title: CLLCCAID2734

description: Gene expression data from CLL sample


title: CLLCCAID2735

status: Public on Jun 30 2021

type: RNA

city: Ulm

first: Johannes

last: Bloehdorn

address: Albert-Einstein-Allee 23

country: Germany

institute: University of Ulm

description: Gene expression data from CLL sample

hyb_protocol: Array hybridization was performed at 45°C for 16-18h in the Affymetrix GeneChip® Hybridization Oven 640, arrays were subsequently washed in the Fluidics Station 450.

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

data_processing: Raw Affymetrix Human Exon array (HuEx-1_0-st-v2) data files have been normalized using the RMA algorithm using aroma.affymetrix

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

label_protocol: Samples from CLL patients were analyzed for mRNA expression using the Affymetrix GeneChip® Human Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA). The experiment was conducted according to the manufacturer’s protocol. In brief, 250 ng RNA per sample were amplified, transcribed to cDNA, fragmented and subsequently labeled with Biotin.

growth_protocol: Peripheral blood mononuclear cells were collected from CLL patients before initiation of treatment on randomized trial with fludarabine and cyclophosphomide +/- rituximab.

extract_protocol: Total RNA for mRNA profiling was extracted from whole cell lysates of CLL patient samples according to the Allprep DNA/RNA mini kit (Qiagen). Quality control was assessed using the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip (Agilent Technologies). RNA for gene expression profiling had a RIN of at least 7.

treatment_protocol: Ficoll density gradient centrifugation for isolation of mononuclear cells with or without subsequent immunomagnetic tumor cell enrichment via CD19.

