title: RMDB_860

description: REMoDLB trial


title: RMDB_857

status: Public on Jan 15 2019

type: RNA

city: Leeds

first: Chulin

last: Sha

address: Woodhouse Lane

department: School of Mole&Cell Biology

country: United Kingdom

institute: University of Leeds

description: REMoDLB trial

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: The data were normalised using lumi package in R

label: Biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Standard Illumina label protocol

extract_protocol: Total RNA was extracted from 5mm paraffin sections using the Ambion RecoverAll kit standard protocol, with the exception of a 16-hour protease digestion. These were routinely collected tissue samples and no attempt was made to standardise fixation or processing protocols

tag: clinic diagnosis

value: Diffuse Large B-cell Lymphoma

tag: molecular subtype

value: ABC

tag: molecular coo subtype


title: RMDB_864

description: REMoDLB trial

value: GCB


title: RMDB_859

description: REMoDLB trial


title: RMDB_867

description: REMoDLB trial

value: UNC


title: RMDB_853

description: REMoDLB trial


title: RMDB_855

description: REMoDLB trial


title: RMDB_856

description: REMoDLB trial


title: RMDB_861

description: REMoDLB trial


title: RMDB_854

description: REMoDLB trial


title: RMDB_858

description: REMoDLB trial


title: RMDB_852

description: REMoDLB trial


title: RMDB_851

description: REMoDLB trial


title: RMDB_844

description: REMoDLB trial


title: RMDB_848

description: REMoDLB trial


title: RMDB_845

description: REMoDLB trial


title: RMDB_847

description: REMoDLB trial


title: RMDB_841

description: REMoDLB trial


title: RMDB_838

description: REMoDLB trial


title: RMDB_849

description: REMoDLB trial


title: RMDB_846

description: REMoDLB trial


title: RMDB_840

description: REMoDLB trial


title: RMDB_843

description: REMoDLB trial


title: RMDB_850

description: REMoDLB trial


title: RMDB_842

description: REMoDLB trial

value: MHG


title: RMDB_832

description: REMoDLB trial


title: RMDB_829

description: REMoDLB trial


title: RMDB_839

description: REMoDLB trial


title: RMDB_837

description: REMoDLB trial


title: RMDB_826

description: REMoDLB trial


title: RMDB_835

description: REMoDLB trial


title: RMDB_836

description: REMoDLB trial


title: RMDB_834

description: REMoDLB trial


title: RMDB_885

description: REMoDLB trial


title: RMDB_833

description: REMoDLB trial


title: RMDB_831

description: REMoDLB trial


title: RMDB_823

description: REMoDLB trial


title: RMDB_828

description: REMoDLB trial


title: RMDB_830

description: REMoDLB trial


title: RMDB_827

description: REMoDLB trial


title: RMDB_825

description: REMoDLB trial


title: RMDB_820

description: REMoDLB trial


title: RMDB_821

description: REMoDLB trial


title: RMDB_822

description: REMoDLB trial


title: RMDB_824

description: REMoDLB trial


title: RMDB_818

description: REMoDLB trial


title: RMDB_816

description: REMoDLB trial


title: RMDB_813

description: REMoDLB trial


title: RMDB_810

description: REMoDLB trial


title: RMDB_817

description: REMoDLB trial


title: RMDB_819

description: REMoDLB trial


title: RMDB_870

description: REMoDLB trial


title: RMDB_815

description: REMoDLB trial


title: RMDB_812

description: REMoDLB trial


title: RMDB_809

description: REMoDLB trial


title: RMDB_806

description: REMoDLB trial


title: RMDB_804

description: REMoDLB trial


title: RMDB_807

description: REMoDLB trial


title: RMDB_814

description: REMoDLB trial


title: RMDB_801

description: REMoDLB trial


title: RMDB_803

description: REMoDLB trial


title: RMDB_811

description: REMoDLB trial


title: RMDB_800

description: REMoDLB trial


title: RMDB_797

description: REMoDLB trial


title: RMDB_808

description: REMoDLB trial


title: RMDB_805

description: REMoDLB trial


title: RMDB_802

description: REMoDLB trial


title: RMDB_798

description: REMoDLB trial


title: RMDB_799

description: REMoDLB trial


title: RMDB_796

description: REMoDLB trial


title: RMDB_794

description: REMoDLB trial


title: RMDB_791

description: REMoDLB trial


title: RMDB_795

description: REMoDLB trial


title: RMDB_787

description: REMoDLB trial


title: RMDB_785

description: REMoDLB trial


title: RMDB_788

description: REMoDLB trial


title: RMDB_792

description: REMoDLB trial


title: RMDB_789

description: REMoDLB trial


title: RMDB_793

description: REMoDLB trial


title: RMDB_782

description: REMoDLB trial


title: RMDB_790

description: REMoDLB trial


title: RMDB_786

description: REMoDLB trial


title: RMDB_784

description: REMoDLB trial


title: RMDB_781

description: REMoDLB trial


title: RMDB_776

description: REMoDLB trial


title: RMDB_783

description: REMoDLB trial


title: RMDB_780

description: REMoDLB trial


title: RMDB_774

description: REMoDLB trial


title: RMDB_771

description: REMoDLB trial


title: RMDB_778

description: REMoDLB trial


title: RMDB_775

description: REMoDLB trial


title: RMDB_773

description: REMoDLB trial


title: RMDB_772

description: REMoDLB trial


title: RMDB_770

description: REMoDLB trial


title: RMDB_779

description: REMoDLB trial


title: RMDB_777

description: REMoDLB trial


title: RMDB_766

description: REMoDLB trial


title: RMDB_768

description: REMoDLB trial


title: RMDB_763

description: REMoDLB trial


title: RMDB_767

description: REMoDLB trial


title: RMDB_757

description: REMoDLB trial


title: RMDB_765

description: REMoDLB trial


title: RMDB_764

description: REMoDLB trial


title: RMDB_759

description: REMoDLB trial


title: RMDB_758

description: REMoDLB trial


title: RMDB_756

description: REMoDLB trial


title: RMDB_769

description: REMoDLB trial


title: RMDB_760

description: REMoDLB trial


title: RMDB_755

description: REMoDLB trial


title: RMDB_754

description: REMoDLB trial


title: RMDB_761

description: REMoDLB trial


title: RMDB_753

description: REMoDLB trial


title: RMDB_762

description: REMoDLB trial


title: RMDB_752

description: REMoDLB trial


title: RMDB_749

description: REMoDLB trial


title: RMDB_744

description: REMoDLB trial


title: RMDB_747

description: REMoDLB trial


title: RMDB_751

description: REMoDLB trial


title: RMDB_734

description: REMoDLB trial


title: RMDB_750

description: REMoDLB trial


title: RMDB_735

description: REMoDLB trial


title: RMDB_748

description: REMoDLB trial


title: RMDB_746

description: REMoDLB trial


title: RMDB_740

description: REMoDLB trial


title: RMDB_741

description: REMoDLB trial


title: RMDB_743

description: REMoDLB trial


title: RMDB_745

description: REMoDLB trial


title: RMDB_737

description: REMoDLB trial


title: RMDB_731

description: REMoDLB trial


title: RMDB_732

description: REMoDLB trial


title: RMDB_739

description: REMoDLB trial


title: RMDB_725

description: REMoDLB trial


title: RMDB_742

description: REMoDLB trial


title: RMDB_728

description: REMoDLB trial


title: RMDB_738

description: REMoDLB trial


title: RMDB_726

description: REMoDLB trial


title: RMDB_729

description: REMoDLB trial


title: RMDB_736

description: REMoDLB trial


title: RMDB_730

description: REMoDLB trial


title: RMDB_733

description: REMoDLB trial


title: RMDB_727

description: REMoDLB trial


title: RMDB_724

description: REMoDLB trial


title: RMDB_723

description: REMoDLB trial


title: RMDB_720

description: REMoDLB trial


title: RMDB_716

description: REMoDLB trial


title: RMDB_717

description: REMoDLB trial


title: RMDB_718

description: REMoDLB trial


title: RMDB_714

description: REMoDLB trial


title: RMDB_715

description: REMoDLB trial


title: RMDB_711

description: REMoDLB trial


title: RMDB_712

description: REMoDLB trial


title: RMDB_721

description: REMoDLB trial


title: RMDB_705

description: REMoDLB trial


title: RMDB_702

description: REMoDLB trial


title: RMDB_708

description: REMoDLB trial


title: RMDB_696

description: REMoDLB trial


title: RMDB_703

description: REMoDLB trial


title: RMDB_699

description: REMoDLB trial


title: RMDB_722

description: REMoDLB trial


title: RMDB_710

description: REMoDLB trial


title: RMDB_697

description: REMoDLB trial


title: RMDB_694

description: REMoDLB trial


title: RMDB_700

description: REMoDLB trial


title: RMDB_709

description: REMoDLB trial


title: RMDB_693

description: REMoDLB trial


title: RMDB_707

description: REMoDLB trial


title: RMDB_719

description: REMoDLB trial


title: RMDB_713

description: REMoDLB trial


title: RMDB_698

description: REMoDLB trial


title: RMDB_704

description: REMoDLB trial


title: RMDB_695

description: REMoDLB trial


title: RMDB_706

description: REMoDLB trial


title: RMDB_692

description: REMoDLB trial


title: RMDB_701

description: REMoDLB trial


title: RMDB_691

description: REMoDLB trial


title: RMDB_687

description: REMoDLB trial


title: RMDB_688

description: REMoDLB trial


title: RMDB_685

description: REMoDLB trial


title: RMDB_682

description: REMoDLB trial


title: RMDB_679

description: REMoDLB trial


title: RMDB_678

description: REMoDLB trial


title: RMDB_676

description: REMoDLB trial


title: RMDB_672

description: REMoDLB trial


title: RMDB_673

description: REMoDLB trial


title: RMDB_689

description: REMoDLB trial


title: RMDB_684

description: REMoDLB trial


title: RMDB_686

description: REMoDLB trial


title: RMDB_675

description: REMoDLB trial


title: RMDB_681

description: REMoDLB trial


title: RMDB_669

description: REMoDLB trial


title: RMDB_667

description: REMoDLB trial


title: RMDB_664

description: REMoDLB trial


title: RMDB_680

description: REMoDLB trial


title: RMDB_663

description: REMoDLB trial


title: RMDB_671

description: REMoDLB trial


title: RMDB_677

description: REMoDLB trial


title: RMDB_674

description: REMoDLB trial


title: RMDB_670

description: REMoDLB trial


title: RMDB_668

description: REMoDLB trial


title: RMDB_666

description: REMoDLB trial


title: RMDB_659

description: REMoDLB trial


title: RMDB_658

description: REMoDLB trial


title: RMDB_665

description: REMoDLB trial


title: RMDB_661

description: REMoDLB trial


title: RMDB_662

description: REMoDLB trial


title: RMDB_660

description: REMoDLB trial


title: RMDB_657

description: REMoDLB trial


title: RMDB_654

description: REMoDLB trial


title: RMDB_656

description: REMoDLB trial


title: RMDB_655

description: REMoDLB trial


title: RMDB_652

description: REMoDLB trial


title: RMDB_651

description: REMoDLB trial


title: RMDB_648

description: REMoDLB trial


title: RMDB_645

description: REMoDLB trial


title: RMDB_649

description: REMoDLB trial


title: RMDB_642

description: REMoDLB trial


title: RMDB_653

description: REMoDLB trial


title: RMDB_646

description: REMoDLB trial


title: RMDB_650

description: REMoDLB trial


title: RMDB_643

description: REMoDLB trial


title: RMDB_647

description: REMoDLB trial


title: RMDB_644

description: REMoDLB trial


title: RMDB_640

description: REMoDLB trial


title: RMDB_637

description: REMoDLB trial


title: RMDB_641

description: REMoDLB trial


title: RMDB_634

description: REMoDLB trial


title: RMDB_638

description: REMoDLB trial


title: RMDB_639

description: REMoDLB trial


title: RMDB_636

description: REMoDLB trial


title: RMDB_629

description: REMoDLB trial


title: RMDB_633

description: REMoDLB trial


title: RMDB_630

description: REMoDLB trial


title: RMDB_631

description: REMoDLB trial


title: RMDB_627

description: REMoDLB trial


title: RMDB_628

description: REMoDLB trial


title: RMDB_635

description: REMoDLB trial


title: RMDB_625

description: REMoDLB trial


title: RMDB_632

description: REMoDLB trial


title: RMDB_626

description: REMoDLB trial


title: RMDB_624

description: REMoDLB trial


title: RMDB_622

description: REMoDLB trial


title: RMDB_619

description: REMoDLB trial


title: RMDB_620

description: REMoDLB trial


title: RMDB_621

description: REMoDLB trial


title: RMDB_617

description: REMoDLB trial


title: RMDB_690

