data_processing:
Chipseq reads were trimmed with fastp v0.23.4 using the following string: --trim_poly_g --trim_poly_x -Q -L --correction
reads were alligned with bwa v0.7.17 on mm39 reference genomne
reads were dedublicated using sambamba v0.8.0 tools
coverage plots and quality control done with ngsplot v2.6 or deeptools v3.5.4
peaks were called with genrich v0.6.1 with significant cutoff of 0.05
Assembly: mm39
Supplementary files format and content: narrow peaks

source_name: primary cells derived from brown adipose tissue

growth_protocol: Cells were grown in standard high glucose DMEM media without pyruvate, and CLPP KO cells were supplemented woth Uridine to bypass growth defect due to OXPHOS deficiency.

extract_protocol:
Cells per condition were cross linked with 1% formaldehyde for 10 minutes at RT. They were then quenched with 0.125M glycine for 5 minutes and washed with PBS, followed by harvesting in cetrifuge at 4000rpm for 5 minutes. Superntant was discarded and pellets were lysed in lysis buffer (50mM HEPES pH 7.9, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 supplemnted with protease inhibitors) using Dounce homogenizor, incubation for 20 minutes followed by centrifugation at 4000 rpm for 5 minutes. Nuclei pellets were then washedin wash buffer followed by washing in shearing buffer (0.1% SDS, 1mM EDTA, 10mM Tris pH 8.0). Cells were resuspended in 2ml shearing buffer, split into 6 tubes of 300 ul each and sonicated suing Bioruptor Pico Sonication system (Diagenode) for 70 cycles (30s on, 30 s off) usig the Easy Mode.
The library construction started with the end repair step of the protocol. Up to 100ng ChIP DNA was used as starting material. After end repair and A-tailing indexing adapters were ligated. The products were then purified and amplified (12 or 15 PCR cycles) to create the final libraries. After validation (TapeStation; Agilent Technologies) and quantification (Qubit System; Invitrogen) libraries were pooled and the library pool was quantified using the KAPA Library Quantification kit (Peqlab) and the 7900HT Sequence Detection System (Applied Biosystems) The pools were sequenced on an Illumina NovaSeq6000 sequencing instrument using a paired-end 2×100 bp protocol.

treatment_protocol: Cells were treated with cell soluble form of 2 hydroxyglutarate in DMSO.

value: mBA cells (primary)

value: primary

value: CLPP knockout


title: Panc-shSmad4_PBS_d2

description:
Library name: T3.shSmad4.588-2
10x Genomics


title: NK_PCI-15B_Durva_1

value: Durvalumab


title: wild type, 2HG treated, mBA cells

description: Library name: Input WT-HG

value: primary cells derived from brown adipose tissue

value: wild type


title: NK_PCI-15B_Ave_1


title: PCI-15B_Durva_3

value: Epithelial cell


title: NK_PCI-15B_Ave_3

value: PCI-15B and NK cells


title: CLPP knockout, untreated, mBA cells, replicate 4

description: Library name: KO-UT4

value: H3K4me3 antibody (Active Motif, 39159)


title: PCI-15B_Durva_2


title: CLPP knockout, untreated, mBA cells, replicate 3

description: Library name: KO-UT3


title: PCI-15B_Ave_3


title: PCI-15B_Ave_2


title: CLPP knockout, untreated, mBA cells, replicate 1

description: Library name: KO-UT1


title: NK_PCI-15B_No_ab_2


title: CLPP knockout, untreated, mBA cells, replicate 2

description: Library name: KO-UT2


title: PCI-15B_Ave_1


title: Lung47_PDO_Tcells_6E7F1_antiPD1

first: Dongxi

last: Xiang

address: No. 25, Lane 2200, Xietu Road

institute: Shanghai Cancer Institute

data_processing:
Analysis of the sequencing data was performed using the Rhapsody Sequence Analysis Pipeline (v2.0) with default parameters, employing the RhapRef_Human_WTA_2023-02 transcriptome for mapping. Quality control, dimensionality reduction, and clustering were conducted using Seurat (v4.0.3). For each sample, cells with high quality, defined as expressing at least 200 genes and up to 7500 genes, with less than 20% mitochondrial genes and less than 5% red blood cell genes, were retained. Additionally, genes had to be expressed in at least 3 cells for retention. Doublet cells identified by DoubletFinder (v2.0.2) were excluded.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every cell in each sample

