title: Blood sample from individual 862

description: Sample ID: 862


title: Blood sample from individual 842

status: Public on Apr 08 2022

type: genomic

city: Darlinghurst

first: Joseph

middle: E

last: Powell

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: Sample ID: 842

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Genomic DNA extracted from blood was genotyped using the Infinium Global Screening Array-24 v1.0 BeadChip (Illumina).
Primary assessment and SNP call rate quality control of SNP intensity output files were performed using GenomeStudio software (Illumina).
Genotype: AA,AB,BB,or NC (no call)
Processed data file onek1k_genotype_matrix.txt.gz is linked as supplementary file at the foot of the Series record.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood sample

label_protocol: Standard Illumina label protocol

extract_protocol: DNA was extracted from blood stored in EDTA tubes using the QIAamp Blood Mini kit.

tag: individual id

tag: gender

value: Male

tag: tissue

value: Blood

tag: disease state

value: No active inflammatory disease


title: Blood sample from individual 840

description: Sample ID: 840

value: Female


title: Blood sample from individual 836

description: Sample ID: 836


title: Blood sample from individual 835

description: Sample ID: 835


title: Blood sample from individual 838

description: Sample ID: 838


title: Blood sample from individual 839

description: Sample ID: 839


title: Blood sample from individual 855

description: Sample ID: 855


title: Blood sample from individual 834

description: Sample ID: 834


title: Blood sample from individual 831

description: Sample ID: 831


title: Blood sample from individual 832

description: Sample ID: 832


title: Blood sample from individual 853

description: Sample ID: 853


title: Blood sample from individual 829

description: Sample ID: 829


title: Blood sample from individual 830

description: Sample ID: 830


title: Blood sample from individual 833

description: Sample ID: 833


title: Blood sample from individual 827

description: Sample ID: 827


title: Blood sample from individual 826

description: Sample ID: 826


title: Blood sample from individual 841

description: Sample ID: 841


title: Blood sample from individual 819

description: Sample ID: 819


title: Blood sample from individual 843

description: Sample ID: 843


title: Blood sample from individual 824

description: Sample ID: 824


title: Blood sample from individual 820

description: Sample ID: 820


title: Blood sample from individual 825

description: Sample ID: 825


title: Blood sample from individual 821

description: Sample ID: 821


title: Blood sample from individual 822

description: Sample ID: 822


title: Blood sample from individual 818

description: Sample ID: 818


title: Blood sample from individual 817

description: Sample ID: 817


title: Blood sample from individual 816

description: Sample ID: 816


title: Blood sample from individual 815

description: Sample ID: 815


title: Blood sample from individual 837

description: Sample ID: 837


title: Blood sample from individual 814

description: Sample ID: 814


title: Blood sample from individual 813

description: Sample ID: 813


title: Blood sample from individual 812

description: Sample ID: 812


title: Blood sample from individual 811

description: Sample ID: 811


title: Blood sample from individual 810

description: Sample ID: 810


title: Blood sample from individual 828

description: Sample ID: 828


title: Blood sample from individual 805

description: Sample ID: 805


title: Blood sample from individual 806

description: Sample ID: 806


title: Blood sample from individual 808

description: Sample ID: 808


title: Blood sample from individual 809

description: Sample ID: 809


title: Blood sample from individual 807

description: Sample ID: 807


title: Blood sample from individual 804

description: Sample ID: 804


title: Blood sample from individual 802

description: Sample ID: 802


title: Blood sample from individual 800

description: Sample ID: 800


title: Blood sample from individual 801

description: Sample ID: 801


title: Blood sample from individual 794

description: Sample ID: 794


title: Blood sample from individual 799

description: Sample ID: 799


title: Blood sample from individual 795

description: Sample ID: 795


title: Blood sample from individual 797

description: Sample ID: 797


title: Blood sample from individual 798

description: Sample ID: 798


title: Blood sample from individual 796

description: Sample ID: 796


title: Blood sample from individual 793

description: Sample ID: 793


title: Blood sample from individual 791

description: Sample ID: 791


title: Blood sample from individual 790

description: Sample ID: 790


title: Blood sample from individual 792

description: Sample ID: 792


title: Blood sample from individual 789

description: Sample ID: 789


title: Blood sample from individual 823

description: Sample ID: 823


title: Blood sample from individual 786

description: Sample ID: 786


title: Blood sample from individual 784

description: Sample ID: 784


title: Blood sample from individual 782

description: Sample ID: 782


title: Blood sample from individual 783

description: Sample ID: 783


title: Blood sample from individual 803

description: Sample ID: 803


title: Blood sample from individual 785

description: Sample ID: 785


title: Blood sample from individual 781

description: Sample ID: 781


title: Blood sample from individual 777

description: Sample ID: 777


title: Blood sample from individual 787

description: Sample ID: 787


title: Blood sample from individual 780

description: Sample ID: 780


title: Blood sample from individual 774

description: Sample ID: 774


title: Blood sample from individual 773

description: Sample ID: 773


title: Blood sample from individual 779

description: Sample ID: 779


title: Blood sample from individual 778

description: Sample ID: 778


title: Blood sample from individual 772

description: Sample ID: 772


title: Blood sample from individual 771

description: Sample ID: 771


title: Blood sample from individual 768

description: Sample ID: 768


title: Blood sample from individual 769

description: Sample ID: 769


title: Blood sample from individual 763

description: Sample ID: 763


title: Blood sample from individual 766

description: Sample ID: 766


title: Blood sample from individual 760

description: Sample ID: 760


title: Blood sample from individual 761

description: Sample ID: 761


title: Blood sample from individual 759

description: Sample ID: 759


title: Blood sample from individual 770

description: Sample ID: 770


title: Blood sample from individual 765

description: Sample ID: 765


title: Blood sample from individual 788

description: Sample ID: 788


title: Blood sample from individual 757

description: Sample ID: 757


title: Blood sample from individual 758

description: Sample ID: 758


title: Blood sample from individual 767

description: Sample ID: 767


title: Blood sample from individual 776

description: Sample ID: 776


title: Blood sample from individual 756

description: Sample ID: 756


title: Blood sample from individual 754

description: Sample ID: 754


title: Blood sample from individual 750

description: Sample ID: 750


title: Blood sample from individual 755

description: Sample ID: 755


title: Blood sample from individual 749

description: Sample ID: 749


title: Blood sample from individual 747

description: Sample ID: 747


title: Blood sample from individual 762

description: Sample ID: 762


title: Blood sample from individual 775

description: Sample ID: 775


title: Blood sample from individual 748

description: Sample ID: 748


title: Blood sample from individual 752

description: Sample ID: 752


title: Blood sample from individual 751

description: Sample ID: 751


title: Blood sample from individual 753

description: Sample ID: 753


title: Blood sample from individual 743

description: Sample ID: 743


title: Blood sample from individual 745

description: Sample ID: 745


title: Blood sample from individual 741

description: Sample ID: 741


title: Blood sample from individual 746

description: Sample ID: 746


title: Blood sample from individual 764

description: Sample ID: 764


title: Blood sample from individual 736

description: Sample ID: 736


title: Blood sample from individual 735

description: Sample ID: 735


title: Blood sample from individual 734

description: Sample ID: 734


title: Blood sample from individual 740

description: Sample ID: 740


title: Blood sample from individual 733

description: Sample ID: 733


title: Blood sample from individual 732

description: Sample ID: 732


title: Blood sample from individual 744

description: Sample ID: 744


title: Blood sample from individual 738

description: Sample ID: 738


title: Blood sample from individual 731

description: Sample ID: 731


title: Blood sample from individual 730

description: Sample ID: 730


title: Blood sample from individual 729

description: Sample ID: 729


title: Blood sample from individual 725

description: Sample ID: 725


title: Blood sample from individual 726

description: Sample ID: 726


title: Blood sample from individual 727

description: Sample ID: 727


title: Blood sample from individual 728

description: Sample ID: 728


title: Blood sample from individual 723

description: Sample ID: 723


title: Blood sample from individual 722

description: Sample ID: 722


title: Blood sample from individual 721

description: Sample ID: 721


title: Blood sample from individual 720

description: Sample ID: 720


title: Blood sample from individual 718

description: Sample ID: 718


title: Blood sample from individual 742

description: Sample ID: 742


title: Blood sample from individual 719

description: Sample ID: 719


title: Blood sample from individual 737

description: Sample ID: 737


title: Blood sample from individual 717

description: Sample ID: 717


title: Blood sample from individual 739

description: Sample ID: 739


title: Blood sample from individual 713

description: Sample ID: 713


title: Blood sample from individual 711

description: Sample ID: 711


title: Blood sample from individual 716

description: Sample ID: 716


title: Blood sample from individual 714

description: Sample ID: 714


title: Blood sample from individual 712

description: Sample ID: 712


title: Blood sample from individual 710

description: Sample ID: 710


title: Blood sample from individual 707

description: Sample ID: 707


title: Blood sample from individual 708

description: Sample ID: 708


title: Blood sample from individual 705

description: Sample ID: 705


title: Blood sample from individual 709

description: Sample ID: 709


title: Blood sample from individual 706

description: Sample ID: 706


title: Blood sample from individual 703

description: Sample ID: 703


title: Blood sample from individual 724

description: Sample ID: 724


title: Blood sample from individual 699

description: Sample ID: 699


title: Blood sample from individual 700

description: Sample ID: 700


title: Blood sample from individual 698

description: Sample ID: 698


title: Blood sample from individual 701

description: Sample ID: 701


title: Blood sample from individual 696

description: Sample ID: 696


title: Blood sample from individual 697

description: Sample ID: 697


title: Blood sample from individual 715

description: Sample ID: 715


title: Blood sample from individual 702

description: Sample ID: 702


title: Blood sample from individual 691

description: Sample ID: 691


title: Blood sample from individual 695

description: Sample ID: 695


title: Blood sample from individual 693

description: Sample ID: 693


title: Blood sample from individual 692

description: Sample ID: 692


title: Blood sample from individual 690

description: Sample ID: 690


title: Blood sample from individual 689

description: Sample ID: 689


title: Blood sample from individual 688

description: Sample ID: 688


title: Blood sample from individual 683

description: Sample ID: 683


title: Blood sample from individual 687

description: Sample ID: 687


title: Blood sample from individual 677

description: Sample ID: 677


title: Blood sample from individual 682

description: Sample ID: 682


title: Blood sample from individual 679

description: Sample ID: 679


title: Blood sample from individual 676

description: Sample ID: 676


title: Blood sample from individual 685

description: Sample ID: 685


title: Blood sample from individual 675

description: Sample ID: 675


title: Blood sample from individual 684

description: Sample ID: 684


title: Blood sample from individual 670

description: Sample ID: 670


title: Blood sample from individual 672

description: Sample ID: 672


title: Blood sample from individual 704

description: Sample ID: 704


title: Blood sample from individual 671

description: Sample ID: 671


title: Blood sample from individual 680

description: Sample ID: 680


title: Blood sample from individual 678

description: Sample ID: 678


title: Blood sample from individual 674

description: Sample ID: 674


title: Blood sample from individual 667

description: Sample ID: 667


title: Blood sample from individual 668

description: Sample ID: 668


title: Blood sample from individual 669

description: Sample ID: 669


title: Blood sample from individual 673

description: Sample ID: 673


title: Blood sample from individual 665

description: Sample ID: 665


title: Blood sample from individual 686

description: Sample ID: 686


title: Blood sample from individual 681

description: Sample ID: 681


title: Blood sample from individual 666

description: Sample ID: 666


title: Blood sample from individual 664

description: Sample ID: 664


title: Blood sample from individual 663

description: Sample ID: 663


title: Blood sample from individual 662

description: Sample ID: 662


title: Blood sample from individual 661

description: Sample ID: 661


title: Blood sample from individual 659

description: Sample ID: 659


title: Blood sample from individual 658

description: Sample ID: 658


title: Blood sample from individual 657

description: Sample ID: 657


title: Blood sample from individual 655

description: Sample ID: 655


title: Blood sample from individual 660

description: Sample ID: 660


title: Blood sample from individual 656

description: Sample ID: 656


