title: Haematopoietic stem cell/multipotent progenitor HSPC_594

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_589

status: Public on Jul 04 2016

type: SRA

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

description: single cell RNA-Seq

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

molecule: total RNA

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
Bone marrow cells were isolated from the femurs, tibiae and iliac crest of 20 8-12 week old C57BL/6 mice.
The cells were lineage depleted and stained with antibodies to separate individual populations by FACS.
Single-cell sorting was done using a FACS Influx5 (BD Biosciences) using unstained cells and single-stained cells are gate-settng controls.
Cells were sorted directly into individual wells of a 96-well PCR plate containing lysis buffer.
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
Pooled libraries were run on the Illumina Hi-Seq 2500.
RNA libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit

tag: cell type

tag: strain

tag: age

value: 8-12 weeks


title: Haematopoietic stem cell/multipotent progenitor HSPC_590

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_600

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_587

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_588

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_601

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_595

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_582

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_581

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_583

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_579

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_576

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_580

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_577

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_574

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_575

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_573

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_568

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_572

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_570

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_585

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_586

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_565

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_566

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_569

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_564

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_561

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_559

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_562

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_558

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_560

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_578

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_553

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_557

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_555

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_563

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_552

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_556

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_554

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_550

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_551

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_549

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_547

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_571

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_546

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_544

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_567

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_542

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_541

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_543

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_540

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_538

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_535

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_536

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_537

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_534

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_531

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_529

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_532

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_523

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_548

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_527

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_530

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_521

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_528

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_522

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_545

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_525

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_526

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_520

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_539

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_519

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_515

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_518

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_533

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_511

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_516

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_514

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_512

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_513

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_508

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_506

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_510

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_505

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_503

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_504

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_501

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_495

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_517

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_496

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_502

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_524

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_492

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_499

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_491

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_493

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_497

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_487

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_509

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_488

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_490

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_507

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_486

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_485

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_484

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_482

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_480

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_481

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_478

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_477

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_479

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_500

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_494

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_483

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_474

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_475

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_473

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_489

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_469

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_470

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_467

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_471

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_468

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_472

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_464

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_465

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_463

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_459

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_460

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_462

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_458

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_461

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_456

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_454

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_453

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_455

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_452

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_451

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_450

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_448

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_476

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_466

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_446

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_441

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_443

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_438

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_439

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_442

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_445

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_440

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_436

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_434

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_435

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_437

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_432

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_457

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_433

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_431

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_449

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_430

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_429

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_427

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_447

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_424

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_425

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_426

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_444

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_423

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_421

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_422

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_420

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_419

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_418

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_414

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_417

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_415

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_413

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_416

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_412

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_409

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_411

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_406

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_407

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_428

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_403

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_402

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_410

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_404

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_400

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_399

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_393

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_395

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_398

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_397

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_391

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_396

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_390

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_387

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_392

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_386

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_405

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_408

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_385

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_383

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_384

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_401

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_389

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_381

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_379

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_382

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_377

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_376

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_375

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_378

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_380

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_374

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_373

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_371

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_370

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_372

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_368

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_367

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_369

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_366

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_365

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_364

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_363

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_362

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_361

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_360

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_358

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_357

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_355

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_353

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_354

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_352

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_351

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_356

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_350

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_347

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_346

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_348

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_345

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_344

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_343

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_342

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_341

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_339

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_359

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_337

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_336

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_334

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_335

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_333

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_332

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_340

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_331

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_330

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_349

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_329

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_328

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_323

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_325

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_324

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_322

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_321

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_498

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_319

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_338

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_320

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_317

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_318

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_316

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_315

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_314

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_313

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_312

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_306

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_310

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_309

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_311

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_303

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_327

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_307

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_305

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_308

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_304

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_302

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_295

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_300

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_291

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_301

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_299

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_297

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_326

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_292