extract_protocol:
Organoids of each treated group were harvested and dissociated into single cells. Organoids were dissociated in Matrigel with TrypLE Express (Gibco) for 1~3min via mechanical pipetting. The cells were washed twice till Matrigel was cleared out, and then resuspended with cold PBS. Subsequently, the cells were stained with Trypan Blue (Gibco) and the viability of the cells was evaluated using phase contrast light microscopy (Olympus,Japan). The viability of the cells was preferably above 80%, and about 30000-50000 cells were needed to generate scRNA-seq.
Single-cell RNA-seq libraries were generated using the BD Rhapsody™ WTA Amplification Kit (No. 633801).

value: Lung

tag: group

value: NSCLC


title: wild type, 2HG treated, mBA cells, replicate 4

description: Library name: WT-HG4


title: wild type, 2HG treated, mBA cells, replicate 3

description: Library name: WT-HG3


title: Lung47_PDO_Tcells_antiPD1


title: wild type, 2HG treated, mBA cells, replicate 2

description: Library name: WT-HG2


title: Lung47_PDO_Tcells_6E7F1


title: wild type untreated, mBA cells, replicate 4

description: Library name: WT-UT4


title: Lung47_PDO

value: PDO


title: wild type untreated, mBA cells, replicate 3

description: Library name: WT-UT3


title: Lung47_Tcells

value: Tcells


title: Lung46_PDO_Tcells_6E7F1_antiPD1


title: wild type untreated, mBA cells, replicate 2

description: Library name: WT-UT2


title: wild type untreated, mBA cells

description: Library name: Input WT-UT


title: wild type untreated, mBA cells, replicate 1

description: Library name: WT-UT1


title: Lung46_PDO_Tcells_antiPD1


title: Lung46_PDO_Tcells_6E7F1


title: Peritoneal lavages of T. brucei brucei infected mice, cDNA

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

institute: Vrije Universiteit Brussel - VIB

description:
Library name: Infected_cDNA
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: GRCm38
Supplementary files format and content: Compressed .h5 files containing UMI RNA/ADT counts in Cellranger output format, and comma-delimited text (.csv) files including metadata per cell as well as ADT antibody barcode information  (ADT_feature_reference.csv)
Library strategy: CITE-seq

source_name: Peritoneal lavage

extract_protocol:
All methods listed in Lebegge et al. VSIG4-EXPRESSING MACROPHAGES CONTRIBUTE TO ANTI-PARASITIC AND ANTI-METASTATIC RESPONSES IN THE PERITONEAL CAVITY. Eur J Immunol. 2025
All methods listed in Lebegge et al. VSIG4-EXPRESSING MACROPHAGES CONTRIBUTE TO ANTI-PARASITIC AND ANTI-METASTATIC RESPONSES IN THE PERITONEAL CAVITY. Eur J Immunol. 2025

value: Peritoneal lavage

value: T. brucei brucei injected


title: PCI-15B_Durva_1

value: Not applicable


title: Peritoneal lavages of naive mice, ADT

description:
Library name: Naive_ADT
ADT: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag sequences

value: HBSS-injected (control)


title: Lung46_PDO


title: Lung46_Tcells


title: Lung43_PDO_Tcells_6E7F1_antiPD1


title: Lung43_PDO_Tcells_antiPD1


title: Lung43_PDO_Tcells_6E7F1


title: wild type, 2HG treated, mBA cells, replicate 1

description: Library name: WT-HG1

value: mBA cells (primary)