description: REMoDLB trial


title: RMDB_615

description: REMoDLB trial


title: RMDB_616

description: REMoDLB trial


title: RMDB_611

description: REMoDLB trial


title: RMDB_609

description: REMoDLB trial


title: RMDB_613

description: REMoDLB trial


title: RMDB_612

description: REMoDLB trial


title: RMDB_610

description: REMoDLB trial


title: RMDB_608

description: REMoDLB trial


title: RMDB_607

description: REMoDLB trial


title: RMDB_623

description: REMoDLB trial


title: RMDB_599

description: REMoDLB trial


title: RMDB_614

description: REMoDLB trial


title: RMDB_602

description: REMoDLB trial


title: RMDB_597

description: REMoDLB trial


title: RMDB_601

description: REMoDLB trial


title: RMDB_603

description: REMoDLB trial


title: RMDB_604

description: REMoDLB trial


title: RMDB_598

description: REMoDLB trial


title: RMDB_594

description: REMoDLB trial


title: RMDB_683

description: REMoDLB trial


title: RMDB_605

description: REMoDLB trial


title: RMDB_596

description: REMoDLB trial


title: RMDB_606

description: REMoDLB trial


title: RMDB_593

description: REMoDLB trial


title: RMDB_600

description: REMoDLB trial


title: RMDB_595

description: REMoDLB trial


title: RMDB_592

description: REMoDLB trial


title: RMDB_586

description: REMoDLB trial


title: RMDB_589

description: REMoDLB trial


title: RMDB_590

description: REMoDLB trial


title: RMDB_591

description: REMoDLB trial


title: RMDB_585

description: REMoDLB trial


title: RMDB_588

description: REMoDLB trial


title: RMDB_576

description: REMoDLB trial


title: RMDB_582

description: REMoDLB trial


title: RMDB_581

description: REMoDLB trial


title: RMDB_587

description: REMoDLB trial


title: RMDB_580

description: REMoDLB trial


title: RMDB_567

description: REMoDLB trial


title: RMDB_584

description: REMoDLB trial


title: RMDB_583

description: REMoDLB trial


title: RMDB_574

description: REMoDLB trial


title: RMDB_577

description: REMoDLB trial


title: RMDB_579

description: REMoDLB trial


title: RMDB_575

description: REMoDLB trial


title: RMDB_570

description: REMoDLB trial


title: RMDB_571

description: REMoDLB trial


title: RMDB_566

description: REMoDLB trial


title: RMDB_565

description: REMoDLB trial


title: RMDB_568

description: REMoDLB trial


title: RMDB_564

description: REMoDLB trial


title: RMDB_573

description: REMoDLB trial


title: RMDB_578

description: REMoDLB trial


title: RMDB_569

description: REMoDLB trial


title: RMDB_572

description: REMoDLB trial


title: RMDB_563

description: REMoDLB trial


title: RMDB_561

description: REMoDLB trial


title: RMDB_562

description: REMoDLB trial


title: RMDB_557

description: REMoDLB trial


title: RMDB_558

description: REMoDLB trial


title: RMDB_554

description: REMoDLB trial


title: RMDB_550

description: REMoDLB trial


title: RMDB_544

description: REMoDLB trial


title: RMDB_552

description: REMoDLB trial


title: RMDB_543

description: REMoDLB trial


title: RMDB_559

description: REMoDLB trial


title: RMDB_553

description: REMoDLB trial


title: RMDB_546

description: REMoDLB trial


title: RMDB_551

description: REMoDLB trial


title: RMDB_547

description: REMoDLB trial


title: RMDB_556

description: REMoDLB trial


title: RMDB_549

description: REMoDLB trial


title: RMDB_541

description: REMoDLB trial


title: RMDB_548

description: REMoDLB trial


title: RMDB_555

description: REMoDLB trial


title: RMDB_538

description: REMoDLB trial


title: RMDB_618

description: REMoDLB trial


title: RMDB_536

description: REMoDLB trial


title: RMDB_532

description: REMoDLB trial


title: RMDB_545

description: REMoDLB trial


title: RMDB_534

description: REMoDLB trial


title: RMDB_540

description: REMoDLB trial


title: RMDB_560

description: REMoDLB trial


title: RMDB_535

description: REMoDLB trial


title: RMDB_542

description: REMoDLB trial


title: RMDB_537

description: REMoDLB trial


title: RMDB_539

description: REMoDLB trial


title: RMDB_531

description: REMoDLB trial


title: RMDB_529

description: REMoDLB trial


title: RMDB_510

description: REMoDLB trial


title: RMDB_504

description: REMoDLB trial


title: RMDB_526

description: REMoDLB trial


title: RMDB_517

description: REMoDLB trial


title: RMDB_513

description: REMoDLB trial


title: RMDB_514

description: REMoDLB trial


title: RMDB_525

description: REMoDLB trial


title: RMDB_528

description: REMoDLB trial


title: RMDB_527

description: REMoDLB trial


title: RMDB_533

description: REMoDLB trial


title: RMDB_515

description: REMoDLB trial


title: RMDB_518

description: REMoDLB trial


title: RMDB_509

description: REMoDLB trial


title: RMDB_506

description: REMoDLB trial


title: RMDB_519

description: REMoDLB trial


title: RMDB_511

description: REMoDLB trial


title: RMDB_521

description: REMoDLB trial


title: RMDB_530

description: REMoDLB trial


title: RMDB_523

description: REMoDLB trial


title: RMDB_524

description: REMoDLB trial


title: RMDB_503

description: REMoDLB trial


title: RMDB_512

description: REMoDLB trial


title: RMDB_520

description: REMoDLB trial


title: RMDB_522

description: REMoDLB trial


title: RMDB_508

description: REMoDLB trial


title: RMDB_516

description: REMoDLB trial


title: RMDB_502

description: REMoDLB trial


title: RMDB_500

description: REMoDLB trial


title: RMDB_494

description: REMoDLB trial


title: RMDB_497

description: REMoDLB trial


title: RMDB_491

description: REMoDLB trial


title: RMDB_498

description: REMoDLB trial


title: RMDB_501

description: REMoDLB trial


title: RMDB_495

description: REMoDLB trial


title: RMDB_492

description: REMoDLB trial


title: RMDB_499

description: REMoDLB trial


title: RMDB_489

description: REMoDLB trial


title: RMDB_496

description: REMoDLB trial


title: RMDB_479

description: REMoDLB trial


title: RMDB_490

description: REMoDLB trial


title: RMDB_476

description: REMoDLB trial


title: RMDB_482

description: REMoDLB trial


title: RMDB_485

description: REMoDLB trial


title: RMDB_493

description: REMoDLB trial


title: RMDB_488

description: REMoDLB trial


title: RMDB_487

description: REMoDLB trial


title: RMDB_505

description: REMoDLB trial


title: RMDB_484

description: REMoDLB trial


title: RMDB_507

description: REMoDLB trial


title: RMDB_481

description: REMoDLB trial


title: RMDB_475

description: REMoDLB trial


title: RMDB_483

description: REMoDLB trial


title: RMDB_486

description: REMoDLB trial


title: RMDB_477

description: REMoDLB trial


title: RMDB_480

description: REMoDLB trial


title: RMDB_473

description: REMoDLB trial


title: RMDB_474

description: REMoDLB trial


title: RMDB_468

description: REMoDLB trial


title: RMDB_471

description: REMoDLB trial


title: RMDB_478

description: REMoDLB trial


title: RMDB_470

description: REMoDLB trial


title: RMDB_465

description: REMoDLB trial


title: RMDB_472

description: REMoDLB trial


title: RMDB_467

description: REMoDLB trial


title: RMDB_459

description: REMoDLB trial


title: RMDB_463

description: REMoDLB trial


title: RMDB_469

description: REMoDLB trial


title: RMDB_466

description: REMoDLB trial


title: RMDB_460

description: REMoDLB trial


title: RMDB_461

description: REMoDLB trial


title: RMDB_455

description: REMoDLB trial


title: RMDB_462

description: REMoDLB trial


title: RMDB_454

description: REMoDLB trial


title: RMDB_457

description: REMoDLB trial


title: RMDB_464

description: REMoDLB trial


title: RMDB_452

description: REMoDLB trial


title: RMDB_458

description: REMoDLB trial


title: RMDB_453

description: REMoDLB trial


title: RMDB_449

description: REMoDLB trial


title: RMDB_451

description: REMoDLB trial


title: RMDB_445

description: REMoDLB trial


title: RMDB_447

description: REMoDLB trial


title: RMDB_446

description: REMoDLB trial


title: RMDB_444

description: REMoDLB trial


title: RMDB_436

description: REMoDLB trial


title: RMDB_440

description: REMoDLB trial


title: RMDB_437

description: REMoDLB trial


title: RMDB_448

description: REMoDLB trial


title: RMDB_439

description: REMoDLB trial


title: RMDB_450

description: REMoDLB trial


title: RMDB_443

description: REMoDLB trial


title: RMDB_456

description: REMoDLB trial


title: RMDB_441

description: REMoDLB trial


title: RMDB_433

description: REMoDLB trial


title: RMDB_430

description: REMoDLB trial


title: RMDB_434

description: REMoDLB trial


title: RMDB_427

description: REMoDLB trial


title: RMDB_428

description: REMoDLB trial


title: RMDB_438

description: REMoDLB trial


title: RMDB_435

description: REMoDLB trial


title: RMDB_425

description: REMoDLB trial


title: RMDB_432

description: REMoDLB trial


title: RMDB_429

description: REMoDLB trial


title: RMDB_426

description: REMoDLB trial


title: RMDB_424

description: REMoDLB trial


title: RMDB_414

description: REMoDLB trial


title: RMDB_422

description: REMoDLB trial


title: RMDB_423

description: REMoDLB trial


title: RMDB_421

description: REMoDLB trial


title: RMDB_413

description: REMoDLB trial


title: RMDB_419

description: REMoDLB trial


title: RMDB_418

description: REMoDLB trial


title: RMDB_415

description: REMoDLB trial


title: RMDB_411

description: REMoDLB trial


title: RMDB_431

description: REMoDLB trial


title: RMDB_412

description: REMoDLB trial


title: RMDB_416

description: REMoDLB trial


title: RMDB_420

description: REMoDLB trial


title: RMDB_417

description: REMoDLB trial


title: RMDB_410

description: REMoDLB trial


title: RMDB_408

description: REMoDLB trial


title: RMDB_409

description: REMoDLB trial


title: RMDB_406

description: REMoDLB trial


title: RMDB_442

description: REMoDLB trial


title: RMDB_400

description: REMoDLB trial


title: RMDB_401

description: REMoDLB trial


title: RMDB_404

description: REMoDLB trial


title: RMDB_397

description: REMoDLB trial


title: RMDB_402

description: REMoDLB trial


title: RMDB_405

description: REMoDLB trial


title: RMDB_403

description: REMoDLB trial


title: RMDB_398

description: REMoDLB trial


title: RMDB_399

description: REMoDLB trial


title: RMDB_407

description: REMoDLB trial


title: RMDB_391

description: REMoDLB trial


title: RMDB_387

description: REMoDLB trial


title: RMDB_394

description: REMoDLB trial


title: RMDB_396

description: REMoDLB trial


title: RMDB_388

description: REMoDLB trial


title: RMDB_390

description: REMoDLB trial


title: RMDB_395

description: REMoDLB trial


title: RMDB_392

description: REMoDLB trial


title: RMDB_389

description: REMoDLB trial


title: RMDB_384

description: REMoDLB trial


title: RMDB_381

description: REMoDLB trial


title: RMDB_379

description: REMoDLB trial


title: RMDB_393

description: REMoDLB trial


title: RMDB_383

description: REMoDLB trial


title: RMDB_376

description: REMoDLB trial


title: RMDB_377

description: REMoDLB trial


title: RMDB_382

description: REMoDLB trial


title: RMDB_386

description: REMoDLB trial


title: RMDB_380

description: REMoDLB trial


title: RMDB_378

description: REMoDLB trial


title: RMDB_373

description: REMoDLB trial


title: RMDB_374

description: REMoDLB trial


title: RMDB_375

description: REMoDLB trial


title: RMDB_372

description: REMoDLB trial


title: RMDB_369

description: REMoDLB trial


title: RMDB_385

description: REMoDLB trial


title: RMDB_371

description: REMoDLB trial


title: RMDB_370

description: REMoDLB trial


title: RMDB_367

description: REMoDLB trial


title: RMDB_361

description: REMoDLB trial


title: RMDB_368

description: REMoDLB trial


title: RMDB_364

description: REMoDLB trial


title: RMDB_358

description: REMoDLB trial


title: RMDB_362

description: REMoDLB trial


title: RMDB_365

description: REMoDLB trial


title: RMDB_357

description: REMoDLB trial


title: RMDB_352

description: REMoDLB trial


title: RMDB_366

description: REMoDLB trial


title: RMDB_355

description: REMoDLB trial


title: RMDB_360

description: REMoDLB trial


title: RMDB_363