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_298

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_294

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_296

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_290

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_293

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_288

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_289

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_276

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_280

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_285

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_287

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_286

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_284

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_281

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_283

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_282

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_274

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_273

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_272

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_265

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_263

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_279

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_277

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_262

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_275

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_271

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_260

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_270

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_259

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_256

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_269

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_267

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_254

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_268

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_266

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_251

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_264

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_278

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_261

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_258

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_388

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_250

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_249

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_394

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_247

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_248

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_244

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_241

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_252

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_238

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_235

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_245

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_234

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_253

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_257

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_246

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_232

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_239

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_236

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_231

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_242

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_243

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_255

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_229

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_240

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_223

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_224

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_226

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_227

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_225

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_221

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_219

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_237

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_222

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_228

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_233

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_217

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_215

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_212

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_214

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_211

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_230

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_210

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_209

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_213

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_208

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_206

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_207

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_203

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_204

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_220

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_218

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_202

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_198

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_195

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_196

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_201

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_193

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_199

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_192

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_191

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_216

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_190

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_194

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_189

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_188

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_200

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_185

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_186

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_183

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_182

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_179

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_181

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_177

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_205

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_178

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_180

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_197

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_176

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_175

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_174

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_173

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_170

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_172

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_168

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_169

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_166

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_167

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_165

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_164

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_187

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_184

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_162

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_161

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_163

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_159

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_157

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_155

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_156

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_158

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_154

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_152

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_153

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_149

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_148

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_150

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_147

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_146

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_151

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_171

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_144

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_145

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_160

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_142

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_138

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_140

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_141

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_139

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_133

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_134

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_137

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_135

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_136

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_131

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_132

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_129

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_124

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_125

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_128

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_123

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_121

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_122

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_120

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_119

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_143

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_117

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_116

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_118

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_115

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_114

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_109

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_110

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_112

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_113

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_111

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_108

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_107

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_130

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_126

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_106

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_105

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_127

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_103

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_104

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_102

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_100

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_097

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_098

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_095

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_094

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_093

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_099

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_092

description: single cell RNA-Seq


title: KasumiSCR_ChIPSeq

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

library_source: genomic

data_processing:
CASSAVA software (llumina)
Data were filtered using trim galore with default settings (phred-score cutt-off set at 20)
ChIP-seq reads were aligned to thehg19 genome assembly using bowtie version 2 using default settings
peaks were called using findPeaks (HOMER version 3.12) with style set to factor and and fold enrichment to 10 (rest were default); overlaps done using CisGenome
tag densities were generated using annotatePeaks (HOMER version 3.12)
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using makeUCSCfile (HOMER version 3.12)

molecule: genomic DNA

organism: Homo sapiens

source_name: Kasumi-1 cell line

growth_protocol: Kasumi-1 cells were cultured in 20% RPMI medium.

extract_protocol:
Chromatin was fixed in 1% formaldehyde for 10 minutes, follwed by shearing them to 200-700bp using a Bioruptor (Diagenode). Samples were immunoprecipitated using AML1-ETO (Diagenode, Cat. C15310197; Lot A706-001) antibody.
Sequencing samples were prepared according to the manufacturer's protocol (Illumina). End repair was performed using the precipitated DNA using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adapters were ligated. The DNA was loaded on gel and a band corresponding to ~300 bp (ChIP fragment + adapters) was excised. The DNA was isolated, amplified by PCR and used for cluster generation. ChIP-seq libraries were further processed according to Illumina's standard protocol.

treatment_protocol: Cells were transduced with scrambled and sh-RNA targetting MEIS2 VCM. Cells were puromycin selected before Chromatin Immunoprecipitation.

tag: transduction

value: SCR

value: leukemic cell line derived from peripheral blood (contains t(8;21) chromosome translocation)

tag: passages

tag: cell line

tag: chip antibody


title: KasumiKDMEIS2_ChIPSeq

value: AML1-ETO (Diagenode, Cat. C15310197; Lot A706-001)


title: Haematopoietic stem cell/multipotent progenitor HSPC_090

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_089

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_086

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_088

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_087

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_091

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_084

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_101

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_083

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_085

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_082

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_079

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_077

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_076

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_074

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_081

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_096

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_080

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_072

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_069

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_078

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_067

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_075

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_073

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_071

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_070

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_068

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_066

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_064

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_063

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_061

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_062

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_065

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_055

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_056

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_053

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_057

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_060

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_059

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_058

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_049

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_046

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_048

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_051

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_045

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_050

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_040

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_042

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_043

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_044

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_038

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_041

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_039

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_037

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_035

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_036

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_034

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_033

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_054

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_032

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_031

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_052

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_030

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_028

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_029

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_027

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_022

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_023

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_021

description: single cell RNA-Seq


title: 30 RM Input

city: Lund

first: Olof

last: Gidlof

address: Solvegatan 19

country: Sweden

institute: Lund University

description:
30 RM Input
rm_input_vs_rm_histone.txt
aar_input_vs_rm_input.txt
201418267-01

data_processing:
alignment Bowtie v. 2.2.2
peak calling SICER v 1.1
differential peak analysis edgeR
Genome_build: genome build mm10
Supplementary_files_format_and_content: peak