title: Lung43_PDO


title: Lung43_Tcells


title: Peritoneal lavages of T. brucei brucei infected mice, ADT

description:
Library name: Infected_ADT
ADT: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag sequences


title: Lung33_PDO_Tcells_antiPD1


title: Lung33_Tcells


title: Lung33_PDO


title: Control IgG, Bleo Lung Tregs, Bulk RNA-seq, pool 3

first: Nicholas

last: Arpaia

state: NY

department: Microbiology & Immunology

institute: Columbia University

description:
Library name: ControlIgG_BleoLungTregs_BulkRNA-seq_pool3
IgGControl_3

data_processing:
Libraries were sequenced using Illumina NovaSeq 6000, yielding paired-end 100bp reads (40 million/sample)
RTA (Illumina) for base calling and bcl2fastq2 (v2.19) for converting BCL to fastq, Trim Galore for adapter trimming
Pseudoalignment using Salmon (1.10.2) from transcriptomic data (Ensembl v96, Mouse GRCm38 p6)
DESeq2 for analysis
Assembly: Ensembl v96, Mouse GRCm38.p6
Supplementary files format and content: tab delimited .txt file with raw counts for each gene/sample
Supplementary files format and content: tab delimited .txt file with normalized DESeq2 values for each gene/sample

source_name: lung

extract_protocol:
Cells were lysed with Trizol Reagent, and RNA was extracted using a Qiagen kit
PolyA pulldown of RNA, RNA amplification using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), cDNA library synthesis with NexteraXT Kit

treatment_protocol: Lung Treg cells from bleomycin-treated mice were sorted, stimulated with control IgG or 4-1BB agonistic antibody (clone 3H3) for 4h, then lysed and prepared for bulk RNA-seq.

value: lung

value: Treg cells

value: male

value: C57BL/6; Foxp3GFP

value: Bleomycin

value: IgGControl


title: Control IgG, Bleo Lung Tregs, Bulk RNA-seq, pool 1

description:
Library name: ControlIgG_BleoLungTregs_BulkRNA-seq_pool1
IgGControl_1


title: Stim 4-1BB agonistic ab, Bleo Lung Tregs, Bulk RNA-seq, pool 4

description:
Library name: Stim41BBAgonisticAntibody_BleoLungTregs_BulkRNA-seq_pool4
Stim41BBab_4


title: Stim 4-1BB agonistic ab, Bleo Lung Tregs, Bulk RNA-seq, pool 3

description:
Library name: Stim41BBAgonisticAntibody_BleoLungTregs_BulkRNA-seq_pool3
Stim41BBab_3


title: Stim 4-1BB agonistic ab, Bleo Lung Tregs, Bulk RNA-seq, pool 2

description:
Library name: Stim41BBAgonisticAntibody_BleoLungTregs_BulkRNA-seq_pool2
Stim41BBab_2


title: Control IgG, Bleo Lung Tregs, Bulk RNA-seq, pool 4

description:
Library name: ControlIgG_BleoLungTregs_BulkRNA-seq_pool4
IgGControl_4


title: Stim 4-1BB agonistic ab, Bleo Lung Tregs, Bulk RNA-seq, pool 1

description:
Library name: Stim41BBAgonisticAntibody_BleoLungTregs_BulkRNA-seq_pool1
Stim41BBab_1


title: Control IgG, Bleo Lung Tregs, Bulk RNA-seq, pool 2

description:
Library name: ControlIgG_BleoLungTregs_BulkRNA-seq_pool2
IgGControl_2


title: Peritoneal lavages of naive mice, cDNA

description:
Library name: Naive_cDNA
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: SK-8-Tumonolide

