title: genomic DNA from eutopic endometrium Sample_741

source_name: endometrium sample 741


title: genomic DNA from eutopic endometrium Sample_740

status: Public on Sep 12 2023

type: genomic

city: Herston

first: Sally

last: Mortlock

state: QLD

address: School of Public Health

department: School of Public Health

country: Australia

institute: University of Queensland

description:
genomic DNA from eutopic endometrium
Control eutopic endometrium sample

hyb_protocol: All DNA samples were adjusted to the same volume and concentration for sodium bisulfite conversion followed by DNAm analysis on the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina scan protocol was performed at the University of Southern California Epigenome Center.

data_processing:
Background correction with dye-bias, signal intensity normalization and Beta value generation performed using the SeSAME R package. Samples with a low overall intensity signal (median unmethylated or methylated signal <9), a detection p-value >0.05 in more than 1% of DNAm sites were removed. Probes with a detection p-value >0.05 in more than 10% of samples and probes not overlapping between batches were removed. Probes were masked based on the SeSAME package. 759,345 DNAm sites for 984 samples remained.
Normalized Beta and Normalized M-value

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: endometrium sample 740

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from endometrial samples

tag: gender

value: Female

tag: sample type

value: endometrium

tag: disease state

value: Control

tag: cycle phase

value: MSE

tag: plate

tag: terminus

tag: batch

tag: euro

value: EUR

tag: recruiment

tag: age


title: genomic DNA from eutopic endometrium Sample_738

description:
genomic DNA from eutopic endometrium
Endometriosis eutopic endometrium sample