description: REMoDLB trial


title: RMDB_343

description: REMoDLB trial


title: RMDB_354

description: REMoDLB trial


title: RMDB_356

description: REMoDLB trial


title: RMDB_351

description: REMoDLB trial


title: RMDB_359

description: REMoDLB trial


title: RMDB_348

description: REMoDLB trial


title: RMDB_346

description: REMoDLB trial


title: RMDB_345

description: REMoDLB trial


title: RMDB_349

description: REMoDLB trial


title: RMDB_353

description: REMoDLB trial


title: RMDB_350

description: REMoDLB trial


title: RMDB_340

description: REMoDLB trial


title: RMDB_347

description: REMoDLB trial


title: RMDB_344

description: REMoDLB trial


title: RMDB_341

description: REMoDLB trial


title: RMDB_342

description: REMoDLB trial


title: RMDB_339

description: REMoDLB trial


title: RMDB_337

description: REMoDLB trial


title: RMDB_335

description: REMoDLB trial


title: ATACseq_pDC-2

type: SRA

city: Aachen

first: Zhijian

last: Li

state: North Rhine-Westphal

address: Pauwelsstr. 19

country: Germany

institute: RWTH Aachen University

library_source: genomic

data_processing:
Illumina NextSeq 500 Platform was used for 75bps paired end reads.
Sequenced reads were trimmed for adapter sequences using Trim Galore with -q 30 --trim1 --paired .
Reads mapped to mm9 whole genome by Bowtie2 with -X 2000 --no-mixed –no-discordant
Duplicates were remove. Reads were filtered for alignment quality of Q > 30 and were required to be properly paired
Reads mapping to chromosome Y, mitochondria and unassembled "random" contigs were removed from all downstream analysis
Peaks were called using MACS2 with -g mm --keep-dup all --call-summits –nomodel
All replicates were merged using samtools to perform footprinting
Genome_build: mm9
Supplementary_files_format_and_content: The counts of the aligned reads of all samples.

molecule: genomic DNA

organism: Mus musculus

source_name: Plasmacytoid dendritic cell (pDC)

extract_protocol: Omni-ATAC-seq was performed according to Corces et al., Nature Methods 14, 959-962, 2017 with minor modifications. Prior to transposition dead cells were removed by centrifugation (800 rpm, 4 min, 4°C). The transposition reaction was with 7.5 µl Tagment DNA Enzyme 1 (TDE1) for 60 min at 37°C. Pre-amplification was with NEBNext Ultra II Q5 Master Mix and Nextera PCR Primers (5 cycles). Quantitative PCR amplification was with NEBNext Ultra II Q5 Master Mix, Nextera PCR Primer and SYBR Gold to determine the number of additional cycles. PCR amplification of additional cycles was as for pre-amplification. PCR fragments were purified with Qiagen MinElute PCR Purification Kit and library concentration and quality were determined by Agilent High Sensitive DNA Kit and Bioanalyzer, respectively.

tag: cell type

value: Plasmacytoid dendritic cell (pDC)


title: ATACseq_cDC1-2

source_name: Classical dendritic cell (cDC)

value: Classical dendritic cell (cDC)


title: RMDB_334

description: REMoDLB trial


title: RMDB_333

description: REMoDLB trial


title: ATACseq_pDC-1


title: ATACseq_cDC1-1


title: poks-ps

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

description: rice-PS-seq-gene-fpkm.xlsx

library_source: transcriptomic

data_processing:
Library strategy: polysome-seq
TopHat was used to align the reads to the genome of rice (MSU v6.1) with option “-G”.
Cufflinks was used to assemble the alignments from TopHat.
Cuffmerge was used to merged assembled transcripts from the individual libraries.
Cuffcompare was used to compare the combined transcripts to annotated transcripts on MSU Rice Genome Annotation Database (v6.1).
Cuffdiff was used to compare expression levels of the transcripts in the control and salt stress libraries.
Genome_build: rice (MSU v6.1)
Supplementary_files_format_and_content: FPKM values of genes

organism: Oryza sativa

source_name: polysomal fractions of Pok salt stress

growth_protocol: Rice seedlings were grown in Yoshida medium in a controlled growth chamber (22–24°C) with a 16h/8h (day/night) photoperiod and 300 µmol m−2 s−1 light intensity.

extract_protocol:
RNA was isolated from 10 µg each of the total RNA and polysomal RNA using MicroPoly(A) Purist ™ kit (Ambion).
Briefly, rice seedlings were ground into a fine powder with liquid nitrogen, then thoroughly mixed with polysome extraction buffer using a spatula and placed on ice for 10 min with occasional mixing by inverting tubes. The lysis was spun for 2 min at 14000 rpm (4  C) and the supernatant was passed through a QIA shredder (QIAGEN) column by centrifugation for 1 min at 14000 rpm (4  C). Approximately 600   microL of the sample was layered on top of the sucrose density gradients (20-60% sucrose, w/v) and centrifuged for 120 min at 40,000 rpm (275,000    g) in a Beckman OPTIMA LE-80 centrifuge. The optical density (OD) of the samples was measured by using a UA-5 detector and a Gradient Fractionator (model 640, ISCO) reading absorbance throughout the sucrose gradient at 254 nm. Fractions with more than two ribosomes were pooled and used for RNA isolation and RNA-Seq library preparation later.
mRNA-Seq libraries were generated by following Illumina mRNA Sequencing Sample Preparation Guide.

treatment_protocol: Approximately 24-day-old seedlings were subjected to salt stress with supplementation of 150 mM NaCl for 24 hours, while control samples were remained on Yoshida medium.

tag: developmental stage

tag: tissue

value: seedlings

tag: cultivar

value: Pokkali (Pok)


title: RMDB_332

description: REMoDLB trial


title: ir29s-ps

description: rice-PS-seq-gene-fpkm.xlsx

source_name: polysomal fractions of IR29 salt stress


title: ir29c-ps

description: rice-PS-seq-gene-fpkm.xlsx

source_name: polysomal fractions of IR29 control


title: pokc-ps

description: rice-PS-seq-gene-fpkm.xlsx

source_name: polysomal fractions of Pok control


title: RMDB_327

description: REMoDLB trial


title: RMDB_324

description: REMoDLB trial


title: RMDB_331

description: REMoDLB trial


title: RMDB_325

description: REMoDLB trial


title: RMDB_329

description: REMoDLB trial


title: poks-rna

description: rice-RNA-seq-gene-fpkm.xlsx

data_processing:
TopHat was used to align the reads to the genome of rice (MSU v6.1) with option “-G”.
Cufflinks was used to assemble the alignments from TopHat.
Cuffmerge was used to merged assembled transcripts from the individual libraries.
Cuffcompare was used to compare the combined transcripts to annotated transcripts on MSU Rice Genome Annotation Database (v6.1).
Cuffdiff was used to compare expression levels of the transcripts in the control and salt stress libraries.
Genome_build: rice (MSU v6.1)
Supplementary_files_format_and_content: FPKM values of genes

source_name: Pok salt stress

extract_protocol:
Total RNA and polysome RNA were isolated using Trizol® Reagent according to the manufacturer’s instructions (Invitrogen).
mRNA-Seq libraries were generated by following Illumina mRNA Sequencing Sample Preparation Guide.

treatment_protocol: Approximately 24-day-old seedlings were subjected to salt stress with supplementation of 150 mM NaCl for 24 hours, while control samples were remained in Yoshida medium.


title: RMDB_326

description: REMoDLB trial


title: RMDB_323

description: REMoDLB trial


title: pokc-rna

description: rice-RNA-seq-gene-fpkm.xlsx

source_name: Pok control


title: RMDB_336

description: REMoDLB trial


title: ir29s-rna

description: rice-RNA-seq-gene-fpkm.xlsx

source_name: IR29 salt stress


title: RMDB_328

description: REMoDLB trial


title: RMDB_322

description: REMoDLB trial


title: RMDB_321

description: REMoDLB trial


title: ir29c-rna

description: rice-RNA-seq-gene-fpkm.xlsx

source_name: IR29 control


title: RMDB_318

description: REMoDLB trial


title: RMDB_316

description: REMoDLB trial


title: RMDB_320

description: REMoDLB trial


title: RMDB_330

description: REMoDLB trial


title: RMDB_314

description: REMoDLB trial


title: RMDB_317

description: REMoDLB trial


title: RMDB_312

description: REMoDLB trial


title: HERS-H1_rep1

city: Chengdu

first: Guoqing

last: Chen

address: No. 14, 3rd Sec., Ren Min Nan Road

department: West China Hospital of Stomatology

institute: Sichuan University

description: Gene expression of immortalized HERS cell line HERS-H1

hyb_protocol: Array hybridization was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, mRNAs that at least 3 out of 9 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

organism: Rattus norvegicus

source_name: HERS cell line HERS-H1

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Cells was cultured with epithelial cell medium (ScienCell, CA, USA) consisting of basal medium, 2% fetal bovine serum, 1% epithelial cell growth supplement, and 1% penicillin/streptomycin solution.

extract_protocol: Total RNA was isolated by the TRIzol (Invitrogen) method following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cell line

value: HERS cell line HERS-H1


title: HERS-H1_rep3


title: HERS-C2_rep3

description: Gene expression of immortalized HERS cell line HERS-C2

source_name: HERS cell line HERS-C2

value: HERS cell line HERS-C2


title: RMDB_315

description: REMoDLB trial


title: RMDB_311

description: REMoDLB trial


title: RMDB_313

description: REMoDLB trial


title: HERS-H1_rep2


title: HERS-C2_rep2


title: RMDB_338

description: REMoDLB trial


title: genomic DNA from FAP87

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description:
SAMPLE 20
low methylation familial adenomatous polyposis tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 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

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from clinical samples using QIAquick DNA mini kit according to standard instructions

value: tumor

tag: gender

value: Male

tag: sample type

value: clinical sample

tag: disease state

value: familial adenomatous polyposis

tag: methylation level

value: low


title: genomic DNA from FAP88

description:
SAMPLE 21
low methylation familial adenomatous polyposis tumor


title: genomic DNA from FAP86

description:
SAMPLE 19
low methylation familial adenomatous polyposis tumor


title: HERS-C2_rep1


title: RMDB_310

description: REMoDLB trial


title: RMDB_308

description: REMoDLB trial


title: genomic DNA from FAP92

description:
SAMPLE 23
low methylation familial adenomatous polyposis tumor

value: Female


title: RMDB_309

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: Primary HERS_rep3

description: Gene expression of primary HERS cells

source_name: Primary HERS cells

value: Primary HERS cells


title: Primary HERS_rep2

description: Gene expression of primary HERS cells


title: Primary HERS_rep1

description: Gene expression of primary HERS cells


title: genomic DNA from FAP41

description:
SAMPLE 12
low methylation familial adenomatous polyposis tumor


title: genomic DNA from FAP51

description:
SAMPLE 15
low methylation familial adenomatous polyposis tumor


title: genomic DNA from FAP45

description:
SAMPLE 14
low methylation familial adenomatous polyposis tumor


title: genomic DNA from FAP42

description:
SAMPLE 13
low methylation familial adenomatous polyposis tumor


title: RMDB_307

description: REMoDLB trial

value: GCB


title: genomic DNA from FAP40

description:
SAMPLE 11
low methylation familial adenomatous polyposis tumor


title: genomic DNA from FAP55

description:
SAMPLE 18
low methylation familial adenomatous polyposis tumor


title: genomic DNA from FAP54

description:
SAMPLE 17
low methylation familial adenomatous polyposis tumor


title: melanoma cell line M117, biological rep1

city: Nantes

first: Delphine

last: Fradin

address: 8 quai Moncousu

country: France

institute: CRCI2NA, Inserm UMR1307, CNRS UMR6075

description:
8_M117-cell1_
miRNA data from melanoma cell line

hyb_protocol: Labeled samples were hybridized to the arrays at 48°C for 20h and then washed and stained with a Streptavidin-PE solution  After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls.  RMA normalization is performed using R with Version 17 of Entrezgene CDF brain array.