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the trimmomatic program to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <50 bases were excluded from RNA-seq analysis.
The cleaned reads of each sample were mapped to the reference sequence using the STAR read mapper (Spliced Transcripts Alignment to a Reference, v2.7.9a) (Dobin et al., 2013).
The mapping results were processed with RSEM, samtools, and scripts developed in house at UF ICBR to count uniquely mapped reads for gene expression analysis.
Differential gene expression analysis was performed with a DESeq2-based R pipeline to identify genes showing significant differential expression.
Assembly: GRCh38
Supplementary files format and content: Raw counts table
Supplementary files format and content: Fold change and P-values for all genes in the Tumonolide vs DMSO comparison.

source_name: Large intestine; Colon

growth_protocol: DMEM plus 10% FBS in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 250 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Ultra II Directional RNA-seq library preparation kit for Illumina according to manufacturer's protocol

treatment_protocol: compound or vehicle control (0.5% DMSO) for 12 h after overnight seeding

value: Large intestine; Colon

value: colorectal carcinoma

value: wt

value: 20 uM tumonolide


title: SK-9-Tumonolide


title: F1-8, PLCG2 Heterozygous Knockout, 5xFAD, 7.5Month, Cortex, female

city: Indianapolis

first: Evan

last: Messenger

state: IN

address: 320 W 15th St

institute: Stark Neuroscience Research Institute

description:
Library name: 7-5M_F1-8_P2KOHET_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_F1-8_P2KOHET_5xFAD_Ctx

data_processing:
Libraries of RNA samples with at least RIN 8 were prepared using KAPA mRNA Hyperprep Kit. Paired-end RNA sequencing (100bp) with ∼100 million reads coverage.
FASTQ files were aligned to the reference mouse genome mm10 with UCSC refGene annotation using STAR (v.2.7.10a), and gene read counts were generated using featureCounts (v. 2.0.3).
No trimming required.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: CSV file includes effective length, expected count, TPM, and FPKM for each sample

source_name: Cortex

extract_protocol:
RNA was extracted using the PureLink RNA mini kit (Invitrogen). 100ng of RNA were used.
KAPA mRNA Hyperprep Kit

value: Cortex

value: PLCG2 Heterozygous Knockout


title: F3-14, PLCG2 Heterozygous Knockout, 5xFAD, 7.5Month, Cortex, female

description:
Library name: 7-5M_F3-14_P2KOHET_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_F3-14_P2KOHET_5xFAD_Ctx


title: M3-3, PLCG2 Heterozygous Knockout, 5xFAD, 7.5Month, Cortex, male

description:
Library name: 7-5M_M3-3_P2KOHET_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M3-3_P2KOHET_5xFAD_Ctx


title: F2-12, PLCG2 Heterozygous Knockout, 5xFAD, 7.5Month, Cortex, female

description:
Library name: 7-5M_F2-12_P2KOHET_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_F2-12_P2KOHET_5xFAD_Ctx


title: SK-7-Tumonolide


title: F2-137, PLCG2 Knockout, 5xFAD, 7.5Month, Cortex, female

description:
Library name: 7-5M_F2-137_P2KOHOM_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_F2-137_P2KOHOM_5xFAD_Ctx

value: PLCG2 Knockout


title: SK-2-DMSOcontrol

value: 0.5% DMSO


title: M1-11, PLCG2 Heterozygous Knockout, 5xFAD, 7.5Month, Cortex, male

description:
Library name: 7-5M_M1-11_P2KOHET_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M1-11_P2KOHET_5xFAD_Ctx


title: M2-13, PLCG2 Heterozygous Knockout, 5xFAD, 7.5Month, Cortex, male

description:
Library name: 7-5M_M2-13_P2KOHET_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M2-13_P2KOHET_5xFAD_Ctx


title: Lung33_PDO_Tcells_6E7F1_antiPD1

value: Lung

value: NSCLC


title: SK-1-DMSOcontrol


title: F1-83, PLCG2 Knockout, 5xFAD, 7.5Month, Cortex, female

description:
Library name: 7-5M_F1-83_P2KOHOM_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_F1-83_P2KOHOM_5xFAD_Ctx