title: Blood sample from individual 654

description: Sample ID: 654


title: Blood sample from individual 653

description: Sample ID: 653


title: Blood sample from individual 650

description: Sample ID: 650


title: Blood sample from individual 647

description: Sample ID: 647


title: Blood sample from individual 651

description: Sample ID: 651


title: Blood sample from individual 652

description: Sample ID: 652


title: Blood sample from individual 645

description: Sample ID: 645


title: Blood sample from individual 646

description: Sample ID: 646


title: Blood sample from individual 644

description: Sample ID: 644


title: Blood sample from individual 641

description: Sample ID: 641


title: Blood sample from individual 642

description: Sample ID: 642


title: Blood sample from individual 648

description: Sample ID: 648


title: Blood sample from individual 638

description: Sample ID: 638


title: Blood sample from individual 643

description: Sample ID: 643


title: Blood sample from individual 640

description: Sample ID: 640


title: Blood sample from individual 636

description: Sample ID: 636


title: Blood sample from individual 635

description: Sample ID: 635


title: Blood sample from individual 694

description: Sample ID: 694


title: Blood sample from individual 634

description: Sample ID: 634


title: Blood sample from individual 637

description: Sample ID: 637


title: Blood sample from individual 633

description: Sample ID: 633


title: Blood sample from individual 649

description: Sample ID: 649


title: Blood sample from individual 631

description: Sample ID: 631


title: Blood sample from individual 629

description: Sample ID: 629


title: Blood sample from individual 621

description: Sample ID: 621


title: Blood sample from individual 630

description: Sample ID: 630


title: Blood sample from individual 626

description: Sample ID: 626


title: Blood sample from individual 632

description: Sample ID: 632


title: Blood sample from individual 619

description: Sample ID: 619


title: Blood sample from individual 628

description: Sample ID: 628


title: Blood sample from individual 625

description: Sample ID: 625


title: Blood sample from individual 620

description: Sample ID: 620


title: Blood sample from individual 623

description: Sample ID: 623


title: Blood sample from individual 627

description: Sample ID: 627


title: Blood sample from individual 624

description: Sample ID: 624


title: Blood sample from individual 615

description: Sample ID: 615


title: Blood sample from individual 617

description: Sample ID: 617


title: Blood sample from individual 622

description: Sample ID: 622


title: Blood sample from individual 612

description: Sample ID: 612


title: Blood sample from individual 611

description: Sample ID: 611


title: Blood sample from individual 639

description: Sample ID: 639


title: Blood sample from individual 614

description: Sample ID: 614


title: Blood sample from individual 610

description: Sample ID: 610


title: Blood sample from individual 613

description: Sample ID: 613


title: Blood sample from individual 608

description: Sample ID: 608


title: Blood sample from individual 609

description: Sample ID: 609


title: Blood sample from individual 606

description: Sample ID: 606


title: Blood sample from individual 607

description: Sample ID: 607


title: Blood sample from individual 605

description: Sample ID: 605


title: Blood sample from individual 604

description: Sample ID: 604


title: Blood sample from individual 618

description: Sample ID: 618


title: Blood sample from individual 602

description: Sample ID: 602


title: Blood sample from individual 599

description: Sample ID: 599


title: Blood sample from individual 600

description: Sample ID: 600


title: Blood sample from individual 603

description: Sample ID: 603


title: Blood sample from individual 593

description: Sample ID: 593


title: Blood sample from individual 598

description: Sample ID: 598


title: Blood sample from individual 616

description: Sample ID: 616


title: Blood sample from individual 596

description: Sample ID: 596


title: Blood sample from individual 590

description: Sample ID: 590


title: Blood sample from individual 595

description: Sample ID: 595


title: Blood sample from individual 594

description: Sample ID: 594


title: Blood sample from individual 589

description: Sample ID: 589


title: Blood sample from individual 592

description: Sample ID: 592


title: Blood sample from individual 585

description: Sample ID: 585


title: Blood sample from individual 584

description: Sample ID: 584


title: Blood sample from individual 586

description: Sample ID: 586


title: Blood sample from individual 583

description: Sample ID: 583


title: Blood sample from individual 582

description: Sample ID: 582


title: Blood sample from individual 581

description: Sample ID: 581


title: Blood sample from individual 578

description: Sample ID: 578


title: Blood sample from individual 579

description: Sample ID: 579


title: Blood sample from individual 580

description: Sample ID: 580


title: Blood sample from individual 597

description: Sample ID: 597


title: Blood sample from individual 601

description: Sample ID: 601


title: Blood sample from individual 576

description: Sample ID: 576


title: Blood sample from individual 591

description: Sample ID: 591


title: Blood sample from individual 577

description: Sample ID: 577


title: Blood sample from individual 572

description: Sample ID: 572


title: Blood sample from individual 575

description: Sample ID: 575


title: Blood sample from individual 573

description: Sample ID: 573


title: Blood sample from individual 588

description: Sample ID: 588


title: Blood sample from individual 568

description: Sample ID: 568


title: Blood sample from individual 571

description: Sample ID: 571


title: Blood sample from individual 564

description: Sample ID: 564


title: Blood sample from individual 569

description: Sample ID: 569


title: Blood sample from individual 567

description: Sample ID: 567


title: Blood sample from individual 570

description: Sample ID: 570


title: Blood sample from individual 562

description: Sample ID: 562


title: Blood sample from individual 587

description: Sample ID: 587


title: Blood sample from individual 566

description: Sample ID: 566


title: Blood sample from individual 565

description: Sample ID: 565


title: Blood sample from individual 557

description: Sample ID: 557


title: Blood sample from individual 561

description: Sample ID: 561


title: Blood sample from individual 555

description: Sample ID: 555


title: Blood sample from individual 559

description: Sample ID: 559


title: Blood sample from individual 554

description: Sample ID: 554


title: Blood sample from individual 560

description: Sample ID: 560


title: Blood sample from individual 558

description: Sample ID: 558


title: Blood sample from individual 563

description: Sample ID: 563


title: Blood sample from individual 552

description: Sample ID: 552


title: Blood sample from individual 556

description: Sample ID: 556


title: Blood sample from individual 574

description: Sample ID: 574


title: Blood sample from individual 553

description: Sample ID: 553


title: Blood sample from individual 549

description: Sample ID: 549


title: Blood sample from individual 551

description: Sample ID: 551


title: Blood sample from individual 544

description: Sample ID: 544


title: Blood sample from individual 548

description: Sample ID: 548


title: Blood sample from individual 542

description: Sample ID: 542


title: Blood sample from individual 547

description: Sample ID: 547


title: Blood sample from individual 545

description: Sample ID: 545


title: Blood sample from individual 538

description: Sample ID: 538


title: Blood sample from individual 546

description: Sample ID: 546


title: Blood sample from individual 536

description: Sample ID: 536


title: Blood sample from individual 550

description: Sample ID: 550


title: Blood sample from individual 541

description: Sample ID: 541


title: Blood sample from individual 543

description: Sample ID: 543


title: Blood sample from individual 534

description: Sample ID: 534


title: Blood sample from individual 540

description: Sample ID: 540


title: Blood sample from individual 533

description: Sample ID: 533


title: Blood sample from individual 537

description: Sample ID: 537


title: Blood sample from individual 535

description: Sample ID: 535


title: Blood sample from individual 532

description: Sample ID: 532


title: Blood sample from individual 527

description: Sample ID: 527


title: Blood sample from individual 525

description: Sample ID: 525


title: Blood sample from individual 524

description: Sample ID: 524


title: Blood sample from individual 531

description: Sample ID: 531


title: Blood sample from individual 529

description: Sample ID: 529


title: Blood sample from individual 528

description: Sample ID: 528


title: Blood sample from individual 520

description: Sample ID: 520


title: Blood sample from individual 523

description: Sample ID: 523


title: Blood sample from individual 530

description: Sample ID: 530


title: Blood sample from individual 522

description: Sample ID: 522


title: Blood sample from individual 516

description: Sample ID: 516


title: Blood sample from individual 521

description: Sample ID: 521


title: Blood sample from individual 539

description: Sample ID: 539


title: Blood sample from individual 519

description: Sample ID: 519


title: Blood sample from individual 518

description: Sample ID: 518


title: Blood sample from individual 512

description: Sample ID: 512


title: Blood sample from individual 515

description: Sample ID: 515


title: Blood sample from individual 509

description: Sample ID: 509


title: Blood sample from individual 513

description: Sample ID: 513


title: Blood sample from individual 511

description: Sample ID: 511


title: Blood sample from individual 510

description: Sample ID: 510


title: Blood sample from individual 508

description: Sample ID: 508


title: Blood sample from individual 514

description: Sample ID: 514


title: Blood sample from individual 526

description: Sample ID: 526


title: Blood sample from individual 505

description: Sample ID: 505


title: Blood sample from individual 506

description: Sample ID: 506


title: Blood sample from individual 500

description: Sample ID: 500


title: Blood sample from individual 503

description: Sample ID: 503


title: Blood sample from individual 504

description: Sample ID: 504


title: Blood sample from individual 501

description: Sample ID: 501


title: Blood sample from individual 497

description: Sample ID: 497


title: Blood sample from individual 498

description: Sample ID: 498


title: Blood sample from individual 517

description: Sample ID: 517


title: Blood sample from individual 496

description: Sample ID: 496


title: Blood sample from individual 495

description: Sample ID: 495


title: Blood sample from individual 494

description: Sample ID: 494


title: Blood sample from individual 499

description: Sample ID: 499


title: Blood sample from individual 507

description: Sample ID: 507


title: Blood sample from individual 492

description: Sample ID: 492


title: Blood sample from individual 491

description: Sample ID: 491


title: Blood sample from individual 490

description: Sample ID: 490


title: Blood sample from individual 486

description: Sample ID: 486


title: Blood sample from individual 483

description: Sample ID: 483


title: Blood sample from individual 489

description: Sample ID: 489


title: Blood sample from individual 487

description: Sample ID: 487


title: Blood sample from individual 484

description: Sample ID: 484


title: Blood sample from individual 488

description: Sample ID: 488


title: Blood sample from individual 502

description: Sample ID: 502


title: Blood sample from individual 482

description: Sample ID: 482


title: Blood sample from individual 481

description: Sample ID: 481


title: Blood sample from individual 485

description: Sample ID: 485


title: Blood sample from individual 477

description: Sample ID: 477


title: Blood sample from individual 480

description: Sample ID: 480


title: Blood sample from individual 493

description: Sample ID: 493


title: Blood sample from individual 479

description: Sample ID: 479


title: Blood sample from individual 478

description: Sample ID: 478


title: Blood sample from individual 475

description: Sample ID: 475


title: Blood sample from individual 472

description: Sample ID: 472


title: Blood sample from individual 470

description: Sample ID: 470


title: Blood sample from individual 474

description: Sample ID: 474


title: Blood sample from individual 473

description: Sample ID: 473


title: Blood sample from individual 471

description: Sample ID: 471


title: HOU_xdrA

type: SRA

city: Tampa

first: Lindsey

middle: N

last: Shaw

state: FL

address: 4202 E Fowler Avenue

department: CMMB

country: USA

institute: University of South Florida

library_source: transcriptomic

data_processing:
Raw data files (.fastq) were exported from the Illumina BaseSpace Server
Raw data files (.fastq) were imported into Qiagen Bioinformatics software platform (version 11) as paired-end reads for analysis and adapter indices trimmed.
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values and fold change for filtered reads were caculated using RNA-Seq Analysis function with experimental fold change feature in Qiagen Bioinformatics software
Expression values and fold change were normalized by quantile normalization
Normalized expression values and fold change comparisons were exported in excel format
Genome_build: The accession number for the Genbank genome file used as references was NC_010079.1
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as TPM values in excel format

molecule: total RNA

organism: Staphylococcus aureus

source_name: bacterial cells, pelleted

growth_protocol: Overnight S. aureus cultures were used to inoculate fresh TSB broth and grown for 3 hours. These exponentially growing cultures were subsequently used to seed fresh TSB medium at OD600 0.05. After 5 hour of growth, 5 mL of cells were harvested for RNA isolation.