source_name: endometrium sample 738

value: Endometriosis

value: PE


title: genomic DNA from eutopic endometrium Sample_739

source_name: endometrium sample 739


title: genomic DNA from eutopic endometrium Sample_737

source_name: endometrium sample 737

value: SE


title: genomic DNA from eutopic endometrium Sample_735

source_name: endometrium sample 735


title: genomic DNA from eutopic endometrium Sample_733

source_name: endometrium sample 733

value: ESE


title: genomic DNA from eutopic endometrium Sample_734

source_name: endometrium sample 734


title: genomic DNA from eutopic endometrium Sample_730

source_name: endometrium sample 730


title: genomic DNA from eutopic endometrium Sample_731

source_name: endometrium sample 731

value: LSE


title: genomic DNA from eutopic endometrium Sample_732

source_name: endometrium sample 732


title: genomic DNA from eutopic endometrium Sample_724

source_name: endometrium sample 724


title: genomic DNA from eutopic endometrium Sample_725

source_name: endometrium sample 725


title: genomic DNA from eutopic endometrium Sample_719

source_name: endometrium sample 719


title: genomic DNA from eutopic endometrium Sample_722

source_name: endometrium sample 722


title: genomic DNA from eutopic endometrium Sample_721

source_name: endometrium sample 721


title: genomic DNA from eutopic endometrium Sample_720

source_name: endometrium sample 720


title: genomic DNA from eutopic endometrium Sample_726

source_name: endometrium sample 726


title: genomic DNA from eutopic endometrium Sample_728

source_name: endometrium sample 728


title: genomic DNA from eutopic endometrium Sample_747

source_name: endometrium sample 747


title: genomic DNA from eutopic endometrium Sample_718

source_name: endometrium sample 718

value: Menstrual


title: genomic DNA from eutopic endometrium Sample_746

source_name: endometrium sample 746


title: genomic DNA from eutopic endometrium Sample_716

source_name: endometrium sample 716


title: genomic DNA from eutopic endometrium Sample_714

source_name: endometrium sample 714


title: genomic DNA from eutopic endometrium Sample_715

source_name: endometrium sample 715


title: genomic DNA from eutopic endometrium Sample_717

source_name: endometrium sample 717


title: genomic DNA from eutopic endometrium Sample_713

source_name: endometrium sample 713


title: genomic DNA from eutopic endometrium Sample_736

source_name: endometrium sample 736


title: genomic DNA from eutopic endometrium Sample_710

source_name: endometrium sample 710


title: genomic DNA from eutopic endometrium Sample_712

source_name: endometrium sample 712


title: genomic DNA from eutopic endometrium Sample_709

source_name: endometrium sample 709


title: genomic DNA from eutopic endometrium Sample_727

source_name: endometrium sample 727


title: genomic DNA from eutopic endometrium Sample_729

source_name: endometrium sample 729


title: genomic DNA from eutopic endometrium Sample_708

source_name: endometrium sample 708


title: genomic DNA from eutopic endometrium Sample_707

source_name: endometrium sample 707


title: genomic DNA from eutopic endometrium Sample_723

source_name: endometrium sample 723


title: genomic DNA from eutopic endometrium Sample_704

source_name: endometrium sample 704


title: genomic DNA from eutopic endometrium Sample_703

source_name: endometrium sample 703


title: genomic DNA from eutopic endometrium Sample_705

source_name: endometrium sample 705


title: genomic DNA from eutopic endometrium Sample_702

source_name: endometrium sample 702


title: genomic DNA from eutopic endometrium Sample_701

source_name: endometrium sample 701


title: genomic DNA from eutopic endometrium Sample_699

source_name: endometrium sample 699


title: genomic DNA from eutopic endometrium Sample_697

source_name: endometrium sample 697


title: genomic DNA from eutopic endometrium Sample_694

source_name: endometrium sample 694


title: genomic DNA from eutopic endometrium Sample_698

source_name: endometrium sample 698


title: genomic DNA from eutopic endometrium Sample_693

source_name: endometrium sample 693


title: genomic DNA from eutopic endometrium Sample_692

source_name: endometrium sample 692


title: genomic DNA from eutopic endometrium Sample_691

source_name: endometrium sample 691


title: genomic DNA from eutopic endometrium Sample_688

source_name: endometrium sample 688


title: genomic DNA from eutopic endometrium Sample_689

source_name: endometrium sample 689


title: genomic DNA from eutopic endometrium Sample_690

source_name: endometrium sample 690


title: genomic DNA from eutopic endometrium Sample_686

source_name: endometrium sample 686


title: genomic DNA from eutopic endometrium Sample_711

source_name: endometrium sample 711


title: genomic DNA from eutopic endometrium Sample_687

source_name: endometrium sample 687


title: genomic DNA from eutopic endometrium Sample_706

source_name: endometrium sample 706


title: genomic DNA from eutopic endometrium Sample_684

source_name: endometrium sample 684


title: genomic DNA from eutopic endometrium Sample_683

source_name: endometrium sample 683


title: genomic DNA from eutopic endometrium Sample_681

source_name: endometrium sample 681


title: genomic DNA from eutopic endometrium Sample_682

source_name: endometrium sample 682


title: genomic DNA from eutopic endometrium Sample_678

source_name: endometrium sample 678


title: genomic DNA from eutopic endometrium Sample_679

source_name: endometrium sample 679


title: genomic DNA from eutopic endometrium Sample_677

source_name: endometrium sample 677


title: genomic DNA from eutopic endometrium Sample_680

source_name: endometrium sample 680


title: genomic DNA from eutopic endometrium Sample_685

source_name: endometrium sample 685


title: genomic DNA from eutopic endometrium Sample_676

source_name: endometrium sample 676


title: genomic DNA from eutopic endometrium Sample_675

source_name: endometrium sample 675


title: genomic DNA from eutopic endometrium Sample_695

source_name: endometrium sample 695


title: genomic DNA from eutopic endometrium Sample_700

source_name: endometrium sample 700


title: genomic DNA from eutopic endometrium Sample_696

source_name: endometrium sample 696


title: genomic DNA from eutopic endometrium Sample_673

source_name: endometrium sample 673


title: genomic DNA from eutopic endometrium Sample_671

source_name: endometrium sample 671


title: genomic DNA from eutopic endometrium Sample_670

source_name: endometrium sample 670


title: genomic DNA from eutopic endometrium Sample_672

source_name: endometrium sample 672


title: genomic DNA from eutopic endometrium Sample_674

source_name: endometrium sample 674


title: genomic DNA from eutopic endometrium Sample_668

source_name: endometrium sample 668


title: genomic DNA from eutopic endometrium Sample_669

source_name: endometrium sample 669


title: genomic DNA from eutopic endometrium Sample_667

source_name: endometrium sample 667


title: genomic DNA from eutopic endometrium Sample_663

source_name: endometrium sample 663


title: genomic DNA from eutopic endometrium Sample_665

source_name: endometrium sample 665


title: genomic DNA from eutopic endometrium Sample_662

source_name: endometrium sample 662


title: genomic DNA from eutopic endometrium Sample_661

source_name: endometrium sample 661


title: genomic DNA from eutopic endometrium Sample_660

source_name: endometrium sample 660


title: genomic DNA from eutopic endometrium Sample_659

source_name: endometrium sample 659


title: genomic DNA from eutopic endometrium Sample_658

source_name: endometrium sample 658


title: genomic DNA from eutopic endometrium Sample_657

source_name: endometrium sample 657


title: genomic DNA from eutopic endometrium Sample_655

source_name: endometrium sample 655


title: genomic DNA from eutopic endometrium Sample_652

source_name: endometrium sample 652


title: genomic DNA from eutopic endometrium Sample_656

source_name: endometrium sample 656


title: genomic DNA from eutopic endometrium Sample_650

source_name: endometrium sample 650


title: genomic DNA from eutopic endometrium Sample_654

source_name: endometrium sample 654


title: genomic DNA from eutopic endometrium Sample_648

source_name: endometrium sample 648


title: genomic DNA from eutopic endometrium Sample_651

source_name: endometrium sample 651


title: genomic DNA from eutopic endometrium Sample_653

source_name: endometrium sample 653


title: genomic DNA from eutopic endometrium Sample_647

source_name: endometrium sample 647


title: genomic DNA from eutopic endometrium Sample_645

source_name: endometrium sample 645


title: genomic DNA from eutopic endometrium Sample_644

source_name: endometrium sample 644


title: genomic DNA from eutopic endometrium Sample_641

source_name: endometrium sample 641


title: genomic DNA from eutopic endometrium Sample_643

source_name: endometrium sample 643


title: genomic DNA from eutopic endometrium Sample_638

source_name: endometrium sample 638


title: genomic DNA from eutopic endometrium Sample_646

source_name: endometrium sample 646


title: genomic DNA from eutopic endometrium Sample_640

source_name: endometrium sample 640


title: genomic DNA from eutopic endometrium Sample_642

source_name: endometrium sample 642


title: genomic DNA from eutopic endometrium Sample_639

source_name: endometrium sample 639


title: genomic DNA from eutopic endometrium Sample_664

source_name: endometrium sample 664


title: genomic DNA from eutopic endometrium Sample_637

source_name: endometrium sample 637


title: genomic DNA from eutopic endometrium Sample_666

source_name: endometrium sample 666


title: genomic DNA from eutopic endometrium Sample_634

source_name: endometrium sample 634


title: genomic DNA from eutopic endometrium Sample_632

source_name: endometrium sample 632


title: genomic DNA from eutopic endometrium Sample_633

source_name: endometrium sample 633


title: genomic DNA from eutopic endometrium Sample_631

source_name: endometrium sample 631


title: genomic DNA from eutopic endometrium Sample_630

source_name: endometrium sample 630


title: genomic DNA from eutopic endometrium Sample_629

source_name: endometrium sample 629