source_name: Cardiac biopsy

extract_protocol:
Chromatin was prepared from ~25 mg cardiac tissue. Homogenized tissue were crosslinked with 1.5 % formaldehyde, nuclei were prepared and chromatin digested using the SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology, Danvers, MA, USA) according to the manufacturers instructions. 5 ug of digested, cross-linked chromatin was used per immunoprecipitation. ChIP was performed with a H3K9me2 antibody (D85B4, Cell Signaling Technology) according to the manufacturers recommendations.
Ten ng of input or ChIP-enriched DNA were used for 2x101 Paired-End Multiplexed library preparation using the NEBNext Ultra DNA Kit (New England Biolabs) and 12 cycles PCR

tag: gender

value: Female

value: 12 months

tag: biopsy type

value: Remote myocardium

tag: sample type

value: Input


title: 30 RM H3K9me2

description:
30 RM H3K9me2
aar_histone_vs_rm_histone.txt
rm_input_vs_rm_histone.txt
201418266-01

value: H3K9me2 ChIP


title: Haematopoietic stem cell/multipotent progenitor HSPC_020

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_024

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_019

description: single cell RNA-Seq


title: 30 AAR Input

description:
30 AAR Input
aar_input_vs_aar_histone.txt
aar_input_vs_rm_input.txt
201418265-01

value: Area at risk


title: Haematopoietic stem cell/multipotent progenitor HSPC_018

description: single cell RNA-Seq


title: 27 AAR H3K9me2

description:
27 AAR H3K9me2
aar_histone_vs_rm_histone.txt
aar_input_vs_aar_histone.txt
201418260-01

value: Male


title: 23 RM Input

description:
23 RM Input
rm_input_vs_rm_histone.txt
aar_input_vs_rm_input.txt
201418259-01


title: 27 RM H3K9me2

description:
27 RM H3K9me2
aar_histone_vs_rm_histone.txt
rm_input_vs_rm_histone.txt
201418262-01


title: 30 AAR H3K9me2

description:
30 AAR H3K9me2
aar_histone_vs_rm_histone.txt
aar_input_vs_aar_histone.txt
201418264-01


title: 27 RM Input

description:
27 RM Input
rm_input_vs_rm_histone.txt
aar_input_vs_rm_input.txt
201418263-01


title: 27 AAR Input

description:
27 AAR Input
aar_input_vs_aar_histone.txt
aar_input_vs_rm_input.txt
201418261-01


title: 23 AAR Input

description:
23 AAR Input
aar_input_vs_aar_histone.txt
aar_input_vs_rm_input.txt
201418257-01


title: Haematopoietic stem cell/multipotent progenitor HSPC_017

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_016

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_026

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_025

description: single cell RNA-Seq


title: 22 AAR H3K9me2

description:
22 AAR H3K9me2
aar_histone_vs_rm_histone.txt
aar_input_vs_aar_histone.txt
201418252-01


title: 22 RM H3K9me2

description:
22 RM H3K9me2
aar_histone_vs_rm_histone.txt
rm_input_vs_rm_histone.txt
201418254-01


title: 19 RM H3K9me2

description:
19 RM H3K9me2
aar_histone_vs_rm_histone.txt
rm_input_vs_rm_histone.txt
201418250-01


title: Haematopoietic stem cell/multipotent progenitor HSPC_014

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_013

description: single cell RNA-Seq


title: 19 RM Input

description:
19 RM Input
rm_input_vs_rm_histone.txt
aar_input_vs_rm_input.txt
201418251-01


title: 23 AAR H3K9me2

description:
23 AAR H3K9me2
aar_histone_vs_rm_histone.txt
aar_input_vs_aar_histone.txt
201418256-01


title: 22 AAR Input

description:
22 AAR Input
aar_input_vs_aar_histone.txt
aar_input_vs_rm_input.txt
201418253-01


title: Haematopoietic stem cell/multipotent progenitor HSPC_012

description: single cell RNA-Seq


title: 19 AAR Input

description:
19 AAR Input
aar_input_vs_aar_histone.txt
aar_input_vs_rm_input.txt
201418249-01


title: 19 AAR H3K9me2

description:
19 AAR H3K9me2
aar_histone_vs_rm_histone.txt
aar_input_vs_aar_histone.txt
201418248-01


title: 17 RM H3K9me2

description:
17 RM H3K9me2
aar_histone_vs_rm_histone.txt
rm_input_vs_rm_histone.txt
201418246-01


title: 17 RM Input

description:
17 RM Input
rm_input_vs_rm_histone.txt
aar_input_vs_rm_input.txt
201418247-01