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free kit. Total RNA was enriched for mRNA using MicrobExpress kit and Illumina RiboZero rRNA removal kit for Gram-positive bacteria.
Library construction was performed using the TruSeq Stranded mRNA Kit from Illumina omitting mRNA enrichment steps.

treatment_protocol: Samples were pelleted and stored at -80°C prior to RNA extraction.

tag: strain

tag: genotype

value: xdrA transposon mutant strain

tag: growth medium

value: TSB

tag: growth conditions

value: 5h/37 degrees C


title: Blood sample from individual 469

description: Sample ID: 469


title: Blood sample from individual 467

description: Sample ID: 467


title: Blood sample from individual 464

description: Sample ID: 464


title: Blood sample from individual 461

description: Sample ID: 461


title: Blood sample from individual 462

description: Sample ID: 462


title: Blood sample from individual 460

description: Sample ID: 460


title: HOU_WT

value: Wildtype parental strain


title: Blood sample from individual 476

description: Sample ID: 476


title: Blood sample from individual 466

description: Sample ID: 466


title: Blood sample from individual 455

description: Sample ID: 455


title: P34_Primary

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

data_processing:
Sequencing adapters were removed from raw reads using Trimmomatic (v0.36).
Trimmed reads were mapped with STAR aligner (v2.5.3a) to GRCh38_r77.
Quantification was performed with Salmon v0.9.1 in alignment-based mode.
Counts were processed and imported into R via package tximport and differential gene expression was performed with DESeq2.
The gene log-scale expression matrix was generated by variance-stabilized transformation (vst).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file with Variance-stabilized log-expression per gene.

source_name: head and neck squamous cell carcinoma

growth_protocol: 34 primary and recurrent tumors were collected as FFPE specimens from surgically resected tumor tissues or pan-endoscopic biopsies.

extract_protocol:
Simultaneous DNA and total RNA extraction using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.
RNA sequencing libraries were prepared with 500 ng (good quality) and 1000 ng (medium/low quality) of total RNA using the TruSeq Stranded Total RNA Library Prep Gold Kit with single-indexing following the manufacturer’s instructions for high sample numbers (Illumina, Inc., USA). Initial RNA fragmentation time was adjusted to the respective RNA quality as follows: 8 min (DV200 >70%), 6 min (DV200 70-60%), 4 min (DV200 59-50), 0 min (DV200 <49%). Quality and quantity of the libraries were evaluated using the Quanti-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific) and the Bioanalyzer High Sensitivity DNA Analysis Kits (Agilent Technologies). Sequencing of 166 libraries was performed in two pools on 17 lanes of an Illumina HiSeq 2000 platform in 150 bp paired-end mode.
150bp paired-end

treatment_protocol: Serial sections of FFPE tumor blocks were macrodissected for the enrichment of tumor cells.

value: HNSCC

tag: cell type

value: tumor cell

tag: pair id

tag: condition

value: Primary


title: Blood sample from individual 465

description: Sample ID: 465


title: primary HNSCC tumor sample [P39_ex_vivo]

data_processing:
Raw base calls have been processed by CellRanger 2.1.1. to demultiplex reads and generate count matrices. Count data were quality controlled with scater 1.10.1 imported into and analyzed by Seurat 2.3.0.
Filtering of cells was based on more than 4000 expression features, more than 25,000 total counts and mitochondrial proportion of reads < 15%.
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered and normalized counts per cell as generated by CellRanger. Each compressed file contains one text file with cell barcodes, gene per count and normalized counts.

growth_protocol: Cells of P39_ex_vivo, P40_ex_vivo and P41_ex_vivo were cultivated for several days to stabilize their transcriptomic status. After growing up to 70-80% confluency cells were harvested and washed according to 10x Genomics Sample Preparation Demonstrated Protocol (10x Genomics, Inc. Pleasanton USA).

extract_protocol:
For each patient < 10,000 cells were loaded into one well of a Chromium Single Cell Chip A.
Library construction was performed with Chromium Single Cell 3’ Reagent Kits v2 (10x Genomics) following the manufacturer’s protocol.

treatment_protocol: The obtained suspensions were microscopically inspected, counted and diluted to a target density of 1000 cells/μl. Cell viability was determined with Trypan Blue to ensure a viability greater than 90% in each preparation.

value: tumor primary culture

value: head and neck squamous cell carcinoma (HNSCC)


title: Blood sample from individual 459

description: Sample ID: 459


title: Blood sample from individual 453

description: Sample ID: 453


title: Blood sample from individual 452

description: Sample ID: 452


title: P33_Primary


title: Blood sample from individual 451

description: Sample ID: 451


title: Blood sample from individual 458

description: Sample ID: 458


title: primary HNSCC tumor sample [P41_ex_vivo]


title: primary HNSCC tumor sample [P40_ex_vivo]