title: genomic DNA from eutopic endometrium Sample_649

source_name: endometrium sample 649


title: genomic DNA from eutopic endometrium Sample_628

source_name: endometrium sample 628


title: genomic DNA from eutopic endometrium Sample_624

source_name: endometrium sample 624


title: genomic DNA from eutopic endometrium Sample_625

source_name: endometrium sample 625


title: genomic DNA from eutopic endometrium Sample_627

source_name: endometrium sample 627


title: genomic DNA from eutopic endometrium Sample_626

source_name: endometrium sample 626


title: genomic DNA from eutopic endometrium Sample_623

source_name: endometrium sample 623


title: genomic DNA from eutopic endometrium Sample_622

source_name: endometrium sample 622


title: genomic DNA from eutopic endometrium Sample_621

source_name: endometrium sample 621


title: genomic DNA from eutopic endometrium Sample_620

source_name: endometrium sample 620


title: genomic DNA from eutopic endometrium Sample_619

source_name: endometrium sample 619


title: genomic DNA from eutopic endometrium Sample_614

source_name: endometrium sample 614


title: genomic DNA from eutopic endometrium Sample_616

source_name: endometrium sample 616


title: genomic DNA from eutopic endometrium Sample_618

source_name: endometrium sample 618


title: genomic DNA from eutopic endometrium Sample_613

source_name: endometrium sample 613


title: genomic DNA from eutopic endometrium Sample_612

source_name: endometrium sample 612


title: genomic DNA from eutopic endometrium Sample_617

source_name: endometrium sample 617


title: genomic DNA from eutopic endometrium Sample_611

source_name: endometrium sample 611


title: genomic DNA from eutopic endometrium Sample_636

source_name: endometrium sample 636


title: genomic DNA from eutopic endometrium Sample_609

source_name: endometrium sample 609


title: genomic DNA from eutopic endometrium Sample_608

source_name: endometrium sample 608


title: genomic DNA from eutopic endometrium Sample_610

source_name: endometrium sample 610


title: genomic DNA from eutopic endometrium Sample_635

source_name: endometrium sample 635


title: genomic DNA from eutopic endometrium Sample_607

source_name: endometrium sample 607


title: genomic DNA from eutopic endometrium Sample_606

source_name: endometrium sample 606


title: genomic DNA from eutopic endometrium Sample_605

source_name: endometrium sample 605


title: genomic DNA from eutopic endometrium Sample_604

source_name: endometrium sample 604


title: genomic DNA from eutopic endometrium Sample_603

source_name: endometrium sample 603


title: genomic DNA from eutopic endometrium Sample_601

source_name: endometrium sample 601


title: genomic DNA from eutopic endometrium Sample_602

source_name: endometrium sample 602


title: genomic DNA from eutopic endometrium Sample_600

source_name: endometrium sample 600


title: genomic DNA from eutopic endometrium Sample_598

source_name: endometrium sample 598


title: genomic DNA from eutopic endometrium Sample_593

source_name: endometrium sample 593


title: genomic DNA from eutopic endometrium Sample_615

source_name: endometrium sample 615


title: genomic DNA from eutopic endometrium Sample_596

source_name: endometrium sample 596


title: genomic DNA from eutopic endometrium Sample_599

source_name: endometrium sample 599


title: genomic DNA from eutopic endometrium Sample_591

source_name: endometrium sample 591


title: genomic DNA from eutopic endometrium Sample_595

source_name: endometrium sample 595


title: genomic DNA from eutopic endometrium Sample_594

source_name: endometrium sample 594


title: genomic DNA from eutopic endometrium Sample_586

source_name: endometrium sample 586


title: genomic DNA from eutopic endometrium Sample_588

source_name: endometrium sample 588


title: genomic DNA from eutopic endometrium Sample_587

source_name: endometrium sample 587


title: genomic DNA from eutopic endometrium Sample_585

source_name: endometrium sample 585


title: genomic DNA from eutopic endometrium Sample_590

source_name: endometrium sample 590


title: genomic DNA from eutopic endometrium Sample_592

source_name: endometrium sample 592


title: genomic DNA from eutopic endometrium Sample_584

source_name: endometrium sample 584


title: genomic DNA from eutopic endometrium Sample_589

source_name: endometrium sample 589


title: genomic DNA from eutopic endometrium Sample_582

source_name: endometrium sample 582


title: genomic DNA from eutopic endometrium Sample_583

source_name: endometrium sample 583


title: genomic DNA from eutopic endometrium Sample_580

source_name: endometrium sample 580


title: genomic DNA from eutopic endometrium Sample_579

source_name: endometrium sample 579


title: genomic DNA from eutopic endometrium Sample_581

source_name: endometrium sample 581


title: genomic DNA from eutopic endometrium Sample_578

source_name: endometrium sample 578


title: genomic DNA from eutopic endometrium Sample_577

source_name: endometrium sample 577


title: genomic DNA from eutopic endometrium Sample_576

source_name: endometrium sample 576


title: genomic DNA from eutopic endometrium Sample_575

source_name: endometrium sample 575


title: genomic DNA from eutopic endometrium Sample_574

source_name: endometrium sample 574


title: genomic DNA from eutopic endometrium Sample_573

source_name: endometrium sample 573


title: genomic DNA from eutopic endometrium Sample_597

source_name: endometrium sample 597


title: genomic DNA from eutopic endometrium Sample_572

source_name: endometrium sample 572


title: genomic DNA from eutopic endometrium Sample_570

source_name: endometrium sample 570


title: genomic DNA from eutopic endometrium Sample_571

source_name: endometrium sample 571


title: genomic DNA from eutopic endometrium Sample_569

source_name: endometrium sample 569


title: genomic DNA from eutopic endometrium Sample_568

source_name: endometrium sample 568


title: genomic DNA from eutopic endometrium Sample_566

source_name: endometrium sample 566


title: genomic DNA from eutopic endometrium Sample_565

source_name: endometrium sample 565


title: genomic DNA from eutopic endometrium Sample_567

source_name: endometrium sample 567


title: genomic DNA from eutopic endometrium Sample_563

source_name: endometrium sample 563


title: genomic DNA from eutopic endometrium Sample_562

source_name: endometrium sample 562


title: genomic DNA from eutopic endometrium Sample_561

source_name: endometrium sample 561


title: genomic DNA from eutopic endometrium Sample_556

source_name: endometrium sample 556


title: genomic DNA from eutopic endometrium Sample_557

source_name: endometrium sample 557


title: genomic DNA from eutopic endometrium Sample_558

source_name: endometrium sample 558


title: genomic DNA from eutopic endometrium Sample_554

source_name: endometrium sample 554


title: genomic DNA from eutopic endometrium Sample_553

source_name: endometrium sample 553


title: genomic DNA from eutopic endometrium Sample_551

source_name: endometrium sample 551


title: genomic DNA from eutopic endometrium Sample_549

source_name: endometrium sample 549


title: genomic DNA from eutopic endometrium Sample_550

source_name: endometrium sample 550


title: genomic DNA from eutopic endometrium Sample_552

source_name: endometrium sample 552


title: genomic DNA from eutopic endometrium Sample_547

source_name: endometrium sample 547


title: genomic DNA from eutopic endometrium Sample_546

source_name: endometrium sample 546


title: genomic DNA from eutopic endometrium Sample_545

source_name: endometrium sample 545


title: genomic DNA from eutopic endometrium Sample_543

source_name: endometrium sample 543


title: genomic DNA from eutopic endometrium Sample_544

source_name: endometrium sample 544


title: genomic DNA from eutopic endometrium Sample_540

source_name: endometrium sample 540


title: genomic DNA from eutopic endometrium Sample_541

source_name: endometrium sample 541


title: genomic DNA from eutopic endometrium Sample_538

source_name: endometrium sample 538


title: genomic DNA from eutopic endometrium Sample_564

source_name: endometrium sample 564


title: genomic DNA from eutopic endometrium Sample_539

source_name: endometrium sample 539


title: genomic DNA from eutopic endometrium Sample_536

source_name: endometrium sample 536


title: genomic DNA from eutopic endometrium Sample_537

source_name: endometrium sample 537


title: genomic DNA from eutopic endometrium Sample_535

source_name: endometrium sample 535


title: genomic DNA from eutopic endometrium Sample_560

source_name: endometrium sample 560


title: genomic DNA from eutopic endometrium Sample_555

source_name: endometrium sample 555


title: genomic DNA from eutopic endometrium Sample_533

source_name: endometrium sample 533


title: genomic DNA from eutopic endometrium Sample_532

source_name: endometrium sample 532


title: genomic DNA from eutopic endometrium Sample_530

source_name: endometrium sample 530


title: genomic DNA from eutopic endometrium Sample_559

source_name: endometrium sample 559


title: genomic DNA from eutopic endometrium Sample_531

source_name: endometrium sample 531


title: genomic DNA from eutopic endometrium Sample_529

source_name: endometrium sample 529


title: genomic DNA from eutopic endometrium Sample_527

source_name: endometrium sample 527


title: genomic DNA from eutopic endometrium Sample_548

source_name: endometrium sample 548


title: genomic DNA from eutopic endometrium Sample_526

source_name: endometrium sample 526


title: genomic DNA from eutopic endometrium Sample_528

source_name: endometrium sample 528


title: genomic DNA from eutopic endometrium Sample_525

source_name: endometrium sample 525


title: genomic DNA from eutopic endometrium Sample_524

source_name: endometrium sample 524


title: genomic DNA from eutopic endometrium Sample_523

source_name: endometrium sample 523


title: genomic DNA from eutopic endometrium Sample_522

source_name: endometrium sample 522


title: genomic DNA from eutopic endometrium Sample_542

source_name: endometrium sample 542


title: genomic DNA from eutopic endometrium Sample_521

source_name: endometrium sample 521


title: genomic DNA from eutopic endometrium Sample_519