tag: disease state

value: chronic lymphocytic leukaemia

tag: prognostic association with gep signature

value: aggressive GEP signature

tag: antibody pretreatment

value: Rituximab-naive

tag: sensitivity to chemotherapy

value: Fludarabine untreated/sensitive

tag: ecog

tag: clinical course

value: early progression


title: CLLCCAID2737

description: Gene expression data from CLL sample

value: indolent GEP signature

value: intermediate/late progression


title: CLLCCAID2744

description: Gene expression data from CLL sample


title: CLLCCAID2730

description: Gene expression data from CLL sample


title: CLLCCAID2731

description: Gene expression data from CLL sample


title: CLLCCAID2725

description: Gene expression data from CLL sample


title: CLLCCAID2726

description: Gene expression data from CLL sample


title: CLLCCAID2724

description: Gene expression data from CLL sample


title: CLLCCAID2729

description: Gene expression data from CLL sample


title: CLLCCAID2723

description: Gene expression data from CLL sample


title: CLLCCAID2728

description: Gene expression data from CLL sample


title: CLLCCAID2722

description: Gene expression data from CLL sample


title: CLLCCAID2727

description: Gene expression data from CLL sample


title: CLLCCAID2721

description: Gene expression data from CLL sample


title: CLLCCAID2720

description: Gene expression data from CLL sample


title: CLLCCAID2716

description: Gene expression data from CLL sample


title: CLLCCAID2719

description: Gene expression data from CLL sample


title: CLLCCAID2717

description: Gene expression data from CLL sample


title: CLLCCAID2709

description: Gene expression data from CLL sample


title: CLLCCAID2708

description: Gene expression data from CLL sample


title: CLLCCAID2712

description: Gene expression data from CLL sample


title: CLLCCAID2704

description: Gene expression data from CLL sample


title: CLLCCAID2718

description: Gene expression data from CLL sample


title: CLLCCAID2710

description: Gene expression data from CLL sample


title: CLLCCAID2701

description: Gene expression data from CLL sample


title: CLLCCAID2702

description: Gene expression data from CLL sample


title: CLLCCAID2693

description: Gene expression data from CLL sample


title: CLLCCAID2715

description: Gene expression data from CLL sample


title: CLLCCAID2714

description: Gene expression data from CLL sample


title: CLLCCAID2705

description: Gene expression data from CLL sample


title: CLLCCAID2694

description: Gene expression data from CLL sample


title: CLLCCAID2706

description: Gene expression data from CLL sample


title: CLLCCAID2698

description: Gene expression data from CLL sample


title: CLLCCAID2700

description: Gene expression data from CLL sample


title: CLLCCAID2713

description: Gene expression data from CLL sample


title: CLLCCAID2707

description: Gene expression data from CLL sample


title: CLLCCAID2699

description: Gene expression data from CLL sample


title: CLLCCAID2695

description: Gene expression data from CLL sample


title: CLLCCAID2697

description: Gene expression data from CLL sample


title: CLLCCAID2703

description: Gene expression data from CLL sample


title: CLLCCAID2692

description: Gene expression data from CLL sample


title: CLLCCAID2711

description: Gene expression data from CLL sample


title: CLLCCAID2845

description: Gene expression data from CLL sample


title: CLLCCAID2696

description: Gene expression data from CLL sample


title: CLLCCAID2691

description: Gene expression data from CLL sample


title: CLLCCAID2688

description: Gene expression data from CLL sample


title: CLLCCAID2689

description: Gene expression data from CLL sample


title: CLLCCAID2690

description: Gene expression data from CLL sample


title: CLLCCAID2687

description: Gene expression data from CLL sample


title: CLLCCAID2673

description: Gene expression data from CLL sample


title: CLLCCAID2675

description: Gene expression data from CLL sample


title: CLLCCAID2671

description: Gene expression data from CLL sample


title: CLLCCAID2678

description: Gene expression data from CLL sample


title: CLLCCAID2676

description: Gene expression data from CLL sample


title: CLLCCAID2684

description: Gene expression data from CLL sample


title: CLLCCAID2674

description: Gene expression data from CLL sample


title: CLLCCAID2680

description: Gene expression data from CLL sample


title: CLLCCAID2668

description: Gene expression data from CLL sample


title: CLLCCAID2677

description: Gene expression data from CLL sample


title: CLLCCAID2682

description: Gene expression data from CLL sample


title: CLLCCAID2679

description: Gene expression data from CLL sample


title: CLLCCAID2685

description: Gene expression data from CLL sample


title: CLLCCAID2686

description: Gene expression data from CLL sample


title: CLLCCAID2683

description: Gene expression data from CLL sample


title: CLLCCAID2666

description: Gene expression data from CLL sample


title: CLLCCAID2681

description: Gene expression data from CLL sample


title: CLLCCAID2670

description: Gene expression data from CLL sample


title: CLLCCAID2672

description: Gene expression data from CLL sample


title: CLLCCAID2665

description: Gene expression data from CLL sample


title: CLLCCAID2667

description: Gene expression data from CLL sample


title: CLLCCAID2669

description: Gene expression data from CLL sample


title: CLLCCAID2664

description: Gene expression data from CLL sample


title: CLLCCAID2663

description: Gene expression data from CLL sample


title: CLLCCAID2661

description: Gene expression data from CLL sample


title: CLLCCAID2659

description: Gene expression data from CLL sample


title: CLLCCAID2662

description: Gene expression data from CLL sample


title: CLLCCAID2657

description: Gene expression data from CLL sample


title: CLLCCAID2658

description: Gene expression data from CLL sample


title: CLLCCAID2654

description: Gene expression data from CLL sample


title: CLLCCAID2655

description: Gene expression data from CLL sample


title: CLLCCAID2660

description: Gene expression data from CLL sample


title: CLLCCAID2651

description: Gene expression data from CLL sample


title: CLLCCAID2649

description: Gene expression data from CLL sample


title: CLLCCAID2646

description: Gene expression data from CLL sample


title: CLLCCAID2653

description: Gene expression data from CLL sample


title: CLLCCAID2647

description: Gene expression data from CLL sample


title: CLLCCAID2648

description: Gene expression data from CLL sample


title: CLLCCAID2650

description: Gene expression data from CLL sample


title: CLLCCAID2640

description: Gene expression data from CLL sample


title: CLLCCAID2652

description: Gene expression data from CLL sample


title: CLLCCAID2656

description: Gene expression data from CLL sample


title: CLLCCAID2638

description: Gene expression data from CLL sample


title: CLLCCAID2644

description: Gene expression data from CLL sample


title: CLLCCAID2641

description: Gene expression data from CLL sample


title: CLLCCAID2635

description: Gene expression data from CLL sample


title: CLLCCAID2643

description: Gene expression data from CLL sample


title: CLLCCAID2642

description: Gene expression data from CLL sample


title: CLLCCAID2633

description: Gene expression data from CLL sample


title: CLLCCAID2637

description: Gene expression data from CLL sample


title: CLLCCAID2645

description: Gene expression data from CLL sample


title: CLLCCAID2634

description: Gene expression data from CLL sample


title: CLLCCAID2631

description: Gene expression data from CLL sample


title: CLLCCAID2636

description: Gene expression data from CLL sample


title: CLLCCAID2632

description: Gene expression data from CLL sample


title: CLLCCAID2630

description: Gene expression data from CLL sample


title: CLLCCAID2625

description: Gene expression data from CLL sample


title: CLLCCAID2622

description: Gene expression data from CLL sample


title: CLLCCAID2623

description: Gene expression data from CLL sample


title: CLLCCAID2627

description: Gene expression data from CLL sample


title: CLLCCAID2624

description: Gene expression data from CLL sample


title: CLLCCAID2626

description: Gene expression data from CLL sample


title: CLLCCAID2629

description: Gene expression data from CLL sample


title: CLLCCAID2628

description: Gene expression data from CLL sample


title: CLLCCAID2639

description: Gene expression data from CLL sample


title: CLLCCAID2616

description: Gene expression data from CLL sample


title: CLLCCAID2621

description: Gene expression data from CLL sample


title: CLLCCAID2619

description: Gene expression data from CLL sample


title: CLLCCAID2617

description: Gene expression data from CLL sample


title: CLLCCAID2615

description: Gene expression data from CLL sample


title: CLLCCAID2620

description: Gene expression data from CLL sample


title: CLLCCAID2618

description: Gene expression data from CLL sample


title: CLLCCAID2605

description: Gene expression data from CLL sample


title: CLLCCAID2610

description: Gene expression data from CLL sample


title: CLLCCAID2613

description: Gene expression data from CLL sample


title: CLLCCAID2608

description: Gene expression data from CLL sample


title: CLLCCAID2614

description: Gene expression data from CLL sample


title: CLLCCAID2609

description: Gene expression data from CLL sample


title: CLLCCAID2601

description: Gene expression data from CLL sample


title: CLLCCAID2602

description: Gene expression data from CLL sample


title: CLLCCAID2612

description: Gene expression data from CLL sample


title: CLLCCAID2604

description: Gene expression data from CLL sample


title: CLLCCAID2603

description: Gene expression data from CLL sample


title: CLLCCAID2599

description: Gene expression data from CLL sample


title: CLLCCAID2611

description: Gene expression data from CLL sample


title: CLLCCAID2600

description: Gene expression data from CLL sample


title: CLLCCAID2595

description: Gene expression data from CLL sample


title: CLLCCAID2598

description: Gene expression data from CLL sample


title: CLLCCAID2593

description: Gene expression data from CLL sample


title: CLLCCAID2597

description: Gene expression data from CLL sample


title: CLLCCAID2589

description: Gene expression data from CLL sample


title: CLLCCAID2594

description: Gene expression data from CLL sample


title: CLLCCAID2607

description: Gene expression data from CLL sample


title: CLLCCAID2606

description: Gene expression data from CLL sample


title: CLLCCAID2590

description: Gene expression data from CLL sample


title: CLLCCAID2586

description: Gene expression data from CLL sample


title: CLLCCAID2592

description: Gene expression data from CLL sample


title: CLLCCAID2581

description: Gene expression data from CLL sample


title: CLLCCAID2577

description: Gene expression data from CLL sample


title: CLLCCAID2591

description: Gene expression data from CLL sample


title: CLLCCAID2596

description: Gene expression data from CLL sample


title: CLLCCAID2585

description: Gene expression data from CLL sample


title: CLLCCAID2588

description: Gene expression data from CLL sample


title: CLLCCAID2587

description: Gene expression data from CLL sample


title: CLLCCAID2579

description: Gene expression data from CLL sample


title: CLLCCAID2572

description: Gene expression data from CLL sample


title: CLLCCAID2571

description: Gene expression data from CLL sample


title: CLLCCAID2580

description: Gene expression data from CLL sample


title: CLLCCAID2569

description: Gene expression data from CLL sample


title: CLLCCAID2584

description: Gene expression data from CLL sample


title: CLLCCAID2568

description: Gene expression data from CLL sample


title: CLLCCAID2583

description: Gene expression data from CLL sample


title: CLLCCAID2578

description: Gene expression data from CLL sample


title: CLLCCAID2575

description: Gene expression data from CLL sample


title: CLLCCAID2566

description: Gene expression data from CLL sample


title: CLLCCAID2576

description: Gene expression data from CLL sample


title: CLLCCAID2582

description: Gene expression data from CLL sample


title: CLLCCAID2574

description: Gene expression data from CLL sample


title: CLLCCAID2563

description: Gene expression data from CLL sample


title: CLLCCAID2564

description: Gene expression data from CLL sample


title: CLLCCAID2570

description: Gene expression data from CLL sample


title: CLLCCAID2573

description: Gene expression data from CLL sample


title: CLLCCAID2560

description: Gene expression data from CLL sample


title: CLLCCAID2567

description: Gene expression data from CLL sample


title: CLLCCAID2558

description: Gene expression data from CLL sample


title: CLLCCAID2556

description: Gene expression data from CLL sample


title: CLLCCAID2565

description: Gene expression data from CLL sample


title: CLLCCAID2553

description: Gene expression data from CLL sample


title: CLLCCAID2555

description: Gene expression data from CLL sample


title: CLLCCAID2551

description: Gene expression data from CLL sample


title: CLLCCAID2557

description: Gene expression data from CLL sample


title: CLLCCAID2547

description: Gene expression data from CLL sample


title: CLLCCAID2550

description: Gene expression data from CLL sample


title: CLLCCAID2548

description: Gene expression data from CLL sample


title: CLLCCAID2562

description: Gene expression data from CLL sample


title: CLLCCAID2554

description: Gene expression data from CLL sample


title: CLLCCAID2549

description: Gene expression data from CLL sample


title: CLLCCAID2559

description: Gene expression data from CLL sample


title: CLLCCAID2545

description: Gene expression data from CLL sample


title: CLLCCAID2540

description: Gene expression data from CLL sample


title: CLLCCAID2546

description: Gene expression data from CLL sample


title: CLLCCAID2543

description: Gene expression data from CLL sample


title: CLLCCAID2542

description: Gene expression data from CLL sample


title: CLLCCAID2541

description: Gene expression data from CLL sample


title: CLLCCAID2538

description: Gene expression data from CLL sample


title: CLLCCAID2552

description: Gene expression data from CLL sample


title: CLLCCAID2544

description: Gene expression data from CLL sample


title: CLLCCAID2539

description: Gene expression data from CLL sample


title: CLLCCAID2537

description: Gene expression data from CLL sample


title: CLLCCAID2561

description: Gene expression data from CLL sample


title: CLLCCAID2534

description: Gene expression data from CLL sample


title: CLLCCAID2530

description: Gene expression data from CLL sample


title: CLLCCAID2533

description: Gene expression data from CLL sample


title: CLLCCAID2531

description: Gene expression data from CLL sample


title: CLLCCAID2532

description: Gene expression data from CLL sample


title: CLLCCAID2529

description: Gene expression data from CLL sample


title: CLLCCAID2536

description: Gene expression data from CLL sample


title: CLLCCAID2535

description: Gene expression data from CLL sample


title: CLLCCAID2525

description: Gene expression data from CLL sample


title: CLLCCAID2524

description: Gene expression data from CLL sample


title: CLLCCAID2527

description: Gene expression data from CLL sample


title: CLLCCAID2528

description: Gene expression data from CLL sample


title: CLLCCAID2521

description: Gene expression data from CLL sample


title: CLLCCAID2522

description: Gene expression data from CLL sample


title: CLLCCAID2514

description: Gene expression data from CLL sample


title: CLLCCAID2518

description: Gene expression data from CLL sample


title: CLLCCAID2516

description: Gene expression data from CLL sample


title: CLLCCAID2523

description: Gene expression data from CLL sample


title: CLLCCAID2515

description: Gene expression data from CLL sample


title: CLLCCAID2508

description: Gene expression data from CLL sample


title: CLLCCAID2513

description: Gene expression data from CLL sample


title: CLLCCAID2512

description: Gene expression data from CLL sample


title: CLLCCAID2510

description: Gene expression data from CLL sample


title: CLLCCAID2511

description: Gene expression data from CLL sample


title: CLLCCAID2526

description: Gene expression data from CLL sample


title: CLLCCAID2507

description: Gene expression data from CLL sample


title: CLLCCAID2503

description: Gene expression data from CLL sample


title: CLLCCAID2520

description: Gene expression data from CLL sample


title: CLLCCAID2504

description: Gene expression data from CLL sample


title: CLLCCAID2517

description: Gene expression data from CLL sample


title: CLLCCAID2509

description: Gene expression data from CLL sample


title: CLLCCAID2505

description: Gene expression data from CLL sample


title: CLLCCAID2519

description: Gene expression data from CLL sample


title: CLLCCAID2499

description: Gene expression data from CLL sample


title: CLLCCAID2500

description: Gene expression data from CLL sample


title: CLLCCAID2501

description: Gene expression data from CLL sample


title: CLLCCAID2502

description: Gene expression data from CLL sample


title: CLLCCAID2492

description: Gene expression data from CLL sample


title: CLLCCAID2494

description: Gene expression data from CLL sample


title: CLLCCAID2496

description: Gene expression data from CLL sample


title: CLLCCAID2493

description: Gene expression data from CLL sample


title: CLLCCAID2485

description: Gene expression data from CLL sample


title: CLLCCAID2486

description: Gene expression data from CLL sample


title: CLLCCAID2495

description: Gene expression data from CLL sample


title: CLLCCAID2497

description: Gene expression data from CLL sample


title: CLLCCAID2483

description: Gene expression data from CLL sample


title: CLLCCAID2487

description: Gene expression data from CLL sample


title: CLLCCAID2489

description: Gene expression data from CLL sample


title: CLLCCAID2488

description: Gene expression data from CLL sample


title: CLLCCAID2484

description: Gene expression data from CLL sample


title: CLLCCAID2490

description: Gene expression data from CLL sample


title: CLLCCAID2498

description: Gene expression data from CLL sample


title: CLLCCAID2481

description: Gene expression data from CLL sample


title: CLLCCAID2482

description: Gene expression data from CLL sample


title: CLLCCAID2479

description: Gene expression data from CLL sample


title: CLLCCAID2480

description: Gene expression data from CLL sample


title: CLLCCAID2491

description: Gene expression data from CLL sample


title: CLLCCAID2475

description: Gene expression data from CLL sample


title: CLLCCAID2478

description: Gene expression data from CLL sample


title: CLLCCAID2472

description: Gene expression data from CLL sample


title: CLLCCAID2473

description: Gene expression data from CLL sample


title: CLLCCAID2506

description: Gene expression data from CLL sample


title: CLLCCAID2476

description: Gene expression data from CLL sample


title: CLLCCAID2477

description: Gene expression data from CLL sample


title: CLLCCAID2372

description: Gene expression data from CLL sample


title: CLLCCAID2474