title: Haematopoietic stem cell/multipotent progenitor HSPC_010

description: single cell RNA-Seq


title: 23 RM H3K9me2

description:
23 RM H3K9me2
aar_histone_vs_rm_histone.txt
rm_input_vs_rm_histone.txt
201418258-01


title: Haematopoietic stem cell/multipotent progenitor HSPC_011

description: single cell RNA-Seq


title: 17 AAR Input

description:
17 AAR Input
aar_input_vs_aar_histone.txt
aar_input_vs_rm_input.txt
201418245-01


title: Haematopoietic stem cell/multipotent progenitor HSPC_007

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_008

description: single cell RNA-Seq


title: AE9a_2

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 using tophat with default parameters
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) calculation, normalization, and differential expression analysis were calculated using Cufflinks and cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: One tab-delimited text file with FPKM values of genes across all samples

source_name: Murine bone marrow cells

growth_protocol: 5FU was injected into mice and 4 days later mice were sacrificed for BM isolation. BM cells were cultured in 15% DMEM medium with cytokine cocktail consisting of IL3,  IL6 and SCF.

extract_protocol:
RNA extraction was done using TRIzol® method following manufacturer's protocol
We used Illumina TruSeq™ RNA Sample preparation Kit version 2 and strictly followed the manufacturer's protocol

treatment_protocol: 5FU BM cells were transduced with either AML1-ETO/Meis2, AML1-ETO9a/Meis2, or AML1-ETO9a. After 48hrs transduction, cells were checked for BM titres and 1x106 cells/mice were transplanted into lethally irradiated mice. RNA was isolated from these mice after they succumbed to leukemia with variable latencies.

tag: tissue

value: Bone marrow

value: Leukemic [median latency = 138 days]


title: Haematopoietic stem cell/multipotent progenitor HSPC_009

description: single cell RNA-Seq


title: AE9a_1


title: Haematopoietic stem cell/multipotent progenitor HSPC_006

description: single cell RNA-Seq


title: 17 AAR H3K9me2

description:
17 AAR H3K9me2
aar_histone_vs_rm_histone.txt
aar_input_vs_aar_histone.txt
201418244-01


title: Haematopoietic stem cell/multipotent progenitor HSPC_015

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_005

description: single cell RNA-Seq


title: Haematopoietic stem cell/multipotent progenitor HSPC_004

description: single cell RNA-Seq


title: AE9aMeis2_3

value: Leukemic [median latency = 102 days]

value: AML1-ETO9a + Meis2


title: AE9aMeis2_2


title: AE9aMeis2_1


title: AEMeis2_3

value: Leukemic [median latency = 171 days]

value: AML1-ETO + Meis2


title: Haematopoietic stem cell/multipotent progenitor HSPC_003

description: single cell RNA-Seq

value: 8-12 weeks


title: Haematopoietic stem cell/multipotent progenitor HSPC_001

description: single cell RNA-Seq


title: AEMeis2_2


title: AEMeis2_1


title: ChIPSeq_327_H3K27me3_0

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

data_processing:
Basecalls were made with RTA1.8_CASAVA1.7
ChIPSeq reads were trimmed of adapter sequence and mapped to v2 of the Fusarium fujikuroi genome with BWA software using default options
samtools were used to convert BWA output to sorted bam files, and BEDTools bamToBed was used to convert alignment files to bed format
EpiChIP_V0.9.7-e3.jar was used to calculate normalized locus chromatin state (NLCS) values for each gene. Window size was each gene without upstream or downstream sequence.
Genome_build: Genome_build: Fusarium fujikuroi v2
Supplementary_files_format_and_content: bed files holding coverage values for the whole genome (chromosomes)

organism: Fusarium fujikuroi

source_name: mycelium

growth_protocol: Strains were grown in liquid synthetic ICI medium in low nitrogen conditions

extract_protocol:
Lysates were clarified from sonicated mycelial tissue and histone-DNA complexes were isolated with antibody [anti-Histone H3K27me3 antibody (pAb)  Active Motif (Catalog No. AM39155)]
DNA obtained by ChIP was end-repaired and ligated to adapters as described in Pomraning KR, Smith KM, Bredeweg EL, Connolly LR, Phatale PA, et al. (2012) Library preparation and data analysis packages for rapid genome sequencing. Methods Mol Biol 944: 1-22.