source_name: endometrium sample 519


title: genomic DNA from eutopic endometrium Sample_516

source_name: endometrium sample 516


title: genomic DNA from eutopic endometrium Sample_518

source_name: endometrium sample 518


title: genomic DNA from eutopic endometrium Sample_517

source_name: endometrium sample 517


title: genomic DNA from eutopic endometrium Sample_534

source_name: endometrium sample 534


title: genomic DNA from eutopic endometrium Sample_515

source_name: endometrium sample 515


title: genomic DNA from eutopic endometrium Sample_514

source_name: endometrium sample 514


title: genomic DNA from eutopic endometrium Sample_512

source_name: endometrium sample 512


title: genomic DNA from eutopic endometrium Sample_511

source_name: endometrium sample 511


title: genomic DNA from eutopic endometrium Sample_510

source_name: endometrium sample 510


title: genomic DNA from eutopic endometrium Sample_507

source_name: endometrium sample 507


title: genomic DNA from eutopic endometrium Sample_508

source_name: endometrium sample 508


title: genomic DNA from eutopic endometrium Sample_509

source_name: endometrium sample 509


title: genomic DNA from eutopic endometrium Sample_503

source_name: endometrium sample 503


title: genomic DNA from eutopic endometrium Sample_504

source_name: endometrium sample 504


title: genomic DNA from eutopic endometrium Sample_502

source_name: endometrium sample 502


title: genomic DNA from eutopic endometrium Sample_506

source_name: endometrium sample 506


title: genomic DNA from eutopic endometrium Sample_505

source_name: endometrium sample 505


title: genomic DNA from eutopic endometrium Sample_500

source_name: endometrium sample 500


title: genomic DNA from eutopic endometrium Sample_499

source_name: endometrium sample 499


title: genomic DNA from eutopic endometrium Sample_501

source_name: endometrium sample 501


title: genomic DNA from eutopic endometrium Sample_495

source_name: endometrium sample 495


title: genomic DNA from eutopic endometrium Sample_496

source_name: endometrium sample 496


title: genomic DNA from eutopic endometrium Sample_498

source_name: endometrium sample 498


title: genomic DNA from eutopic endometrium Sample_497

source_name: endometrium sample 497


title: genomic DNA from eutopic endometrium Sample_493

source_name: endometrium sample 493


title: genomic DNA from eutopic endometrium Sample_520

source_name: endometrium sample 520


title: genomic DNA from eutopic endometrium Sample_491

source_name: endometrium sample 491


title: genomic DNA from eutopic endometrium Sample_492

source_name: endometrium sample 492


title: genomic DNA from eutopic endometrium Sample_489

source_name: endometrium sample 489


title: genomic DNA from eutopic endometrium Sample_488

source_name: endometrium sample 488


title: genomic DNA from eutopic endometrium Sample_494

source_name: endometrium sample 494


title: genomic DNA from eutopic endometrium Sample_513

source_name: endometrium sample 513


title: genomic DNA from eutopic endometrium Sample_487

source_name: endometrium sample 487


title: genomic DNA from eutopic endometrium Sample_485

source_name: endometrium sample 485


title: genomic DNA from eutopic endometrium Sample_486

source_name: endometrium sample 486


title: genomic DNA from eutopic endometrium Sample_484

source_name: endometrium sample 484


title: genomic DNA from eutopic endometrium Sample_483

source_name: endometrium sample 483


title: genomic DNA from eutopic endometrium Sample_481

source_name: endometrium sample 481


title: genomic DNA from eutopic endometrium Sample_480

source_name: endometrium sample 480


title: genomic DNA from eutopic endometrium Sample_482

source_name: endometrium sample 482


title: genomic DNA from eutopic endometrium Sample_479

source_name: endometrium sample 479


title: genomic DNA from eutopic endometrium Sample_476

source_name: endometrium sample 476


title: genomic DNA from eutopic endometrium Sample_475

source_name: endometrium sample 475


title: genomic DNA from eutopic endometrium Sample_477

source_name: endometrium sample 477


title: genomic DNA from eutopic endometrium Sample_473

source_name: endometrium sample 473


title: genomic DNA from eutopic endometrium Sample_474

source_name: endometrium sample 474


title: genomic DNA from eutopic endometrium Sample_471

source_name: endometrium sample 471


title: genomic DNA from eutopic endometrium Sample_472

source_name: endometrium sample 472


title: genomic DNA from eutopic endometrium Sample_470

source_name: endometrium sample 470


title: genomic DNA from eutopic endometrium Sample_467

source_name: endometrium sample 467


title: genomic DNA from eutopic endometrium Sample_466

source_name: endometrium sample 466


title: genomic DNA from eutopic endometrium Sample_469

source_name: endometrium sample 469


title: genomic DNA from eutopic endometrium Sample_468

source_name: endometrium sample 468


title: genomic DNA from eutopic endometrium Sample_465

source_name: endometrium sample 465


title: genomic DNA from eutopic endometrium Sample_463

source_name: endometrium sample 463


title: genomic DNA from eutopic endometrium Sample_464

source_name: endometrium sample 464


title: genomic DNA from eutopic endometrium Sample_490

source_name: endometrium sample 490


title: genomic DNA from eutopic endometrium Sample_462

source_name: endometrium sample 462


title: genomic DNA from eutopic endometrium Sample_460

source_name: endometrium sample 460


title: genomic DNA from eutopic endometrium Sample_461

source_name: endometrium sample 461


title: genomic DNA from eutopic endometrium Sample_458

source_name: endometrium sample 458


title: genomic DNA from eutopic endometrium Sample_457

source_name: endometrium sample 457


title: genomic DNA from eutopic endometrium Sample_456

source_name: endometrium sample 456


title: genomic DNA from eutopic endometrium Sample_459

source_name: endometrium sample 459


title: genomic DNA from eutopic endometrium Sample_455

source_name: endometrium sample 455


title: genomic DNA from eutopic endometrium Sample_454

source_name: endometrium sample 454


title: genomic DNA from eutopic endometrium Sample_478

source_name: endometrium sample 478


title: genomic DNA from eutopic endometrium Sample_453

source_name: endometrium sample 453


title: genomic DNA from eutopic endometrium Sample_452

source_name: endometrium sample 452


title: genomic DNA from eutopic endometrium Sample_451

source_name: endometrium sample 451


title: genomic DNA from eutopic endometrium Sample_450

source_name: endometrium sample 450


title: genomic DNA from eutopic endometrium Sample_447

source_name: endometrium sample 447


title: genomic DNA from eutopic endometrium Sample_449

source_name: endometrium sample 449


title: genomic DNA from eutopic endometrium Sample_446

source_name: endometrium sample 446


title: genomic DNA from eutopic endometrium Sample_445

source_name: endometrium sample 445


title: genomic DNA from eutopic endometrium Sample_443

source_name: endometrium sample 443


title: genomic DNA from eutopic endometrium Sample_442

source_name: endometrium sample 442


title: genomic DNA from eutopic endometrium Sample_444

source_name: endometrium sample 444


title: genomic DNA from eutopic endometrium Sample_441

source_name: endometrium sample 441


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title: genomic DNA from eutopic endometrium Sample_201

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title: genomic DNA from eutopic endometrium Sample_199

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title: genomic DNA from eutopic endometrium Sample_192

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title: genomic DNA from eutopic endometrium Sample_191

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title: genomic DNA from eutopic endometrium Sample_188

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title: genomic DNA from eutopic endometrium Sample_189

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title: genomic DNA from eutopic endometrium Sample_178

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title: genomic DNA from eutopic endometrium Sample_139

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title: genomic DNA from eutopic endometrium Sample_137

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title: genomic DNA from eutopic endometrium Sample_160

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title: genomic DNA from eutopic endometrium Sample_129

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title: genomic DNA from eutopic endometrium Sample_128

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title: genomic DNA from eutopic endometrium Sample_127

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title: genomic DNA from eutopic endometrium Sample_125

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title: genomic DNA from eutopic endometrium Sample_126

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title: genomic DNA from eutopic endometrium Sample_145

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title: genomic DNA from eutopic endometrium Sample_122

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title: genomic DNA from eutopic endometrium Sample_123

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title: genomic DNA from eutopic endometrium Sample_124

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title: genomic DNA from eutopic endometrium Sample_120

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title: genomic DNA from eutopic endometrium Sample_121

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title: genomic DNA from eutopic endometrium Sample_118

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title: genomic DNA from eutopic endometrium Sample_119

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title: genomic DNA from eutopic endometrium Sample_115

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title: genomic DNA from eutopic endometrium Sample_112

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title: genomic DNA from eutopic endometrium Sample_117

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title: genomic DNA from eutopic endometrium Sample_113