description: Gene expression data from CLL sample


title: CLLCCAID2365

description: Gene expression data from CLL sample


title: CLLCCAID2359

description: Gene expression data from CLL sample


title: CLLCCAID2371

description: Gene expression data from CLL sample


title: CLLCCAID2364

description: Gene expression data from CLL sample


title: CLLCCAID2370

description: Gene expression data from CLL sample


title: CLLCCAID2349

description: Gene expression data from CLL sample


title: CLLCCAID2353

description: Gene expression data from CLL sample


title: CLLCCAID2362

description: Gene expression data from CLL sample


title: CLLCCAID2366

description: Gene expression data from CLL sample


title: CLLCCAID2369

description: Gene expression data from CLL sample


title: CLLCCAID2358

description: Gene expression data from CLL sample


title: CLLCCAID2350

description: Gene expression data from CLL sample


title: CLLCCAID2368

description: Gene expression data from CLL sample


title: CLLCCAID2356

description: Gene expression data from CLL sample


title: CLLCCAID2355

description: Gene expression data from CLL sample


title: CLLCCAID2360

description: Gene expression data from CLL sample


title: CLLCCAID2357

description: Gene expression data from CLL sample


title: CLLCCAID2361

description: Gene expression data from CLL sample


title: CLLCCAID2354

description: Gene expression data from CLL sample


title: CLLCCAID2352

description: Gene expression data from CLL sample


title: CLLCCAID2367

description: Gene expression data from CLL sample


title: CLLCCAID2351

description: Gene expression data from CLL sample


title: CLLCCAID2348

description: Gene expression data from CLL sample


title: CLLCCAID2363

description: Gene expression data from CLL sample


title: CLLCCAID2347

description: Gene expression data from CLL sample


title: CLLCCAID2346

description: Gene expression data from CLL sample


title: CLLCCAID2344

description: Gene expression data from CLL sample


title: CLLCCAID2345

description: Gene expression data from CLL sample


title: CLLCCAID2343

description: Gene expression data from CLL sample


title: CLLCCAID2340

description: Gene expression data from CLL sample


title: CLLCCAID2451

description: Gene expression data from CLL sample


title: CLLCCAID2450

description: Gene expression data from CLL sample


title: CLLCCAID2342

description: Gene expression data from CLL sample


title: CLLCCAID2341

description: Gene expression data from CLL sample


title: CLLCCAID2443

description: Gene expression data from CLL sample


title: CLLCCAID2440

description: Gene expression data from CLL sample


title: CLLCCAID2442

description: Gene expression data from CLL sample


title: CLLCCAID2438

description: Gene expression data from CLL sample


title: CLLCCAID2449

description: Gene expression data from CLL sample


title: CLLCCAID2448

description: Gene expression data from CLL sample


title: CLLCCAID2434

description: Gene expression data from CLL sample


title: CLLCCAID2436

description: Gene expression data from CLL sample


title: CLLCCAID2431

description: Gene expression data from CLL sample


title: CLLCCAID2435

description: Gene expression data from CLL sample


title: CLLCCAID2437

description: Gene expression data from CLL sample


title: CLLCCAID2433

description: Gene expression data from CLL sample


title: CLLCCAID2439

description: Gene expression data from CLL sample


title: CLLCCAID2446

description: Gene expression data from CLL sample


title: CLLCCAID2447

description: Gene expression data from CLL sample


title: CLLCCAID2445

description: Gene expression data from CLL sample


title: CLLCCAID2429

description: Gene expression data from CLL sample


title: CLLCCAID2432

description: Gene expression data from CLL sample


title: CLLCCAID2430

description: Gene expression data from CLL sample


title: CLLCCAID2427

description: Gene expression data from CLL sample


title: CLLCCAID2444

description: Gene expression data from CLL sample


title: CLLCCAID2441

description: Gene expression data from CLL sample


title: CLLCCAID2425

description: Gene expression data from CLL sample


title: CLLCCAID2422

description: Gene expression data from CLL sample


title: CLLCCAID2428

description: Gene expression data from CLL sample


title: CLLCCAID2426

description: Gene expression data from CLL sample


title: CLLCCAID2421

description: Gene expression data from CLL sample


title: CLLCCAID2424

description: Gene expression data from CLL sample


title: CLLCCAID2423

description: Gene expression data from CLL sample


title: CLLCCAID2419

description: Gene expression data from CLL sample


title: CLLCCAID2418

description: Gene expression data from CLL sample


title: CLLCCAID2420

description: Gene expression data from CLL sample


title: CLLCCAID2415

description: Gene expression data from CLL sample


title: CLLCCAID2412

description: Gene expression data from CLL sample


title: CLLCCAID2411

description: Gene expression data from CLL sample


title: CLLCCAID2410

description: Gene expression data from CLL sample


title: CLLCCAID2417

description: Gene expression data from CLL sample


title: CLLCCAID2409

description: Gene expression data from CLL sample


title: CLLCCAID2413

description: Gene expression data from CLL sample


title: CLLCCAID2406

description: Gene expression data from CLL sample


title: CLLCCAID2403

description: Gene expression data from CLL sample


title: CLLCCAID2404

description: Gene expression data from CLL sample


title: CLLCCAID2401

description: Gene expression data from CLL sample


title: CLLCCAID2405

description: Gene expression data from CLL sample


title: CLLCCAID2414

description: Gene expression data from CLL sample


title: CLLCCAID2416

description: Gene expression data from CLL sample


title: CLLCCAID2408

description: Gene expression data from CLL sample


title: CLLCCAID2402

description: Gene expression data from CLL sample


title: CLLCCAID2397

description: Gene expression data from CLL sample


title: CLLCCAID2400

description: Gene expression data from CLL sample


title: CLLCCAID2396

description: Gene expression data from CLL sample


title: CLLCCAID2393

description: Gene expression data from CLL sample


title: CLLCCAID2394

description: Gene expression data from CLL sample


title: CLLCCAID2398

description: Gene expression data from CLL sample


title: CLLCCAID2407

description: Gene expression data from CLL sample


title: CLLCCAID2392

description: Gene expression data from CLL sample


title: CLLCCAID2399

description: Gene expression data from CLL sample


title: CLLCCAID2395

description: Gene expression data from CLL sample


title: CLLCCAID2390

description: Gene expression data from CLL sample


title: CLLCCAID2391

description: Gene expression data from CLL sample


title: CLLCCAID2383

description: Gene expression data from CLL sample


title: CLLCCAID2384

description: Gene expression data from CLL sample


title: CLLCCAID2388

description: Gene expression data from CLL sample


title: CLLCCAID2387

description: Gene expression data from CLL sample


title: CLLCCAID2385

description: Gene expression data from CLL sample


title: CLLCCAID2386

description: Gene expression data from CLL sample


title: CLLCCAID2379

description: Gene expression data from CLL sample


title: CLLCCAID2378

description: Gene expression data from CLL sample


title: CLLCCAID2377

description: Gene expression data from CLL sample


title: CLLCCAID2381

description: Gene expression data from CLL sample


title: CLLCCAID2375

description: Gene expression data from CLL sample


title: CLLCCAID2389

description: Gene expression data from CLL sample


title: CLLCCAID2382

description: Gene expression data from CLL sample


title: CLLCCAID2374

description: Gene expression data from CLL sample


title: CLLCCAID2470

description: Gene expression data from CLL sample


title: CLLCCAID2469

description: Gene expression data from CLL sample


title: CLLCCAID2376

description: Gene expression data from CLL sample


title: CLLCCAID2471

description: Gene expression data from CLL sample


title: CLLCCAID2468

description: Gene expression data from CLL sample


title: CLLCCAID2463

description: Gene expression data from CLL sample


title: CLLCCAID2467

description: Gene expression data from CLL sample


title: CLLCCAID2464

description: Gene expression data from CLL sample


title: CLLCCAID2373

description: Gene expression data from CLL sample


title: CLLCCAID2461

description: Gene expression data from CLL sample


title: CLLCCAID2465

description: Gene expression data from CLL sample


title: CLLCCAID2466

description: Gene expression data from CLL sample


title: CLLCCAID2380

description: Gene expression data from CLL sample


title: OACre132T

status: Public on May 06 2021

type: SRA

city: Southampton

first: Tim

last: Underwood

address: Somers Cancer Research Building, General Hospital

department: Cancer Sciences

country: United Kingdom

institute: University of Southampton

description: DropSeq Barcoded Libraries

library_source: transcriptomic

data_processing:
Raw reads were converted to fastqs using bcl2fastq v2.18 (Illumina)
Fastqs were ultimately processed through the DropSeq alignment cookbook v2.1 pipeline
https://github.com/broadinstitute/Drop-seq/releases/tag/v2.1.0
During the pipeline, captured transcripts were aligned to hg38 using STAR alignment (STAR 2.6.0a)
https://github.com/broadinstitute/Drop-seq/releases/tag/v2.1.0
Dropseq was performed following a modified DropSeq protocol v3.1 (Macosko et al., 2015), where single cells from the suspension were co-encapsulated with a barcoded bead in nanolitre droplets. Droplets were broken and the bead yield underwent reverse transcription (Maxima H- RTase; ThermoFisher), followed by an exonuclease (Exonuclease I; NEB) and PCR step (KAPA HiFi HotStart ReadyMix; Roche). Each PCR reaction consisted of 2000 beads (estimated 100 cell transcriptomes) for 16 cycles. Products were purified (Ampure Beads XP at a 0.6 ratio), pooled (10 reactions estimated at 1000 cells), and re-purified (again at a 0.6 ratio). For each sample, 500pg of cDNA were used for a Nextera XT library prep kit (Illumina) before sequencing on a NextSeq 500, 75 cycle High output cartridge with a loading concentration 2.3pM.
Genome_build: hg38
Supplementary_files_format_and_content: Digital Gene Expression Matrix

molecule: cytoplasmic RNA

source_name: Esophageal Adenocarcinoma

extract_protocol:
Samples were relocated to the laboratory and placed in a tissue culture hood, moved to a petri dish and washed with PBS-A and then minced with a scalpel to approximately 1mm chunks. Minced tissue was transferred to a 50ml Falcon tube with 5ml of DMEM complete 100 ul of 150 U/ml Collagenase P and 100 ul of10 mg/ml DNase. The samples were placed in an incubator at 37o C with agitation for 60 minutes and disturbed at 15 minutes and 30 minutes with pipettes. Samples were then passed through a 70 um strainer and 10 ml of empty DMEM added.
Cells were then pelleted using centrifugation and media aspirated. Cells were resuspended in RBC lysis solution and incubated at 4oC for 10 minutes, 10 ml of empty DMEM was added and the suspension was passed through a 40 um strainer before being pelleted and resuspended in either 1 ml PBS or 1 ml of cell suspension buffer.
10 ul of cells in suspension and 10 ul of trypan blue was mixed together and cells were counted on a C-chip Fuchs-Rosenthal haemocytometer. A 150,000-cell aliquot was made up to 1.5 mls with cell suspension buffer and prepared for DropSeq.
scRNA-seq

tag: tissue

value: Esophageal Adenocarcinoma


title: OAC3010NT

description: DropSeq Barcoded Libraries

source_name: Normal Esophagus

value: Normal Esophagus


title: OAC3010TT

description: DropSeq Barcoded Libraries


title: CLLCCAID2462

description: Gene expression data from CLL sample


title: OAC2811T

description: DropSeq Barcoded Libraries


title: CLLCCAID2458

description: Gene expression data from CLL sample


title: CLLCCAID2455

description: Gene expression data from CLL sample


title: OAC2610T

description: DropSeq Barcoded Libraries


title: OAC2210L

description: DropSeq Barcoded Libraries


title: OAC2210T3

description: DropSeq Barcoded Libraries


title: CLLCCAID2453

description: Gene expression data from CLL sample


title: CLLCCAID2459

description: Gene expression data from CLL sample


title: OAC1711N

description: DropSeq Barcoded Libraries


title: CLLCCAID2456

description: Gene expression data from CLL sample


title: OAC1710N1T

description: DropSeq Barcoded Libraries


title: OAC1710T2C

description: DropSeq Barcoded Libraries


title: OAC1512T

description: DropSeq Barcoded Libraries


title: CLLCCAID2457

description: Gene expression data from CLL sample


title: OAC1411NT

description: DropSeq Barcoded Libraries


title: OAC1411T

description: DropSeq Barcoded Libraries


title: OAC1212T3

description: DropSeq Barcoded Libraries


title: OAC1212T4

description: DropSeq Barcoded Libraries


title: OAC1212T2

description: DropSeq Barcoded Libraries


title: OAC1212T1

description: DropSeq Barcoded Libraries


title: CLLCCAID2452

description: Gene expression data from CLL sample


title: OAC1212T5

description: DropSeq Barcoded Libraries


title: OAC1710T1C

description: DropSeq Barcoded Libraries


title: CLLCCAID2454

description: Gene expression data from CLL sample


title: CLLCCAID2460

description: Gene expression data from CLL sample


title: OAC1210T2

description: DropSeq Barcoded Libraries


title: OAC1711T

description: DropSeq Barcoded Libraries


title: OAC307CP

description: DropSeq Barcoded Libraries


title: OAC1210T1

description: DropSeq Barcoded Libraries


title: OAC276T

description: DropSeq Barcoded Libraries


title: OAC263N

description: DropSeq Barcoded Libraries


title: OAC233TM

description: DropSeq Barcoded Libraries


title: OAC233TC

description: DropSeq Barcoded Libraries


title: OAC307PS

description: DropSeq Barcoded Libraries


title: OAC233NC

description: DropSeq Barcoded Libraries


title: OAC174N

description: DropSeq Barcoded Libraries


title: OAC174T

description: DropSeq Barcoded Libraries


title: OAC166T

description: DropSeq Barcoded Libraries


title: OAC67T

description: DropSeq Barcoded Libraries


title: OAC55N2

description: DropSeq Barcoded Libraries


title: OAC55N

description: DropSeq Barcoded Libraries


title: OAC46T

description: DropSeq Barcoded Libraries


title: OAC55B

description: DropSeq Barcoded Libraries


title: OAC44T2

description: DropSeq Barcoded Libraries


title: OAC55B2

description: DropSeq Barcoded Libraries


title: OAC46N

description: DropSeq Barcoded Libraries


title: OAC44N

description: DropSeq Barcoded Libraries


title: OAC22B

description: DropSeq Barcoded Libraries


title: Aged Uninjured MuSCs [d0_Aged_v2]

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2200 Bonisteel Blvd

department: Biomedical Engineering

country: USA

institute: University of Michigan

data_processing:
Base calling, alignment, filtering, barcode counting, and UMI counting: CellRanger v3.1 (10x Genomics) was used to process raw data. The CellRanger count command was run with default parameters with the exception of the --expect-cells parameter which was set at 10000.
Data filtering and quality control: Datasets were loaded into LIGER using the read10x function followed by createLiger, and cells with less than 300umis were removed. Data scaling, identification of highly variable features, and normalization was performed using LIGER.
Batch correction: Batch effects were removed using LIGER following normalization (k = 30, lambda = 3). Factors dominated by ribosomal or mitochondrial genes were removed. For scVelo analysis, aged timecourse datasets were batch corrected using Seurat v3.
Dimension reduction and community detection: Batch-corrected LIGER objects were imported into Seurat objects after running UMAP dimensional reduction using LIGER. Dimensional reduction and community detection was then performed using RunUMAP (reduction = 'inmf') and FindNeighbors in Seurat.
Celltype annotation: Cell types were annotated using scCATCH to compare with mouse muscle databases in combination with markergene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Seurat objects containing raw counts, normalized, scaled, and dimensionally reduced datasets, with metadata for the timepoint, age, and original dataset identity.

organism: Mus musculus

source_name: TA and EDL muscle

extract_protocol:
For tissue collection, mice were anesthetized with 3% isoflurane, then euthanized by cervical dislocation, bilateral pneumothorax and removal of the heart. Hind limb muscles (tibialis anterior and gastrocnemius) of control and experimental mice were quickly harvested using sterile surgical tools and placed in separate plastic petri dishes containing cold PBS. Using surgical scissors, muscle tissues were minced and transferred into 50 mL conical tubes containing 20 mL of digest solution (2.5 U/mL Dispase II and 0.2% [~5,500 U/mL] Collagenase Type II in DMEM media per mouse). Samples were incubated on a rocker placed in a 37oC incubator for 60 min with manual pipetting the solution up and down to break up tissue every 30 minutes using an FBS coated 10 mL serological pipette. Once the digestion was completed, 20 mL of F10 media containing 20% heat inactivated FBS was added into each sample to inactivate enzyme activity. The solution was then filtered through a 70 µm cell strainer into a new 50 mL conical tube and centrifuged again at 350xg for 5 min. The pellets were re-suspended in 6 mL of staining media (2% heat inactivated FBS in Hank’s Buffered Salt Solution - HBSS) and divided into separate FACS tubes. The FACS tubes were centrifuged at 350xg for 5 min and supernatants discarded. The cell pellets were then re-suspended in 200 µL of staining media and antibody cocktail containing Sca-1:APC (1:400), CD45:APC (1:400), CD11b:APC (1:400), Ter119:APC (1:400), CD29/b1-integrin:PE (1:200), and CD184/CXCR-4: BIOTIN (1:100) and incubated for 30 minutes on ice in the dark. Cells and antibodies were diluted in 3mL of staining solution, centrifuged at 350xg for 5 min, and supernatants discarded. Pellets were resuspended in 200uL staining solution containing PECy7:STREPTAVIDIN (1:100) and incubated on ice for 20 minutes in the dark. Again, samples were diluted in 3mL staining solution, centrifuged, supernatants discarded, and pellets re-suspended in 200uL staining buffer. Live cells were sorted from the suspension via addition of 1 µg of propidium iodide (PI) stain into each experimental sample and all samples were filtered through 70 μm cell strainers before the FACS. Cell sorting was done using a BD FACSAria III Cell Sorter (BD Biosciences, San Jose, CA) and APC negative, PE/PECy7 double-positive MuSCs were sorted into staining solution for immediate processing.
Freshly isolated MuSCs were sorted into staining solution, enumerated by hemocytometer, and re-suspended into PBS. Cells were loaded into the 10x Genomics chromium single cell controller for each time point and age group were captured into nanoliter-scale gel bead-in-emulsions (GEMs). cDNAs were prepared using the single cell 3′ Protocol as per manufacturer’s instructions and sequenced on a NextSeq 500 instrument (Illumina) or NovaSeq instrument (Illumina) with 26 bases for read1 and 98 bases for read2.