title: Blood sample from individual 450

description: Sample ID: 450


title: Blood sample from individual 456

description: Sample ID: 456


title: P32_Primary


title: P31_Relapse

value: Relapse


title: Blood sample from individual 449

description: Sample ID: 449


title: P34_Relapse


title: Blood sample from individual 447

description: Sample ID: 447


title: Blood sample from individual 454

description: Sample ID: 454


title: P33_Relapse


title: P32_Relapse


title: Blood sample from individual 468

description: Sample ID: 468


title: Blood sample from individual 463

description: Sample ID: 463


title: P29_Relapse


title: Blood sample from individual 443

description: Sample ID: 443


title: Blood sample from individual 444

description: Sample ID: 444


title: P28_Relapse


title: P31_Primary


title: P28_Primary


title: Blood sample from individual 448

description: Sample ID: 448


title: Blood sample from individual 457

description: Sample ID: 457


title: P27_Relapse


title: Blood sample from individual 441

description: Sample ID: 441


title: P30_Relapse


title: Blood sample from individual 439

description: Sample ID: 439


title: Blood sample from individual 438

description: Sample ID: 438


title: Blood sample from individual 445

description: Sample ID: 445


title: P26_Primary


title: P24_Relapse


title: Blood sample from individual 435

description: Sample ID: 435


title: Blood sample from individual 442

description: Sample ID: 442


title: P30_Primary


title: Blood sample from individual 434

description: Sample ID: 434


title: Blood sample from individual 440

description: Sample ID: 440


title: P29_Primary


title: P26_Relapse


title: P27_Primary


title: Blood sample from individual 446

description: Sample ID: 446


title: P25_Relapse


title: Blood sample from individual 432

description: Sample ID: 432


title: P22_Relapse


title: Blood sample from individual 437

description: Sample ID: 437


title: Blood sample from individual 436

description: Sample ID: 436


title: Blood sample from individual 430

description: Sample ID: 430


title: P22_Primary


title: P21_Relapse


title: P21_Primary


title: Blood sample from individual 428

description: Sample ID: 428


title: P24_Primary


title: P20_Relapse


title: Blood sample from individual 429

description: Sample ID: 429


title: Blood sample from individual 425

description: Sample ID: 425


title: P23_Relapse


title: P18_Relapse


title: Blood sample from individual 433

description: Sample ID: 433


title: P19_Relapse


title: Blood sample from individual 423

description: Sample ID: 423


title: P25_Primary


title: Blood sample from individual 426

description: Sample ID: 426


title: P18_Primary


title: Blood sample from individual 420

description: Sample ID: 420


title: P19_Primary


title: Blood sample from individual 427

description: Sample ID: 427


title: P20_Primary


title: P23_Primary


title: Blood sample from individual 431

description: Sample ID: 431


title: Blood sample from individual 424

description: Sample ID: 424


title: Blood sample from individual 421

description: Sample ID: 421


title: P17_Relapse


title: P16_Primary


title: Blood sample from individual 417

description: Sample ID: 417


title: P17_Primary


title: P16_Relapse


title: Blood sample from individual 416

description: Sample ID: 416


title: P14_Relapse


title: Blood sample from individual 418

description: Sample ID: 418


title: P14_Primary


title: P13_Relapse


title: Blood sample from individual 414

description: Sample ID: 414


title: Blood sample from individual 422

description: Sample ID: 422


title: P13_Primary


title: P12_Relapse


title: Blood sample from individual 410

description: Sample ID: 410


title: Blood sample from individual 412

description: Sample ID: 412


title: Blood sample from individual 415

description: Sample ID: 415


title: Blood sample from individual 409

description: Sample ID: 409


title: P11_Relapse


title: P12_Primary


title: Blood sample from individual 419

description: Sample ID: 419


title: Blood sample from individual 411

description: Sample ID: 411


title: Blood sample from individual 406

description: Sample ID: 406


title: P11_Primary


title: P09_Primary


title: P09_Relapse


title: P15_Relapse


title: Blood sample from individual 403

description: Sample ID: 403


title: Blood sample from individual 408

description: Sample ID: 408


title: P15_Primary


title: Blood sample from individual 407

description: Sample ID: 407


title: Blood sample from individual 413

description: Sample ID: 413


title: P10_Relapse


title: P08_Primary


title: Blood sample from individual 405

description: Sample ID: 405


title: Blood sample from individual 404

description: Sample ID: 404


title: P10_Primary


title: Blood sample from individual 401

description: Sample ID: 401


title: P07_Relapse


title: P08_Relapse


title: Blood sample from individual 402

description: Sample ID: 402


title: Blood sample from individual 400

description: Sample ID: 400


title: Blood sample from individual 399

description: Sample ID: 399


title: Blood sample from individual 398

description: Sample ID: 398


title: P06_Relapse


title: P06_Primary


title: P05_Primary


title: P07_Primary


title: Blood sample from individual 397

description: Sample ID: 397


title: P05_Relapse


title: Blood sample from individual 396

description: Sample ID: 396


title: P04_Relapse


title: Blood sample from individual 395

description: Sample ID: 395


title: P04_Primary


title: Blood sample from individual 393

description: Sample ID: 393


title: P03_Relapse


title: P03_Primary


title: Blood sample from individual 394

description: Sample ID: 394


title: Blood sample from individual 391

description: Sample ID: 391


title: Blood sample from individual 389

description: Sample ID: 389


title: Blood sample from individual 390

description: Sample ID: 390


title: Blood sample from individual 388

description: Sample ID: 388


title: P02_Primary


title: Blood sample from individual 387

description: Sample ID: 387


title: Blood sample from individual 392

description: Sample ID: 392


title: Blood sample from individual 384

description: Sample ID: 384


title: P01_Primary


title: Blood sample from individual 382

description: Sample ID: 382


title: Blood sample from individual 383

description: Sample ID: 383


title: Blood sample from individual 381

description: Sample ID: 381


title: Blood sample from individual 386

description: Sample ID: 386


title: Blood sample from individual 380

description: Sample ID: 380


title: Blood sample from individual 379

description: Sample ID: 379


title: Blood sample from individual 377

description: Sample ID: 377


title: P02_Relapse


title: Blood sample from individual 378

description: Sample ID: 378


title: Blood sample from individual 375

description: Sample ID: 375


title: Blood sample from individual 385

description: Sample ID: 385


title: P01_Relapse


title: Blood sample from individual 371

description: Sample ID: 371


title: Blood sample from individual 372

description: Sample ID: 372


title: Blood sample from individual 374

description: Sample ID: 374


title: Blood sample from individual 370

description: Sample ID: 370


title: Blood sample from individual 369

description: Sample ID: 369


title: Blood sample from individual 367

description: Sample ID: 367


title: Blood sample from individual 366

description: Sample ID: 366


title: Blood sample from individual 376

description: Sample ID: 376


title: Blood sample from individual 373

description: Sample ID: 373


title: Blood sample from individual 365

description: Sample ID: 365


title: Wnt4-lineage cells, Wt atac, S13

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Paired-end reads were processed by first trimming the adapter sequences using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Trimmed reads were mapped to the mm10 Ensembl v90 mouse genome using HISATv2.2.1
Duplicate fragments were discarded, leaving only high-quality unique reads.
Reads were sorted by the chromosomal coordinates using samtools (https://doi.org/10.1093/bioinformatics/btp352).
Peak calling was performed using Genrich with the setting ‘-j-r-y-d100-q0.15’ (https://github.com/jsh58/Genrich).
Assembly: mm10
Supplementary files format and content: Tab-delimited peaks text file

organism: Mus musculus

source_name: Kidney

extract_protocol:
ATAC-seq was performed using FACS-purified tdTomato cells from control or Brg1cKO/cKO with previously published methods.28, 57, 58 Briefly, we obtained nuclei by resuspending 50000 cells in 0.5 ml of lysis buffer (0.1% Tween-20 in RSB buffer) and incubated them for 10 min on ice. Nuclei were pelleted by centrifugation for 10 min at 500g, resuspended in 50 μl of transposition mix [1× Tagmentation DNA buffer, 2.5 μl Tagment DNA enzyme (Illumina)], and incubated for 30 min at 37 °C. DNA was purified with a MinElute PCR purification kit (Qiagen), and libraries were amplified by PCR with barcoded Nextera primers (Illumina).
For sequencing, libraries were size-selected with Agencourt AMPure XP (Beckman Coulter) for fragments between ~50 and 1,000 bp in length according to the manufacturer's instructions. Libraries were sequenced in paired-end mode on a NovaSeq Instrument (Illumina) targeting a depth of 5  104-1 105 reads per cell.

value: Kidney

value: WT control

value: control


title: Blood sample from individual 364

description: Sample ID: 364


title: CWnt4-lineage cells, ko atac, S14

value: Wnt4-lineage cells


title: CSR002: Sub-confluent Caco-2, biological rep2

type: RNA

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description: Gene expression data from non-infected Caco-2 cells grown to 80% confluency

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on a Human Gene 2.0 ST GeneChip array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1. Signal summarization was performed independently in two groups. Samples CaI003, CaI004, CaU001, CaU002 were summarized in one group, while samples COR001, C)R002, CSR001, CSR002 were summarized in the second group.

label: biotin

source_name: Non-infected Caco-2 cells grown to 80% confluency, biological rep2

label_protocol: For samples CaI003, CaI004, CaU001, CaU002: sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).  For samples COR001, C)R002, CSR001, CSR002: sense target cDNA was prepared from 100ng of total RNA using the Affymetrix GeneChip WT Plus (Applied Biosystems P/N 902281). cDNA was fragmented and biotin-labeled using the GeneChip™ WT Terminal Labeling Kit (Applied Biosystems P/N 900670).

growth_protocol: Caco-2 cells were grown in minimum essential medium supplemented with 20% fetal bovine serum, GlutaMax-I, and 1 mM sodium pyruvate.

extract_protocol: Total RNA extraction was performed using Qiagen RNeasy Kit according to the manufacturer's instructions.

treatment_protocol: Cells were serum-starved for 1 hour prior to infection or non-infection. Following infection or non-infection, cells were washed with phosphate buffered saline and replaced with minimum essential medium supplemented with 1% bovine serum albumin. Cells were harvested at 24 hours following infection or non-infection.

value: Colon epithelial cells


title: CSR001: Sub-confluent Caco-2, biological rep1

source_name: Non-infected Caco-2 cells grown to 80% confluency, biological rep1


title: CaI004: Infected Caco-2 cells, biological rep2

description: Gene expression data from HAstV-1 infected Caco-2 cells

source_name: HAstV-1 infected Caco-2 cells at 24 hpi, biological rep2


title: COR002: Over-confluent Caco-2 cells, biological rep2

description: Gene expression data from non-infected Caco-2 cells grown to differentiation

source_name: Non-infected Caco-2 cells grown to differentiation, biological rep2


title: COR001: Over-confluent Caco-2 cells, biological rep1

source_name: Non-infected Caco-2 cells grown to differentiation, biological rep1


title: CaU001: Uninfected Caco-2 cells, biological rep1

description: Gene expression data from non-infected Caco-2 cells

source_name: Non-infected Caco-2 cells, biological rep1


title: Blood sample from individual 363

description: Sample ID: 363

value: Blood

value: No active inflammatory disease


title: CaI003: Infected Caco-2 cells, biological rep1

source_name: HAstV-1 infected Caco-2 cells at 24 hpi, biological rep1


title: D5-6 ATO DLL4 DN2a Bcl11b+ 21140

city: Pasadena

first: Wen

last: Zhou

state: California

address: 1200 E California Blvd, Mail Code 250-86

department: BBE

institute: California Institute of Technology

description:
D5-6 ATO DLL4 DN2a Bcl11b+
NEBNext Ultra RNA

data_processing:
Base calls were performed with RTA 1.13.48.0
conversion to FASTQ with bcl2fastq 1.8.4
FASTQ files were mapped onto the mouse genome build GRCm38(mm10) with STAR (v2.4.0) (Dobin et al., 2013) and post-processed with RSEM (v1.2.25; http://deweylab.github.io/RSEM/) (Li and Dewey, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings ?--output-genome-bam --sampling-for-bam? was added to rsem-calculate-expression.
STAR and RSEM reference libraries were created from genome build GRCm38(mm10) together with the Ensembl gene model file Mus_musculus.GRCm38.gtf.The resulting bam-files were used to create HOMER (Heinz et al., 2010) tag directories (makeTagDirectory with ?keepAll setting).
For analysis of statistical significance among differentially expressed genes the raw gene counts were derived from each tag directory with analyzeRepeats.pl with the ?noadj -condenseGenes options followed by the getDiffExpression.pl command using EdgeR (v3.6.8; http://bioconductor.org/packages/release/bioc/html/edgeR.html) (Robinson et al., 2010).
single cell data was processed with Cellranger 2.0 is run on the FASTQ files to generate matrix
Genome_build: GRCm38(mm10)

source_name: Bone Marrow

growth_protocol: Lineage purified bone marrow cells (Lin-) were cultured with stromal cells (OP9 or MS5) following the previously published conditions and recommended setups.(T. M. Schmitt, J. C. Zúñiga-Pflücker, Induction of T cell development from hematopoietic progenitor cells by Delta-like-1 in vitro. Immunity. 17, 749–756 (2002). A. Montel-Hagen, V. Sun, D. Casero, S. Tsai, A. Zampieri, N. Jackson, S. Li, S. Lopez, Y. Zhu, B. Chick, C. He, S. C. de Barros, C. S. Seet, G. M. Crooks, In Vitro Recapitulation of Murine Thymopoiesis from Single Hematopoietic Stem Cells. Cell Rep. 33, 108320 (2020)). The cells were cultured for 4-6 days, purified through FACS sorting as described.

extract_protocol:
RNAeasy MicroKit (Qiagen) for bulk RNA-seq
NEBNext Ultra RNA

tag: facs purification gate

value: Lin- 7AAD- CD44+ Kit+ CD25+ YFP+


title: Myxoid liposarcoma tumor Round-cell type_2

city: Gothenburg

first: Pierre

last: Åman

address: Medicinaregatan 1G

department: Institute of Biomedicine, University of Gothenburg

country: Sweden

institute: Sahlgrenska Center for Cancer Research

hyb_protocol: Equal quantities of labeled cDNA and reference cDNA were hybridized to Agilent Whole Human Genome Microarray 4x44K G4112F microarrays (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using an Agilent G2565CA microarray scanner and analysis was performed with Agilent’s Feature Extraction 10.4 Image Analysis Software

data_processing: Agilent’s Feature Extraction 10.4 Image Analysis Software was used for background substraction and LOWESS normalization

label_protocol: Tumor and reference (HT1080 wt) RNA were labeled with Cy3 and Cy5 nucleotides during cDNA synthesis  according to the instructions for the Pronto Plus 6 labeling kit (Corning) followed by microarray analysis.

growth_protocol: Frozen MLS tumor samples

extract_protocol: Total RNA was extracted using Trizol (Thermo Fisher Scientific) from the frozen tumor tissue according to the manufacturer's instructions