source_name: endometrium sample 113


title: genomic DNA from eutopic endometrium Sample_114

source_name: endometrium sample 114


title: genomic DNA from eutopic endometrium Sample_111

source_name: endometrium sample 111


title: genomic DNA from eutopic endometrium Sample_110

source_name: endometrium sample 110


title: genomic DNA from eutopic endometrium Sample_116

source_name: endometrium sample 116


title: genomic DNA from eutopic endometrium Sample_109

source_name: endometrium sample 109


title: genomic DNA from eutopic endometrium Sample_135

source_name: endometrium sample 135


title: genomic DNA from eutopic endometrium Sample_105

source_name: endometrium sample 105


title: genomic DNA from eutopic endometrium Sample_107

source_name: endometrium sample 107


title: genomic DNA from eutopic endometrium Sample_108

source_name: endometrium sample 108


title: genomic DNA from eutopic endometrium Sample_104

source_name: endometrium sample 104


title: genomic DNA from eutopic endometrium Sample_103

source_name: endometrium sample 103


title: genomic DNA from eutopic endometrium Sample_102

source_name: endometrium sample 102


title: genomic DNA from eutopic endometrium Sample_101

source_name: endometrium sample 101


title: genomic DNA from eutopic endometrium Sample_106

source_name: endometrium sample 106


title: genomic DNA from eutopic endometrium Sample_100

source_name: endometrium sample 100


title: genomic DNA from eutopic endometrium Sample_99

source_name: endometrium sample 99


title: genomic DNA from eutopic endometrium Sample_98

source_name: endometrium sample 98


title: genomic DNA from eutopic endometrium Sample_97

source_name: endometrium sample 97


title: genomic DNA from eutopic endometrium Sample_96

source_name: endometrium sample 96


title: genomic DNA from eutopic endometrium Sample_94

source_name: endometrium sample 94


title: genomic DNA from eutopic endometrium Sample_92

source_name: endometrium sample 92


title: genomic DNA from eutopic endometrium Sample_93

source_name: endometrium sample 93


title: genomic DNA from eutopic endometrium Sample_91

source_name: endometrium sample 91


title: genomic DNA from eutopic endometrium Sample_89

source_name: endometrium sample 89


title: genomic DNA from eutopic endometrium Sample_90

source_name: endometrium sample 90


title: genomic DNA from eutopic endometrium Sample_87

source_name: endometrium sample 87


title: genomic DNA from eutopic endometrium Sample_88

source_name: endometrium sample 88


title: genomic DNA from eutopic endometrium Sample_85

source_name: endometrium sample 85


title: genomic DNA from eutopic endometrium Sample_83

source_name: endometrium sample 83


title: genomic DNA from eutopic endometrium Sample_84

source_name: endometrium sample 84


title: genomic DNA from eutopic endometrium Sample_82

source_name: endometrium sample 82


title: genomic DNA from eutopic endometrium Sample_80

source_name: endometrium sample 80


title: genomic DNA from eutopic endometrium Sample_131

source_name: endometrium sample 131


title: genomic DNA from eutopic endometrium Sample_79

source_name: endometrium sample 79


title: genomic DNA from eutopic endometrium Sample_78

source_name: endometrium sample 78


title: genomic DNA from eutopic endometrium Sample_77

source_name: endometrium sample 77


title: genomic DNA from eutopic endometrium Sample_76

source_name: endometrium sample 76


title: genomic DNA from eutopic endometrium Sample_72

source_name: endometrium sample 72


title: genomic DNA from eutopic endometrium Sample_74

source_name: endometrium sample 74


title: genomic DNA from eutopic endometrium Sample_71

source_name: endometrium sample 71


title: genomic DNA from eutopic endometrium Sample_95

source_name: endometrium sample 95


title: genomic DNA from eutopic endometrium Sample_69

source_name: endometrium sample 69


title: genomic DNA from eutopic endometrium Sample_68

source_name: endometrium sample 68


title: genomic DNA from eutopic endometrium Sample_70

source_name: endometrium sample 70


title: genomic DNA from eutopic endometrium Sample_67

source_name: endometrium sample 67


title: genomic DNA from eutopic endometrium Sample_65

source_name: endometrium sample 65


title: genomic DNA from eutopic endometrium Sample_66

source_name: endometrium sample 66


title: genomic DNA from eutopic endometrium Sample_63

source_name: endometrium sample 63


title: genomic DNA from eutopic endometrium Sample_64

source_name: endometrium sample 64


title: genomic DNA from eutopic endometrium Sample_61

source_name: endometrium sample 61


title: genomic DNA from eutopic endometrium Sample_62

source_name: endometrium sample 62


title: genomic DNA from eutopic endometrium Sample_86

source_name: endometrium sample 86


title: genomic DNA from eutopic endometrium Sample_60

source_name: endometrium sample 60


title: genomic DNA from eutopic endometrium Sample_59

source_name: endometrium sample 59


title: genomic DNA from eutopic endometrium Sample_81

source_name: endometrium sample 81


title: genomic DNA from eutopic endometrium Sample_55

source_name: endometrium sample 55


title: genomic DNA from eutopic endometrium Sample_56

source_name: endometrium sample 56


title: genomic DNA from eutopic endometrium Sample_57

source_name: endometrium sample 57


title: genomic DNA from eutopic endometrium Sample_73

source_name: endometrium sample 73


title: genomic DNA from eutopic endometrium Sample_75

source_name: endometrium sample 75


title: genomic DNA from eutopic endometrium Sample_54

source_name: endometrium sample 54


title: genomic DNA from eutopic endometrium Sample_50

source_name: endometrium sample 50


title: genomic DNA from eutopic endometrium Sample_51

source_name: endometrium sample 51


title: genomic DNA from eutopic endometrium Sample_49

source_name: endometrium sample 49


title: genomic DNA from eutopic endometrium Sample_52

source_name: endometrium sample 52


title: genomic DNA from eutopic endometrium Sample_53

source_name: endometrium sample 53


title: genomic DNA from eutopic endometrium Sample_48

source_name: endometrium sample 48


title: genomic DNA from eutopic endometrium Sample_47

source_name: endometrium sample 47


title: genomic DNA from eutopic endometrium Sample_46

source_name: endometrium sample 46


title: genomic DNA from eutopic endometrium Sample_43

source_name: endometrium sample 43


title: genomic DNA from eutopic endometrium Sample_44

source_name: endometrium sample 44


title: genomic DNA from eutopic endometrium Sample_45

source_name: endometrium sample 45


title: genomic DNA from eutopic endometrium Sample_41

source_name: endometrium sample 41


title: genomic DNA from eutopic endometrium Sample_40

source_name: endometrium sample 40


title: genomic DNA from eutopic endometrium Sample_37

source_name: endometrium sample 37


title: genomic DNA from eutopic endometrium Sample_38

source_name: endometrium sample 38


title: genomic DNA from eutopic endometrium Sample_58

source_name: endometrium sample 58


title: genomic DNA from eutopic endometrium Sample_35

source_name: endometrium sample 35


title: genomic DNA from eutopic endometrium Sample_33

source_name: endometrium sample 33


title: genomic DNA from eutopic endometrium Sample_34

source_name: endometrium sample 34


title: genomic DNA from eutopic endometrium Sample_31

source_name: endometrium sample 31


title: genomic DNA from eutopic endometrium Sample_29

source_name: endometrium sample 29


title: genomic DNA from eutopic endometrium Sample_30

source_name: endometrium sample 30


title: genomic DNA from eutopic endometrium Sample_23

source_name: endometrium sample 23


title: genomic DNA from eutopic endometrium Sample_25

source_name: endometrium sample 25


title: genomic DNA from eutopic endometrium Sample_21

source_name: endometrium sample 21


title: genomic DNA from eutopic endometrium Sample_26

source_name: endometrium sample 26


title: genomic DNA from eutopic endometrium Sample_24

source_name: endometrium sample 24


title: genomic DNA from eutopic endometrium Sample_22

source_name: endometrium sample 22


title: genomic DNA from eutopic endometrium Sample_27

source_name: endometrium sample 27


title: genomic DNA from eutopic endometrium Sample_20

source_name: endometrium sample 20


title: genomic DNA from eutopic endometrium Sample_18

source_name: endometrium sample 18


title: genomic DNA from eutopic endometrium Sample_17

source_name: endometrium sample 17


title: genomic DNA from eutopic endometrium Sample_42

source_name: endometrium sample 42


title: genomic DNA from eutopic endometrium Sample_16

source_name: endometrium sample 16


title: genomic DNA from eutopic endometrium Sample_14

source_name: endometrium sample 14


title: genomic DNA from eutopic endometrium Sample_13

source_name: endometrium sample 13


title: genomic DNA from eutopic endometrium Sample_15

source_name: endometrium sample 15


title: genomic DNA from eutopic endometrium Sample_36

source_name: endometrium sample 36


title: genomic DNA from eutopic endometrium Sample_12

source_name: endometrium sample 12


title: genomic DNA from eutopic endometrium Sample_32

source_name: endometrium sample 32


title: genomic DNA from eutopic endometrium Sample_28

source_name: endometrium sample 28


title: genomic DNA from eutopic endometrium Sample_9

source_name: endometrium sample 9


title: genomic DNA from eutopic endometrium Sample_11

source_name: endometrium sample 11


title: genomic DNA from eutopic endometrium Sample_10

source_name: endometrium sample 10


title: genomic DNA from eutopic endometrium Sample_6

source_name: endometrium sample 6


title: genomic DNA from eutopic endometrium Sample_7

source_name: endometrium sample 7


title: genomic DNA from eutopic endometrium Sample_5

source_name: endometrium sample 5


title: genomic DNA from eutopic endometrium Sample_19

source_name: endometrium sample 19


title: genomic DNA from eutopic endometrium Sample_4

source_name: endometrium sample 4


title: genomic DNA from eutopic endometrium Sample_3

source_name: endometrium sample 3


title: genomic DNA from eutopic endometrium Sample_1

source_name: endometrium sample 1


title: genomic DNA from eutopic endometrium Sample_2

source_name: endometrium sample 2


title: genomic DNA from eutopic endometrium Sample_39

source_name: endometrium sample 39


title: E13.5/14.5/E18.5 mouse intestine enriched cells

status: Public on Sep 11 2023

type: SRA

city: Los Angeles

first: Dario

last: Boffelli

state: CA

address: 700 N San Vicente Blvd

department: Pediatrics

country: USA

institute: Cedars Sinai

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Barcode processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Aggregated raw RNA UMI count matrices were analyzed using Seurat, excluding cells with < 1e3 total RNA UMIs and genes with <= 3 total counts across cells. Cells were further filtered to remove gene expression clusters associated with high proportions of mitochondrial reads and/or low total RNA UMIs. Using this filtered set of cell barcodes, MULTI-seq FASTQs were then pre-processed and subjected to the sample classification and semi-supervised negative cell reclassification workflows as implemented in the deMULTIplex R package
Seurat objects were normalized using SCTransform. Integration of Seurat objects from two different experimental days were performed following the Seurat integration workflow.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Mus musculus

source_name: small intestine

extract_protocol:
Tissue segments were dissociated to single cells in HBSS buffer containing 10mM HEPES, 1% BSA, 0.3mg/mL DNase and 0.1W/mL Liberase TL on an orbital shaker at 37C for 30 min with trituration with P200 pipette every 15 mins. Single-cell suspensions were then transferred to 96-well U-bottom plates and washed twice in fetal gut media to remove any remaining BSA. MULTIseq lipid barcode labeling was performed in 96 well plates following the MULTI-seq protocol (McGinnis et al., 2019). Once the cells are incubated with lipid modified oligos (barcode, anchor and co-anchor) in total of 100uL volume reaction, 150uL of HBSS with 2% BSA solution were added to quench the reaction and pooled together in 15ml conical tubes. The cells were pelleted and stained with APC/Cy7 anti-mouse Ter119, APC anti-mouse CD31, BV605 anti-mouse CD45, PE/Cy7 Epcam (all from Biolegend) for 30min on ice followed by a wash with FACS buffer. The collected cells were resuspended in FACS buffer with DAPI to stain dead cells and passed through a 35um cell strainer.
Using BD FACS Aria II, live (DAPI-, Ter119-) cells as well as enriched rare cells (CD31+, CD45+, Epcam+, or PDGFRa GFP-high) were sorted separately in a desired ratio. 35,000 cells were loaded to each well of GEM chip (2 wells of live-sorted cells and 1 well of enriched rare cells for each experimental day) for single-cell capture using the 10x Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics) for aimed target recovery of 20,000 cells per well. Library preparation for both cDNA and MULTI-seq barcodes were performed following 10X library preparation protocol along with MULTI-seq library preparation protocol. Libraries were pooled and subjected to sequencing in a single lane of an Illumina NovaSeq6000 for each experiment.

tag: cell type

value: tissue

tag: tissue

value: small intestine

tag: strain


title: E15.5/16.5 mouse intestine all cells lane 2

description: 10x Genomics


title: E13.5/14.5/E18.5 mouse intestine all cells lane 2

description: 10x Genomics


title: E15.5/16.5 mouse intestine all cells lane 1

description: 10x Genomics


title: MSM6

status: Public on Sep 05 2023

city: Bronx

first: Marija

last: Kundakovic

state: NY

address: 441 E. Fordham Road

department: Biological Sciences

institute: Fordham University

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.6.1b with parameters -outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8  --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20  --alignIntronMax 1000000 --alignMatesGapMax 1000000 --sjdbGTFfile GENCODE_vM15.gtf
The generated counts were analyzed with DESeq2.
Assembly: mm10
Supplementary files format and content: GeneCounts: column 1: gene ID, column 2: counts for unstranded RNA-seq, column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes), column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)

molecule: total RNA

source_name: Bilateral nucleus accumbens

extract_protocol:
Upon sacrifice, whole brains were removed and snap frozen in hexane. Bilateral NAc were dissected inside a cryostat using a brain matrix and 1.5 mm biopsy tissue punch. RNA was isolated from the NAc using the RNeasy Micro Kit (Qiagen).
cDNA libraries were prepared from RNA samples using the RNA HyperPrep Kit with RiboErase (KAPA Biosystems). First, rRNA was depleted from the RNA samples by hybridizing complementary DNA oligonucleotides to rRNA followed by treatment with RNase H and DNase. Following rRNA depletion, RNA was fragmented at 94°C for 5 minutes in the presence of Mg2+ and first and second cDNA strands were synthesized, followed by A-tailing. Single-indexed adaptors (KAPA) were ligated and libraries were amplified by PCR. After bead-based purification, library quality was determined with the Fragment Analyzer (Agilent), and quantification was performed using the Qubit High-Sensitivity DNA assay (Thermo Fisher Scientific).