label: biotin

source_name: melanoma cell line M117 in culture

label_protocol: 4 ng of total RNA was labeled using the FlashTag Biotin RNA Labeling Kit (Thermofisher).Briefly,  RNA was poly-A tailed and a proprietary biotin-labeled dendramer molecule was joined to the 3′ end using DNA ligase

growth_protocol: melanoma cell lines were cultured during 24h in exoFree media

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Exoquick TC reagent was used to purified exosomes from supernatant

value: melanoma cell line

tag: tumor stage

value: metastatic

value: melanoma cell line culture


title: genomic DNA from FAP37

description:
SAMPLE 8
low methylation familial adenomatous polyposis tumor


title: RMDB_306

description: REMoDLB trial

value: UNC


title: genomic DNA from FAP39

description:
SAMPLE 10
low methylation familial adenomatous polyposis tumor


title: 5Fu_Ncad_tdT_marrow_rep3

city: Kansas City

first: Shiyuan

middle: (Cynthia)

state: MO

department: Computational Biology

country: USA

institute: Stowers Institute for Medical Research

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
RNA-seq was aligned to genome mm10 from UCSC using tophat 2.0.13.
FPKM was generated using Cufflinks v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: FPKM in excel file

extract_protocol:
Bone marrow and bone cells were harvested from femur and tibia, enzymatically digested, antibody stained and FACS sorted.
RNA-seq libraries were prepared using the SMARTer ultra low input RNA kit for sequencing - v3 (Clontech Nextera)

value: femur and tibia

value: Bone marrow

tag: treatment

value: Fluorouracil (5FU)

tag: marker

value: Tomato postivie


title: genomic DNA from FAP52

description:
SAMPLE 16
low methylation familial adenomatous polyposis tumor

value: tumor


title: 5Fu_Ncad_tdT_marrow_rep1


title: RMDB_319

description: REMoDLB trial


title: 5Fu_Ncad_tdT_bone_rep3

value: bone cells


title: melanoma-derived exosome M113, biological rep3

description:
5_M113-exo_
miRNA data from melanoma-derived exosome

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

source_name: exosomes from melanoma cell line M113 in culture supernatant

value: melanoma-derived exosome


title: 5Fu_Ncad_tdT_marrow_rep2


title: melanoma-derived exosome M117, biological rep1

description:
7_M117-exo1_
miRNA data from melanoma-derived exosome

source_name: exosomes from melanoma cell line M117 in culture supernatant


title: genomic DNA from FAP28

description:
SAMPLE 5
intermediate methylation familial adenomatous polyposis tumor

value: clinical sample

value: familial adenomatous polyposis

value: intermediate


title: genomic DNA from FAP36

description:
SAMPLE 7
low methylation familial adenomatous polyposis tumor

value: Male

value: low


title: genomic DNA from FAP27

description:
SAMPLE 4
intermediate methylation familial adenomatous polyposis tumor

value: Female


title: genomic DNA from FAP23

description:
SAMPLE 3
intermediate methylation familial adenomatous polyposis tumor


title: 5Fu_Ncad_tdT_bone_rep2


title: genomic DNA from FAP29

description:
SAMPLE 6
intermediate methylation familial adenomatous polyposis tumor


title: melanoma-derived exosome M117, biological rep2

description:
9_M117-exo2_
miRNA data from melanoma-derived exosome

value: melanoma cell line


title: melanoma-derived exosome M113, biological rep1

description:
1_M113-exo1_
miRNA data from melanoma-derived exosome

value: metastatic


title: melanoma cell line M117, biological rep2

description:
10_M117-cell2
miRNA data from melanoma cell line

value: melanoma cell line culture


title: RMDB_302

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma

value: GCB


title: melanoma-derived exosome M113, biological rep2

description:
3_M113-exo2_
miRNA data from melanoma-derived exosome


title: genomic DNA from FAP38

description:
SAMPLE 9
low methylation familial adenomatous polyposis tumor


title: small RNA of Medicago sativa L. (Altet) Shoots

description: grown in greenhouse, Oklahoma State University, Stillwater, Oklahoma, USA

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Keep the sequenecs whose lengths are greater than or equal to 18 bp (the 3' adapter sequenecs of reads had been removed by the sequencing facility)
Sort and remove repetitive sequenecs
Calculate the counts of unique sequenecs
The unique sequenecs were aligned to a self-assembled transcriptome with SOAP2
Genome_build: JCVI.Medtr.v4
Supplementary_files_format_and_content: sequenecs and count values

organism: Medicago sativa

source_name: shoots

growth_protocol: Rooted stem cuttings were cultured on Murashige and Skoog media and grown in a Conviron growth room, Noble Research Institute, Ardmore, OK.

extract_protocol:
Total RNA was isolated from the whole plantlets, roots and shoots of three genotypes of Alfalfa using TRIzol (Invitrogen) according to the manufacturer’s instructions
Small RNA libraries were generated following the protocol as described by Illumina Truseq Small RNA Preparation kit (Illumina, San Diego, USA)

treatment_protocol: no treatment

value: shoots


title: RMDB_304

description: REMoDLB trial


title: small RNA of Medicago sativa L. (NECS) Shoots


title: RMDB_303

description: REMoDLB trial

value: ABC


title: RMDB_305

description: REMoDLB trial


title: 5Fu_Ncad_tdT_bone_rep1

value: femur and tibia

value: Fluorouracil (5FU)

value: Tomato postivie


title: RMDB_301

description: REMoDLB trial


title: genomic DNA from FAP21

description:
SAMPLE 2
intermediate methylation familial adenomatous polyposis tumor

value: tumor


title: small RNA of Medicago sativa L. (NF08ALF06) Roots

source_name: root

value: root


title: genomic DNA from FAP91

description:
SAMPLE 22
low methylation familial adenomatous polyposis tumor

value: clinical sample

value: familial adenomatous polyposis


title: genomic DNA from FAP15

description:
SAMPLE 1
low methylation familial adenomatous polyposis tumor


title: small RNA of Medicago sativa L. (NECS) plantlets

value: whole plantlets


title: IDH1 FBioCLIP-seq-2

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

data_processing:
Library strategy: CLIP-seq
Illumina Casava software used for basecalling.
CLIP-seq reads were mapped to the mouse reference genome (mm9) using the novoalign software.
Peaks were called using Piranha software.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph files

source_name: embryonic stem cells

growth_protocol: ESCs expressing 3 × FLAG and biotin tagged proteins were maintained in complete ESC culture medium: DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 15% heat-inactivated FCS (fetal calf serum), 2 mM GlutaMax (100 × Life Technology), 1% Nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 0.1 mM Non-Essential Amino Acids (NEAA), 0.1 mM β-mercaptoethanol and supplied with 1000 U/mL recombinant Leukemia Inhibitory Factor (LIF, Millipore). ESCs were cultured on plates which were pre-coated with 0.1% gelatin.

extract_protocol:
UV-crosslinked cells were lysed in ice-cold Lysis Buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% Triton X-100, 5% glycerol, supplemented with 1 mM DTT, 1 mM PMSF, 1:500 PI cocktail and 400 U/mL RNase Inhibitor), tandem immunoprecipitation, fragmented RNA transcripts were purified using TRIzol according to manufacturer's protocol.
The pre-adenylated 3’ linker was ligated to the end of fragmented RNAs with T4 RNA ligase (NEB) at 16 °C overnight. Then, after four times washes with PNK Buffer, the bead-bound RNA fragments were phosphorylated by T4 PNK (NEB) for 10 min at 37 °C and the reaction was stopped by washing three times with PNK-EGTA Buffer. The protein-bound RNA fragments were eluted by Proteinase K treatment. The purified RNAs were ligated with 5’ RNA adaptor. The RNA fragments were then reverse transcribed by Superscript III (Invitrogen) with RT primer and amplified for 20 cycles with 2 × NEB HF PCR mix (NEB). Library index sequence was introduced by PCR with index primers for 8 more cycles.

value: ESCs stably expressing FBioIDH1

tag: tags for clip

value: FLAG and Biotin


title: small RNA of Medicago sativa L. (NF08ALF06) plantlets


title: IDH1 FBioCLIP-seq-1


title: IDH1 FBioCLIP-seq-3


title: melanoma cell line M113, biological rep2

description:
4_M113-cell2_
miRNA data from melanoma cell line

source_name: melanoma cell line M113 in culture

value: melanoma cell line


title: small RNA of Medicago sativa L. (Altet) Roots


title: RMDB_299

description: REMoDLB trial

value: UNC


title: small RNA of Medicago sativa L. (NECS) Roots


title: 48hpf_sib_heart_3 [RNA-seq]

city: Beijing

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

institute: Peking University Third Hospital

data_processing:
Raw reads were aligned using STAR v2.3.0e_r291
Read counting was performed using htseq-count v0.6.0
Genome_build: GRCz10
Supplementary_files_format_and_content: counts

organism: Danio rerio

growth_protocol: Embryos were raised at 28.5°C and morphologically staged as described (Kimmel et al., 1995); all procedures were carried out as approved by the WCMC IACUC. Wild-type embryos were derived from crosses of the AB and TU lines. For heart RNA seq, 48hpf embryonic hearts are dissected manually unders microscope.

extract_protocol:
For 48hpf dissected heart, total RNA was isolated with the RNeasy Micro Kit. Then 1 ng total RNA was used to prepare amplified double-stranded cDNA using the Ovation RNA-Seq System V2 (Nugen). Amplified cDNA was purified using a QIAquick PCR purification kit (Qiagen) and 200 ng of amplified cDNA was fragmented in a final volume of 50 l using S220 Focused-ultrasonicator (Covaris) to obtain 150 bp DNA fragment size (peak incident power: 175W, duty factor: 10%, cycles per burst: 200, time: 280s). For 25hpf whole embryo RNA seq, total RNA was isolated with the RNeasy Mini Kit. Fragmented DNA samples and whole embryo RNA samples were used to prepare libraries with the TruSeq RNA Library Prep Kit v2 (Illumina)
Illumina TruSeq RNA Library Prep Kit v2

treatment_protocol: No treatments were applied prior to RNA extraction

tag: strain background

value: AB

value: zebrafish dissected heart

tag: genotype/variation

value: mixture of wild type  and tet2 and/or tet3 heterozygous mutant


title: 48hpf_sib_heart_1 [RNA-seq]


title: 48hpf_WT_heart_1 [RNA-seq]

value: Wild type sequence


title: RMDB_300

description: REMoDLB trial

tag: clinic diagnosis

value: Diffuse Large B-cell Lymphoma

tag: molecular subtype

value: GCB


title: 25hpf_tet2/3DM_3 [RNA-seq]

value: zebrafish embryo

value: Inactivating mutations in  tet2 and tet3


title: 25hpf_tet2/3DM_2 [RNA-seq]


title: 48hpf_tet2/3DM_heart_3 [RNA-seq]


title: 25hpf_tet2/3DM_1 [RNA-seq]


title: RMDB_297

description: REMoDLB trial

tag: molecular coo subtype


title: RMDB_298

description: REMoDLB trial


title: 48hpf_WT_heart_3 [RNA-seq]


title: 25hpf_sibling_3 [RNA-seq]


title: 25hpf_sibling_2 [RNA-seq]


title: 25hpf_sibling_1 [RNA-seq]


title: small RNA of Medicago sativa L. (Altet) plantlets


title: WT heart 5hmC 5hMe-BIC-seq_input 2

data_processing:
FASTQ sequence files were aligned using BWA.
Peaks identification was performed using nonduplicate reads with Model-based Analysis of ChIP-Seq data (MACS).
Genome_build: danRer7
Supplementary_files_format_and_content: peak files in .txt format

source_name: WT heart 5hmC 5hMe-BIC-seq_input

growth_protocol: Embryos were raised at 28.5°C and morphologically staged as described (Kimmel et al., 1995); all procedures were carried out as approved by the WCMC IACUC. Wild-type embryos were derived from crosses of the AB and TU lines. For heart CHIP seq, 48hpf embryonic hearts are dissected manually unders microscope.

extract_protocol:
Library prep. 250 ngs of genomic DNA were sonicated in a Covaris S220 instrument (Covaris, Woburn, MA) to obtain mean fragment sizes of 250bp (Peak Incident Power 175, Duty Factor 10%, Cycles per Burst 200, 150secs) and DNA was end-repaired and A-tailed using New England Biolabs enzymes (Ipswich, MA). 10ng of this DNA was used as Input control by adding TruSeq barcoded adapters.  The rest of the sample was used to selectively label 5-hydroxymethylcytosine with azido-modified-glucose (UDP-6-N3_Glucose, P19-11019, Proactive Molecular Research, Alachua, FL) in the presence of b-glucosyltransferase (New England Biolabs, Ipswich, MA) by a 16 hr incubation at 37oC. Biotin was added through Click chemistry with Dibenzocyclooctyne-PEG4-biotin (BP-22295, BroadPharm, San Diego, CA), and the biotinylated-gluco-modified DNA was isolated by affinity capture with streptavidin magnetic beads (Dynabeads ® MyOne™Streptavidin, ThermoFisher/LifeTechnologies, Waltham, MA). After ligation of TruSeq barcode adapters the 5hmC-enriched sample was PCR amplified using 12 cycles with Turbo Pfu Cx Polymerase (Agilent, Santa Clara, CA). To control the labeling and enrichment of 5hmC-containing DNA, a parallel reaction containing sheared Ecoli spiked in with the 5-hydroxymethylcytosine APC-spike control (cat # 55008) obtained from Active Motif (Carlsbad, CA) was performed.