value: mycelium

tag: glutamine

value: 6 mM

tag: antibody


title: tilapia_8_0h_gill_3

status: Public on Jul 03 2016

city: Shanghai

first: Peng

last: Hu

address: Huchenghuan Road 999

country: China

institute: Shanghai Ocean University

data_processing:
Illumina Casava1.7 software used for basecalling.
Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First, the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then, the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20, and post-trimming length of 50 bases or longer are enforced. Finally, the trimmed reads that were paired were kept for the mapping.
Tophat 2.0.13 was used to map the reads to the reference genomes.
Samtools was used to first sort the bam files of the aligned reads by the read name.
HTSeq-count was then applied to count the number of reads that are mapped to the genes.
Genome_build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78
Supplementary_files_format_and_content: tab-delimited text files include raw reads count for each Sample

organism: Oreochromis niloticus

source_name: gill

growth_protocol: Tilapia and zebrafish were raised and maintained at 28±1°C in well-managed aquariums.

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fishes were subjected to a stepped cooling by lowering 1°C /h, to 8°C, and then maintained at 8°C. When temperature declined to 8°C, tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C, 0h of LOE,6h of LOE and 12h of LOE, gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition, after 6h of LOE, tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA-seq.

value: gill

tag: species

value: tilapia

tag: replicate

tag: time point

tag: temperature

value: 8 degreeC

value: Six months old


title: ChIPSeq_350_H3K27me3_0


title: ChIPSeq_365_H3K27me3_10


title: 22 RM Input

description:
22 RM Input
rm_input_vs_rm_histone.txt
aar_input_vs_rm_input.txt
201418255-01

value: 12 months

value: Remote myocardium

value: Input


title: tilapia_8_6h_gill_3


title: BHI 1 control

city: Tel Aviv

first: Lior

last: Lobel

state: Israel

address: Ramat Aviv

department: Molecular Microbiology

country: Israel

institute: Tel Aviv University

data_processing:
Quality control using the SeqMonk software
Trimming if needed using the FASTX tool kit
Alignment using Bowtie2
Peak calling using MACS
Fold change and FDR values were calculated by the MACS [Zhang, Y et al, Model-based analysis of ChIP-Seq (MACS). Genome biology. 2008] algorithm
The "exp" column represents the existence of CodY regulation on the genes asssociated with the peaks.
The CodY motifs and P-values were identified using the MAST algorithem [Bailey TL et al,  Combining evidence using p-values: application to sequence homology searches. Bioinformatics. 1998].
Genome_build: Listeria monocytogenes 10430S genome (the Broad Institute)
Supplementary_files_format_and_content: Excel file with peak call and  CodY binding site analysis for both BHI and LBMM conditions

organism: Listeria monocytogenes

growth_protocol: L. monocytogenes CodY-6his were grown to mid exponenital growth phase (OD 600nm = 0.3) in BHI or low BCAAs minimal medium (LBMM) and then fixed with 1% paraformaldhyde

extract_protocol:
Bacterial ChIP was performed according to Waldminghaus T et al, BMC genomics. 2010.
ChIP libraries were prepared for sequencing using standard Illumina protocols - TruSeq ChIP kit