treatment_protocol: C57BL/6 wild-type female mice were obtained from Charles River Breeding Laboratories, the National Institute on Aging, or from a breeding colony at the University of Michigan (UM). All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and were in accordance with the U.S. National Institute of Health (NIH). Young female mice (3-4 months) and aged female mice (20-24 months) were randomly assigned to one of five groups: uninjured, day 3, and day 7 injured (n=4 per group). To induce skeletal muscle injury, mice were first anesthetized with 2% isoflurane and administered a 1.2% barium chloride (BaCl2) solution injected intramuscularly into several points of the tibialis anterior and gastrocnemius muscles for a total of 80 µL per hindlimb.

tag: strain

tag: age

value: 22-24 months

tag: 10x chemistry

tag: timepoint (days post injury)


title: Young Uninjured MuSCs [d0_Young_v2]

value: 3-4 months


title: OAC263T

description: DropSeq Barcoded Libraries


title: Young Uninjured MuSCs [d0_Young]


title: SOD1 Rescue MuSCs

value: 10-12 months


title: SOD1 Knockout MuSCs


title: Aged MuSCs 7dpi


title: Aged MuSCs 3dpi


title: OAC233T2C

description: DropSeq Barcoded Libraries


title: MZspg_rep3_5.5hpf

status: Public on Mar 03 2021

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

institute: University of Freiburg

data_processing:
Clean raw data were uploaded into Galaxy EU (https://galaxy.uni-freiburg.de) and passed fastQC quality check. Following analysis are all performed on Galaxy server.
Clean raw data were trimmed on 5' end for 5bp by Trim Galore! according to the sequencing quality.
Trimmed reads were mapped to GRCz11/danRer11 ensGene using RNA STAR.
Number of reads for each gene was counted in Featurecount using GRCz11/danRer11 ensGene reference genome.
All Featurecount reads from each sample were normalized in Deseq2. We used genotypes as factor level 1. The rest parameters are default.
Genome_build: GRCz11/danRer11
Supplementary_files_format_and_content: text files with normalized reads for each Sample

organism: Danio rerio

source_name: whole zebrafish embryos

extract_protocol:
40-45 zebrafish embryos were collected, sorted and fixed in liquid nitrogen for each time point. Total RNA was isolated with QIAGEN RNeasy kit following the user’s manual.  RNA was eluted in ddH2O.
Eukaryotic Poly-A enriched library preparation

value: whole embryos

tag: Stage

tag: genotype

value: MZspg

tag: biological replicates number


title: MZspg_rep3_6hpf


title: MZspg_rep3_5hpf


title: R595K_19

status: Public on May 01 2021

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

description: DNA was isolated from 3-week old leaf tissue, bisulfite converted, library prepped, and sequenced

library_source: genomic

data_processing:
1x50 bp bisulfite reads were aligned to the TAIR10 genome using the BSMAP program (Xi Y, Li W,. BMC Bioinformatics. 2009) using a QC trim score >= 33, -n 0 mapping type  and filtering for less than 5 n using 8% or less overall read mismatch. Aligned reads were converted to bisulfite methylation values via methratio.py (from BSMAP).  Methylation ratios at each cytosine were converted to bedGraph files using awk and to bigWig files using the UCSC executable script "bedGraphToBigWig". Methylation ratios were also used to call differentially methylated cytosines (DMCs) via the R package MethylKit (https://bioconductor.org/packages/release/bioc/vignettes/methylKit/inst/doc/methylKit.html) and methdiff.py (from BSMAP). DMCs called by both MethylKit and methdiff.py were used for subsequent analysis and were identified by using BEDtools overlap function between the two sets of DMCs.
Genome_build: TAIR10
Supplementary_files_format_and_content: Methratio output files  were converted to bedGraph via custom awk scripts and bedGraph files were converted to BigWig files via the UCSC "bedGraphToBigWig" executable script.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 3-week old leaf tissue

growth_protocol: Plants were grown on 1/2X MS agar (0.7%) + 50mg/mL hygromycein for 10 days under long day conditions (16hrs light/8hrs dark) and then transferred to soil under long day conditions. After three weeks of growth from seedlings, leaf tissue was harvested and frozen in liquid nitrogen for DNA extraction for sequencing.

extract_protocol:
DNA extracted using  Qiagen DNeasy Plant Mini Kit (catalog # 69104)
Bisulfite-seq were prepared as Pignatta, D. et al Bio-Protocols 2015.

treatment_protocol: (See Growth)

value: drm1-2 drm2-2 cmt3-1 mutations and R595K-FLAG transgene

tag: ecotype


title: MZspg_rep3_3.5hpf


title: MZspg_rep3_4hpf


title: MZsox19b_rep3_6hpf


title: ddc

value: drm1-2 drm2-2 cmt3-1 mutations


title: MZspg_rep3_3hpf


title: MZsox19b_rep3_5hpf


title: MZsox19b_rep3_4hpf


title: MZsox19b_rep3_4.5hpf


title: WT_rep5_5.5hpf

value: wild-type


title: MZsox19b_rep3_3.5hpf


title: MZsox19b_rep3_2.5hpf


title: Aged Uninjured MuSCs [d0_Aged]

description:
aged_timecourse_cca_filtered_v2.rds
sod1ko_v_rescue_seurat.rds


title: WT_rep5_5hpf


title: Aged Uninjured MuSCs [d0_Geriatric]

value: 26 months


title: WT_rep5_3.5hpf


title: WT_rep5_4hpf


title: WT_rep5_2.5hpf


title: WT_rep5_3hpf


title: MZsox19bspg rep2_5.5hpf

extract_protocol:
40-45 zebrafish embryos were collected, sorted and fixed in liquid nitrogen for each time point. Total RNA was isolated with QIAGEN RNeasy kit following the user’s manual.  RNA was eluted in ddH2O.
Eukaryotic Poly-A enriched library preparation; 250-300bp insert cDNA library

value: whole embryo


title: MZsox19bspg rep2_6hpf


title: MZsox19bspg rep2_5hpf


title: WT_rep5_4.5hpf


title: MZsox19bspg rep2_4.5hpf


title: MZsox19bspg rep2_4hpf


title: MZspg_rep3_4.5hpf


title: MZspg_rep3_2.5hpf


title: MZsox19b_rep3_5.5hpf


title: MZsox19bspg rep2_3hpf


title: MZsox19bspg rep2_3.5hpf


title: MZsox19bspg rep2_2.5hpf


title: MZsox19b_rep3_3hpf


title: MZsox19bspg rep1_5.5hpf


title: MZsox19bspg rep1_5hpf


title: MZsox19bspg rep1_4hpf


title: MZsox19bspg rep1_3.5hpf


title: MZsox19bspg rep1_3hpf


title: MZsox19bspg rep1_4.5hpf


title: MZsox19bspg rep1_2.5hpf


title: MZspg rep2_6hpf


title: MZspg rep2_4.5hpf


title: MZspg rep2_5hpf


title: MZspg rep2_5.5hpf


title: MZspg rep2_3.5hpf


title: MZspg rep2_4hpf


title: MZspg rep2_2.5hpf


title: MZspg rep2_3hpf


title: MZspg rep1_4.5hpf


title: MZspg rep1_4hpf


title: MZspg rep1_5hpf


title: MZspg rep1_5.5hpf


title: MZspg rep1_6hpf


title: MZspg rep1_3.5hpf


title: MZspg rep1_3hpf


title: MZspg rep1_2.5hpf


title: MZsox19b rep2_4.5hpf


title: MZsox19b rep2_5.5hpf


title: MZsox19b rep2_4hpf


title: MZsox19b rep2_3.5hpf


title: MZsox19b rep2_6hpf


title: MZsox19b rep1_6hpf


title: MZsox19b rep2_3hpf


title: MZsox19b rep2_2.5hpf


title: MZsox19b rep1_5.5hpf


title: MZsox19b rep1_5hpf


title: MZsox19b rep1_4.5hpf


title: MZsox19b rep1_3hpf


title: MZsox19b rep1_4hpf


title: MZsox19b rep1_3.5hpf


title: MZsox19b rep1_2.5hpf


title: WT rep4_6hpf


title: WT rep4_5hpf


title: WT rep4_4.5hpf


title: WT rep4_5.5hpf


title: WT rep4_4hpf


title: WT rep4_3.5hpf


title: WT rep3_6hpf


title: WT rep3_5hpf


title: WT rep4_3hpf


title: WT rep3_2.5hpf


title: WT rep3_3.5hpf


title: WT rep2_6hpf


title: WT rep3_3hpf


title: WT rep2_5.5hpf


title: WT rep2_5hpf


title: WT rep2_4hpf


title: MZsox19b rep2_5hpf


title: WT rep2_3hpf


title: WT rep1_5.5hpf


title: WT rep1_4.5hpf


title: WT rep1_4hpf


title: WT rep1_5hpf


title: WT rep1_3.5hpf


title: WT rep1_2.5hpf


title: WT rep3_4hpf


title: WT rep3_4.5hpf


title: WT rep3_5.5hpf


title: thyroid tissue-from male PTC patients

status: Public on Dec 31 2020

city: Guangzhou

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

country: China

institute: Forevergen

data_processing:
The raw data were processed thought the BD Rhapsody™ WTA Analysis Pipeline (v1.8), including filtering, alignment, annontation and cell calling. R1 reads were used to identify cell label sequences and unique molecular identifiers (UMIs). R2 reads were mapped to reference to determine mRNA origin.
R1 contains only barcode sequence in the following orientation from 5' to 3':  CLS1 (bp 1-9), L1 (12 bp), CLS2 (bp 22-30), L2 (13 bp), CLS3 (bp 44-42), UMI (bp 53-60), polyT (18 bp), where CLS: cell label section sequence, L: common sequences, UMI: Unique Molecular Identifier.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files generated by BD Rhapsody pipeline, expression matrix with molecule counts per gene per cell index

source_name: thyroid

extract_protocol:
tissue was isolated using Trypsin and Collagense II, isolated cells were labeled via BD Rahposidy single-cell system for single-cell sequecing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Papillary thyroid carcinoma (PTC)

tag: tissue source

value: male PTC patients


title: WT-2

status: Public on Nov 12 2020

city: St. Louis

first: Emily

last: Landy

state: Missouri

address: 425 S. Euclid Ave

data_processing:
sequenced on the Illumina NextSeq500
mapped to Mus_musculus_ensembl_v80 reference sequence, and quantified using CLC Genomics Workbench software (V8.1.6, Qiagen)
Differentially expressed genes were those defined as having a maximum group mean RPKM>5, |FC|>2, and FDR p<0.05.
Fold changes were not calculated directly from RPKM values but from the generalized linear model, which corrects for differences in library size between the samples and the effects of confounding factors.
Genome_build: Mus_musculus_ensembl_v80 reference sequence
Supplementary_files_format_and_content: .txt is RMKM tables of mapped genes

molecule: polyA RNA

source_name: WT_Day 8 splenic GP33+ CD8 T Cells

growth_protocol: Mice were infected 8 days prior to isolation with 2e5 PFU of LCMV-armstrong

extract_protocol:
fluorescence-activated cell sorting directly into lysis/stabilization media
Messenger RNA purification and fragmentation, complementary DNA synthesis and target amplification were performed with Smart-Seq v4 ultra Low input RNA sequencing preparation kit. Pooled complementary DNA libraries were sequenced on the Illumina NextSeq500.

treatment_protocol: FACS sorted CD8 T lymphocytes

tag: strain background

tag: genotype/variation

value: WT

value: Spleen

tag: cell type

value: GP33+ CD8 T cells

tag: days post infection

value: day 8 post LCMV-Armstrong infection


title: Il18tg-2

source_name: Il18tg_Day 8 splenic GP33+ CD8 T Cells


title: WT-1


title: Il18tg-3


title: thyroid tissue-from goiters

value: goiters


title: WT rep2_4.5hpf


title: Prf1KO-2

source_name: Prf1KO_Day 8 splenic GP33+ CD8 T Cells


title: Prf1KO-1


title: Il18tg-1


title: WT rep2_3.5hpf


title: obcrn8_es7

status: Public on Oct 20 2020

city: Leicester

first: Marcin

last: Wozniak

address: Leicester

institute: University of Leicester

data_processing:
Sequencing data was quality-checked with Fastqc
Data was quantified with Salmon after indexing with a decoy
Data Annotations was done with GENCODE 34/Ensembl v100
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix of transcript quantities in length-scaled transcripts per million normalized values

source_name: Tissue

growth_protocol: Atrial biopsies (50 – 100 mg) were collected from patients undergoing surgery

extract_protocol:
RNA was isolated from 20mg of tissue using ISOLATE II RNA Mini Kit;Sample quality was assessed using the RNA ScreenTape assay on the Agilent Tapestation 4200
The Stranded total RNA libraries were prepared in accordance to the Illumina TruSeq Stranded Total RNA Sample Preparation Guide with Ribo-Zero Human/Mouse/Rat for Illumina Paired-End Multiplexed Sequencing

treatment_protocol: biopsies immediately snap-frozen in liquid nitrogen.