tag: fusion oncoprotein

source_name: HT1080 reference

tag: cell line

value: HT1080 fibrosarcoma


title: Myxoid liposarcoma tumor_3

source_name: Myxoid liposarcoma tumor


title: CaU002: Uninfected Caco-2 cells, biological rep2

source_name: Non-infected Caco-2 cells, biological rep2


title: Blood sample from individual 361

description: Sample ID: 361

value: Female


title: D6 ATO DLL4 DN2a  Bcl11b- 21139

description:
D6 ATO DLL4 DN2a  Bcl11b-
NEBNext Ultra RNA

value: Lin- 7AAD- CD44+ Kit+ CD25+ YFP-


title: Blood sample from individual 368

description: Sample ID: 368


title: Blood sample from individual 362

description: Sample ID: 362


title: D5 ATO DLL4 DN2a Bcl11b- 21137

description:
D5 ATO DLL4 DN2a Bcl11b-
NEBNext Ultra RNA


title: Myxoid liposarcoma tumor Round-cell type_1


title: D5 ATO DLL4 DN1 21136

description:
D5 ATO DLL4 DN1
NEBNext Ultra RNA

value: Lin- 7AAD- CD44+ Kit+ CD25-


title: Blood sample from individual 360

description: Sample ID: 360

value: Male


title: Blood sample from individual 359

description: Sample ID: 359


title: D5-6 ATO DLL1 DN2a Bcl11b+ 21101

description:
D5-6 ATO DLL1 DN2a Bcl11b+
NEBNext Ultra RNA


title: Blood sample from individual 358

description: Sample ID: 358


title: D6 ATO DLL1 DN2a Bcl11b- 21100

description:
D6 ATO DLL1 DN2a Bcl11b-
NEBNext Ultra RNA


title: Blood sample from individual 356

description: Sample ID: 356


title: D6 ATO DLL1 DN1 21099

description:
D6 ATO DLL1 DN1
NEBNext Ultra RNA


title: Myxoid liposarcoma tumor_1


title: Blood sample from individual 353

description: Sample ID: 353


title: Blood sample from individual 352

description: Sample ID: 352


title: Blood sample from individual 351

description: Sample ID: 351


title: Blood sample from individual 350

description: Sample ID: 350


title: Myxoid liposarcoma tumor_2


title: D6 ATO DLL4 DN1 21138

description:
D6 ATO DLL4 DN1
NEBNext Ultra RNA


title: Blood sample from individual 354

description: Sample ID: 354


title: Blood sample from individual 355

description: Sample ID: 355


title: BM_DN2a  Bcl11b+_D6_OP9_dll4 20939

description:
BM_DN2a  Bcl11b+_D6_OP9_dll4
NEBNext Ultra RNA


title: BM_DN2a  Bcl11b-_D6_OP9_dll4 20938

description:
BM_DN2a  Bcl11b-_D6_OP9_dll4
NEBNext Ultra RNA


title: Blood sample from individual 349

description: Sample ID: 349


title: D5 ATO DLL1 DN1 21097

description:
D5 ATO DLL1 DN1
NEBNext Ultra RNA


title: BM_DN1_d4_OP9_dll4 20935

description:
BM_DN1_d4_OP9_dll4
NEBNext Ultra RNA


title: DN2a Y + thymocytes 20722

description:
DN2a Y + thymocytes
NEBNext Ultra RNA


title: Blood sample from individual 348

description: Sample ID: 348


title: BM_DN2a  Bcl11b-_d4_OP9_dll4 20936

description:
BM_DN2a  Bcl11b-_d4_OP9_dll4
NEBNext Ultra RNA


title: ETP total thymocytes 20720

description:
ETP total thymocytes
NEBNext Ultra RNA


title: Blood sample from individual 345

description: Sample ID: 345


title: ETP total thymocytes 20719

description:
ETP total thymocytes
NEBNext Ultra RNA


title: Blood sample from individual 357

description: Sample ID: 357


title: DN2a Y - thymocytes 20721

description:
DN2a Y - thymocytes
NEBNext Ultra RNA


title: Blood sample from individual 347

description: Sample ID: 347


title: C100_vpLeftBoundary_rep1

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: genomic

data_processing:
Reads were mapped and processed using pipe4C (Krijger et al., 2020) (github.com/deLaatLab/pipe4C) with the following parameters: normalization to 1 million reads in cis, non-blind fragments only, window size 21, top 2 read counts removed.
Assembly: Modified versions of hg19 containing the sequences of the integrated regulatory elements at their respective integration site.
Supplementary files format and content: 4C: interaction coverage file (wig files generated using pipe4C)
Library strategy: 4C

growth_protocol: Human erythroleukemia K562 cells were grown at 37°C at 5% CO2 in RPMI 1640 (Gibco) with 10% FBS (Sigma) and 1% Penicillin-Streptomycin (Gibco). Density was kept between 1x10^5 and 5x10^5 cells per ml medium. Cells were routinely tested for mycoplasma. Prior to every experiment, cells were weekly bulk sorted for two consecutive weeks on Becton Dickinson SORP FACSAria FUSION Flow Cytometer. To obtain irreversibly silenced populations of cells, GFP negative cells where weekly sorted GFP-negative for six (E100) or nine (E407) consecutive weeks.

extract_protocol:
4C experiments were performed as described (Krijger et al., 2020). Eight to ten million cells were cross-linked with formaldehyde. DNA was digested in situ with Csp6I (first cutter) and NlaIII (second cutter).
Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy as described in Krijger et al., 2020.

treatment_protocol: For differentiation, culture medium was supplemented with porcine hemin (Sigma, 30 µM final concentration) one day after sorting. Hemin and medium were refreshed one day later.

tag: knock down

tag: hemin treatment

tag: facs

tag: viewpoint

value: LeftBoundary

tag: barcode

value: GATCAAAAATGAGTGAAAGGT


title: Blood sample from individual 346

description: Sample ID: 346

tag: individual id

tag: gender

tag: tissue


title: Blood sample from individual 344

description: Sample ID: 344

tag: disease state


title: C100_vpLeftBoundary_rep2

tag: genotype


title: C0_vpLeftBoundary_rep2

value: ATCAAAAATGAGTGAAAGGT


title: D5 ATO DLL1 DN2a Bcl11b- 21098

description:
D5 ATO DLL1 DN2a Bcl11b-
NEBNext Ultra RNA

tag: strain


title: Blood sample from individual 342

description: Sample ID: 342


title: Blood sample from individual 343

description: Sample ID: 343


title: Blood sample from individual 339

description: Sample ID: 339


title: Blood sample from individual 341

description: Sample ID: 341


title: BM_DN1_d6_OP9_dll4 20937

description:
BM_DN1_d6_OP9_dll4
NEBNext Ultra RNA


title: E407_vpGFP_LongTermNegative_rep6

value: GFP

value: GGGGCACAAGCTGGAGTA


title: C0_vpLeftBoundary_rep1


title: C0_vpLeftBoundary_rep3


title: Blood sample from individual 340

description: Sample ID: 340


title: E407_vpGFP_LongTermNegative_rep7


title: Blood sample from individual 336

description: Sample ID: 336


title: Blood sample from individual 337

description: Sample ID: 337


title: Blood sample from individual 338

description: Sample ID: 338


title: E407_vpGFP_LongTermNegative_rep4


title: E407_vpGFP_LongTermNegative_rep5


title: E100_vpGFP_LongTermNegative_rep4


title: Blood sample from individual 334

description: Sample ID: 334


title: E407_vpGFP_rep5


title: E100_vpGFP_LongTermNegative_rep3


title: Blood sample from individual 333

description: Sample ID: 333


title: Blood sample from individual 332

description: Sample ID: 332


title: E407_vpGFP_rep4


title: Blood sample from individual 331

description: Sample ID: 331


title: E100_vpGFP_rep4


title: E47_vpGFP_rep4


title: Blood sample from individual 329

description: Sample ID: 329


title: Blood sample from individual 326

description: Sample ID: 326


title: Blood sample from individual 327

description: Sample ID: 327


title: E47_vpGFP_rep3


title: linear RNA miR-21 sponge bulge with stemloop

city: Giessen

first: Oliver

last: Rossbach

address: Heinrich-Buff-Ring 17

department: Biology and Chemistry (FB08)

institute: Institute of Biochemistry - University of Giessen

data_processing:
Adapters were trimmed using Trim_Galore (version 0.6.4) which used cutadapt (version 2.8) with parameters –length 30
Low quality bases were removed with fastq_quality_filter from the FASTX-toolkit (version 0.0.14) with parameters -q 20 -p 90
Preprocessed reads were aligned to hg38 with STAR (version 2.7.3a)
Features were counted in R (version 3.6.3) via featureCounts from the package Rsubread (version 2.2.6) with parameters countMultiMappedReads=TRUE
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and sample
Supplementary_files_format_and_content: Matrix table with DESeq2 results containing metrics for every gene

source_name: A549 cell culture cells

growth_protocol: A549 cells were cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum at 37°C and 5% CO2.

extract_protocol:
Cells were lysed and total RNA was isolated using TRIzol (Thermo Fisher Scientific, Cat. no.: 15596026) reagent.
Library preparation was performed using SMARTer Stranded Total RNA Sample Prep Kit (Takara, Cat. no.: 634873), which includes rRNA removal.
Sequencing was performed using a NextSeq 500 High Output Kit (75 cycles).

treatment_protocol: 24 h prior transfection 4.2x105 cells were seeded on 6-well plates. The transfection of cells was performed using Lipofectamine 2000 (Thermo Fisher Scientific; Cat. no.: 11668019) according to manufacturer’s instructions. Depending on the approach 250 ng of the circular RNA sponges were added to the transfection reaction.

value: adenocarcinomic alveolar basal epithelial cells

tag: treatment


title: Blood sample from individual 335

description: Sample ID: 335


title: linear RNA miR-21 sponge bulge without stemloop


title: circular RNA miR-21 sponge bulge without stemloop


title: circular RNA miR-21 sponge bulge with stemloop


title: linear RNA miR-21 random control with stemloop


title: Blood sample from individual 323

description: Sample ID: 323


title: Blood sample from individual 325

description: Sample ID: 325


title: circular RNA miR-21 random control without stemloop


title: Blood sample from individual 324

description: Sample ID: 324


title: linear RNA miR-21 random control without stemloop


title: Blood sample from individual 319

description: Sample ID: 319


title: Blood sample from individual 322

description: Sample ID: 322


title: non-transfected

value: Liposome


title: circular RNA miR-21 random control with stemloop


title: Blood sample from individual 330

description: Sample ID: 330


title: E100_vpGFP_rep3


title: mock transfected (liposome only)


title: Blood sample from individual 328

description: Sample ID: 328


title: Ctrl-KO_uninduced Rep1

city: BOSTON

first: Stephanie

middle: Pei Tung

last: Yiu

state: Massachusetts(MA)

address: 181 Longwood Ave

department: Virology

institute: Harvard University

description: Sample 7

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using Salmon
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental group and the control group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Genome_build: GRCh37.83
Supplementary_files_format_and_content: Comma-delimited text files include Log2FoldChange value (experimental vs. control), p value and FDR corrected p value (padj). Separate tab-delimited text files are also provided for raw counts and normalized counts of genes, respectively

molecule: polyA RNA

growth_protocol: P3HR1-Z/R-HT cells were cultured in GIBCO RPMI 1650 medium (Life Technologies) with 10% fetal bovine serum (FBS) and 1% Pen/Strep in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
Total RNAs were subsequently isolated using Rneasy Mini Kit (Qiagen) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination
To construct RNA-seq libraries, 1000 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: P3HR1-Z/R-HT cells were transduced with lentiviruses expressing control or BNRF1 sgRNA. At day 8 post-transduction, cells were either untreated or induced into EBV lytic cycle by 4HT and sodium butyrate.

value: P3HR1-Z/R-HT Burkitt Lymphoma cell line

tag: transduction

value: Cells expressing Control sgRNA

value: Control-KO

value: control


title: Blood sample from individual 321

description: Sample ID: 321

value: Blood

value: No active inflammatory disease


title: Blood sample from individual 316

description: Sample ID: 316


title: Ctrl-KO_uninduced Rep2

description: Sample 8


title: Blood sample from individual 317

description: Sample ID: 317

value: Female


title: Blood sample from individual 315

description: Sample ID: 315


title: Ctrl-KO_induced Rep1

description: Sample 5

value: lytic induction


title: Ctrl-KO_induced Rep2

description: Sample 6


title: Blood sample from individual 313

description: Sample ID: 313


title: Blood sample from individual 320

description: Sample ID: 320


title: BNRF1-KO_induced Rep2

description: Sample 2

value: Cells expressing BNRF1 sgRNA


title: Blood sample from individual 314

description: Sample ID: 314


title: Blood sample from individual 312

description: Sample ID: 312


title: Blood sample from individual 311

description: Sample ID: 311


title: BNRF1-KO_uninduced Rep1

description: Sample 3


title: BNRF1-KO_uninduced Rep2

description: Sample 4


title: BNRF1-KO_induced Rep1

description: Sample 1


title: EC100_vpCBS_Control_KD2_rep1

data_processing:
Reads were mapped and processed using pipe4C (Krijger et al., 2020) (github.com/deLaatLab/pipe4C) with the following parameters: normalization to 1 million reads in cis, non-blind fragments only, window size 21, top 2 read counts removed
Genome_build: Modified versions of hg19 containing the sequences of the integrated regulatory elements at their respective integration site.
Supplementary_files_format_and_content: 4C:  interaction coverage file (wig files generated using pipe4C)

growth_protocol: Human erythroleukemia K562 cells were grown at 37°C at 5% CO2 in RPMI 1640 (Gibco) with 10% FBS (Sigma) and 1% Penicillin-Streptomycin (Gibco). Density was kept between 1x105 and 5x105 cells per ml medium. Cells were routinely tested for mycoplasma. Prior to every experiment, cells were weekly bulk sorted for two consecutive weeks on Becton Dickinson SORP FACSAria FUSION Flow Cytometer. To obtain irreversibly silenced populations of cells, GFP negative cells where weekly sorted GFP-negative for six (E100) or nine (E407) consecutive weeks.