tag: strain background

tag: genotype/variation

tag: media

value: BHI

tag: chip/no-chip

value: no-ChIP


title: BHI 1

value: ChIP


title: BHI 2 control


title: tilapia_8_12h_gill_3

tag: age


title: zebrafish_8_6h_gill_1

organism: Danio rerio

value: zebrafish


title: zebrafish_8_6h_gill_3


title: zebrafish_8_0h_gill_3


title: BHI 2


title: zebrafish_8_12h_gill_3


title: Haematopoietic stem cell/multipotent progenitor HSPC_002

description: single cell RNA-Seq

tag: cell type

tag: strain


title: zebrafish_8_6h_gill_2


title: tilapia_8_6h_gill_2

description: LOE: tilapia loss of equilibrium

value: Six months

tag: group

tag: condition


title: tilapia_8_12h_gill_2

description: LOE: tilapia loss of equilibrium


title: tilapia_8_0h_gill_2

description: LOE: tilapia loss of equilibrium


title: LBMM 2 control

value: Low BCAA Minimal Medium


title: zebrafish_8_12h_gill_2

description: LOE: tilapia loss of equilibrium


title: tilapia_8_12h_gill_1

description: LOE: tilapia loss of equilibrium


title: tilapia_8_6h_gill_1

description: LOE: tilapia loss of equilibrium


title: zebrafish_8_0h_gill_2

description: LOE: tilapia loss of equilibrium


title: tilapia_28_gill_3


title: LBMM 2


title: tilapia_8_0h_gill_1

description: LOE: tilapia loss of equilibrium


title: zebrafish_8_0h_gill_1

description: LOE: tilapia loss of equilibrium


title: zebrafish_28_gill_3


title: zebrafish_28_gill_2


title: tilapia_28_gill_2


title: LBMM 1


title: tilapia_28_gill_1


title: Nppa viewpoint in the E12.5 ventricles

status: Public on Jul 02 2016

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

data_processing:
Library strategy: 4C-seq
4C templates were mixed and sequenced simultaneously in 1 Illumina HiSeq 2000 lane. The sequence tags generated by the procedure were prefixed by the 4C reading primer, which includes the DpnII restriction site sequence. The 4C reading primer sequences were separated from multiplexed 4C-seq libraries, and the suffixes were extracted for further processing.
Mapping and filtering of the sequence reads was done as previously described (Werken et al., 2012, Nat Methods). The algorithm constructs a background model for remote intra- and interchromosomal contacts to correct for systematic biases that can occur during the 4C-seq experimental protocol. The algorithm is designed to use controls for sequencing errors and nonunique sequences while considering the high coverage (100×–100,000×) of fragment ends that are proximal to the viewpoint fragment.
To normalize the interactions in close proximity to the viewpoint, the algorithm was used to calculate the median of normalized coverage for running windows of size 4 kb and sliding windows of 2–50 kb of linearly increasing size. All median values represent enrichment relative to the maximum attainable 4-kb median value, whereas sliding windows represent enrichment relative to the maximum attainable 12-kb median value. The 20th and 80th percentiles were also computed and depicted as the gray area around the 4-kb running windows.
The 4C-seq contact profile comparison plots were generated combining the mapping (Werken et al., 2012, Methods Enzymol) and normalization (Werken et al., 2012, Nat Methods) strategies. Within samples the distribution of the blind fragment-end reads and the distribution of the non-blind fragment-end reads were quantile normalized after linear interpolation of the center of the fragment-end using R's limma package (Smyth, 2005). The reads between samples were normalized based on library size within the locus. Subsequently, a running trimmed (10%) mean was calculated on 21 fragment-ends to smoothen the 4C-seq data. The R statistical package version 3.1.0 was used for the statistical calculations and for generating the 4C-Seq plots (R Core Team, 2013).
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle tracks contain uniquely mapped reads at 4C fragment ends on the cis chromosome, i.e. the chromosome on which the bait/viewpoint fragment is located (chr4). Scores represent the number of reads mapping to a DpnII restriction fragment end.

source_name: embryonic heart ventricles

growth_protocol: control and TAC-operated mice were used, where TAC (transverse aortic constriction) induces cardiac hypertrophy

extract_protocol:
4C templates was prepared as described previously (Simonis et al., 2009). Adult mouse hearts and liver were dissociated and homogenized in ice-cold PBS with 10%FCS to obtain single cell suspension. Chromatin was cross-linked with 2% formaldehyde in 40ml PBS with 10% FCS for 10 min at room temperature, nuclei were isolated in 25ml cold lysis buffer for 1h, and cross-linked DNA was digested with DpnII. Digestion was followed by proximity ligation, removal of cross-links, a secondary restriction digestion with Csp6I and a second proximity ligation.
200 ng of the resulting 4C template was used for the subsequent PCR reaction using Expand Long Template Polymerase (Roche). The PCR products were purified using the High Pure PCR Product Purification Kit (Roche) and the QIAquick PCR purification kit (Qiagen).

treatment_protocol: cells are cross linked using 2% formaldehyde for 10minutes at room temperature in 10%FCS/PBS

value: heart ventricles

value: FVB/N

tag: Stage

tag: bait


title: Nppa viewpoint in the ventricles

source_name: heart ventricles

tag: tissue

value: adult


title: Nppb viewpoint in the liver

source_name: liver

value: liver


title: Nppa viewpoint in the atria

source_name: heart atria

value: heart atria


title: Haematopoietic stem cell/multipotent progenitor HSPC_047

description: single cell RNA-Seq

value: 8-12 weeks


title: Nppb viewpoint in the E12.5 ventricles


title: Nppb viewpoint in the ventricles after TAC

source_name: heart ventricles_TAC


title: Nppb viewpoint in the ventricles


title: zebrafish_8_12h_gill_1

description: LOE: tilapia loss of equilibrium

value: gill


title: rFSL3

status: Public on Jul 01 2016

city: New York

first: Carla

last: Nasca

state: NY

address: 1 Park Avenue

country: USA

institute: NYU Grossman School of Medicine

data_processing:
FastQC v0.11.3
Trimmomatic v0.33 SE -phred33 ILLUMINACLIP:TruSeq3.fa:2:30:10 TRAILING:3 MINLEN:36
Tophat v2.0.9 --library-type  fr-firststrand --GTF rattus_norvegicus_genes_UCSC_igenome.gtf --min-coverage-intron 50 --max-coverage-intron 20000
merge bam files
htseq-count v0.6.1 -s 'reverse'
EdgeR v3.12.0
Genome_build: RGSC 5.0/rn5
Supplementary_files_format_and_content: Tab delimited files with raw counts for each sample