value: myocardium (atrial biopsy)

tag: group

tag: bmi

tag: gender

value: Male

tag: ethnicity

value: Any other White background

tag: batch

tag: comorbidities

tag: multimorbid

value: No


title: WT rep2_2.5hpf

tag: tissue


title: obcrn9_es8

value: White British

value: Yes


title: WT rep4_2.5hpf

tag: Stage


title: obcrn6_es5


title: obcrn7_es6

value: Female


title: obcrn54_es37


title: obcrn60_es41


title: thyroid tissue-from female PTC patients

value: female PTC patients


title: obcrn58_es40


title: WT rep1_3hpf

tag: genotype

value: wild-type


title: obcrn5_es4

value: Any other Asian background


title: obcrn55_es38


title: obcrn53_es36


title: obcrn49_es34


title: obcrn51_es35


title: obcrn46_es32

value: Asian or Asian British Indian


title: obcrn44_es30


title: obcrn43_es29


title: obcrn45_es31


title: obcrn40_es26


title: obcrn48_es33


title: obcrn42_es28


title: obcrn39_es25


title: obcrn4_es3


title: obcrn36_es22


title: obcrn56_es39


title: obcrn33_es20


title: obcrn37_es23


title: obcrn30_es18


title: obcrn3_es2


title: obcrn27_es15


title: obcrn29_es17


title: obcrn26_es14


title: obcrn28_es16


title: obcrn23_es22


title: obcrn21_es20


title: obcrn24_es23

value: Any other ethnic group


title: obcrn22_es21


title: obcrn20_es19


title: obcrn41_es27


title: obcrn38_es24


title: obcrn25_es13


title: obcrn16_es15


title: obcrn18_es17


title: obcrn2_es1


title: obcrn17_es16


title: obcrn13_es12


title: obcrn12_es11


title: obcrn10_es9


title: obcrn11_es10


title: obcrn31_es19


title: obcrn34_es21


title: obcrn19_es18


title: MZnanog_H3K4me3_ChIP-seq

status: Public on May 07 2020

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq paired  reads were aligned to the Zv9 genome assembly using Bowtie2  (Galaxy Version 2.3.2.2);  with parameters 0 (-I) 400 (-X)
BAM files were filtered to keep only properly mapped paired reads with BAM filter bedtools command ( Galaxy Version 0.5.8.1)
log2 ratio between ChIP and  input BAM  files was computed using  bamCompare command from deeptools2 suite (Galaxy Version 3.0.2.0). Bin size 10, normalization method -RPKM, pseudocount 1.0
Genome_build: Zv9 (danrer7)
Supplementary_files_format_and_content: bigwig files for vizualization in UCSC browser were generated using bamCompare. Scores represent log2 ChIP/input ratio.

source_name: whole embryo

growth_protocol: The mutant  line MZnanog  were maintained as described previously (Veil et al. 2018). Embryos obtained from natural  crosses were collected within 10 minutes and raised in egg water at 28.5°C. Staging was performed following the 1995 Kimmel staging series (Kimmel et al. 1995). Stages of the mutant embryos were indirectly determined by observation of wild-type embryos born at the same time and incubated under identical conditions. All experiments were performed in accordance with German Animal Protection Law (TierSchG)

extract_protocol:
Fixation of embryos and nuclei extraction. 1000-4000  embryos  were enzymatically dechorionated with pronase E (0.3 mg/ml),homogenized and immediately fixed with 1 % (v/v) Methanol-free Formaldehyde (Thermo scientific , 28906)  for 10 min at room temperature.The fixation was stopped with 0.125 M Glycine. Cells were pelleted by centrifugation and resuspended  in Wardle cell lysis buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 0.5 % NP-40, 1 ml/1000 embryos), followed by 5 min incubation on ice. Cells were pelleted by 1 min centrifugation, 2700 g at 4 °C. the pellet was washed 2 times with 1 ml ice cold 1x x PBST; a 10ul aliquote was used for scoring the nuclei.  The pellets were frozen atb -80°.   2.5 million nuclei were used to perform one ChIP-Seq experiment.  Chromatin was sonified to 200 bp fragments using Covaris S2 sonicator (DC 20 %, Intensity 5, Cycles of Burst 200, Time = 3*40 cycles with 30 sec each (3*20 min),  1/10 of the sample was taken as an input control. The rest was immunoprecipitated with the anti-H3K27ac or anti-H3K4me3 antibodies.
ChIP and Input libraries for each sample were  prepared using NEBNext® Ultra™ DNA Library Prep Kit according to the manufacturer instructions
For each sample, ChIP libraries were sequenced to 70 mln reads, Input libraries to 30 mln reads

tag: background strain

value: AB/TL

tag: developmental stage

value: dome (4.3 hpf)

value: MZnanog

tag: chip antibody

value: Anti-Histone H3 (tri-methyl K4) rabbit, 1/100 dilution, Millipore 07-449


title: MZnanog_intput_for_H3K27ac

value: none (input)


title: MZnanog_input_for_H3K4me3


title: MZnanog_H3K27ac_rep1_ChIP-seq

value: Anti-Histone H3 (acetyl K27), rabbit, 1/100 dilution, Abcam ab 4729


title: obcrn1_es24

value: myocardium (atrial biopsy)

value: Male


title: WT_K27ac_Input

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq paired reads were aligned to the danrer11 genome assembly using Bowtie2 (Galaxy Version 2.3.2.2); with parameters 0 (-I) 400 (-X)
BAM files were filtered to keep only properly mapped paired reads with BAM filter bedtools command ( Galaxy Version 0.5.8.1)
Input BAM files for each modification (H3K27ac or H3K4me3) in all genotypes were merged together using "Merge BAM Files" bedtools command (Galaxy Version 1.2.0)
log2 ratio between each ChIP and merged input BAM files was computed using bamCompare command from deeptools2 suite (Galaxy Version 3.0.2.0). Bin size 10, normalization method -RPKM, pseudocount 1.0
Peaks were called with MACS2 (Feng, J., et al.,Nat Protoc 7, 1728-1740, (2012)), with the parameters Effective Genome Size=1370000000, --mfold= 5 to 50, --bw=300,  --qvalue=0.05.
Pooled input files from all four genotypes were used as a background.
Genome_build: danrer11
Supplementary_files_format_and_content: log2 (ChIP/input) bigwig files bin=10, peak bed files

growth_protocol: Wild-type fish of AB/TL strain were raised, maintained and crossed under standard conditions as described by Westerfield (Westerfield 2000, Zebrafish Book). The mutant  lines were maintained as described previously (Lunde et al. 2004; Veil et al. 2018). Embryos obtained from natural  crosses were collected within 10 minutes and raised in egg water at 28.5°C. Staging was performed following the 1995 Kimmel staging series (Kimmel et al. 1995). Stages of the mutant embryos were indirectly determined by observation of wild-type embryos born at the same time and incubated under identical conditions. All experiments were performed in accordance with German Animal Protection Law (TierSchG)

tag: strain background

value: WT

value: whole embryo


title: WT_K27ac_ChIP

tag: genotype/variation


title: MZspg_K4me3_Input

value: MZspg


title: MZspg_K27ac_Input


title: MZspg_K27ac_ChIP


title: MZsox19b_K27ac_rep2_input


title: MZspg_K4me3_ChIP


title: WT_K4me3_Input


title: MZsox19b_K27ac_rep1_input


title: obcrn15_es14

value: Any other White background

value: Yes


title: MZsox19b_K27ac_rep2_ChIP


title: WT_K4me3_ChIP


title: MZsox19b_K4me3_input


title: MZsox19b_K27ac_rep1_ChIP


title: K562_INP_100cells_rep1

status: Public on Nov 15 2019

city: Tartu

first: Tõnis

last: Org

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

data_processing:
Basecalling was done using Illumina Casava software
Alignment of fastq files was done using Bowtie 2 version 2.2.9with following parameters: -k 2 -N 1 --mm -x
sam files were converted to bam files and sorted using Samtools version: 1.4.1
Genome_build: hg19 and BosTau8
Supplementary_files_format_and_content: bigwig files, genarated using deepTools version 2.5.1 bamCoverage --normalizeTo1x  --ignoreDuplicates --minMappingQuality 40

source_name: K562 cells

growth_protocol: Human K562cells were grown in IMDM and DMEM  respectively, supplemented with 10% of FBS and penicillin/streptomycin in the presence of 5% CO2 at 37C.

extract_protocol:
1µl ProtG Dynabeads (Thermo Fisher Scientific) were bound with 0.25µg of corresponding antibody (H3K4me3 (07-473, Millipore), H3K27me3 (07-449, Millipore)) in 5µl of complete immunoprecipitation (IP) buffer (20mM Tris-HCl pH 7.4, 2mM EDTA, 150mM NaCl, 0.1% Triton X-100) at RT for 2 h followed by two washes using IP buffer. The density of cultured K562 or H1299 cells was determined using haemocytometer. Cells were spun down and resuspended in PBS at a density 100 or 1,000 cells per 0.5µl. Subsequently 0.5µl of lysis-restriction mix (1µl FD (FastDigest) buffer combined with 3.75µl of 2x nuclear lysis buffer (20mM TrisHCl, pH 7.4, 20mM NaCl, 6mM MgCl, 0.2% NP-40)) and 0.25µl 4x restriction enzyme mix (AluI #FD0014, SaqAI#FD2174, HinfI#FD0804, MvaI#FD0554, all FastDigest enzymes from Thermo Scientific) was added to the cells and incubated 15 min on ice and thereafter 5 min at 37¡C. Next, 1µl of 0.2% NaDOC, 0.2% TritonX-100 with protease inhibitors was added to the samples and incubated 15 min on ice after which 8µl of IP buffer (20mM Tris-HCl, pH 7.4, 150mM NaCl, 2mM EDTA and 1%TritonX-100) and 1µl of ProtG Dynabeads (Thermo Fisher Scientific) prebound with corresponding antibody was  added to the samples. Chromatin immunoprecipitation was performed at 4¡C for four hours with end-over end mixing. After IP, beads were washed twice with 100µl of following buffers: low salt washing buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl (pH 8.1)), high salt washing buffer, IP buffer and 20mM TrisHCl, pH 7.4. Tagging was performed by resuspending the beads in 2.5µl of transposase mix (prepared by mixing 5µl of 2x buffer with 4µl mQ and 1µl Transposase) (Illumina Nextera kit) and incubation of 1 min at 37¡C. Beads were washed once with 100µl of low salt washing buffer, once with 20mM TrisHCl pH 7.4 and resuspended in 5µl of 20mM TrisHCl, pH 7.4. 16 cycles of PCR was performed using bead bound DNA as a template by mixing 5µl of beads with 2,5µl of 5µM forward and reverse primers and 10µl of 2x NEBNext enzyme. The following PCR program was used: (72C 5 min, 98C 2 min, 98C 10 sec, 63C 10 sec, 7¡C 1 min, repeat steps 3-5 15 times, hold at 4C). PCR products were purified with Agencourt RNA XP magnetic beads (Coulter Beckman), eluted in 10µl of TrisHCl pH 7.4 followed by DNA quantification using Nanodrop. The resulting library was subjected to 50 or 75bp paired end Illumina sequencing using either HiSeq2500 or NextSeq 500 platforms. RAT-ChIP-seq with bovine blastocysts was performed as described above except that after dissection the cells were collected in 3µl of embryo medium. Lysis/restriction buffer was prepared by combining 4.75µl of 10x NL (100mM TrisHCl, pH 7.4, 100mM NaCl, 30mM MgCl) buffer, 4.75µl of 10x FastDigest buffer and 0.5µl of mix of 4x restrictases. 0.75µl of lysis/restriction buffer was added to 3µl of cells and incubated 15 min on ice and 5 min at 37¡C. Next, 1µl of mix of 0.5% NaDOC, 0.5% TritonX100 with protease inhibitor cocktail was added to the samples and incubated 15 min on after which 15µl of IP buffer (20mM Tris-HCl pH 7.4, 2mM EDTA, 150mM NaCl, 0.1% Triton X-100) was added and sample was divided into 2 tubes, 10µl each for subsequent IP with Dynabeads bound with corresponding antibodies.
Library was constructed using tagging resuspending the beads in 2.5µl of transposase mix (prepared by mixing 5µl of 2x buffer with 4µl mQ and 1µl Transposase) (Illumina Nextera kit) and incubation of 1 min at 37¡C. Beads were washed once with 100µl of low salt washing buffer, once with 20mM TrisHCl pH 7.4 and resuspended in 5µl of 20mM TrisHCl, pH 7.4. 16 cycles of PCR was performed using bead bound DNA as a template by mixing 5µl of beads with 2,5µl of 5µM forward and reverse primers and 10µl of 2x NEBNext enzyme. The following PCR program was used: (72C 5 min, 98C 2 min, 98C 10 sec, 63C 10 sec, 7¡C 1 min, repeat steps 3-5 15 times, hold at 4C). PCR products were purified with Agencourt RNA XP magnetic beads (Coulter Beckman), eluted in 10µl of TrisHCl pH 7.4 followed by DNA quantification using Nanodrop.
Library was constructed using tagging with Tn5 Transposase (Illumina Nextera kit)