Sequencing. Input and 5hmC-enriched libraries were clustered on a pair end read flow cell and sequenced for 50 cycles on an Illumina HiSeq 2500 to obtain about 30M reads per libraries.

Data processing. Primary processing of sequencing images was done using Illumina’s Real Time Analysis software (RTA) as suggested by the Illumina. CASAVA 1.8.2 software was used to perform image capture, base calling and demultiplexing. Reads passing Illumina’s purity filter were adapter trimmed and aligned to the genome using the BWA aligner.

treatment_protocol: No treatments were applied prior to chromatin isolation and fixation.

tag: age

value: 2d; 48hpf

tag: genotype

value: Wild type

value: dissected zebrafish heart


title: RMDB_296

description: REMoDLB trial

value: MHG


title: WT heart 5hmC 5hMe-BIC-seq_input 1

tag: tissue


title: WT heart 5hmC 5hMe-BIC-seq 2

source_name: WT heart 5hmC 5hMe-BIC-seq


title: 48hpf_tet2/3DM_heart_1 [RNA-seq]


title: WT heart 5hmC 5hMe-BIC-seq 1


title: RMDB_295

description: REMoDLB trial


title: RMDB_291

description: REMoDLB trial

value: ABC


title: RMDB_294

description: REMoDLB trial


title: plateA5.positionG12.single.cell

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

institute: Chinese Academy of Sciences

description:
all.single.cell.gene.counts.txt
A5-G12

data_processing:
Reads were mapped to the mouse GRCm38 genome assemblies by HISAT2 using default settings
Uniquely aligned reads were counted using the ‘htseq-count’ tool of HTSeq
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes counts values for each single cell

source_name: Sftpc-TD

extract_protocol:
Lungs were digest with Collagenase, Dispase and Elastase sollution, Single epithelial cell was sorted by BD AriaII. Cell was lysed by single cell RNA lysis buffer containing 0.45% (vol/vol) NP40, followed by reverse transcription using SuperScript II reverse transcriptase (Invitrogen) and whole transcription amplification using KAPA HiFi HotStart ReadyMix (2X; KAPA Biosystems). PCR product was purified using AMPure XP beads (Agencourt) and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher).
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

value: Lung

tag: cell type

value: epithelial cell

tag: cell sub-type


title: plateA5.positionH12.single.cell

description:
all.single.cell.gene.counts.txt
A5-H12


title: RMDB_290

description: REMoDLB trial


title: plateA5.positionB12.single.cell

description:
all.single.cell.gene.counts.txt
A5-B12


title: plateA5.positionE12.single.cell

description:
all.single.cell.gene.counts.txt
A5-E12


title: plateA5.positionD12.single.cell

description:
all.single.cell.gene.counts.txt
A5-D12


title: plateA5.positionA12.single.cell

description:
all.single.cell.gene.counts.txt
A5-A12


title: plateA5.positionC12.single.cell

description:
all.single.cell.gene.counts.txt
A5-C12


title: plateA5.positionH11.single.cell

description:
all.single.cell.gene.counts.txt
A5-H11


title: plateA5.positionG11.single.cell

description:
all.single.cell.gene.counts.txt
A5-G11


title: plateA5.positionE11.single.cell

description:
all.single.cell.gene.counts.txt
A5-E11

value: BASCs


title: plateA5.positionF11.single.cell

description:
all.single.cell.gene.counts.txt
A5-F11


title: plateA5.positionF12.single.cell

description:
all.single.cell.gene.counts.txt
A5-F12


title: RMDB_289

description: REMoDLB trial


title: RMDB_286

description: REMoDLB trial


title: RMDB_288

description: REMoDLB trial


title: RMDB_292

description: REMoDLB trial

value: UNC


title: RMDB_285

description: REMoDLB trial


title: RMDB_282

description: REMoDLB trial


title: RMDB_293

description: REMoDLB trial


title: RMDB_287

description: REMoDLB trial


title: RMDB_283

description: REMoDLB trial


title: RMDB_284

description: REMoDLB trial


title: plateA5.positionH10.single.cell

description:
all.single.cell.gene.counts.txt
A5-H10


title: plateA5.positionE10.single.cell

description:
all.single.cell.gene.counts.txt
A5-E10


title: plateA5.positionF10.single.cell

description:
all.single.cell.gene.counts.txt
A5-F10


title: RMDB_281

description: REMoDLB trial


title: plateA5.positionC11.single.cell

description:
all.single.cell.gene.counts.txt
A5-C11


title: plateA5.positionA11.single.cell

description:
all.single.cell.gene.counts.txt
A5-A11


title: plateA5.positionB11.single.cell

description:
all.single.cell.gene.counts.txt
A5-B11


title: plateA5.positionD11.single.cell

description:
all.single.cell.gene.counts.txt
A5-D11


title: plateA5.positionD10.single.cell

description:
all.single.cell.gene.counts.txt
A5-D10


title: melanoma cell line M113, biological rep3

description:
6_M113-cell_
miRNA data from melanoma cell line

tag: cell line

value: melanoma cell line

value: metastatic

tag: sample type

value: melanoma cell line culture


title: plateA5.positionA10.single.cell

description:
all.single.cell.gene.counts.txt
A5-A10


title: plateA5.positionH9.single.cell

description:
all.single.cell.gene.counts.txt
A5-H9


title: plateA5.positionG10.single.cell

description:
all.single.cell.gene.counts.txt
A5-G10


title: plateA5.positionG9.single.cell

description:
all.single.cell.gene.counts.txt
A5-G9


title: plateA5.positionF9.single.cell

description:
all.single.cell.gene.counts.txt
A5-F9


title: plateA5.positionE9.single.cell

description:
all.single.cell.gene.counts.txt
A5-E9


title: plateA5.positionD9.single.cell

description:
all.single.cell.gene.counts.txt
A5-D9


title: plateA5.positionB10.single.cell

description:
all.single.cell.gene.counts.txt
A5-B10


title: plateA5.positionC9.single.cell

description:
all.single.cell.gene.counts.txt
A5-C9


title: RMDB_279

description: REMoDLB trial


title: RMDB_280

description: REMoDLB trial


title: plateA5.positionA9.single.cell

description:
all.single.cell.gene.counts.txt
A5-A9


title: plateA5.positionB9.single.cell

description:
all.single.cell.gene.counts.txt
A5-B9


title: RMDB_278

description: REMoDLB trial


title: RMDB_273

description: REMoDLB trial


title: RMDB_277

description: REMoDLB trial


title: RMDB_275

description: REMoDLB trial


title: plateA5.positionE8.single.cell

description:
all.single.cell.gene.counts.txt
A5-E8


title: melanoma cell line M113, biological rep1

description:
2_M113-cell1_
miRNA data from melanoma cell line


title: plateA5.positionD8.single.cell

description:
all.single.cell.gene.counts.txt
A5-D8


title: RMDB_274

description: REMoDLB trial


title: plateA5.positionC10.single.cell

description:
all.single.cell.gene.counts.txt
A5-C10


title: RMDB_276

description: REMoDLB trial


title: plateA5.positionC8.single.cell

description:
all.single.cell.gene.counts.txt
A5-C8


title: plateA5.positionH8.single.cell

description:
all.single.cell.gene.counts.txt
A5-H8


title: plateA5.positionA8.single.cell

description:
all.single.cell.gene.counts.txt
A5-A8


title: plateA5.positionH7.single.cell

description:
all.single.cell.gene.counts.txt
A5-H7


title: plateA5.positionB8.single.cell

description:
all.single.cell.gene.counts.txt
A5-B8


title: RMDB_268

description: REMoDLB trial


title: RMDB_271

description: REMoDLB trial


title: RMDB_270

description: REMoDLB trial


title: RMDB_269

description: REMoDLB trial


title: plateA5.positionG7.single.cell

description:
all.single.cell.gene.counts.txt
A5-G7


title: plateA5.positionF7.single.cell

description:
all.single.cell.gene.counts.txt
A5-F7


title: plateA5.positionF8.single.cell

description:
all.single.cell.gene.counts.txt
A5-F8


title: plateA5.positionD7.single.cell

description:
all.single.cell.gene.counts.txt
A5-D7


title: WT-St3

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Tophat with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR package of R.
Genome_build: mm9

source_name: Day 4 epithelial cells

extract_protocol:
Epithelium and stroma were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: day

value: Day 4

value: Uterus

value: stromal


title: WT-St1


title: RMDB_272

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma

value: GCB


title: plateA5.positionE7.single.cell

description:
all.single.cell.gene.counts.txt
A5-E7


title: WT-St2


title: RMDB_267

description: REMoDLB trial


title: RMDB_266

description: REMoDLB trial


title: plateA5.positionC7.single.cell

description:
all.single.cell.gene.counts.txt
A5-C7


title: WT-LE3

value: epithelial


title: WT-LE2


title: plateA5.positionB7.single.cell

description:
all.single.cell.gene.counts.txt
A5-B7


title: plateA5.positionG8.single.cell

description:
all.single.cell.gene.counts.txt
A5-G8


title: plateA5.positionH6.single.cell

description:
all.single.cell.gene.counts.txt
A5-H6


title: RMDB_265

description: REMoDLB trial


title: RMDB_262

description: REMoDLB trial


title: plateA5.positionG6.single.cell

description:
all.single.cell.gene.counts.txt
A5-G6


title: plateA5.positionE6.single.cell

description:
all.single.cell.gene.counts.txt
A5-E6


title: RMDB_263

description: REMoDLB trial


title: plateA5.positionD6.single.cell

description:
all.single.cell.gene.counts.txt
A5-D6


title: plateA5.positionF6.single.cell

description:
all.single.cell.gene.counts.txt
A5-F6


title: Prdm9-mut 16dpp rep5

city: Bar Harbor

first: Gregory

last: Carter

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Two technical replicates for each paired-end were run in different lanes and then merged.
Sequenced reads were filtered to keep reads for which 70% of the base pair quality score was > 20, and the 3’ end was trimmed if the base pair quality score was < 20
All RNA-seq samples were aligned with Bowtie 1.0.0 and expression levels were estimated by RSEM 1.2.8
A Bowtie index was prepared for alignment to a combined (mm10) transcriptome of Ensembl Genome Reference Consortium, build 38, release 75, NONCODE v4 lncRNA, and piRNA precursor transcripts. The 214 piRNA precursors were obtained from Dr. Christian Roy. Both the NONCODE lncRNA and piRNA precursors were converted to mm10 coordinates using liftOver.
We used log2(TPM+1) as the expression level, where TPM is transcripts per million, defined by RSEM
Prdm9-het 12dpp rep4 and Prdm9-mut 12dpp rep5 were removed, due to mismatch between annotated genotype and RNAseq based genotype
Data were merged with previously published data (GSE72833) and adjusted for systematic variation using ComBat in R
Only transcripts having ComBat-adjusted log2(TPM+1) >= 1 for at least one of the samples was used in this study.
Genome_build: (mm10) Ensembl Genome Reference Consortium, build 38, release 75
Supplementary_files_format_and_content: Gene_Exp_w_Analysis.xls : Gene expression in log-transformed transcripts per million (log2(TPM+1)) for transcripts that reach > 1 log2(TPM+1). Results of differential expression analysis, stage specificity, and gene information included.
Supplementary_files_format_and_content: all_samples_gene_expression_RSEM_TPM_GRCm38-75_lnc-piRNA.txt : Gene expression in Transcripts per Million (TPM) by RSEM of genes for samples collected for this project.

molecule: polyA RNA

source_name: Spermatocytes

extract_protocol:
The procedure was as previously described with some modifications (Cobb 1997, La Salle 2009). Briefly, seminiferous tubules were transferred into 20 ml DMEM (Gibco, Life Technologies, Carlsbad, CA, USA) containing 0.5 mg of Liberase TL Research Grade (05401020001, Roche, Basel, Switzerland) and incubated for 20 min at 32 °C. To remove interstitial cells, tubules were washed three times with the same media.
Isolated germ cell samples were resuspended in QIAzol Lysis Reagent according to the manufacturer's instructions, and total RNAs were purified from homogenized cells using Qiagen RNeasy Mini Kit (74104).