organism: Rattus norvegicus

source_name: ventral dentate gyrus

extract_protocol:
Ventral dentate gyrus tissues were dissected and weighed before homogenization and about 130 mg of tissue was lysed. Total RNA was extracted using Qiazol reagent and RNeasy mini Kit (Qiagen, US), according to the manufacturer’s instructions. RNA quality was checked using the 2100 Bioanalyzer (Agilent Technologies, US) and quantified spectrophotometrically. The acceptance criteria for RNA quality were a 260/280 ratio ≥ 1.80 and ≤ 2.20.
After checking RNA for quality, Total RNA was extracted according to the manufacturer’s instructions (TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat).

treatment_protocol: Tap water (vehicle), or L-acetyl-carnitine (LAC, Sigma, Stockholm, SE), dissolved in tap water, at a concentration of 0.3% (w/v), was available ad libitum in standard rat sipping bottles. The treatment was available for a total of 7 days, with fresh water and LAC prepared after 3 days. LAC intake (30 ml) did not differ from water intake (31 ml) per day. This corresponded to a daily LAC consumption of approximately 210 mg/kg body weight (p.o.).

value: Sprague-Dawley

tag: Sex

value: male

tag: line

value: Flinders Sensitive Line (FSL)

tag: lac phenotype

value: responder

tag: treatment

value: LAC


title: upstream CTCF viewpoint in the liver


title: downstream CTCF viewpoint in the ventricles


title: nrFSL2

value: non-responder


title: nrFSL3


title: downstream CTCF viewpoint in the liver


title: rFSL2


title: rFSL1


title: FSL3

value: vehicle


title: LBMM 1 control

value: no-ChIP


title: Nppa viewpoint in the liver


title: zebrafish_28_gill_1

value: Six months

tag: replicate

tag: temperature


title: upstream CTCF viewpoint in the ventricles


title: FRL2

value: Flinders Resistant Line (FRL)


title: FRL1


title: Nppb viewpoint in the atria


title: FRL3


title: LNCaP non-treated 0 h

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
The illumina GAIIX-generated RNA-Seq reads was in 35 bp length and an initial filtering process was taken to remove any non-desirable contamination sequences.
The reads were mapped to the human RefSeq mRNA database.
The expression levels of mapped transcripts were normalized into transcript parts per Million mapped reads (PPM) to faciliate comparison among different samples.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited .txt file of PPM values for each Sample

source_name: prostate cancer cells

growth_protocol: LNCaP cells were cultured in RPMI 1640 containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol:
Total RNA was extracted using ISOGEN reagent.
RNA sequencing (RNA-seq) library construction and sequencing was performed according to the manufacturer’s protocol for Illumina GAIIX.

treatment_protocol: Cells were treated with DHT 10 nM for 0, 3, 6, 12, 24 and 48 h.

tag: cell line

value: LNCaP

value: non-treatment

tag: time

value: 0 h


title: LNCaP DHT treated 12 h

value: DHT 10nM


title: LNCaP DHT treated 6 h

value: 6 h


title: LNCaP DHT treated 24 h


title: H3 ChIP-seq, Brown adipose tissue

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
All the ChIP-seq libraries were sequenced by the Functional Genomics Core at the University of Pennsylvania using HiSeq 2000.
ChIP-seq reads were aligned to mouse genome (mm9) using Bowtie with options, ‘-k 1 -m 1 --best --strata’. All redundant reads were discarded except one per genomic position.
BigWig files for RPM-normalized stack-height profiles were generated using Homer and bedGraphToBigWig command.
Genome_build: mm9
Supplementary_files_format_and_content: RPM-normalized bigWig files

source_name: Brown adipose tissue

growth_protocol: C57BL/6J male mice were maintained in a 12 hour dark /light cycle, and sacrificed at 5 pm between 10 and 12 weeks of age for tissue collection.