tag: cell line

tag: cell type

value: bone marrow lymfoblast cells from chronic myelogenous leukemia patient - K562 cells

value: adult - 53 year female


title: K562_INP_100cells_rep2


title: K562_INP_1000cells_rep3


title: MZsox19b_Mnase-seq

data_processing:
All sequenced reads were mapped  to the zebrafish genome (zv9 assembly) using CLC Workbench, with the default parameters and repeated sequences were mapped randomly.
Bigwig files made for both Zv9 and GRCz11 genome builds.
Genome_build: zv9 danio rerio
Supplementary_files_format_and_content: Danio rerio Zv9 and GRCz11 bigwig

source_name: embryos

growth_protocol: Fish were raised, maintained and crossed under standard conditions as described (Westerfield, 2000). Embryos obtained from crosses were raised in egg water at 28.5°C. Developmental stage of MZsox19b embryos was indirectly determined by observation of wild type embryos born at the same time and incubated under identical conditions. For controls, we used the AB-TL wild type embryos. Staging was performed according to Kimmel publication (Kimmel et al., 1995).

extract_protocol:
MZsox19b embryos were collected and staged to dome stage. With them, the Mnase digestion was performed as previously described by Zhang et al, 2014.
Library preparation and high throughput sequencing was performed according to standard Illumina HiSeq 2500 protocols.

value: dome stage (4.3 hpf)

value: embryos


title: In vivo-icSHAPE-HEK293T-DMSO rep2

status: Public on Mar 06 2020

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

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

department: Division of Genomic Medicine

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: RNA structure probing using icSHAPE

data_processing:
To ensure sufficient sequencing depth, the sequence data from two Illumina HiSeq runs were merged together for each replicate and standard icSHAPE bioinformatics pipeline was used (PMID:26766114).
After PCR duplicates removal and adapter (13 nt from 5ʹ end) trimming, sequencing reads were mapped to human transcriptome (GRCh38) and custom EGFP and SINEUP transcripts index using Bowtie2. In case of SINEUP, the mapping was focused on the region starting from 1 bp upstream of the SINE B2 till 88 bp downstream of it (to encompass all the reads strating with in the inverted SINE B2 region of SINEUP). Following the icSHAPE pipeline, RT stops were calculated and normalized, and subsequently enrichment reactivity scores were calculated for each base by subtracting the background signal (DMSO data).
Genome_build: Homo sapiens GRCh38 (hg38)
Supplementary_files_format_and_content: SINEUP-GFP_invSINEB2_icSHAPE_reactivity_score.txt: Valid enrichment reactivity score for each base of SINEUP-GFP inverted SINE B2 (starting from 1 nt upstream and up to 88 nt downstream of SINE B2). Format: Each base position is represented by a different row. Columns 1-5 correspond to Transcript name, Position of each base in mapped sequence (used for RT stop calculation), Position of actual modified base (+1 nt from RT stop), valid enrichment reactivity score for each modified base (bases with null values were not detected by icSHAPE), and sequence of the modified base.
Supplementary_files_format_and_content: All_SINEB2_icSHAPE_reactivity_scores.txt: Valid enrichment reactivity score for each base of SINEB2 (starting from 1 nt upstream and up to 88 nt downstream of SINEB2). Format: Each base position is represented by a different row. Columns 1-5 correspond to Transcript name, Position of each base in mapped sequence (used for RT stop calculation), Position of actual modified base (+1 nt from RT stop), valid enrichment reactivity score for each modified base (bases with null values were not detected by icSHAPE), and sequence of the modified base.

growth_protocol: HEK293T/17 cells were grown in 6-well culture dish in DMEM (1×) + GlutaMAX-1 supplemented with 10% fetal bovine serum and 1% penicillin streptomycin solution at 37°C, 5% CO2 until ~80% confluent.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and digested with DNaseI to remove DNA contamination. Purified RNA was ribo-depleted and used for further library construction.
icSHAPE library preparation protocol was followed (PMID:26766114). Briefly, ribo-depleted RNA was biotin-clicked, fragmented and end-repaired. Next, RNA was 3' end ligated followed by cDNA synthesis and circularization. Final library was PCR amplified.

treatment_protocol: Different SINEUP-EGFP construts were co-transfected with pEGFP-C2 in each well of 6-well plate. 24 h post-transfection, all the wells pooled together and cells were treated with either NAI-N3 or DMSO (mock) following the icSHAPE protocol (PMID:26766114).

value: Human embryonic kidney cell line

tag: transfection

value: Co-transfection with SINEUP-GFP and pEGFP-C2

tag: treatment

value: DMSO (mock)


title: In vivo-icSHAPE-HEK293T-NAI-N3 rep2

description: RNA structure probing using icSHAPE


title: K562_INP

growth_protocol: Human K562 and H1299 cells were grown in IMDM and DMEM  respectively, supplemented with 10% of FBS and penicillin/streptomycin in the presence of 5% CO2 at 37C.

treatment_protocol: Oocyte collection and in vitro maturation: All chemicals used for in vitro embryo production were purchased from IVF Limited T/A IVF Bioscience. Slaughterhouse derived ovaries were transported to the laboratory in a 0.9% sterile NaCl solution within 4 h after slaughter at approximately 32-37¡C and washed twice in a 0.9% NaCl solution. Using a vacuum pump (MinitŸb GmbH), cumulus oocyte complexes (COC) from follicles with a diameter of 2-8mm were aspirated. Grade 1 COCs were washed and matured in groups of 50 in 500µl of in vitro maturation medium in four-well plates (Nunc). Oocytes were incubated at 38.5¡C with humidified 5% CO2 in air for 22-24 h. In vitro fertilization: Frozen-thawed semen from a Holstein bull ZIARD (id EE 13993023) was used to fertilize the matured oocytes. Oocytes and sperm were co-incubated in groups of 50 in 500µl of BO-IVM media in four-well plates (Nunc) at 38.5°C with humidified 5% CO2 in air for 22-24 h. In vitro cultivation: Zygotes were individually cultured in 60µl droplets BO-IVC media for 8 days at 38.5°C, 5% CO2, 5% O2 and 90% N2 with maximum humidity. Embryos having reached blastocyst stage by day 8 were collected and used for laser assisted microdissection. Laser assisted microdissection to obtain ICM and TE fractions: Integra 3 micromanipulator (Research Instruments Limited) equipped with Saturn 5 Active™ laser system was used to manually separate bovine blastocysts into ICM and TE fractions. Separated fractions from three blastocysts were pooled and used for subsequent RAT-ChIP-seq experiments .


title: In vivo-icSHAPE-HEK293T-NAI-N3 rep1

description: RNA structure probing using icSHAPE


title: MZsox19b_K4me3_ChIP

value: AB/TL

value: dome (4.3 hpf)

value: Anti-Histone H3 (tri-methyl K4) rabbit, 1/100 dilution, Millipore 07-449


title: H1299_INP

source_name: H1299 cells

value: non-small cell lung cancer metastatic cells from lymph node - H1299 cells

value: adult - 43 year male


title: In vivo-icSHAPE-HEK293T-DMSO rep1

description: RNA structure probing using icSHAPE


title: K562_H3K4me3_1000cells_rep3

value: H3K4me3 (07-473, Millipore)


title: K562_INP_1000cells_rep2


title: K562_H3K4me3_100cells_rep1


title: K562_INP_1000cells_rep1


title: K562_H3K4me3_100cells_rep3


title: obcrn14_es13

value: myocardium (atrial biopsy)

tag: group

tag: bmi

tag: gender

value: Male

value: White British


title: K562_H3K27me3_100cells_rep2

value: H3K27me3 (07-449, Millipore)


title: K562_H3K4me3_1000cells_rep1

value: bone marrow lymfoblast cells from chronic myelogenous leukemia patient - K562 cells


title: K562_H3K27me3_100cells_rep1

value: adult - 53 year female


title: K562_H3K4me3_100cells_rep2


title: K562_H3K27me3_100cells_rep3


title: K562_INP_100cells_rep3


title: H1299_H3K4me3_100cells

extract_protocol:
1µl ProtG Dynabeads (Thermo Fisher Scientific) were bound with 0.25µg of corresponding antibody (H3K4me3 (07-473, Millipore), H3K27me3 (07-449, Millipore)) in 5µl of complete immunoprecipitation (IP) buffer (20mM Tris-HCl pH 7.4, 2mM EDTA, 150mM NaCl, 0.1% Triton X-100) at RT for 2 h followed by two washes using IP buffer. The density of cultured K562 or H1299 cells was determined using haemocytometer. Cells were spun down and resuspended in PBS at a density 100 or 1,000 cells per 0.5µl. Subsequently 0.5µl of lysis-restriction mix (1µl FD (FastDigest) buffer combined with 3.75µl of 2x nuclear lysis buffer (20mM TrisHCl, pH 7.4, 20mM NaCl, 6mM MgCl, 0.2% NP-40)) and 0.25µl 4x restriction enzyme mix (AluI #FD0014, SaqAI#FD2174, HinfI#FD0804, MvaI#FD0554, all FastDigest enzymes from Thermo Scientific) was added to the cells and incubated 15 min on ice and thereafter 5 min at 37¡C. Next, 1µl of 0.2% NaDOC, 0.2% TritonX-100 with protease inhibitors was added to the samples and incubated 15 min on ice after which 8µl of IP buffer (20mM Tris-HCl, pH 7.4, 150mM NaCl, 2mM EDTA and 1%TritonX-100) and 1µl of ProtG Dynabeads (Thermo Fisher Scientific) prebound with corresponding antibody was  added to the samples. Chromatin immunoprecipitation was performed at 4¡C for four hours with end-over end mixing. After IP, beads were washed twice with 100µl of following buffers: low salt washing buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl (pH 8.1)), high salt washing buffer, IP buffer and 20mM TrisHCl, pH 7.4. Tagging was performed by resuspending the beads in 2.5µl of transposase mix (prepared by mixing 5µl of 2x buffer with 4µl mQ and 1µl Transposase) (Illumina Nextera kit) and incubation of 1 min at 37¡C. Beads were washed once with 100µl of low salt washing buffer, once with 20mM TrisHCl pH 7.4 and resuspended in 5µl of 20mM TrisHCl, pH 7.4. 16 cycles of PCR was performed using bead bound DNA as a template by mixing 5µl of beads with 2,5µl of 5µM forward and reverse primers and 10µl of 2x NEBNext enzyme. The following PCR program was used: (72C 5 min, 98C 2 min, 98C 10 sec, 63C 10 sec, 7¡C 1 min, repeat steps 3-5 15 times, hold at 4C). PCR products were purified with Agencourt RNA XP magnetic beads (Coulter Beckman), eluted in 10µl of TrisHCl pH 7.4 followed by DNA quantification using Nanodrop. The resulting library was subjected to 50 or 75bp paired end Illumina sequencing using either HiSeq2500 or NextSeq platforms. RAT-ChIP-seq with bovine blastocysts was performed as described above except that after dissection the cells were collected in 3µl of embryo medium. Lysis/restriction buffer was prepared by combining 4.75µl of 10x NL (100mM TrisHCl, pH 7.4, 100mM NaCl, 30mM MgCl) buffer, 4.75µl of 10x FastDigest buffer and 0.5µl of mix of 4x restrictases. 0.75µl of lysis/restriction buffer was added to 3µl of cells and incubated 15 min on ice and 5 min at 37¡C. Next, 1µl of mix of 0.5% NaDOC, 0.5% TritonX100 with protease inhibitor cocktail was added to the samples and incubated 15 min on after which 15µl of IP buffer (20mM Tris-HCl pH 7.4, 2mM EDTA, 150mM NaCl, 0.1% Triton X-100) was added and sample was divided into 2 tubes, 10µl each for subsequent IP with Dynabeads bound with corresponding antibodies.
Library was constructed using tagging resuspending the beads in 2.5µl of transposase mix (prepared by mixing 5µl of 2x buffer with 4µl mQ and 1µl Transposase) (Illumina Nextera kit) and incubation of 1 min at 37¡C. Beads were washed once with 100µl of low salt washing buffer, once with 20mM TrisHCl pH 7.4 and resuspended in 5µl of 20mM TrisHCl, pH 7.4. 16 cycles of PCR was performed using bead bound DNA as a template by mixing 5µl of beads with 2,5µl of 5µM forward and reverse primers and 10µl of 2x NEBNext enzyme. The following PCR program was used: (72C 5 min, 98C 2 min, 98C 10 sec, 63C 10 sec, 7¡C 1 min, repeat steps 3-5 15 times, hold at 4C). PCR products were purified with Agencourt RNA XP magnetic beads (Coulter Beckman), eluted in 10µl of TrisHCl pH 7.4 followed by DNA quantification using Nanodrop.
Library was constructed using tagging with Tn5 Transposase (Illumina Nextera kit)