value: Germ cells enriched from testes

tag: Sex

value: Male

value: 16 days postpartum


title: plateA5.positionC6.single.cell

description:
all.single.cell.gene.counts.txt
A5-C6


title: plateA5.positionB6.single.cell

description:
all.single.cell.gene.counts.txt
A5-B6


title: Prdm9-mut 16dpp rep4


title: plateA5.positionH5.single.cell

description:
all.single.cell.gene.counts.txt
A5-H5


title: Prdm9-mut 16dpp rep3


title: plateA5.positionA6.single.cell

description:
all.single.cell.gene.counts.txt
A5-A6


title: plateA5.positionA7.single.cell

description:
all.single.cell.gene.counts.txt
A5-A7


title: Prdm9-mut 16dpp rep2


title: Prdm9-mut 16dpp rep1


title: RMDB_264

description: REMoDLB trial

value: ABC


title: plateA5.positionF5.single.cell

description:
all.single.cell.gene.counts.txt
A5-F5

value: Lung


title: plateA5.positionE5.single.cell

description:
all.single.cell.gene.counts.txt
A5-E5

value: epithelial cell


title: Prdm9-het 16dpp rep3


title: plateA5.positionD5.single.cell

description:
all.single.cell.gene.counts.txt
A5-D5


title: plateA5.positionC5.single.cell

description:
all.single.cell.gene.counts.txt
A5-C5


title: plateA5.positionG5.single.cell

description:
all.single.cell.gene.counts.txt
A5-G5


title: RMDB_261

description: REMoDLB trial


title: RMDB_256

description: REMoDLB trial


title: RMDB_260

description: REMoDLB trial


title: RMDB_258

description: REMoDLB trial


title: plateA5.positionB5.single.cell

description:
all.single.cell.gene.counts.txt
A5-B5


title: RMDB_257

description: REMoDLB trial


title: plateA5.positionA5.single.cell

description:
all.single.cell.gene.counts.txt
A5-A5


title: WT-LE1


title: plateA5.positionG4.single.cell

description:
all.single.cell.gene.counts.txt
A5-G4


title: Prdm9-het 16dpp rep2


title: plateA5.positionF4.single.cell

description:
all.single.cell.gene.counts.txt
A5-F4


title: plateA5.positionE4.single.cell

description:
all.single.cell.gene.counts.txt
A5-E4


title: Prdm9-het 16dpp rep1


title: Wild-type 16dpp rep1


title: Wild-type 16dpp rep2


title: plateA5.positionH4.single.cell

description:
all.single.cell.gene.counts.txt
A5-H4


title: Prdm9-mut 12dpp rep3

value: 12 days postpartum


title: Prdm9-mut 12dpp rep4


title: Prdm9-mut 12dpp rep2


title: Prdm9-mut 12dpp rep5


title: Prdm9-mut 12dpp rep1


title: plateA5.positionG2.single.cell

description:
all.single.cell.gene.counts.txt
A5-G2


title: plateA5.positionA4.single.cell

description:
all.single.cell.gene.counts.txt
A5-A4


title: plateA5.positionH2.single.cell

description:
all.single.cell.gene.counts.txt
A5-H2


title: plateA5.positionH3.single.cell

description:
all.single.cell.gene.counts.txt
A5-H3


title: plateA5.positionD4.single.cell

description:
all.single.cell.gene.counts.txt
A5-D4


title: plateA5.positionE3.single.cell

description:
all.single.cell.gene.counts.txt
A5-E3


title: plateA5.positionB3.single.cell

description:
all.single.cell.gene.counts.txt
A5-B3


title: plateA5.positionB4.single.cell

description:
all.single.cell.gene.counts.txt
A5-B4


title: plateA5.positionC4.single.cell

description:
all.single.cell.gene.counts.txt
A5-C4


title: plateA5.positionG3.single.cell

description:
all.single.cell.gene.counts.txt
A5-G3


title: plateA5.positionD3.single.cell

description:
all.single.cell.gene.counts.txt
A5-D3


title: plateA5.positionC3.single.cell

description:
all.single.cell.gene.counts.txt
A5-C3


title: plateA5.positionA3.single.cell

description:
all.single.cell.gene.counts.txt
A5-A3


title: plateA5.positionF3.single.cell

description:
all.single.cell.gene.counts.txt
A5-F3


title: RMDB_254

description: REMoDLB trial

value: UNC


title: RMDB_248

description: REMoDLB trial


title: plateA5.positionF2.single.cell

description:
all.single.cell.gene.counts.txt
A5-F2


title: plateA5.positionE2.single.cell

description:
all.single.cell.gene.counts.txt
A5-E2


title: RMDB_251

description: REMoDLB trial


title: Prdm9-het 12dpp rep4


title: RMDB_259

description: REMoDLB trial


title: plateA5.positionD2.single.cell

description:
all.single.cell.gene.counts.txt
A5-D2


title: RMDB_255

description: REMoDLB trial


title: RMDB_252

description: REMoDLB trial


title: RMDB_249

description: REMoDLB trial


title: RMDB_246

description: REMoDLB trial


title: Prdm9-het 12dpp rep2


title: plateA5.positionB2.single.cell

description:
all.single.cell.gene.counts.txt
A5-B2


title: plateA5.positionC2.single.cell

description:
all.single.cell.gene.counts.txt
A5-C2


title: plateA5.positionG1.single.cell

description:
all.single.cell.gene.counts.txt
A5-G1

value: BASCs


title: plateA5.positionH1.single.cell

description:
all.single.cell.gene.counts.txt
A5-H1


title: plateA5.positionA2.single.cell

description:
all.single.cell.gene.counts.txt
A5-A2


title: RMDB_245

description: REMoDLB trial


title: Wild-type 12dpp rep1


title: RMDB_250

description: REMoDLB trial


title: RMDB_253

description: REMoDLB trial


title: Prdm9-het 12dpp rep3


title: plateA5.positionF1.single.cell

description:
all.single.cell.gene.counts.txt
A5-F1


title: RMDB_247

description: REMoDLB trial


title: Prdm9-mut 8dpp rep5

value: 8 days postpartum


title: Prdm9-het 12dpp rep1


title: plateA5.positionE1.single.cell

description:
all.single.cell.gene.counts.txt
A5-E1


title: plateA5.positionD1.single.cell

description:
all.single.cell.gene.counts.txt
A5-D1


title: plateA5.positionC1.single.cell

description:
all.single.cell.gene.counts.txt
A5-C1


title: Prdm9-mut 8dpp rep4


title: plateA5.positionB1.single.cell

description:
all.single.cell.gene.counts.txt
A5-B1


title: plateA5.positionA1.single.cell

description:
all.single.cell.gene.counts.txt
A5-A1


title: RMDB_244

description: REMoDLB trial


title: plateA4.positionH12.single.cell

description:
all.single.cell.gene.counts.txt
A4-H12


title: RMDB_242

description: REMoDLB trial

value: MHG


title: Prdm9-mut 8dpp rep3


title: RMDB_243

description: REMoDLB trial


title: Prdm9-mut 8dpp rep2


title: plateA4.positionF12.single.cell

description:
all.single.cell.gene.counts.txt
A4-F12


title: plateA4.positionE12.single.cell

description:
all.single.cell.gene.counts.txt
A4-E12


title: Prdm9-mut 8dpp rep1


title: Prdm9-het 8dpp rep1


title: Prdm9-het 8dpp rep2


title: plateA4.positionH11.single.cell

description:
all.single.cell.gene.counts.txt
A4-H11


title: plateA4.positionG11.single.cell

description:
all.single.cell.gene.counts.txt
A4-G11


title: plateA4.positionB12.single.cell

description:
all.single.cell.gene.counts.txt
A4-B12


title: plateA4.positionA12.single.cell

description:
all.single.cell.gene.counts.txt
A4-A12


title: Wild-type 8dpp rep3


title: plateA4.positionC12.single.cell

description:
all.single.cell.gene.counts.txt
A4-C12


title: plateA4.positionE11.single.cell

description:
all.single.cell.gene.counts.txt
A4-E11


title: plateA4.positionG12.single.cell

description:
all.single.cell.gene.counts.txt
A4-G12


title: plateA4.positionD11.single.cell

description:
all.single.cell.gene.counts.txt
A4-D11


title: Wild-type 8dpp rep2


title: plateA4.positionD12.single.cell

description:
all.single.cell.gene.counts.txt
A4-D12


title: plateA4.positionC11.single.cell

description:
all.single.cell.gene.counts.txt
A4-C11


title: RMDB_239

description: REMoDLB trial


title: Wild-type 8dpp rep1


title: RMDB_240

description: REMoDLB trial


title: RMDB_237

description: REMoDLB trial


title: plateA4.positionA11.single.cell

description:
all.single.cell.gene.counts.txt
A4-A11


title: RMDB_241

description: REMoDLB trial


title: RMDB_238

description: REMoDLB trial


title: plateA4.positionH10.single.cell

description:
all.single.cell.gene.counts.txt
A4-H10


title: plateA4.positionF11.single.cell

description:
all.single.cell.gene.counts.txt
A4-F11


title: plateA4.positionG10.single.cell

description:
all.single.cell.gene.counts.txt
A4-G10


title: RMDB_235

description: REMoDLB trial


title: RMDB_236

description: REMoDLB trial


title: plateA4.positionD10.single.cell

description:
all.single.cell.gene.counts.txt
A4-D10


title: Pecam_GFP rep3

source_name: Pecam_GFP rep3

tag: marker


title: Pecam_GFP rep4

source_name: Pecam_GFP rep4


title: RMDB_233

description: REMoDLB trial


title: Pecam_GFP rep2

source_name: Pecam_GFP rep2


title: RMDB_234

description: REMoDLB trial


title: plateA4.positionC10.single.cell

description:
all.single.cell.gene.counts.txt
A4-C10


title: RMDB_232

description: REMoDLB trial


title: plateA4.positionE10.single.cell

description:
all.single.cell.gene.counts.txt
A4-E10


title: Pecam_GFP rep1

source_name: Pecam_GFP rep1


title: Ng2 rFP rep4

source_name: Ng2 rFP rep4


title: plateA4.positionA10.single.cell

description:
all.single.cell.gene.counts.txt
A4-A10


title: plateA4.positionH9.single.cell

description:
all.single.cell.gene.counts.txt
A4-H9


title: plateA4.positionB11.single.cell

description:
all.single.cell.gene.counts.txt
A4-B11


title: plateA4.positionB10.single.cell

description:
all.single.cell.gene.counts.txt
A4-B10


title: plateA4.positionG9.single.cell

description:
all.single.cell.gene.counts.txt
A4-G9


title: Ng2 rFP rep3

source_name: Ng2 rFP rep3


title: plateA4.positionD9.single.cell

description:
all.single.cell.gene.counts.txt
A4-D9


title: plateA4.positionE9.single.cell

description:
all.single.cell.gene.counts.txt
A4-E9


title: Ng2 rFP rep2

source_name: Ng2 rFP rep2


title: plateA4.positionC9.single.cell

description:
all.single.cell.gene.counts.txt
A4-C9


title: plateA4.positionA9.single.cell

description:
all.single.cell.gene.counts.txt
A4-A9


title: plateA4.positionB9.single.cell

description:
all.single.cell.gene.counts.txt
A4-B9


title: Ng2 rFP rep1

source_name: Ng2 rFP rep1


title: RMDB_230

description: REMoDLB trial


title: Nestin_GFP rep4

source_name: Nestin_GFP rep4


title: plateA4.positionH8.single.cell

description:
all.single.cell.gene.counts.txt
A4-H8


title: plateA4.positionG8.single.cell

description:
all.single.cell.gene.counts.txt
A4-G8


title: Nestin_GFP rep3

source_name: Nestin_GFP rep3


title: Nestin_GFP rep2

source_name: Nestin_GFP rep2


title: plateA4.positionF8.single.cell

description:
all.single.cell.gene.counts.txt
A4-F8


title: plateA4.positionE8.single.cell

description:
all.single.cell.gene.counts.txt
A4-E8


title: plateA4.positionF9.single.cell

description:
all.single.cell.gene.counts.txt
A4-F9


title: plateA4.positionD8.single.cell

description:
all.single.cell.gene.counts.txt
A4-D8


title: plateA4.positionC8.single.cell

description:
all.single.cell.gene.counts.txt
A4-C8


title: Nestin_GFP rep1

source_name: Nestin_GFP rep1


title: RMDB_231

description: REMoDLB trial


title: RMDB_228

description: REMoDLB trial


title: plateA4.positionB8.single.cell

description:
all.single.cell.gene.counts.txt
A4-B8


title: RMDB_227

description: REMoDLB trial


title: RMDB_225

description: REMoDLB trial


title: plateA4.positionA8.single.cell

description:
all.single.cell.gene.counts.txt
A4-A8


title: plateA4.positionH7.single.cell

description:
all.single.cell.gene.counts.txt
A4-H7


title: Ncad_marrow rep4

source_name: Ncad_marrow rep4


title: RMDB_229

description: REMoDLB trial


title: plateA4.positionG7.single.cell

description:
all.single.cell.gene.counts.txt
A4-G7


title: Ncad_marrow rep3

source_name: Ncad_marrow rep3


title: RMDB_226

description: REMoDLB trial


title: plateA4.positionF7.single.cell

description:
all.single.cell.gene.counts.txt
A4-F7

source_name: Sftpc-TD


title: RMDB_223

description: REMoDLB trial


title: Ncad_marrow rep2

source_name: Ncad_marrow rep2


title: plateA4.positionC7.single.cell

description:
all.single.cell.gene.counts.txt
A4-C7


title: Ncad_marrow rep1

source_name: Ncad_marrow rep1


title: RMDB_222

description: REMoDLB trial


title: RMDB_220

description: REMoDLB trial


title: plateA4.positionB7.single.cell

description:
all.single.cell.gene.counts.txt
A4-B7


title: RMDB_224

description: REMoDLB trial


title: RMDB_221

description: REMoDLB trial


title: Ncad_bone rep4

source_name: Ncad_bone rep4

value: Bone CD45Ter119CD31-Tomato+


title: plateA4.positionA7.single.cell

description:
all.single.cell.gene.counts.txt
A4-A7


title: RMDB_219

description: REMoDLB trial


title: plateA4.positionH6.single.cell

description:
all.single.cell.gene.counts.txt
A4-H6


title: RMDB_218

description: REMoDLB trial


title: plateA4.positionE7.single.cell

description:
all.single.cell.gene.counts.txt
A4-E7


title: RMDB_217

description: REMoDLB trial


title: Ncad_bone rep3

source_name: Ncad_bone rep3


title: RMDB_216

description: REMoDLB trial


title: plateA4.positionF6.single.cell

description:
all.single.cell.gene.counts.txt
A4-F6


title: plateA4.positionD7.single.cell

description:
all.single.cell.gene.counts.txt
A4-D7


title: plateA4.positionD6.single.cell

description:
all.single.cell.gene.counts.txt
A4-D6


title: Ncad_bone rep2

source_name: Ncad_bone rep2


title: plateA4.positionE6.single.cell

description:
all.single.cell.gene.counts.txt
A4-E6


title: plateA4.positionB6.single.cell

description:
all.single.cell.gene.counts.txt
A4-B6


title: plateA4.positionA6.single.cell

description:
all.single.cell.gene.counts.txt
A4-A6


title: Ncad_bone rep1

source_name: Ncad_bone rep1


title: RMDB_213

description: REMoDLB trial


title: MK rep4

source_name: MK rep4


title: plateA4.positionH5.single.cell

description:
all.single.cell.gene.counts.txt
A4-H5


title: plateA4.positionG6.single.cell

description:
all.single.cell.gene.counts.txt
A4-G6


title: plateA4.positionG5.single.cell

description:
all.single.cell.gene.counts.txt
A4-G5


title: MK rep3

source_name: MK rep3


title: plateA4.positionF10.single.cell

description:
all.single.cell.gene.counts.txt
A4-F10


title: RMDB_214

description: REMoDLB trial


title: plateA4.positionC6.single.cell

description:
all.single.cell.gene.counts.txt
A4-C6


title: plateA4.positionF5.single.cell

description:
all.single.cell.gene.counts.txt
A4-F5


title: plateA4.positionE5.single.cell

description:
all.single.cell.gene.counts.txt
A4-E5


title: MK rep2

source_name: MK rep2


title: plateA4.positionA5.single.cell

description:
all.single.cell.gene.counts.txt
A4-A5


title: plateA4.positionB5.single.cell

description:
all.single.cell.gene.counts.txt
A4-B5


title: plateA4.positionD5.single.cell

description:
all.single.cell.gene.counts.txt
A4-D5


title: Mac rep4

source_name: Mac rep4


title: RMDB_211

description: REMoDLB trial


title: plateA4.positionH4.single.cell

description:
all.single.cell.gene.counts.txt
A4-H4

value: Club cell


title: MK rep1

source_name: MK rep1


title: plateA4.positionC5.single.cell

description:
all.single.cell.gene.counts.txt
A4-C5


title: plateA4.positionG4.single.cell

description:
all.single.cell.gene.counts.txt
A4-G4


title: Mac rep3

source_name: Mac rep3


title: plateA4.positionF4.single.cell

description:
all.single.cell.gene.counts.txt
A4-F4


title: plateA4.positionE4.single.cell

description:
all.single.cell.gene.counts.txt
A4-E4


title: plateA4.positionD4.single.cell

description:
all.single.cell.gene.counts.txt
A4-D4


title: plateA4.positionC4.single.cell

description:
all.single.cell.gene.counts.txt
A4-C4


title: RMDB_215

description: REMoDLB trial


title: plateA4.positionB4.single.cell

description:
all.single.cell.gene.counts.txt
A4-B4

value: Ciliated cell


title: RMDB_212

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: plateA4.positionA4.single.cell