extract_protocol:
4C experiments were performed as described (Krijger et al., 2020).  Eight to ten million cells were cross-linked with formaldehyde. DNA was digested in situ with Csp6I (first cutter) and NlaIII (second cutter).
Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy as described in Krijger et al., 2020.
OTHER:  4C

value: CBS

value: GGAATCTCGCTCTGATCGTC


title: Blood sample from individual 309

description: Sample ID: 309


title: EC100_vpCBS_Control_KD2_rep2


title: Blood sample from individual 310

description: Sample ID: 310

value: Male


title: E407_vpuLCR_RAD21_KD_rep1

value: uLCR

value: CATTTAATATGCTTTAAGTTCTGGGGTAC


title: Blood sample from individual 318

description: Sample ID: 318


title: Blood sample from individual 306

description: Sample ID: 306


title: Blood sample from individual 304

description: Sample ID: 304


title: Blood sample from individual 308

description: Sample ID: 308


title: Blood sample from individual 301

description: Sample ID: 301


title: E407_vpGFP_RAD21_KD_rep1

value: GFP

value: GGGGCACAAGCTGGAGTA


title: Blood sample from individual 300

description: Sample ID: 300


title: Blood sample from individual 302

description: Sample ID: 302


title: EC100_vpuLCR_Control_KD2_rep1

value: TTTAATATGCTTTAAGTTCTGGGGTAC


title: Blood sample from individual 307

description: Sample ID: 307


title: EC100_vpuLCR_Control_KD1_rep1

value: GTTTAATATGCTTTAAGTTCTGGGGTAC


title: Blood sample from individual 298

description: Sample ID: 298


title: EC100_vpCBS_Control_KD1_rep2


title: Blood sample from individual 305

description: Sample ID: 305


title: E100C0C100_vpLeftBoundary_rep1

value: LeftBoundary

value: GATCAAAAATGAGTGAAAGGTAC


title: EC100_vpCBS_Control_KD1_rep1


title: EC100_vpuLCR_Control_KD2_rep2


title: Blood sample from individual 295

description: Sample ID: 295


title: E0C0C100_vpLeftBoundary_rep1


title: Blood sample from individual 303

description: Sample ID: 303


title: EC100_vpLeftBoundary_rep2

value: GATCAAAAATGAGTGAAAGGT


title: Blood sample from individual 293

description: Sample ID: 293

value: Blood


title: EC100_vpGFP_Control_KD2_rep1

value: AGGGGCACAAGCTGGAGTA


title: EC100_vpGFP_Control_KD2_rep2


title: EC100_vpLeftBoundary_rep1


title: Blood sample from individual 299

description: Sample ID: 299

value: No active inflammatory disease


title: EC0_vpLeftBoundary_rep2

value: ATCAAAAATGAGTGAAAGGT


title: E100C0C100_vpLeftBoundary_rep2


title: Blood sample from individual 297

description: Sample ID: 297

value: Female


title: Blood sample from individual 291

description: Sample ID: 291


title: E0C0C100_vpLeftBoundary_rep2


title: Blood sample from individual 294

description: Sample ID: 294


title: Blood sample from individual 296

description: Sample ID: 296


title: noE_vpLeftBoundary_rep1

value: noE


title: Blood sample from individual 288

description: Sample ID: 288


title: Blood sample from individual 292

description: Sample ID: 292


title: Blood sample from individual 286

description: Sample ID: 286


title: Blood sample from individual 287

description: Sample ID: 287


title: EC0_vpLeftBoundary_rep1


title: Blood sample from individual 290

description: Sample ID: 290


title: noE_vpLeftBoundary_rep2


title: Blood sample from individual 289

description: Sample ID: 289


title: E407_vpuLCR_rep1


title: E47_vpuLCR_rep1


title: E47_vpuLCR_rep2


title: E407_vpuLCR_rep3


title: Sample98 pituispheres RNA

city: Riga

first: Raitis

last: Peculis

address: Ratsupites str 1 k-1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

data_processing:
Paired end data was trimmed with fastp(v0.23.2) software to retain reads with average quality of at least 20 (Phred score) and minimum read length of 100 base pairs.
Ribosomal RNA (rRNA) read alignment and removal was performed with SortMeRNA.
Quality and rRNA filtered reads were further quasi-mapped and quantified using Salmon(v1.6.0) against the GENCODE(v38) Homo sapiens genome for tissue and pituisphere samples  while simultaneously performing GC bias, sequence level bias and positional bias correction to increase the number of high quality mappings. Tissue samples with quasi-mapping rate of at least 45% were selected for differential expression analysis.
Quality and rRNA filtered reads were further quasi-mapped and quantified using Salmon(v1.6.0) against Ensembl(v105) Rattus Norvegicus genome for the GH3 cell lines while simultaneously performing GC bias, sequence level bias and positional bias correction to increase the number of high quality mappings.
The quantified transcripts were imported in the R software and summarized to gene level counts using the tximeta package. Differential expression analysis was performed by DESeq2. Quantified read counts were filtered by frequency setting the count threshold at 10 and the sample frequency threshold as 33% of the smallest comparison group contrast size.  Parametric dispersion fit type was chosen to model the counts, after also checking the fit of mean and local fits. Euclidean distances between samples and PCA graphs of 500 most variable genes were used to check for unforeseen variability within the comparison groups and possible batch effects. Subsequently Wald test was performed to determine expression differences both in PitNET type and SSA/DA therapy contrasts.   The default independent filtering function was replaced with independent hypotheses weighing from the IHW package.  Adjustment p values based on the mean expression level of each gene which was followed with multiple testing correction using the Benjamini-Hochberg adjustment.
Assembly: GENCODE v38 GRCh38
Assembly: Ensembl 105 mRatBN7.2
Supplementary files format and content: raw counts

source_name: Pituitary neuroendocrine tumor pituispheres

growth_protocol: Within 12 hours after surgery, PitNET tissue samples were processed for propagation. Tissue material was mechanically sliced into small pieces and washed in DMEM with 1x Antibiotic-Antimycotic solution (Thermo Fisher Scientific, USA). Enzymatic dissociation using Accutase solution (Thermo Fisher Scientific, USA) was carried out on a rotating platform for 20 min at 37°C in a humidified environment with 5% CO2. The cells were centrifuged for 5 min at 360 x g after the incubation period to obtain cell pellets. The cell pellet was treated with a red blood cell lysis solution (154 mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA, pH 7.4) for 10 min to reduce contamination with red blood cells. To remove red blood cell debris, the sample was centrifuged and the cell pellet was washed twice. The obtained pellet was split into two portions. To obtain PitNET tissue-derived free-floating spheres, cells were grown in DMEM-F12 (Thermo Fisher Scientific, USA), containing 1x penicillin/streptomycin solution, 20 ng/ml epidermal growth factor (EGF) (Sigma-Aldrich, Germany), 10 ng/ml basic fibroblast growth factor (bFGF) (Sigma-Aldrich, Germany), and 1x B27 supplement (GIBCO, USA).  To obtain MSC, culture cells were grown in DMEM-F12, supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Fisher Scientific, USA), 1% ITS (Corning, USA), and 100 µg/ml primocin (InvivoGen, USA) until confluent, then propagated and passaged 2–6 times. All cell culture cultivations and incubations were performed at 37°C, 95% air, and 5% CO2.

extract_protocol:
Total RNA for transcriptome sequencing was extracted using AllPrep DNA/RNA/miRNA universal kit (Qiagen, Germany) according to manufacturer’s instructions from tumor tissue samples stored in RNAlater Tissue Storage Reagent (Sigma-Aldrich, USA). The concentrations of extracted RNA were measured using Qubit 2.0 with Qubit RNA HS kit (Thermo Fisher, USA). The quality of extracted RNA was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Following this the RIN and DV200 values were calculated to calculate the RNA input amounts for RNA-seq compatible library preparation.
Prior to the library preparation rRNA removal was performed using MGIEasy rRNA Depletion kit (MGI, China). After the rRNA depletion reverse transcription, second strand synthesis, and cDNA library preparation for NGS were carried out using MGIEasy RNA Directional Library Prep Set (MGI, China). The libraries were sequenced on DNBSEQ-G400 platform (MGI, China) with 35 M reads per sample and with 2 x 150 bp read length.

treatment_protocol:
To obtain PitNET tissue-derived free-floating spheres, cells were grown in DMEM-F12 (Thermo Fisher Scientific, USA), containing 1x penicillin/streptomycin solution, 20 ng/ml epidermal growth factor (EGF) (Sigma-Aldrich, Germany), 10 ng/ml basic fibroblast growth factor (bFGF) (Sigma-Aldrich, Germany), and 1x B27 supplement (GIBCO, USA). Cell culture cultivation and incubation was performed at 37°C, 95% air, and 5% CO2. For the gene expression experiments, pituispheres were grown on a 6-well plate and treated with 10 μM octreotide or 10 μM cabergoline for 4, 8, 24, 48, and 72 h.
The GH3 cells were maintained in F12-K medium containing 15% horse serum, 2.5% FBS and  1x penicillin/streptomycin solution. For studying the effects of PitNET drugs on gene expression, the cells were incubated for  4, 8, 24, 48, and 72 h with 10 μM octreotide and 10 μM cabergoline. Cell culture cultivation and incubation was performed at 37°C, 95% air, and 5% CO2.
To obtain MSC cells were grown in DMEM-F12, supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Fisher Scientific, USA), 1% ITS (Corning, USA), and 100 µg/ml primocin (InvivoGen, USA) until confluent, then propagated and passaged 2–6 times. Cell culture cultivation and incubation was performed at 37°C, 95% air, and 5% CO2.