title: K562_H3_1000cells

value: H3 (Diagenode)


title: H1299_H3K27me3_100cells


title: K562_H3K4me3_1000cells


title: H1299_H3K27me3_1000cells


title: H1299_H3K4me3_1000cells


title: K562_H3K4me3_100cells


title: TE_H3K4me3_rep2

organism: Bos taurus

source_name: Trophoectoderm of day 8 embryos

value: trophoectoderm of in vitro fertilized bovine embryos

value: day 8 blastocyst


title: ICM_H3K27me3_rep2

source_name: Inner cell mass of day 8 embryos

value: inner cell mass of in vitro fertilized bovine embryos


title: TE_H3K27me3_rep2


title: ICM_H3K4me3_rep2


title: K562_H3K4me3_1000cells_rep2


title: K562_H3K27me3_1000cells


title: K562_H3K27me3_1000cells_rep3


title: K562_H3K27me3_1000cells_rep1


title: ICM_H3K27me3_rep1


title: TE_H3K4me3_rep1


title: TE_H3K27me3_rep3


title: TE_H3K4me3_rep3


title: ICM_H3K27me3_rep3


title: ICM_H3K4me3_rep3


title: ICM_INP_merged


title: TE_INP_merged


title: K562_H3K27me3_100cells


title: K562_H3K27me3_1000cells_rep2


title: ICM_H3K4me3_rep1


title: TE_H3K27me3_rep1


title: NP_9408_CTRL

status: Public on Sep 02 2019

city: Oxford

first: Amber

last: Barton

address: Centre for Clinical Vaccinology and Tropical Medicine

institute: Oxford Vaccine Group

hyb_protocol: Standard Illumina hybridisation protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was quantile normalized, background subtracted and log2 transformed using neqc() in R.

label: biotin

source_name: Whole blood

label_protocol: Standard Illumina TotalPrep RNA Amplification kits.

growth_protocol: NA - whole blood samples from clinical trial

extract_protocol: Tempus tube RNA isolation kit.

value: CTRL

value: Whole blood


title: NP_7537_sEF

value: sEF

value: Negative


title: NP_1182_sEF


title: NP_5030_EF

value: EF

value: ST


title: NP_185_EF

value: SPT


title: NP_214_EF


title: NP_119_2_EF


title: NP_1183_EF


title: NP_7398_EF


title: NP_6655_EF


title: NP_9103_CTRL


title: NP_2853_EF


title: NP_6691_EF


title: NP_8944_EF


title: NP_3876_CTRL


title: NP_499_sEF


title: NP_1839_EF


title: NP_6281_EF


title: NP_8427_EF


title: NP_559_EF


title: NP_8794_EF


title: NP_9484_CTRL


title: NP_5235_sEF


title: NP_6438_CTRL


title: NP_4273_sEF


title: NP_4346_sEF


title: NP_7286_EF


title: NP_4040_CTRL


title: NP_7166_EF


title: NP_9233_EF


title: NP_1071_sEF


title: NP_6174_CTRL


title: NP_5413_CTRL


title: NP_2478_CTRL


title: NP_7038_sEF


title: NP_6497_CTRL


title: NP_7069_sEF


title: NP_83_sEF


title: NP_8237_sEF


title: NP_468_EF


title: NP_7725_sEF


title: NP_3539_EF


title: NP_1398_sEF


title: NP_833_sEF


title: NP_8767_CTRL


title: NP_54_CTRL


title: NP_6292_CTRL


title: NP_5128_sEF


title: NP_6329_CTRL


title: NP_6104_sEF


title: NP_1227_sEF


title: NP_8380_CTRL


title: NP_4781_sEF


title: NP_4590_CTRL


title: NP_8108_sEF


title: NP_9723_sEF


title: NP_9577_EF


title: NP_7490_sEF


title: NP_1532_sEF


title: NP_9908_sEF


title: NP_9486_sEF


title: NP_7643_sEF


title: NP_8617_CTRL


title: NP_3218_sEF


title: NP_7847_sEF


title: NP_3257_EF


title: NP_7883_EF


title: NP_7335_CTRL


title: NP_4987_sEF


title: NP_6087_CTRL


title: NP_127_sEF


title: NP_5459_sEF


title: NP_4267_sEF


title: NP_6170_CTRL


title: NP_8600_sEF


title: NP_9127_CTRL


title: NP_1870_sEF


title: NP_7355_CTRL


title: NP_1958_sEF


title: NP_6152_sEF


title: NP_5145_sEF


title: NP_4204_CTRL


title: NP_7784_sEF


title: NP_7973_sEF


title: NP_3409_sEF


title: NP_2248_EF


title: NP_762_sEF


title: NP_6537_CTRL


title: NP_7314_CTRL


title: NP_6171_sEF


title: NP_8505_CTRL


title: NP_2496_sEF


title: NP_7209_sEF


title: NP_9162_CTRL


title: NP_6220_sEF


title: NP_1077_CTRL


title: NP_3088_EF


title: NP_8321_CTRL


title: NP_6498_CTRL


title: NP_5607_CTRL


title: NP_5791_sEF


title: NP_2681_sEF


title: NP_501_sEF


title: NP_4882_sEF


title: NP_8125_sEF


title: NP_7465_CTRL


title: NP_721_sEF


title: NP_2378_sEF


title: NP_3236_EF


title: NP_6379_CTRL


title: NP_9158_CTRL


title: NP_8625_sEF


title: NP_1094_CTRL


title: NP_6520_sEF


title: NP_7109_EF


title: NP_8192_CTRL


title: NP_7988_sEF


title: NP_4430_CTRL


title: NP_1440_EF


title: NP_5942_sEF


title: NP_7461_CTRL


title: NP_8925_sEF


title: NP_8844_sEF


title: NP_3828_sEF


title: NP_6018_EF


title: NP_403_sEF


title: NP_7251_CTRL


title: NP_3464_sEF


title: NP_9131_sEF


title: NP_8630_CTRL


title: NP_1416_sEF


title: NP_2812_sEF


title: NP_3294_sEF


title: NP_5426_sEF


title: NP_6523_sEF


title: NP_6958_EF


title: NP_7859_CTRL


title: NP_9820_CTRL


title: NP_578_sEF


title: NP_9754_sEF


title: NP_7064_sEF


title: NP_4134_sEF


title: NP_390_CTRL


title: NP_6584_CTRL


title: NP_4166_EF


title: NP_8879_CTRL


title: NP_2394_CTRL


title: NP_2962_sEF


title: NP_3080_CTRL


title: T2_3655


title: T2_9956


title: T2_7367


title: T2_528


title: T2_4575


title: T2_7575


title: T2_2467


title: T2_9932

value: S. Typhi


title: T2_3663


title: T2_2329


title: T2_5180


title: T2_7765


title: T2_3415


title: T2_6664


title: T2_7625


title: T2_2911


title: T2_1387


title: T2_1640


title: T2_4559


title: T2_2525


title: T2_6425


title: T2_4811


title: T2_3710


title: T2_6522


title: T2_9180


title: T2_1735


title: T2_4241


title: T2_6462


title: T2_3443


title: T2_2120


title: T2_2625


title: T2_6715


title: T2_330


title: T2_6236


title: T2_5693


title: P1_6600

description:
featureCounts.tsv
featureCounts_voom.tsv

data_processing:
Illumina Casava v1.8 was used for basecalling.
Reads were adapter removed, quality filtered and trimmed to 65Bp using trimmomatic 0.35 with parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 HEADCROP:5 CROP:65 SLIDINGWINDOW:5:6 MINLEN:65
Sequences were mapped to hg38 using STAR aligner v2.5.2b with parameter --outSAMmultNmax 20
tab-delimited text files include per gene read counts. Counts were calculated using featureCounts v1.5.1 with parameters: -T 10  -C -B -M -s 2 -p -S fr and the reference gtf file containing ENSEMBL gene definitions was downloaded from Gencode v25 basic; voom transformed log2 CPM values were calculated as follows: only genes with cpm values greater 1 in at least 20 samples were kept for the analysis;  To scale raw library sizes, the calcNormFactors method of the edgeR package was used in R with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: featureCounts.tsv, featureCounts_voom.tsv

source_name: Tempus tubes (Whole Blood)

extract_protocol:
Peripheral venous blood (3mL) was collected in TempusTM Blood RNA tubes (Applied Biosystems)
Libraries were contstructed using Illumina's kit's and standard protocols

value: Whole Blood


title: P1_263


title: P1_9588


title: T2_8628


title: P1_4423


title: T2_9617


title: T2_6749


title: T2_8138


title: T2_5406


title: T2_8982


title: T2_314


title: T2_4692


title: T2_523


title: T2_7878


title: T2_2031


title: T2_5207


title: T2_8414


title: T2_3665


title: T2_6297


title: T2_8196


title: T2_4837


title: T2_9566


title: T2_8973


title: T2_8984


title: P1_6936


title: P1_7270


title: P1_5339


title: P1_9400


title: P1_7778


title: P1_327


title: P1_4495


title: P1_3338


title: P1_4362


title: P1_7648


title: P1_7561


title: P1_8081


title: T2_1843


title: T2_8823


title: T2_5446


title: T2_1202


title: T2_3258


title: P1_1979


title: P1_156


title: T2_1029


title: T2_9725


title: T2_3170


title: T2_2063


title: T2_6296


title: T2_8763


title: T2_4459


title: P1_4789


title: T2_955


title: P1_7759


title: T2_5549


title: P1_6201


title: T2_836


title: T2_6160


title: P1_3726


title: P1_8383


title: P1_4638


title: P1_2038


title: P1_1103


title: T2_4891


title: P1_1341


title: T2_8156


title: T2_8161


title: T2_5888


title: T2_1841


title: P1_4742


title: P1_4903


title: T2_508


title: P1_7481


title: P1_914


title: P1_2209


title: P1_1888


title: P1_5614


title: P1_2696


title: P1_5241


title: P1_3634


title: T2_2770


title: P1_3627


title: T2_7899


title: T2_7136


title: T2_5594


title: P1_2730


title: P1_1783


title: T2_8191


title: P1_7796


title: P1_1361


title: P1_1683


title: T2_3079


title: T2_1846


title: P1_5271


title: P1_6566


title: T2_5921


title: T2_4505


title: T2_5557


title: T2_3072


title: P1_1797


title: P1_9480


title: T2_787


title: P1_2135


title: P1_5625


title: P1_9981


title: P1_262


title: P1_304


title: T2_2973


title: T2_6613


title: T2_6744


title: T2_1434


title: P1_4881


title: P1_8921


title: T2_2527


title: T2_772


title: P1_2299


title: P1_8593


title: T2_2044


title: T2_5009


title: P1_2190


title: T2_3310


title: P1_35


title: P1_5163


title: P1_7433


title: P1_4785


title: T2_2062


title: P1_9079


title: P1_7338


title: P1_3381


title: P1_2222


title: P1_3429


title: T2_6929


title: T2_8053


title: P1_2134


title: T2_9780


title: P1_4703


title: P1_9815


title: P1_4883


title: P1_715


title: P1_7470


title: T2_2491


title: P1_570


title: P1_974


title: T2_3867


title: P1_1088


title: T2_5411


title: T2_2013


title: T2_5092


title: T2_1322


title: T2_8093


title: T2_2356


title: T2_9631


title: T2_6805


title: T2_7192


title: T2_8938


title: T2_2474


title: T2_57


title: T2_3893


title: T2_9416


title: T2_3280


title: T2_5938


title: T2_7927


title: T2_1864


title: T2_4534


title: T2_6337


title: T2_4936


title: T2_1831


title: T2_6366


title: T2_8312


title: T2_3662


title: T2_735


title: T2_7028


title: T2_3316


title: T2_6705


title: T2_5001


title: T2_384


title: T2_8743


title: T2_4569


title: T2_5968


title: T2_5781


title: T2_9984


title: T2_1558


title: T2_6878


title: T2_7552


title: T2_5824


title: T2_7176


title: T2_3068


title: T2_6360


title: T2_506


title: T2_3787


title: T2_3484


title: T2_4350


title: T2_2058


title: T2_4538


title: T2_6084


title: T2_1236


title: T2_856


title: T2_4958


title: T2_726


title: T2_6558


title: T2_2032


title: T2_239


title: T2_2087


title: T2_7884


title: T2_3573


title: T2_8202


title: T2_5119


title: WT_dome stage_Mnase-seq

status: Public on Jan 15 2019

description: WT_TTAGGC_L001_R1_001 postMBT

data_processing:
All mapped reads were extended to 147 bp in their 3' direction and truncated to the middle 61 bp.
Bigwig files made for both Zv9 and GRCz11 genome builds.
Genome_build: Danio rerio Zv9 and GRCz11
Supplementary_files_format_and_content: bigwig

growth_protocol: Fish were raised, maintained and crossed under standard conditions as described (Westerfield, 2000). Embryos obtained from crosses were raised in egg water at 28.5°C. Developmental stage of MZspg and MZnanog embryos was indirectly determined by observation of wild type embryos born at the same time and incubated under identical conditions. For controls, we used the AB-TL wild type embryos. Staging was performed according to Kimmel publication (Kimmel et al., 1995).