value: nucleus accumbens

value: 50 days

tag: Sex

value: male

tag: estrous cycle stage

tag: group

value: MS


title: MSM4


title: MSM2


title: CONM4

value: CON


title: CONM6


title: MSF4

value: female


title: MSF6


title: CONM2


title: genomic DNA from eutopic endometrium Sample_8

source_name: endometrium sample 8

value: Female

value: endometrium


title: CONF6


title: CONF2


title: MSF2


title: MSM5

value: Diestrus


title: CONF4


title: MSM1

value: Proestrus/Estrus


title: MSM3

value: Estrus/Metestrus


title: CONM3

value: Metestrus/Diestrus


title: CONM5

value: Proestrus


title: E13.5/14.5/E18.5 mouse intestine all cells lane 1

description: 10x Genomics


title: MSF5


title: MSF3


title: MSF1


title: E15.5/16.5 mouse intestine enriched cells

description: 10x Genomics


title: CONM1


title: CONF1


title: MALE_Cocaine_2

library_source: genomic

data_processing:
The obtained sequences were adapter trimmed and aligned to the mouse reference genome (mm10 including small contigs) using the BWA-MEM software (arXiv:1303.3997v1).
We selected and used only uniquely aligned reads for the analysis. Reads aligned to mitochondrial DNA and PCR duplicate reads were eliminated from further analysis.
We performed peak calling using MACS2.
The featureCounts function of the Rsubreads package was used to count the reads in each peak across replicates.
The resulting count matrix was analyzed using DESeq2.
Assembly: mm10

source_name: FACS-sorted neuronal (NeuN+) nuclei

extract_protocol:
Whole brains were removed, bilateral NAc were dissected immediately and snap frozen in liquid nitrogen.  Total nuclei were extracted using sucrose gradient centrifugation. Neuronal (NeuN+) nuclei were isolated by fluorescence-activated nuclei sorting  with anti-NeuN antibody conjugated to AlexaFluor 488 on a FACSAria instrument. Detailed protocol for total nuclei isolation and purification of neuronal nuclei is provided in Kundakovic et al, 2017 (PMID:27113501).
ATAC-seq libraries were prepared according to Buenrostro et al. 2013 (PMID:24097267) with some modifications. Illumina Nextera DNA Library Prep kit (FC-121-1030) and Nextera Index kit (FC 121-1011) were used to prepare the libraries.

value: Bilateral nucleus accumbens

tag: treatment

value: 10mg/kg Cocaine (i.p.), 1 hour


title: CONF3

value: Metestrus


title: MALE_Control_3

value: Control


title: PRO_Cocaine_4

value: proestrus


title: CONF5

value: nucleus accumbens

value: 50 days


title: DIE_Cocaine_3

value: diestrus


title: PRO_Control_2


title: DIE_Control_2


title: PRO_Cocaine_2


title: DIE_Cocaine_2


title: MALE_Cocaine_1

value: male


title: PRO_Control_3

value: female


title: MALE_Control_2


title: DIE_Cocaine_1


title: DIE_Control_1


title: PRO_Control_1


title: PRO_Cocaine_1


title: MALE_Control_1


title: 97_0618_tumor [COTC022-0618-T]

status: Public on Aug 01 2023

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

data_processing:
The HiSeq Real Time Analysis software (RTA v.3.4.4) was used for processing raw data files. The Illumina bcl2fastq2.17 was used to demultiplex and convert binary base calls and qualities to fastq format. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt.  The trimmed reads were mapped to the CanFam4 reference genome (GSD_1.032 from NCBI) using STAR aligner (version 2.7.0f) with two-pass alignment option. RSEM (version 1.3.1) was used for gene and transcript quantification based on the CanFam4 GTF file.
Supplementary files format and content: tab delimited text files with raw counts for each sample
Supplementary files format and content: tab delimited text files with TPM values for each sample

organism: Canis lupus familiaris

source_name: primary osteosarcoma

extract_protocol:
100 ng to 1µg was used as input to TruSeq Stranded mRNA library kit (Illumina) and generated according to the manufactures protocol
libraries were pooled and sequenced on NovaSeq S1 using a 2x150 cycle kit

value: tumor


title: 96_0606_tumor [COTC022-0606-T]


title: 95_0411_tumor [COTC022-0411-T]


title: 99_0318_tumor [COTC022-0318-T]


title: 98_0306_tumor [COTC022-0306-T]


title: 93_0406_tumor [COTC022-0406-T]


title: 9_2312_Tumor [COTC021-2312-T]


title: 94_0410_tumor [COTC022-0410-T]


title: 91_0402_tumor [COTC022-0402-T]


title: 92_0404_tumor [COTC022-0404-T]


title: DIE_Control_3


title: 90_0224_tumor [COTC022-0224-T]


title: 9_0510_Tumor [COTC022-0510-T]


title: 88_0712_tumor [COTC022-0712-T]


title: 87_0204_tumor [COTC022-0204-T]


title: 86_2215_tumor [COTC021-2215-T]


title: 89_0216_tumor [COTC022-0216-T]


title: 84_1908_tumor [COTC021-1908-T]


title: 8_2202_Tumor [COTC022-2202-T]


title: 85_2205_tumor [COTC021-2205-T]


title: 83_1907_tumor [COTC021-1907-T]


title: 8_0335_Tumor [COTC021-0335-T]


title: 80_1806_tumor [COTC021-1806-T]


title: 82_1905_tumor [COTC021-1905-T]


title: 79_1713_tumor [COTC021-1713-T]


title: 76_1106_tumor [COTC021-1106-T]


title: 77_1417_tumor [COTC021-1417-T]


title: 75_0819_tumor [COTC021-0819-T]


title: 78_1419_tumor [COTC021-1419-T]


title: 71_0643_tumor [COTC021-0643-T]


title: 72_0732_tumor [COTC021-0732-T]


title: 74_0815_tumor [COTC021-0815-T]


title: 7_0309_Tumor [COTC021-0309-T]


title: 7_1022_Tumor [COTC022-1022-T]


title: 70_0225_tumor [COTC022-0225-T]


title: 69_0222_tumor [COTC022-0222-T]


title: 68_0210_tumor [COTC022-0210-T]


title: 73_0813_tumor [COTC021-0813-T]


title: 65_2009_tumor [COTC021-2009-T]


title: 66_0206_tumor [COTC022-0206-T]


title: 64_1009_tumor [COTC021-1009-T]


title: 67_1909_tumor [COTC021-1909-T]


title: 63_1411_tumor [COTC021-1411-T]


title: 61_1005_tumor [COTC021-1005-T]


title: 81_1904_tumor [COTC021-1904-T]


title: 6_1012_Tumor [COTC022-1012-T]


title: 6_0305_Tumor [COTC021-0305-T]


title: 59_1003_tumor [COTC021-1003-T]


title: 57_0709_tumor [COTC021-0709-T]


title: 55_2308_Tumor [COTC022-2308-T]


title: 60_1415_tumor [COTC021-1415-T]


title: 53_2011_Tumor [COTC022-2011-T]


title: 54_2303_Tumor [COTC022-2303-T]


title: 53_0717_tumor [COTC021-0717-T]


title: 56_1001_tumor [COTC021-1001-T]


title: 52_2006_Tumor [COTC022-2006-T]


title: 52_2317_tumor [COTC021-2317-T]


title: 51_0803_tumor [COTC021-0803-T]


title: 5_0220_Tumor [COTC022-0220-T]


title: 50_0703_tumor [COTC021-0703-T]


title: 48_0705_tumor [COTC021-0705-T]


title: 48_1712_Tumor [COTC022-1712-T]


title: 62_2003_tumor [COTC021-2003-T]


title: 47_2321_tumor [COTC021-2321-T]


title: 49_1803_Tumor [COTC022-1803-T]


title: 51_1902_Tumor [COTC022-1902-T]


title: 58_1104_tumor [COTC021-1104-T]


title: 46_1405_tumor [COTC021-1405-T]


title: 46_1703_Tumor [COTC021-1703-T]


title: 45_1024_tumor [COTC021-1024-T]


title: 47_1709_Tumor [COTC022-1709-T]


title: 44_1412_Tumor [COTC022-1412-T]


title: 44_0713_tumor [COTC021-0713-T]


title: 43_1410_Tumor [COTC022-1410-T]


title: 55_2307_tumor [COTC021-2307-T]