tag: tumor functional type

value: GH

tag: therapy


title: Sample99 pituispheres RNA


title: Blood sample from individual 284

description: Sample ID: 284

source_name: Blood sample

value: Male


title: Blood sample from individual 285

description: Sample ID: 285


title: Sample94 pituispheres RNA


title: Blood sample from individual 282

description: Sample ID: 282


title: E407_vpuLCR_rep2

value: uLCR


title: Sample92 pituispheres RNA


title: E11_vpuLCR_rep1


title: E11_vpuLCR_rep2


title: Sample95 pituispheres RNA


title: Sample96 pituispheres RNA


title: Blood sample from individual 283

description: Sample ID: 283


title: noE_vpPos407_rep2

value: GGGTTTCCAGGCAAGTA


title: Blood sample from individual 281

description: Sample ID: 281


title: Sample93 pituispheres RNA


title: Sample91 pituispheres RNA


title: Blood sample from individual 280

description: Sample ID: 280


title: noE_vpPos47_rep2

value: AGGAGAACAAGGCCTTCAGTA


title: Blood sample from individual 279

description: Sample ID: 279


title: Sample87 pituispheres RNA


title: noE_vpPos407_rep1


title: Sample90 pituispheres RNA


title: Sample85 pituispheres RNA


title: Sample97 pituispheres RNA


title: Sample89 pituispheres RNA


title: Sample84 pituispheres RNA


title: Blood sample from individual 277

description: Sample ID: 277


title: Sample151 pituispheres RNA


title: Blood sample from individual 276

description: Sample ID: 276


title: Sample149 pituispheres RNA


title: Sample86 pituispheres RNA


title: Sample83 pituispheres RNA


title: E407_vpGFP_LongTermNegative_rep2

value: GFP

value: GGGGCACAAGCTGGAGTA


title: Sample145 pituispheres RNA


title: noE_vpPos47_rep1


title: Sample150 pituispheres RNA


title: E407_vpGFP_LongTermNegative_rep3


title: Sample147 pituispheres RNA


title: noE_vpPos11_rep1

value: GAAACCTCAGGACTAGGCAT


title: Sample88 pituispheres RNA


title: Blood sample from individual 275

description: Sample ID: 275


title: Sample144 pituispheres RNA

value: non-secreting


title: Blood sample from individual 274

description: Sample ID: 274


title: E407_vpGFP_LongTermNegative_rep1


title: Blood sample from individual 278

description: Sample ID: 278


title: Blood sample from individual 273

description: Sample ID: 273


title: Sample143 pituispheres RNA


title: Sample142 pituispheres RNA


title: E100_vpGFP_LongTermNegative_rep2


title: Blood sample from individual 272

description: Sample ID: 272


title: Sample140 pituispheres RNA


title: noE_vpPos11_rep2


title: Sample138 pituispheres RNA


title: Sample141 pituispheres RNA


title: E100_vpGFP_LongTermNegative_rep1


title: Blood sample from individual 271

description: Sample ID: 271


title: Sample148 pituispheres RNA


title: Sample137 pituispheres RNA


title: E407_vpGFP_plusHemin_rep3

value: CAGGGGCACAAGCTGGAGTA


title: Blood sample from individual 270

description: Sample ID: 270


title: Sample136 pituispheres RNA


title: Sample135 pituispheres RNA


title: Blood sample from individual 269

description: Sample ID: 269


title: Sample131 pituispheres RNA


title: Sample133 pituispheres RNA


title: Sample130 pituispheres RNA


title: Sample129 pituispheres RNA


title: Sample127 pituispheres RNA


title: E407_vpGFP_plusHemin_rep1


title: E407_vpGFP_plusHemin_rep2


title: Blood sample from individual 266

description: Sample ID: 266


title: Sample126 pituispheres RNA


title: E100_vpGFP_plusHemin_rep2


title: Sample125 pituispheres RNA


title: Blood sample from individual 265

description: Sample ID: 265


title: Sample123 pituispheres RNA


title: Sample124 pituispheres RNA


title: Sample122 pituispheres RNA


title: Blood sample from individual 264

description: Sample ID: 264


title: E47_vpGFP_plusHemin_rep2


title: Sample134 pituispheres RNA


title: E47_vpGFP_plusHemin_rep1


title: Sample120 pituispheres RNA


title: Blood sample from individual 268

description: Sample ID: 268


title: E11_vpGFP_plusHemin_rep2


title: Blood sample from individual 262

description: Sample ID: 262


title: Sample117 pituispheres RNA


title: Sample119 pituispheres RNA


title: Sample118 pituispheres RNA


title: E100_vpGFP_plusHemin_rep3


title: Sample116 pituispheres RNA


title: E11_vpGFP_plusHemin_rep1


title: Blood sample from individual 267

description: Sample ID: 267


title: E100_vpGFP_plusHemin_rep1


title: Sample115 pituispheres RNA


title: Blood sample from individual 261

description: Sample ID: 261


title: Sample114 pituispheres RNA


title: E0_vpGFP_plusHemin_rep2


title: Sample112 pituispheres RNA


title: Blood sample from individual 260

description: Sample ID: 260


title: E0_vpGFP_plusHemin_rep1


title: Sample111 pituispheres RNA


title: Sample108 pituispheres RNA


title: Sample110 pituispheres RNA


title: E100C0C100_vpGFP_rep2


title: Blood sample from individual 259

description: Sample ID: 259


title: Sample107 pituispheres RNA


title: Blood sample from individual 263

description: Sample ID: 263


title: Sample106 pituispheres RNA


title: E100C0C100_vpGFP_rep1


title: Blood sample from individual 257

description: Sample ID: 257


title: Sample104 pituispheres RNA


title: Blood sample from individual 256

description: Sample ID: 256


title: Sample105 pituispheres RNA


title: Blood sample from individual 255

description: Sample ID: 255


title: Sample113 pituispheres RNA


title: E0C0C100_vpGFP_rep1


title: E0C0C100_vpGFP_rep2


title: Blood sample from individual 254

description: Sample ID: 254


title: E407_vpuLCR_SMC1A_KD_rep1

value: CATTTAATATGCTTTAAGTTCTGGGGTAC


title: Sample102 pituispheres RNA


title: Sample103 pituispheres RNA


title: Sample139 mesenchymal stromal cells RNA

source_name: Pituitary neuroendocrine tumor mesenchymal stromal cells


title: Sample101 pituispheres RNA


title: E407_vpuLCR_Control_KD_rep2


title: Blood sample from individual 258

description: Sample ID: 258

value: Blood


title: Sample132 mesenchymal stromal cells RNA


title: Sample109 mesenchymal stromal cells RNA


title: Blood sample from individual 253

description: Sample ID: 253


title: Blood sample from individual 252

description: Sample ID: 252


title: Sample146 mesenchymal stromal cells RNA


title: Sample121 mesenchymal stromal cells RNA


title: E407_vpuLCR_Control_KD_rep1


title: Blood sample from individual 251

description: Sample ID: 251


title: Sample82 PitNET tissue RNA

source_name: Pituitary neuroendocrine tumor


title: E407_vpGFP_Control_SMC1A_rep1


title: Sample128 mesenchymal stromal cells RNA


title: Sample100 mesenchymal stromal cells RNA


title: E407_vpGFP_Control_KD_rep3


title: E407_vpGFP_Control_KD_rep2


title: Sample79 PitNET tissue RNA


title: Sample81 PitNET tissue RNA


title: Blood sample from individual 250

description: Sample ID: 250


title: Sample78 PitNET tissue RNA


title: Blood sample from individual 249

description: Sample ID: 249


title: Sample77 PitNET tissue RNA


title: Blood sample from individual 248

description: Sample ID: 248


title: Blood sample from individual 247

description: Sample ID: 247


title: EC100_vpCBS_RAD21_KD_rep1

value: CBS

value: GGAATCTCGCTCTGATCGTC


title: Blood sample from individual 246

description: Sample ID: 246

value: No active inflammatory disease


title: EC100_vpCBS_SMC1A_KD_rep1


title: Sample76 PitNET tissue RNA


title: Sample75 PitNET tissue RNA


title: Sample74 PitNET tissue RNA

value: No


title: Sample73 PitNET tissue RNA


title: EC100_vpuLCR_RAD21_KD_rep1

value: TTTAATATGCTTTAAGTTCTGGGGTAC


title: Sample71 PitNET tissue RNA


title: Blood sample from individual 245

description: Sample ID: 245

value: Female


title: Sample70 PitNET tissue RNA


title: EC100_vpuLCR_SMC1A_KD_rep1


title: Sample68 PitNET tissue RNA


title: Blood sample from individual 244

description: Sample ID: 244


title: Blood sample from individual 243

description: Sample ID: 243


title: Sample80 PitNET tissue RNA

value: Yes


title: Sample65 PitNET tissue RNA


title: EC100_vpGFP_RAD21_KD_rep1


title: Sample67 PitNET tissue RNA


title: Sample66 PitNET tissue RNA


title: E407_vpGFP_Control_KD_rep1


title: E100_vpuLCR_RAD21_KD_rep1

value: uLCR

value: GTTTAATATGCTTTAAGTTCTGGGGTAC


title: Sample63 PitNET tissue RNA


title: Sample64 PitNET tissue RNA


title: Sample72 PitNET tissue RNA


title: Blood sample from individual 241

description: Sample ID: 241


title: Sample62 PitNET tissue RNA


title: Blood sample from individual 240

description: Sample ID: 240

value: Male


title: Sample69 PitNET tissue RNA


title: noE_vpPos100_rep2

value: noE

value: CAGGGTCTCACTCTGTGGAG


title: Sample60 PitNET tissue RNA


title: Sample61 PitNET tissue RNA


title: Blood sample from individual 239

description: Sample ID: 239


title: Sample57 PitNET tissue RNA


title: Sample56 PitNET tissue RNA


title: noE_vpPos100_rep1


title: Sample59 PitNET tissue RNA


title: EC100_vpGFP_SMC1A_KD_rep1

value: GFP

value: GGGGCACAAGCTGGAGTA


title: E100_vpGFP_RAD21_KD_rep1

value: AGGGGCACAAGCTGGAGTA


title: Blood sample from individual 238

description: Sample ID: 238


title: E100_vpuLCR_SMC1A_KD_rep1


title: Sample54 PitNET tissue RNA


title: Blood sample from individual 242

description: Sample ID: 242

value: Unknown


title: Sample55 PitNET tissue RNA


title: Sample52 PitNET tissue RNA


title: Sample51 PitNET tissue RNA


title: EC100_vpGFP_Control_KD1_rep1


title: Blood sample from individual 237

description: Sample ID: 237

value: Blood


title: Sample53 PitNET tissue RNA


title: Blood sample from individual 236

description: Sample ID: 236


title: Sample58 PitNET tissue RNA


title: EC100_vpGFP_Control_KD1_rep2


title: Sample49 PitNET tissue RNA


title: Sample50 PitNET tissue RNA


title: Sample48 PitNET tissue RNA


title: Blood sample from individual 233

description: Sample ID: 233


title: Blood sample from individual 234

description: Sample ID: 234


title: C-0E100_vpuLCR_rep3


title: E100_vpGFP_Control_KD_rep1


title: Sample45 PitNET tissue RNA


title: Sample47 PitNET tissue RNA


title: Blood sample from individual 232

description: Sample ID: 232


title: Sample44 PitNET tissue RNA


title: Sample43 PitNET tissue RNA


title: Blood sample from individual 231

description: Sample ID: 231


title: E100_vpGFP_SMC1A_KD_rep1


title: C-0E100_vpuLCR_rep2


title: Blood sample from individual 235

description: Sample ID: 235


title: Blood sample from individual 230

description: Sample ID: 230


title: Sample41 PitNET tissue RNA


title: Sample40 PitNET tissue RNA


title: C-0E100_vpGFP_rep3


title: Sample39 PitNET tissue RNA


title: C-0E100_vpuLCR_rep1


title: Blood sample from individual 229

description: Sample ID: 229


title: Blood sample from individual 228

description: Sample ID: 228


title: Sample38 PitNET tissue RNA


title: Sample37 PitNET tissue RNA


title: Sample36 PitNET tissue RNA


title: C-0E100_vpGFP_rep1


title: Sample46 PitNET tissue RNA


title: Sample34 PitNET tissue RNA


title: Sample32 PitNET tissue RNA


title: Sample35 PitNET tissue RNA


title: Sample33 PitNET tissue RNA


title: Sample42 PitNET tissue RNA


title: EC100_vpCBS_rep1

value: CBS


title: Blood sample from individual 226

description: Sample ID: 226


title: EC100_vpCBS_rep2

value: GGAATCTCGCTCTGATCGTC


title: Blood sample from individual 224