extract_protocol:
Wild-type, MZspg and MZnanog embryos were collected and staged to 512-cell or dome stage. With them the Mnase digestion was performed as previously described by Zhang et al., 2014.
Library preparation and high throughput sequencing was performed according to standard Illumina HiSeq 2500 protocols.

value: wild type

value: dome stage (4.3 hpf)

value: embryos


title: MZnanog mutant_512-cell stage_Mnase-seq

value: Nanog -/-

value: 512-cell stage (2.75 hpf)


title: MZspg mutant_dome stage_Mnase-seq

description: MZspg_GATCAG_L001_R1_001 postMBT


title: Donor 1 Day 0

status: Public on Jul 11 2018

first: Farshid

last: Guilak

address: Couch Building, 3rd Floor, #3213

department: Orthopaedics

institute: Washington University in St Louis

data_processing:
Raw fastq files were processed with Trim Galore! (Babraham Bioinformatics) to eliminate low quality reads and remnant adapter sequences.
After trimming, processed reads were aligned to the human genome (STAR pre-assembled GRCh38 genome) by STAR
The number of aligned reads to each annotated genes or transcripts (GENCODE v21) were counted using HTseq
Normalized counts and differential gene expression analysis was carried out with DESeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for genes for each sample by gene symbol and ENSEMBL ID
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for genes for all samples by gene symbol and ENSEMBL ID

source_name: Mesenchymal stem cells

growth_protocol: At the end of passage 4, MSCs were dissociated from the culture vessels with 0.05% Trypsin-EDTA (Sigma). Trypsin was subsequently inactivated with equal volume of expansion medium. Detached cells were collected by centrifugation (200 x g for 5 min), followed by 3 washes in pre-warmed DMEM-high glucose (Gibco). The resulting cell mixtures were resuspended at 5.0 x 105 cells/mL in chondrogenic medium: DMEM-high glucose (Gibco), 1% Penicillin/streptomycin (Gibco), 1% ITS+ (Corning), 100 nM dexamethasone (Sigma), 50 µg/mL ascorbic acid (Sigma), 40 µg/mL L-proline (Sigma), and 10 ng/mL rhTGF-β3 (R&D Systems). To form pellets, 2.5 x 105 cells (500 µL) was dispended into each 15 mL conical tube, then centrifuged at 200 x g for 5 min. Pellets were cultured for 21 days at 37ºC and 5% CO2 with medium exchange every three days. Pellets were harvested on day 0, day 1, day 3, day 7, day 14, and day 21 for RNA isolation, and on day 3, day 14, and day 21 for histological and biochemical analyses.

extract_protocol:
On day of harvest, pellets were washed once with PBS, snap frozen in liquid nitrogen, and stored at -80ºC until processing. Isolation of RNA was performed following manufacturer’s protocol (Norgen #48500) with the following modifications: for each time point, three pellets were homogenized with a pestle prior to addition of lysis buffer RL; RNA was eluted in 20 µL of DEPC-treated water.
Libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina). Sequencing was performed on a HiSeq2500 (paired end and 100 base-pair reads) with sequencing depth of 100 million reads per samples.

tag: donor

value: Donor 1

tag: day

value: Day 0

value: MSCs harvested after trypsin digestion


title: Donor 2 Day 21

source_name: MSC derived pellets day 21

value: Donor 2

value: Day 21

tag: source

value: pooled from 3 pellets


title: Donor 3 Day 21

value: Donor 3


title: Donor 1 Day 21


title: Donor 3 Day 0


title: T2_6102

value: sEF

value: Negative

tag: tissue

value: Whole blood


title: Donor 2 Day 0


title: T2_8729

value: CTRL


title: T2_8909

value: EF

value: S. Typhi


title: MZnanog mutant_dome stage_Mnase-seq

description: MZnanog_CGTACG_L001_R1_001 postMBT

value: dome stage (4.3 hpf)


title: T2_145


title: T2_9476


title: T2_5822


title: T2_3691


title: T2_7151


title: MZspg mutant_512-cell stage_Mnase-seq

value: embryos


title: T2_4567


title: T2_4968


title: WT_512-cell stage_Mnase-seq

value: wild type


title: S2-007_RNA-seq rep3

status: Public on Apr 18 2018

city: Brighton

first: Leandro

last: Castellano

address: Falmer, JMS Building

institute: University of Sussex

data_processing:
Basecalls performed using CASAVA version 1.4
Sequence reads were mapped to the hg19 genome assembly using TopHat
Data was normalized using DESeq2 package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values from DESeq2 for each Sample

growth_protocol: BxPC-3 cells were cultured in RPMI supplemented with 10%FCS and 1%Pen-Sprep-Glutamine, whereas S2-007 cells were cultured in DMEM supplemented with 10%FCS and 1%Pen-Sprep-Glutamine.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions (TRI Reagent, Sigma).
Libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer's instructions.

treatment_protocol: Cells were washed twice with cold PBS and Trizol was added for RNA extraction.

value: pancreatic cancer cell line

tag: cell phenotype

value: mesenchymal phenotype


title: S2-007_RNA-seq rep1


title: S2-007_RNA-seq rep2


title: BxPC-3_RNA-seq rep2

value: epithelial phenotype


title: BxPC-3_RNA-seq rep1


title: BxPC-3_RNA-seq rep3


title: T2_5879


title: Veh_72h_rep2

data_processing:
Basecalls performed using CASAVA version 1.4
Sequence reads were mapped to the hg19 genome assembly using TopHat
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek Genomic Suite (Partek Incorporated)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: PANC-1 cells

growth_protocol: PANC-1 cells were cultured in DMEM supplemented with 10%FCS and 1%Pen-Sprep-Glutamine.

treatment_protocol: For RIP-seq and RNA-seq PANC-1 cells were transiently transfected with either miR-100 or miR-125b (0.5nM) mimic using HiPerfect transfection reagent (Qiagen). For TGFb expression profiling PANC-1 cells were treated with 5nM of TGFb or vehicle control for 72 hours.

value: Pancreatic ductal adenocarcinoma

value: Vehicle

tag: duration of treatment

value: 72 hours


title: Total_miR-125b_rep2

value: 24 hours


title: TGFb_72h_rep3

value: TGFb


title: Veh_72h_rep1


title: TGFb_72h_rep2


title: Total_miR-100_rep2


title: Total_nc_rep1

value: mimic:negative control


title: SMAD2/3_rep1

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 300 bp to create summary windows. Alignments were done using Bowtie 1.0.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) using default settings.
Genome_build: hg19
Supplementary_files_format_and_content: wig files

extract_protocol:
Lysates were clarified from sonicated nuclei and SMAD2/3--DNA complexes were isolated with antibody.
Libraries were prepared according to NEB DNA UltraKit's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated using Ampure SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the H-Seq2000 following the manufacturer's protocols.

treatment_protocol: PANC-1 cells were treated with 5nM of TGFb or vehicle control for 1 hour.

value: pancreatic carcinoma

value: 1 hour


title: Total_nc_rep2


title: Total_miR-100_rep1


title: Input DNA


title: AGO2_IP_miR-125b_rep1


title: AGO2_IP_miR-125b_rep2


title: AGO2_IP_miR-100_rep2


title: AGO2_IP_nc_rep1


title: AGO2_IP_miR-100_rep1


title: AGO2_IP_nc_rep2


title: TGFb_72h_rep1


title: SMAD2/3_rep2


title: Veh_72h_rep3


title: Total_miR-125b_rep1


title: S2-007_rep2

hyb_protocol: Hybridization reactions were performed according to NanoString protocol.

scan_protocol: Data collection was carried out on the nCounter Digital Analyzer following NanoString protocol.

data_processing: Each dataset was normalised and analysed using DESeq2.

label: specific miRTag sequence

source_name: S2-007 cells

label_protocol: Samples were processed according to NanoString protocol.

growth_protocol: PANC-1 and S2-007 cells were cultured in DMEM and BxPC-3 in RPMI medium, all supplemented with 10%FCS and 1%Pen-Sprep-Glutamine.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (TRI Reagent, Sigma).

treatment_protocol: PANC-1 cells were treated with 5nM of TGFb or vehicle control for 72 hours.


title: S2-007_rep3


title: S2-007_rep1


title: PANC-1_TGFb_72h_rep2


title: PANC-1_TGFb_72h_rep3


title: PANC-1_TGFb_72h_rep1


title: PANC-1_veh_72h_rep1


title: PANC-1_veh_72h_rep2


title: PANC-1_veh_72h_rep3


title: BxPC-3_rep2

source_name: BxPC-3 cells


title: BxPC-3_rep1


title: BxPC-3_rep3


title: T2S_367_Ty21a_TD_Va

status: Public on Oct 12 2017

data_processing: Data was quantile normalised, background subtracted and log2 transformed using neqc() in R.

growth_protocol: NA - whole blood samples from clinical trial.

value: Whole blood

tag: condition

value: TD

tag: date

tag: timepoint

value: Va


title: T2S_8406_Ty21a_TD_PREV

value: PREV


title: T2S_7508_Ty21a_nonTD_PREV

value: nonTD


title: T2S_9536_Ty21a_TD_Va


title: T2S_8429_M01ZH09_nonTD_PREV


title: T2S_8184_Ty21a_nonTD_Va


title: T2S_3082_M01ZH09_nonTD_Va


title: T2S_704_Ty21a_nonTD_Va


title: T2S_8807_Ty21a_TD_Va


title: T2S_1553_M01ZH09_nonTD_PREV


title: T2S_4172_Ty21a_TD_PREV


title: T2S_8496_M01ZH09_nonTD_Va


title: T2S_1696_M01ZH09_TD_Va


title: T2S_2860_Ty21a_TD_Va


title: T2S_8901_M01ZH09_TD_Va


title: T2S_7587_Ty21a_nonTD_PREV


title: T2S_331_M01ZH09_TD_PREV


title: T2S_3533_Ty21a_TD_PREV


title: T2S_5454_Ty21a_nonTD_PREV


title: T2S_6742_Ty21a_TD_PREV


title: T2S_4163_Ty21a_nonTD_PREV


title: T2S_6875_Ty21a_nonTD_Va


title: T2S_2586_Ty21a_nonTD_Va


title: T2S_4287_Ty21a_TD_Va


title: T2S_6306_M01ZH09_TD_PREV


title: T2S_2273_Ty21a_TD_Va


title: T2S_1459_Ty21a_nonTD_PREV


title: T2S_3556_Ty21a_TD_PREV


title: T2S_5379_M01ZH09_nonTD_PREV


title: T2S_1447_M01ZH09_nonTD_PREV


title: T2S_481_M01ZH09_TD_PREV


title: T2S_5431_M01ZH09_nonTD_PREV


title: T2S_6136_M01ZH09_nonTD_PREV


title: T2S_4578_M01ZH09_TD_PREV


title: T2S_4281_M01ZH09_nonTD_Va


title: T2S_3818_M01ZH09_TD_Va


title: T2S_4924_M01ZH09_TD_Va