title: 43_1401_tumor [COTC021-1401-T]


title: 42_1409_Tumor [COTC021-1409-T]


title: 54_1013_tumor [COTC021-1013-T]


title: 42_0715_tumor [COTC021-0715-T]


title: 41_2007_tumor [COTC021-2007-T]


title: 4_0215_Tumor [COTC021-0215-T]


title: 41_1407_Tumor [COTC021-1407-T]


title: 50_1805_Tumor [COTC021-1805-T]


title: 5_0817_Tumor [COTC021-0817-T]


title: 49_1903_tumor [COTC021-1903-T]


title: 40_1107_Tumor [COTC022-1107-T]


title: 4_0214_Tumor [COTC022-0214-T]


title: 39_1103_Tumor [COTC021-1103-T]


title: 39_0701_tumor [COTC021-0701-T]


title: 38_0630_tumor [COTC021-0630-T]


title: 36_0607_tumor [COTC021-0607-T]


title: 36_1014_Tumor [COTC022-1014-T]


title: 37_1015_Tumor [COTC021-1015-T]


title: 34_1004_Tumor [COTC022-1004-T]


title: 35_1007_Tumor [COTC021-1007-T]


title: 35_0603_tumor [COTC021-0603-T]


title: 32_0904_Tumor [COTC022-0904-T]


title: 32_0523_tumor [COTC021-0523-T]


title: 33_0524_tumor [COTC021-0524-T]


title: 34_0601_tumor [COTC021-0601-T]


title: 31_0519_tumor [COTC021-0519-T]


title: 33_1002_Tumor [COTC022-1002-T]


title: 3_0212_Tumor [COTC022-0212-T]


title: 30_0814_RNAla_Ter_tumor [COTC021-0814-T]


title: 30_0517_tumor [COTC021-0517-T]


title: 29_0515_tumor [COTC021-0515-T]


title: 28_0725_Tumor [COTC021-0725-T]


title: 29_0729_Tumor [COTC022-0729-T]


title: 40_1101_tumor [COTC021-1101-T]


title: 27_0723_Tumor [COTC021-0723-T]


title: 28_0513_tumor [COTC021-0513-T]


title: 27_0511_tumor [COTC021-0511-T]


title: 38_1016_Tumor [COTC022-1016-T]


title: 24_0704_Tumor [COTC022-0704-T]


title: 37_0625_tumor [COTC021-0625-T]


title: 25_0706_Tumor [COTC022-0706-T]


title: 26_0722_Tumor [COTC021-0722-T]


title: 26_0509_tumor [COTC021-0509-T]


title: 25_0505_tumor [COTC021-0505-T]


title: 23_0642_Tumor [COTC022-0642-T]


title: 23_0329_tumor [COTC021-0329-T]


title: 24_0405_tumor [COTC021-0405-T]


title: 22_0317_tumor [COTC021-0317-T]


title: 3_0207_Tumor [COTC021-0207-T]


title: 20_0307_tumor [COTC021-0307-T]


title: 2_0209_Tumor [COTC021-0209-T]


title: 19_0303_tumor [COTC021-0303-T]


title: 2_0203_Tumor [COTC021-0203-T]


title: 19_0621_Tumor [COTC021-0621-T]


title: 18_0301_tumor [COTC021-0301-T]


title: 21_0631_Tumor [COTC021-0631-T]


title: 17_0620_Tumor [COTC022-0620-T]


title: 141_1707_tumor [COTC022-1707-T]


title: 143_1916_tumor [COTC022-1916-T]


title: 15_0615_Tumor [COTC022-0615-T]


title: 16_0616_Tumor [COTC022-0616-T]


title: 142_1710_tumor [COTC022-1710-T]


title: 16_0211_tumor [COTC021-0211-T]


title: 14_0614_Tumor [COTC022-0614-T]


title: 140_0905_tumor [COTC022-0905-T]


title: 139_0733_tumor [COTC022-0733-T]


title: 17_0226_tumor [COTC021-0226-T]


title: 136_0105_tumor [COTC021-0105-T]


title: 134_2208_tumor [COTC022-2208-T]


title: 22_0640_Tumor [COTC021-0640-T]


title: 135_0102_tumor [COTC022-0102-T]


title: 138_0314_tumor [COTC021-0314-T]


title: 21_0311_tumor [COTC021-0311-T]


title: 133_0907_tumor [COTC022-0907-T]


title: 131_2012_tumor [COTC022-2012-T]


title: 128_1023_tumor [COTC022-1023-T]


title: 129_1414_tumor [COTC022-1414-T]


title: 127_2010_tumor [COTC022-2010-T]


title: 132_1025_tumor [COTC022-1025-T]


title: 13_0613_Tumor [COTC022-0613-T]


title: 126_0228_tumor [COTC022-0228-T]


title: 123_2316_tumor [COTC022-2316-T]


title: 122_0504_tumor [COTC022-0504-T]


title: 121_2322_tumor [COTC022-2322-T]


title: 125_2004_tumor [COTC022-2004-T]


title: 12_0608_Tumor [COTC022-0608-T]


title: 137_0106_tumor [COTC022-0106-T]


title: 119_0516_tumor [COTC022-0516-T]


title: 115_2318_tumor [COTC022-2318-T]


title: 114_1704_tumor [COTC022-1704-T]


title: 117_1011_tumor [COTC022-1011-T]


title: 118_2304_tumor [COTC022-2304-T]


title: 116_0506_tumor [COTC022-0506-T]


title: 120_2306_tumor [COTC022-2306-T]


title: 112_0502_tumor [COTC022-0502-T]


title: 113_1010_tumor [COTC022-1010-T]


title: 111_1708_tumor [COTC022-1708-T]


title: 109_0721_tumor [COTC022-0721-T]


title: 11_0602_Tumor [COTC022-0602-T]


title: 105_0710_tumor [COTC022-0710-T]


title: 107_0719_tumor [COTC022-0719-T]


title: 110_0522_tumor [COTC022-0522-T]


title: 108_0720_tumor [COTC022-0720-T]


title: 104_0702_tumor [COTC022-0702-T]


title: 1_0202_tumor [COTC022-0202-T]


title: 106_0716_tumor [COTC022-0716-T]


title: 101_0518_tumor [COTC022-0518-T]


title: 10_0512_Tumor [COTC022-0512-T]


title: 1_0201_tumor [COTC021-0201-T]


title: 103_0639_tumor [COTC022-0639-T]


title: 100_0514_tumor [COTC022-0514-T]


title: RPTEC cells, input, KO2, rep1

status: Public on Jul 12 2023

city: Rochester

first: Keith

middle: Darrell

last: Robertson

state: MN

address: 200 First Street SW, Stabile 12-70

department: Pharmacology

institute: Mayo Clinic

data_processing:
ChIP-seq reads were aligned to the UCSC hg38 genome using bowtie2 v2.3.3.1.
ChIP-seq reads for KO were normalized to Drosophila spike-in control and the broad peaks were called using Spiker pipeline (https://spiker.readthedocs.io/en/latest/installation.html). For WT and rescue, the peaks are called using MACS v2.2.7.1 with the significance cut-off q-value <=0.05
Differential analysis of peaks were analyzed using DiffBind v2.14.0
Assembly: hg38
Supplementary files format and content: bed (except for Input sample)

source_name: RPTEC

growth_protocol: RPTEC epithelial cells were maintained in DMEM:F12 supplemented with 10% fetal bovine serum (FBS), MEM non-essential amino acids, MEM sodium pyruvate, RPTEC growth kit supplement A 5ml and supplement B 8ml. 250 ug/ml G418 is used for maintaining selection of hTERT

extract_protocol:
6 million cells were fixed with 1% formaldehyde for 10 minutes. After quenching with glycine and cell lysis, chromatin was sonicated using a Diagenode Twin Sonicator. Input was then taken from supernatant. IP fraction was pulled down using H3K36me3 antibody. A Drosophila spike-in chromatin was also prepared as a control.
ChIP-seq libraries were prepared using the ThruPLEX DNA-seq kit.

tag: cell line

value: RPTEC

value: Human renal epithelial cells

tag: chip antibody

value: input

tag: genotype


title: RPTEC cells, input, KO1, rep1


title: RPTEC cells, input, WT, rep1

value: WT


title: RPTEC cells, H3K36me3, Rescue1, input, rep1


title: RPTEC cells, H3K36me3, Rescue2, rep1

value: H3K36me3 (Active Motif 61021)


title: RPTEC cells, input, WT, rep2


title: RPTEC cells, input, KO2, rep2


title: RPTEC cells, H3K36me3, Rescue2, rep2


title: RPTEC cells, H3K36me3, Rescue2, input, rep2


title: RPTEC cells, input, KO1, rep2


title: RPTEC cells, H3K36me3, Rescue2, input, rep1


title: RPTEC cells, H3K36me3, Rescue1, rep1


title: RPTEC cells, H3K36me3, KO2, rep1


title: RPTEC cells, H3K36me3, Rescue1, rep2


title: RPTEC cells, H3K36me3, KO2, rep2


title: RPTEC cells, H3K36me3, WT, rep2


title: RPTEC cells, H3K36me3, WT, rep1


title: RPTEC cells, H3K36me3, Rescue1, input, rep2


title: 102_0619_tumor [COTC022-0619-T]


title: RPTEC cells, ATAC, KO2, rep2

data_processing:
ATAC-seq reads were aligned to the UCSC hg38 genome using bwa v0.7.17.
Narrow peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=0.05
Differential analysis of peaks were analyzed using DiffBind v2.14.0
Assembly: hg38
Supplementary files format and content: bed (except for Input sample)

extract_protocol:
50,000 cells were harvested for Tn5 transposition reaction
Nextera DNA Sample Preparation kit is specifically used for library prep.