description: Sample ID: 224

value: No active inflammatory disease


title: Sample31 PitNET tissue RNA


title: C100_vpCBS_rep1


title: Blood sample from individual 223

description: Sample ID: 223


title: C-0E100_vpGFP_rep2


title: Sample29 PitNET tissue RNA


title: Sample27 PitNET tissue RNA


title: Sample28 PitNET tissue RNA


title: Sample25 PitNET tissue RNA


title: C100_vpGFP_rep2

value: CAGGGGCACAAGCTGGAGTA


title: Blood sample from individual 222

description: Sample ID: 222


title: Sample23 PitNET tissue RNA

value: No


title: Blood sample from individual 227

description: Sample ID: 227

value: Female


title: Blood sample from individual 221

description: Sample ID: 221


title: Sample24 PitNET tissue RNA


title: C100_vpGFP_rep1


title: Sample22 PitNET tissue RNA


title: EC0_vpCBS_rep2


title: Sample21 PitNET tissue RNA


title: Sample20 PitNET tissue RNA


title: Blood sample from individual 220

description: Sample ID: 220


title: Sample30 PitNET tissue RNA


title: Blood sample from individual 219

description: Sample ID: 219


title: Sample19 PitNET tissue RNA


title: Blood sample from individual 225

description: Sample ID: 225


title: C100_vpCBS_rep2


title: Sample17 PitNET tissue RNA


title: EC0_vpCBS_rep1


title: Sample18 PitNET tissue RNA


title: C0_vpCBS_rep2


title: Blood sample from individual 218

description: Sample ID: 218


title: Sample26 PitNET tissue RNA


title: Blood sample from individual 217

description: Sample ID: 217


title: Sample14 PitNET tissue RNA


title: Sample16 PitNET tissue RNA


title: C0_vpCBS_rep1


title: Sample15 PitNET tissue RNA


title: C0_vpGFP_rep3


title: Sample13 PitNET tissue RNA


title: Blood sample from individual 216

description: Sample ID: 216


title: C0_vpGFP_rep2


title: Blood sample from individual 215

description: Sample ID: 215


title: Sample12 PitNET tissue RNA


title: Sample10 PitNET tissue RNA


title: Sample09 PitNET tissue RNA


title: Sample11 PitNET tissue RNA

value: Yes


title: EC100_vpuLCR_rep3

value: uLCR


title: C0_vpGFP_rep1


title: Blood sample from individual 214

description: Sample ID: 214


title: Sample07 PitNET tissue RNA


title: Blood sample from individual 213

description: Sample ID: 213


title: Sample08 PitNET tissue RNA


title: EC100_vpuLCR_rep2

value: GTTTAATATGCTTTAAGTTCTGGGGTAC


title: Sample03 PitNET tissue RNA


title: Sample04 PitNET tissue RNA


title: E100_vpuLCR_rep2

value: TTTAATATGCTTTAAGTTCTGGGGTAC


title: Blood sample from individual 212

description: Sample ID: 212


title: Blood sample from individual 210

description: Sample ID: 210

value: Male


title: Sample06 PitNET tissue RNA


title: Blood sample from individual 211

description: Sample ID: 211


title: Sample05 PitNET tissue RNA


title: EC100_vpuLCR_rep1


title: Sample02 PitNET tissue RNA


title: Sample01 PitNET tissue RNA


title: Blood sample from individual 209

description: Sample ID: 209


title: Brn1-FRB + rapa chip for Red1 rep 1

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq and MNase-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009).  Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis. The RNA-seq reads were mapped to the SK1 genome using Tophat2 with first strand library type, no novel junctions, and otherwise default options.
For ChIP-seq, 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. For MNase-seq, 3' ends were extended to a final length of 146 and bandwidth was set to 350 using MACS2 2.1.1. For RNA-seq, mapped reads were counted using featureCounts and statistical analysis was performed using a count-based workflow with the edgeR Bioconductor package.
For ChIP-seq, the input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses. For MNase-seq, the pileup was SPMR-normalized and used for further analyses. For RNA-seq, gene counts were normalized to counts per million and were then gene length-corrected for transcripts per million (tpm).
Axis sites (Red1 summits in wild type conditions) were identified using MACS2 narrow and -log10 qvalue of 20.
Peaks were identified using MACS broad flag.
Genome_build: SK1 (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: csv (count of mRNAs in tmp)

organism: Saccharomyces cerevisiae

source_name: Brn1-FRB chip for Red1 rep 1

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C, except for H7606  which was innoculated at OD600 = 0.8 in BYTA medium and grown for 20 hours at room temperature. H7797 was also grown in BYTA medium at room temperature for the 34C experiments. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 1.9 or 2.0 at 30°C (details are described in (Blitzblau et al., 2012)). Rapamycin was added at 0h where indicated.

extract_protocol:
For ChIP-seq samples, 25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. For MNase-seq samples, 50 ml of the meiotic cells were collected at the 3-hr time point and fixed for 30 min in 1% formaldehyde.  The formaldehyde was quenched with 125 mM glycine. ChIP-seq samples were processed as described in (Blitzblau et al., 2012). MNase-seq samples were processed as described in (Pan et al., 2011). A second sonication step was added just before library prep where indicated using a Bioruptor Pico (Diagenode, NJ, USA) with the following settings: 30 secs ON and 30 secs OFF for 5 cycles. For RNA-seq, 1.5 ml meiotic culture was taken at the 3-hr time point and RNA was extracted from mechanically lysed cells using the Qiagen RNeasy RNA isolation Kit and mRNA was extracted using Sera-Mag oligo-dT beads and fragmented.
For MNase-seq and ChIP-seq, libraries were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). For RNA-seq, libraries were prepared according to the Illumina TruSeq Stranded mRNA sample preparation kit, and sequencing libraries were prepared by PCR from the cDNA samples after ligation of adapters. Quality of all libraries was checked on 2200 Tapestation or Agilent 2100 Bioanalyzer. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads or 100 bp single-end reads.

treatment_protocol: For 34C experiments, strains were shaken in SPO medium at room temperature for 1 hour and shifted to 34 degrees Celsius for the remaining time.

tag: meiotic time point

tag: antibody


title: E100_vpuLCR_rep1

tag: knock down


title: Brn1-FRB + rapa input for Red1 rep 1

source_name: Brn1-FRB input for Red1 rep 1


title: EC100_vpGFP_rep2

tag: hemin treatment


title: anchor away no tag control  + rapa input for Red1 rep 1

source_name: anchor away no tag control input for Red1 rep 1


title: Blood sample from individual 208

description: Sample ID: 208


title: anchor away no tag control  + rapa chip for Red1 rep 1

source_name: anchor away no tag control chip for Red1 rep 1


title: pch2Δ ndt80Δ chip for Hop1 rep 2

description: reanalysis of: GSM2818434

source_name: pch2Δ ndt80Δ chip for Hop1 rep 2


title: EC100_vpGFP_rep1

tag: facs


title: pch2Δ ndt80Δ input for Hop1 rep 2

description: reanalysis of: GSM2818435

source_name: pch2Δ ndt80Δ input for Hop1 rep 2


title: Blood sample from individual 207

description: Sample ID: 207


title: pch2Δ ndt80Δ chip for Hop1 rep 1

description: reanalysis of: GSM2818430

source_name: pch2Δ ndt80Δ chip for Hop1 rep 1


title: EC0_vpuLCR_rep3

tag: viewpoint


title: EC0_vpuLCR_rep2

tag: barcode


title: wild type 3h Mnase rep 1

description: reanalysis of: GSM649328

source_name: wild type 3h Mnase rep 1


title: SCC2-3HA chip for HA rep 1

description: reanalysis of: GSM4677833

source_name: SCC2-3HA chip for HA rep 1

value: anti-HA


title: Blood sample from individual 205

description: Sample ID: 205

tag: individual id


title: Blood sample from individual 204

description: Sample ID: 204

tag: gender


title: E0_vpuLCR_rep1


title: Blood sample from individual 203

description: Sample ID: 203

tag: tissue


title: E0_vpuLCR_rep2


title: EC0_vpuLCR_rep1


title: wild type chip for H3 rep 3

source_name: wild type chip for H3 rep 3


title: Blood sample from individual 202

description: Sample ID: 202

tag: disease state


title: SMC4-PK9 resonicated chip for PK9 rep 2

description: reanalysis of: GSM4677855

source_name: SMC4-PK9 resonicated chip for PK9 rep 2

tag: genotype


title: SMC4-PK9 resonicated input for PK9 rep 1

description: reanalysis of: GSM4677852

tag: strain


title: SMC4-PK9 resonicated input for PK9 rep 2

description: reanalysis of: GSM4677854


title: Blood sample from individual 201

description: Sample ID: 201


title: wild type RNA seq 3h

description: reanalysis of: GSM3834085

source_name: wild type RNA seq 3h


title: SMC4-PK9 resonicated chip for PK9 rep 1

description: reanalysis of: GSM4677853

source_name: SMC4-PK9 resonicated chip for PK9 rep 1


title: wild type chip for H3 rep 2

source_name: wild type chip for H3 rep 2


title: wild type input for H3 rep 3

source_name: wild type input for H3 rep 3


title: EC0_vpGFP_rep3

value: GFP


title: EC0_vpGFP_rep2


title: Blood sample from individual 206

description: Sample ID: 206

source_name: Blood sample


title: Blood sample from individual 200

description: Sample ID: 200


title: wild type input for H3 rep 2

source_name: wild type input for H3 rep 2


title: EC0_vpGFP_rep1


title: SCC2-3HA input for HA rep 1

description: reanalysis of: GSM4677832

source_name: SCC2-3HA input for HA rep 1


title: Blood sample from individual 199

description: Sample ID: 199


title: pch2Δ ndt80Δ input for Hop1 rep 1

description: reanalysis of: GSM2818431

source_name: pch2Δ ndt80Δ input for Hop1 rep 1


title: rec8Δ chip for Red1 rep 3

description: reanalysis of: GSM2320255

source_name: rec8Δ chip for Red1 rep 3


title: Blood sample from individual 198

description: Sample ID: 198


title: rec8Δ input for Red1 rep 4

description: reanalysis of: GSM4677911

source_name: rec8Δ input for Red1 rep 4


title: rec8Δ input for Red1 rep 3

description: reanalysis of: GSM2320253

source_name: rec8Δ input for Red1 rep 3


title: E407_vpGFP_rep3


title: rec8Δ chip for Red1 rep 2

description: reanalysis of: GSM1695731

source_name: rec8Δ chip for Red1 rep 2


title: rec8Δ chip for Red1 rep 1

description: reanalysis of: GSM1695730

source_name: rec8Δ chip for Red1 rep 1


title: Blood sample from individual 197

description: Sample ID: 197


title: E407_vpGFP_rep2


title: E407_vpGFP_rep1


title: rec8Δ input for Red1 rep 2

description: reanalysis of: GSM1695729

source_name: rec8Δ input for Red1 rep 2


title: E100_vpGFP_rep2

value: GGGGCACAAGCTGGAGTA


title: Blood sample from individual 195

description: Sample ID: 195


title: E100_vpGFP_rep1


title: wild type Rec8 chip rep 1

description: reanalysis of: GSM1695724

source_name: wild type Rec8 chip rep 1


title: rec8Δ input for Red1 rep 1

description: reanalysis of: GSM1695728

source_name: rec8Δ input for Red1 rep 1


title: wild type input for Rec8 rep 1

description: reanalysis of: GSM1695722

source_name: wild type input for Rec8 rep 1


title: Blood sample from individual 194

description: Sample ID: 194


title: rec8Δ chip for Red1 rep 4

description: reanalysis of: GSM4677912

source_name: rec8Δ chip for Red1 rep 4


title: Blood sample from individual 196

description: Sample ID: 196


title: wild type Red1 chip rep 4

description: reanalysis of: GSM1695719

source_name: wild type Red1 chip rep 4