description:
all.single.cell.gene.counts.txt
A4-A4


title: Mac rep1

source_name: Mac rep1


title: Lepr rep6

source_name: Lepr rep6


title: plateA4.positionH3.single.cell

description:
all.single.cell.gene.counts.txt
A4-H3


title: RMDB_210

description: REMoDLB trial


title: plateA4.positionF3.single.cell

description:
all.single.cell.gene.counts.txt
A4-F3


title: plateA4.positionG3.single.cell

description:
all.single.cell.gene.counts.txt
A4-G3


title: RMDB_206

description: REMoDLB trial


title: Lepr rep4

source_name: Lepr rep4


title: Mac rep2

source_name: Mac rep2


title: plateA4.positionD3.single.cell

description:
all.single.cell.gene.counts.txt
A4-D3


title: Lepr rep3

source_name: Lepr rep3


title: plateA4.positionC3.single.cell

description:
all.single.cell.gene.counts.txt
A4-C3


title: RMDB_209

description: REMoDLB trial

value: GCB


title: RMDB_204

description: REMoDLB trial


title: RMDB_208

description: REMoDLB trial


title: RMDB_205

description: REMoDLB trial


title: RMDB_207

description: REMoDLB trial


title: plateA4.positionB3.single.cell

description:
all.single.cell.gene.counts.txt
A4-B3


title: RMDB_201

description: REMoDLB trial


title: plateA4.positionA3.single.cell

description:
all.single.cell.gene.counts.txt
A4-A3


title: RMDB_202

description: REMoDLB trial


title: RMDB_203

description: REMoDLB trial


title: plateA4.positionH2.single.cell

description:
all.single.cell.gene.counts.txt
A4-H2


title: Lepr rep2

source_name: Lepr rep2


title: plateA4.positionG2.single.cell

description:
all.single.cell.gene.counts.txt
A4-G2


title: Lepr rep1

source_name: Lepr rep1


title: plateA4.positionE3.single.cell

description:
all.single.cell.gene.counts.txt
A4-E3


title: plateA4.positionF2.single.cell

description:
all.single.cell.gene.counts.txt
A4-F2


title: RMDB_199

description: REMoDLB trial


title: Cxcl12 rFP rep4

source_name: Cxcl12 rFP rep4


title: RMDB_200

description: REMoDLB trial


title: plateA4.positionD2.single.cell

description:
all.single.cell.gene.counts.txt
A4-D2


title: Lepr rep5

source_name: Lepr rep5


title: plateA4.positionE2.single.cell

description:
all.single.cell.gene.counts.txt
A4-E2


title: plateA4.positionA2.single.cell

description:
all.single.cell.gene.counts.txt
A4-A2


title: Cxcl12 rFP rep2

source_name: Cxcl12 rFP rep2


title: plateA4.positionH1.single.cell

description:
all.single.cell.gene.counts.txt
A4-H1


title: Cxcl12 rFP rep3

source_name: Cxcl12 rFP rep3


title: plateA4.positionG1.single.cell

description:
all.single.cell.gene.counts.txt
A4-G1


title: Cxcl12 rFP rep1

source_name: Cxcl12 rFP rep1


title: plateA4.positionF1.single.cell

description:
all.single.cell.gene.counts.txt
A4-F1


title: plateA4.positionE1.single.cell

description:
all.single.cell.gene.counts.txt
A4-E1


title: Col23._GFP rep4

source_name: Col23._GFP rep4


title: RMDB_197

description: REMoDLB trial


title: RMDB_196

description: REMoDLB trial


title: Col23._GFP rep3

source_name: Col23._GFP rep3


title: RMDB_198

description: REMoDLB trial


title: plateA4.positionC2.single.cell

description:
all.single.cell.gene.counts.txt
A4-C2


title: plateA4.positionB2.single.cell

description:
all.single.cell.gene.counts.txt
A4-B2


title: RMDB_195

description: REMoDLB trial


title: plateA4.positionA1.single.cell

description:
all.single.cell.gene.counts.txt
A4-A1


title: plateA4.positionC1.single.cell

description:
all.single.cell.gene.counts.txt
A4-C1


title: plateA3.positionH12.single.cell

description:
all.single.cell.gene.counts.txt
A3-H12


title: Col23._GFP rep2

source_name: Col23._GFP rep2


title: RMDB_193

description: REMoDLB trial


title: RMDB_194

description: REMoDLB trial


title: plateA4.positionB1.single.cell

description:
all.single.cell.gene.counts.txt
A4-B1


title: plateA3.positionG12.single.cell

description:
all.single.cell.gene.counts.txt
A3-G12


title: RMDB_192

description: REMoDLB trial


title: Col23._GFP rep1

source_name: Col23._GFP rep1


title: plateA3.positionF12.single.cell

description:
all.single.cell.gene.counts.txt
A3-F12


title: plateA4.positionD1.single.cell

description:
all.single.cell.gene.counts.txt
A4-D1


title: ST rep3

source_name: ST rep3


title: plateA3.positionD12.single.cell

description:
all.single.cell.gene.counts.txt
A3-D12


title: plateA3.positionB12.single.cell

description:
all.single.cell.gene.counts.txt
A3-B12


title: ST rep2

source_name: ST rep2


title: plateA3.positionC12.single.cell

description:
all.single.cell.gene.counts.txt
A3-C12


title: ST rep1

source_name: ST rep1


title: plateA3.positionH11.single.cell

description:
all.single.cell.gene.counts.txt
A3-H11


title: RMDB_191

description: REMoDLB trial


title: plateA3.positionE12.single.cell

description:
all.single.cell.gene.counts.txt
A3-E12


title: RMDB_189

description: REMoDLB trial


title: plateA3.positionA12.single.cell

description:
all.single.cell.gene.counts.txt
A3-A12


title: RMDB_190

description: REMoDLB trial


title: plateA3.positionF11.single.cell

description:
all.single.cell.gene.counts.txt
A3-F11


title: plateA3.positionE11.single.cell

description:
all.single.cell.gene.counts.txt
A3-E11


title: plateA3.positionG11.single.cell

description:
all.single.cell.gene.counts.txt
A3-G11


title: plateA3.positionD11.single.cell

description:
all.single.cell.gene.counts.txt
A3-D11


title: RMDB_187

description: REMoDLB trial


title: plateA3.positionC11.single.cell

description:
all.single.cell.gene.counts.txt
A3-C11


title: plateA3.positionB11.single.cell

description:
all.single.cell.gene.counts.txt
A3-B11


title: Reserve rep2

source_name: Reserve rep2


title: plateA3.positionA11.single.cell

description:
all.single.cell.gene.counts.txt
A3-A11


title: Reserve rep4

source_name: Reserve rep4


title: Reserve rep3

source_name: Reserve rep3


title: plateA3.positionH10.single.cell

description:
all.single.cell.gene.counts.txt
A3-H10


title: RMDB_188

description: REMoDLB trial


title: Reserve rep1

source_name: Reserve rep1


title: RMDB_186

description: REMoDLB trial


title: plateA3.positionE10.single.cell

description:
all.single.cell.gene.counts.txt
A3-E10


title: plateA3.positionF10.single.cell

description:
all.single.cell.gene.counts.txt
A3-F10


title: plateA3.positionG10.single.cell

description:
all.single.cell.gene.counts.txt
A3-G10


title: Primed rep2

source_name: Primed rep2


title: plateA3.positionD10.single.cell

description:
all.single.cell.gene.counts.txt
A3-D10


title: Primed rep1

source_name: Primed rep1


title: plateA3.positionC10.single.cell

description:
all.single.cell.gene.counts.txt
A3-C10


title: RMDB_182

description: REMoDLB trial


title: RMDB_184

description: REMoDLB trial


title: RMDB_183

description: REMoDLB trial


title: RMDB_185

description: REMoDLB trial


title: RMDB_181

description: REMoDLB trial


title: plateA3.positionB10.single.cell

description:
all.single.cell.gene.counts.txt
A3-B10


title: RMDB_180

description: REMoDLB trial


title: plateA3.positionA10.single.cell

description:
all.single.cell.gene.counts.txt
A3-A10


title: Primed rep3

source_name: Primed rep3


title: plateA3.positionH9.single.cell

description:
all.single.cell.gene.counts.txt
A3-H9


title: plateA3.positionF9.single.cell

description:
all.single.cell.gene.counts.txt
A3-F9


title: plateA3.positionG9.single.cell

description:
all.single.cell.gene.counts.txt
A3-G9


title: MPP rep2

source_name: MPP rep2


title: plateA3.positionC9.single.cell

description:
all.single.cell.gene.counts.txt
A3-C9


title: plateA3.positionH8.single.cell

description:
all.single.cell.gene.counts.txt
A3-H8


title: MPP rep3

source_name: MPP rep3


title: plateA3.positionD9.single.cell

description:
all.single.cell.gene.counts.txt
A3-D9


title: plateA3.positionE9.single.cell

description:
all.single.cell.gene.counts.txt
A3-E9


title: MPP rep4

source_name: MPP rep4


title: plateA3.positionG8.single.cell

description:
all.single.cell.gene.counts.txt
A3-G8


title: 5FuReserve rep2

source_name: 5FuReserve rep2

value: D3 post 5Fu treatment LSKFlk2-CD34-CD49b-


title: plateA3.positionA9.single.cell

description:
all.single.cell.gene.counts.txt
A3-A9


title: 5FuReserve rep3

source_name: 5FuReserve rep3

value: D3 post 5Fu treatment LSKFlk2-CD34-CD49-


title: plateA3.positionF8.single.cell

description:
all.single.cell.gene.counts.txt
A3-F8


title: plateA3.positionE8.single.cell

description:
all.single.cell.gene.counts.txt
A3-E8


title: 5FuReserve rep1

source_name: 5FuReserve rep1


title: MPP rep1

source_name: MPP rep1


title: plateA3.positionD8.single.cell

description:
all.single.cell.gene.counts.txt
A3-D8


title: plateA3.positionB9.single.cell

description:
all.single.cell.gene.counts.txt
A3-B9


title: plateA3.positionC8.single.cell

description:
all.single.cell.gene.counts.txt
A3-C8


title: RMDB_178

description: REMoDLB trial


title: plateA3.positionB8.single.cell

description:
all.single.cell.gene.counts.txt
A3-B8


title: RMDB_175

description: REMoDLB trial


title: RMDB_177

description: REMoDLB trial


title: plateA3.positionA8.single.cell

description:
all.single.cell.gene.counts.txt
A3-A8


title: RMDB_174

description: REMoDLB trial


title: RMDB_176

description: REMoDLB trial


title: RMDB_179

description: REMoDLB trial


title: plateA3.positionG7.single.cell

description:
all.single.cell.gene.counts.txt
A3-G7


title: RMDB_172