title: RPTEC cells, ATAC, KO2, rep3


title: RPTEC cells, ATAC, Rescue2, rep1


title: RPTEC cells, ATAC, KO2, rep1


title: RPTEC cells, ATAC, Rescue1, rep2


title: RPTEC cells, ATAC, Rescue2, rep3


title: RPTEC cells, ATAC, Rescue1, rep3


title: RPTEC cells, ATAC, KO1, rep2


title: RPTEC cells, WT, lentiviral transduction, SOX2, rep1

data_processing:
Sequence reads were quantified and mapped to reference transcripts using Salmon v1.9.0
Estimated raw counts were extracted using tximport v1.14.2. The counts is normalized by VST (variance stabilizing transformation).
Differential analysis is then performed by DESeq2 v1.26.0
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample

growth_protocol: RPTEC epithelial cells were maintained in DMEM:F12 supplemented with 10% fetal bovine serum (FBS), MEM non-essential amino acids, MEM sodium pyruvate, RPTEC growth kit supplement A 5ml and supplement B 8ml. 250 ug/ml G418 is used for maintaining selection of hTERT. SETD2 expression is maintained in rescue cell lines using 5ug/ml blasticidin.

extract_protocol:
RNA was extracted using Trizol and chloroform. 3 ug of total RNA was used for the construction of sequencing libraries.
Libraries for RNA-seq were prepared using TruSeq Stranded mRNA Kit following manufacturer's protocols.

treatment_protocol: For inducing mesenchymal differentiation, RPTEC WT cells were pretreated with 2%FBS for 24h followed by 10ng/ml TGFβ treatment for 72h. WT and KO cells treated with 2%FBS are used as control. Rescue cells were cultured in regular media containing 10%FBS.

value: Regular media

tag: time


title: RPTEC cells, ATAC, KO1, rep1


title: RPTEC cells, ATAC, KO1, rep3


title: RPTEC cells, ATAC, WT, rep3


title: RPTEC cells, H3K36me3, KO1, rep2


title: RPTEC cells, WT, lentiviral transduction, OCT2, rep2


title: RPTEC cells, WT, lentiviral transduction, PRRX1, rep2


title: RPTEC cells, H3K36me3, KO1, rep1


title: RPTEC cells, ATAC, WT, rep2


title: RPTEC cells, ATAC, WT, rep1


title: RPTEC cells, WT, lentiviral transduction, SOX2, rep2


title: RPTEC cells, WT, lentiviral transduction, OCT2, rep1


title: RPTEC cells, Rescue2, rep2


title: RPTEC cells, Rescue2, rep1


title: RPTEC cells, Rescue1, rep2


title: RPTEC cells, ATAC, Rescue2, rep2


title: RPTEC cells, ATAC, Rescue1, rep1


title: RPTEC cells, WT, lentiviral transduction, empty vector, rep1


title: RPTEC cells, WT, lentiviral transduction, empty vector, rep2


title: RPTEC cells, Rescue1, rep1


title: RPTEC cells, KO2_Rescue, untreated, rep1


title: RPTEC cells, KO1, untreated, rep1


title: RPTEC cells, KO2_Rescue, untreated, rep2


title: RPTEC cells, KO1, untreated, rep2


title: RPTEC cells, KO2, untreated, rep2


title: RPTEC cells, WT, TGFβ-treated, 72h, rep1

value: 2%FBS, TGFβ


title: RPTEC cells, WT, TGFβ-treated, 72h, rep2


title: RPTEC cells, WT, untreated, rep2


title: RPTEC cells, WT, untreated, rep1


title: UPN3 PrePost Not T Enriched CITE

status: Public on Jun 26 2023

city: New York

first: Sanam

last: Shahid

state: New York

address: 1275 York Avenue

department: Department of Pediatrics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Filtered gene expression matrices were generated using 10X CellRanger (version 6.0.1).
Paired single-cell VDJ sequences and annotations were generated using 10X Cellranger VDJ (version 6.0.1) and high confidence sequences were mapped to gene expression barcodes.
Feature barcode matrices were generated for each CITE-seq sample using antibody barcode patterns from TotalSeq.
Assembly: GRCh38
Supplementary files format and content: *_GEX.h5 CellRanger h5 Gene by Cell Matrix
Supplementary files format and content: *_FB.h5 CellRanger h5 Gene by Cell Matrix
Supplementary files format and content: *_VDJ.csv CellRanger h5 Gene by Cell Matrix
Library strategy: CITE-seq

source_name: Bone Marrow Aspirate

extract_protocol:
Frozen human bone marrow specimens were thawed and transferred into 5mL polypropylene FACS tubes and resuspended in 4mL PBS + 2mM EDTA + 2% FBS (staining buffer). Cell suspensions were centrifuged at 500g for 5 minutes at 4°C and supernatant was discarded (all subsequent wash steps performed the same way). Cell pellets were re-suspended in staining buffer and counted. For each sample with > 106 live cells, 70% was used for T cell sorting (described below). The remaining 30% of the sample, or the entire sample for those with < 106 live cells, were washed and proceeded to dead cell removal (Miltenyi Biotec). Dead cells were depleted according to manufacturer’s instructions, with the exception of the incubation period shortened to 5 minutes and column washes reduced to 3 times. The live cell fraction was washed, resuspended in staining buffer, and counted. Samples were re-suspended in PBS + 2% FBS (labeling buffer) and Human FcR Blocking Reagent (1:50, Miltenyi Biotec) and incubated on ice for 5 minutes. Samples were tagged with cell hashing (Stoeckius et al., 2018) oligo-tagged antibodies (TotalSeq-C0251 anti-human hashtag 1 antibody and TotalSeq-C0252 anti-human hashtag 2 antibody, BioLegend) according to manufacturer’s instructions. After tagging, samples were washed 3 times in labeling buffer, and then each patient’s samples were pooled together and washed. Samples were re-suspended in labeling buffer and Human FcR Blocking Reagent (1:50, Miltenyi Biotec) and incubated on ice for 5 minutes. CITE-Seq antibodies (TotalSeq-C Human Universal Cocktail, BioLegend) were stained according to manufacturer’s instructions (https://cite-seq.com/protocol/) using the above described labeling buffer for all steps. After staining, samples were washed 3 times in labeling buffer and resuspended at a concentration of 103 cells per μL in cold PBS + 0.04% BSA (sequencing buffer).
Fresh cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following quality control (QC), the single cell suspension was loaded onto a Chromium Next GEM Chip K (10X Genomics PN 1000286). GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 2,000-14,000 cells proceeded using the Chromium Next GEM Single Cell 5’ Kit v2 (10X Genomics PN 1000263) according to the manufacturer’s protocol. cDNA amplification included 13-14 cycles, and 38-50ng of the material was used to prepare sequencing libraries with 14 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/91 run using the NovaSeq 6000 S1 or S2 Reagent Kit (100 or 200 cycles) (Illumina). An average of 263 million paired reads were generated per sample.

value: Bone Marrow Aspirate

tag: disease state

value: AML


title: HD T Enriched VDJ

data_processing:
Filtered gene expression matrices were generated using 10X CellRanger (version 6.0.1).
Paired single-cell VDJ sequences and annotations were generated using 10X Cellranger VDJ (version 6.0.1) and high confidence sequences were mapped to gene expression barcodes.
Feature barcode matrices were generated for each CITE-seq sample using antibody barcode patterns from TotalSeq.
Assembly: GRCh38
Supplementary files format and content: *_GEX.h5 CellRanger h5 Gene by Cell Matrix
Supplementary files format and content: *_FB.h5 CellRanger h5 Gene by Cell Matrix
Supplementary files format and content: *_VDJ.csv CellRanger h5 Gene by Cell Matrix
Library strategy: VDJ-seq


title: UPN1 PrePost Not T Enriched CITE


title: UPN4 PrePost Not T Enriched CITE


title: UPN4 PrePost T Enriched VDJ


title: UPN2 Pre T Enriched VDJ


title: UPN2 PrePost Not T Enriched CITE