description: REMoDLB trial


title: RMDB_173

description: REMoDLB trial


title: plateA3.positionH7.single.cell

description:
all.single.cell.gene.counts.txt
A3-H7


title: plateA3.positionF7.single.cell

description:
all.single.cell.gene.counts.txt
A3-F7


title: plateA3.positionD7.single.cell

description:
all.single.cell.gene.counts.txt
A3-D7


title: plateA3.positionC7.single.cell

description:
all.single.cell.gene.counts.txt
A3-C7


title: plateA3.positionB7.single.cell

description:
all.single.cell.gene.counts.txt
A3-B7


title: plateA3.positionA7.single.cell

description:
all.single.cell.gene.counts.txt
A3-A7


title: plateA3.positionH6.single.cell

description:
all.single.cell.gene.counts.txt
A3-H6


title: plateA3.positionF6.single.cell

description:
all.single.cell.gene.counts.txt
A3-F6


title: plateA3.positionE7.single.cell

description:
all.single.cell.gene.counts.txt
A3-E7


title: plateA3.positionG6.single.cell

description:
all.single.cell.gene.counts.txt
A3-G6


title: plateA3.positionE6.single.cell

description:
all.single.cell.gene.counts.txt
A3-E6


title: RMDB_170

description: REMoDLB trial


title: Ectromelia virus at 16H, biological rep1

city: Singapore

first: Richard

middle: J

last: Sugrue

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description: Mouse RAW_ectromelia virus_16H-1

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45˚C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing:
The data were analyzed with GeneChip Operating Software 5.0 (GCOS 5.0) using Affymetrix default analysis settings. Further analysis was done in GeneSpring 11.0. The normalization was done using internal and external control genes as assigned by Affymetrix. The target intensity of each array on a given time point was first filtered by the flagging of Present (P) in 3 replicates at one time-point, which then further calculated in fold change up- or downregulation with respect to the signal intensity in MOCK infected cells, after analyzed by ANOVA with p value ≤ 0.05.
Algorithm: ExpressionStat 5.0

source_name: Ectromelia virus infected mouse RAW 16 hpi

label_protocol: Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: The cells were grown in DMEM L929 (30%) cell condition media (Gibco) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2

extract_protocol: RNA extraction was performed using RNAeasy MiniKit (Qiagen) according to the manufacturer's instruction at 4˚C

treatment_protocol: The cells were infected with ectromelia virus at 95% confluence at MOI=10 and incubated for 1 hr in DMEM with 2% Fetal Bovine Serum (FBS) at 37˚C, 5% CO2

value: RAW 264.7 cells

value: murine macrophage cell line

tag: infection

value: ectromelia virus

tag: time point

value: 16 hpi


title: plateA3.positionD6.single.cell

description:
all.single.cell.gene.counts.txt
A3-D6

value: Lung

value: epithelial cell


title: Ectromelia virus at 16H, biological rep3

description: Mouse RAW_ectromelia virus_16H-3


title: RMDB_171

description: REMoDLB trial


title: RMDB_167

description: REMoDLB trial


title: Ectromelia virus at 2H, biological rep2

description: Mouse RAW_ectromelia virus_2H-2

source_name: Ectromelia virus infected mouse RAW 2 hpi

value: 2 hpi


title: plateA3.positionC6.single.cell

description:
all.single.cell.gene.counts.txt
A3-C6


title: RMDB_169

description: REMoDLB trial

value: ABC


title: Ectromelia virus at 2H, biological rep1

description: Mouse RAW_ectromelia virus_2H-1


title: plateA3.positionB6.single.cell

description:
all.single.cell.gene.counts.txt
A3-B6


title: Ectromelia virus at 2H, biological rep3

description: Mouse RAW_ectromelia virus_2H-3


title: RMDB_168

description: REMoDLB trial


title: RMDB_166

description: REMoDLB trial

value: UNC


title: RMDB_165

description: REMoDLB trial


title: Ectromelia virus at 16H, biological rep2

description: Mouse RAW_ectromelia virus_16H-2


title: plateA3.positionA6.single.cell

description:
all.single.cell.gene.counts.txt
A3-A6

value: BASCs


title: plateA3.positionH5.single.cell

description:
all.single.cell.gene.counts.txt
A3-H5


title: plateA3.positionF5.single.cell

description:
all.single.cell.gene.counts.txt
A3-F5


title: plateA3.positionG5.single.cell

description:
all.single.cell.gene.counts.txt
A3-G5


title: Vaccinia virus at 16H, biological rep2

description: Mouse RAW_vaccinia virus_16H-2

source_name: Vaccinia virus infected mouse RAW 16 hpi

treatment_protocol: The cells were infected with vaccinia virus at 95% confluence at MOI=10 and incubated for 1 hr in DMEM with 2% Fetal Bovine Serum (FBS) at 37˚C, 5% CO2

value: Vaccinia virus


title: plateA3.positionD5.single.cell

description:
all.single.cell.gene.counts.txt
A3-D5


title: RMDB_163

description: REMoDLB trial


title: plateA3.positionC5.single.cell

description:
all.single.cell.gene.counts.txt
A3-C5


title: plateA3.positionB5.single.cell

description:
all.single.cell.gene.counts.txt
A3-B5


title: plateA3.positionH4.single.cell

description:
all.single.cell.gene.counts.txt
A3-H4

value: Club cell


title: plateA3.positionG4.single.cell

description:
all.single.cell.gene.counts.txt
A3-G4


title: RMDB_162

description: REMoDLB trial


title: RMDB_161

description: REMoDLB trial

value: MHG


title: plateA3.positionA5.single.cell

description:
all.single.cell.gene.counts.txt
A3-A5


title: Vaccinia virus at 16H, biological rep3

description: Mouse RAW_vaccinia virus_16H-3


title: plateA3.positionF4.single.cell

description:
all.single.cell.gene.counts.txt
A3-F4


title: Vaccinia virus at 16H, biological rep1

description: Mouse RAW_vaccinia virus_16H-1


title: Vaccinia virus at 2H, biological rep1

description: Mouse RAW_vaccinia virus_2H-1

source_name: Vaccinia virus infected mouse RAW 2 hpi


title: Vaccinia virus at 2H, biological rep2

description: Mouse RAW_vaccinia virus_2H-2


title: Vaccinia virus at 0H, biological rep2

description: Mouse RAW_vaccinia virus_0H-2

source_name: Mock infected mouse RAW


title: plateA3.positionD4.single.cell

description:
all.single.cell.gene.counts.txt
A3-D4


title: plateA3.positionC4.single.cell

description:
all.single.cell.gene.counts.txt
A3-C4


title: RMDB_159

description: REMoDLB trial

value: Diffuse Large B-cell Lymphoma


title: plateA3.positionE5.single.cell

description:
all.single.cell.gene.counts.txt
A3-E5


title: plateA3.positionE4.single.cell

description:
all.single.cell.gene.counts.txt
A3-E4


title: RMDB_164

description: REMoDLB trial

value: GCB


title: plateA3.positionB4.single.cell

description:
all.single.cell.gene.counts.txt
A3-B4


title: Vaccinia virus at 2H, biological rep3

description: Mouse RAW_vaccinia virus_2H-3


title: plateA3.positionA4.single.cell

description:
all.single.cell.gene.counts.txt
A3-A4


title: cowpox virus at 16H, biological rep3

description: Mouse RAW_Cowpox virus_16H-3

source_name: Cowpox virus infected mouse RAW 16 hpi

treatment_protocol: The cells were infected with cowpox virus at 95% confluence at MOI=10 and incubated for 1 hr in DMEM with 2% Fetal Bovine Serum (FBS) at 37˚C, 5% CO2

value: Cowpox virus


title: plateA3.positionH3.single.cell

description:
all.single.cell.gene.counts.txt
A3-H3


title: RMDB_157

description: REMoDLB trial


title: RMDB_160

description: REMoDLB trial


title: RMDB_155

description: REMoDLB trial


title: RMDB_158

description: REMoDLB trial


title: plateA3.positionF3.single.cell

description:
all.single.cell.gene.counts.txt
A3-F3


title: plateA3.positionC3.single.cell

description:
all.single.cell.gene.counts.txt
A3-C3


title: Vaccinia virus at 0H, biological rep1

description: Mouse RAW_vaccinia virus_0H-1


title: plateA3.positionE3.single.cell

description:
all.single.cell.gene.counts.txt
A3-E3


title: plateA3.positionD3.single.cell

description:
all.single.cell.gene.counts.txt
A3-D3

value: Ciliated cell


title: plateA3.positionA3.single.cell

description:
all.single.cell.gene.counts.txt
A3-A3


title: RMDB_154

description: REMoDLB trial


title: plateA3.positionG2.single.cell

description:
all.single.cell.gene.counts.txt
A3-G2


title: plateA3.positionH2.single.cell

description:
all.single.cell.gene.counts.txt
A3-H2


title: plateA3.positionG3.single.cell

description:
all.single.cell.gene.counts.txt
A3-G3


title: RMDB_153

description: REMoDLB trial


title: plateA3.positionF2.single.cell

description:
all.single.cell.gene.counts.txt
A3-F2


title: cowpox virus at 16H, biological rep1

description: Mouse RAW_Cowpox virus_16H-1

value: RAW 264.7 cells


title: Vaccinia virus at 0H, biological rep3

description: Mouse RAW_vaccinia virus_0H-3

value: murine macrophage cell line


title: cowpox virus at 16H, biological rep2

description: Mouse RAW_Cowpox virus_16H-2


title: RMDB_152

description: REMoDLB trial


title: RMDB_151

description: REMoDLB trial


title: Mock infected mouse RAW rep 3

description: Mock infected mouse RAW-3


title: RMDB_150

description: REMoDLB trial


title: plateA3.positionE2.single.cell

description:
all.single.cell.gene.counts.txt
A3-E2


title: cowpox virus at 2H, biological rep2

description: Mouse RAW_Cowpox virus_2H-2

source_name: Cowpox virus infected mouse RAW 2 hpi


title: plateA3.positionB3.single.cell

description:
all.single.cell.gene.counts.txt
A3-B3


title: plateA3.positionC2.single.cell

description:
all.single.cell.gene.counts.txt
A3-C2


title: cowpox virus at 2H, biological rep1

description: Mouse RAW_Cowpox virus_2H-1