extract_protocol:
Interscapular BAT and epididymal WAT were isolated and processed separately for each sacrificed mouse. The tissues were immediately minced, crosslinked in 1 % formaldehyde/PBS, and stored at -80 C. For each fat pad, material from 3-4 mice was used for sequencing. To prepare ChIP extracts, frozen crosslinked tissue was thawed and suspended ChIP buffer (50 mM HEPES/NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate and Complete protease inhibitor) supplemented with 0.1% SDS. Samples were incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency. Extracts were cleared of insoluble lipid by microfuge centrifugation at full speed followed by extract transfer to a new tube. The process was repeated until minimal lipid accumulated at the top of the extract after centrifugation.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

treatment_protocol: Male mice were delivered from the vendor at seven weeks of age. After arrival, placed on a normal chow diet and allowed to acclimate for 3-5 weeks.

value: Brown adipose tissue

tag: antibody

value: H3 (Abcam ab1791)


title: LNCaP DHT treated 48 h


title: H3K4me1 ChIP-seq, Brown adipose tissue

value: H3K4me1 (Abcam ab8895)


title: H3K4me1 ChIP-seq, Epididymal white adipose tissue

source_name: Epididymal white adipose tissue

value: Epididymal white adipose tissue


title: nrFSL1

value: Sprague-Dawley

value: male

value: Flinders Sensitive Line (FSL)


title: P6 Cochlea GFP- 1

city: Houston

first: Andrew

last: Groves

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: mRNA enriched ds cDNA was sequenced paired end

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm9) using TopHat (v1.4.0) with default parameters except -G Ensembl GTF gene annotation.
Read counts for each gene were determined using htseq -count (python) function.
Reads were normalized across samples using DESeq Bioconductor package (v1.9.2).
Genome_build: mm9
Supplementary_files_format_and_content: Text files inclue read counts value for each gene; individual file for each sample.

source_name: Purified LFng-GFP- cells from P6 mouse cochlea

growth_protocol: Cochleas were freshly dissected, dissociated and sorted without culture

extract_protocol:
Total RNA was extracted using Trizol (Thermo Fisher Scientific) and PelletPaint (Novagen EMD Millipore). Briefly, samples were homogenized in 300µl of Trizol and shaken with 60µl chloroform and 2µl PelletPaint and centrifuged for 15 minutes. The supernatant containing RNA was precipitated with 1 volume of isopropanol, centrifuged for 30 minutes, washed in 75% ethanol, resuspended in 100µl water and re-precipitated with 10µl 3M sodium acetate and 250µl ethanol. After a final wash in 75% ethanol, the pellet was allowed to dry, resuspended in 20µl RNAse-free water and stored at -80°C.
cDNA libraries for RNAseq were generated using RNA Seq Truseq RNA sample preparation kit v2 (Illumina) following the “low sample” protocol according to the manufacturer's instructions for mRNA extraction, cDNA synthesis, indexing and amplification. cDNA generated from less than 20,000 cells received an initial amplification using the NuGen Ovation Kit.  The quality and integrity of RNA samples and the final quality of the sequencing libraries was checked by electrophenogram in an Agilent Bioanalyzer.
paired end 100bp sequencing

treatment_protocol: Cochleas were freshly dissected, dissociated and sorted without treatment

value: LFng-GFP BAC Transgenic Mouse (B6;FVB-Tg(Lfng-EGFP)HM340Gsat/Mmucd)

tag: tissue type

value: P6 cochlea


title: P6 Cochlea GFP- 2


title: FSL2

value: vehicle


title: P1 Cochlea GFP- 2

source_name: Purified LFng-GFP- cells from P1 mouse cochlea

value: P1 cochlea


title: P6 Cochlea GFP+ 2

source_name: Purified LFng-GFP+ cells from P6 mouse cochlea


title: P5 Cochlea DAPT GFP- 2

source_name: Purified LFng-GFP- cells from P5 mouse cochlea cultured for 24 hours in DAPT

growth_protocol: P0 and P5 cochleas were cultured in DMEM/F12 (buffered with Hepes; Thermo Fisher Scientific) supplemented with B27 (Thermo Fisher Scientific), 1mM N-acetylcysteine (Sigma), 5 ng/ml EGF and 2.5 ng/ml FGF2 and 67 µg/ml penicillin. For Notch inhibition experiments, cultures were treated with 10µM DAPT (Gamma secretase inhibitor IX, Calbiochem EMD) or 0.04% v/v DMSO (vehicle control; Thermo Fisher Scientific) for 24 hours

tag: agent

value: DAPT

value: P5  cochlea


title: P6 Cochlea GFP+ 1

tag: strain


title: P1 Cochlea GFP+ 1

source_name: Purified LFng-GFP+ cells from P1 mouse cochlea


title: P1 Cochlea GFP+ 2


title: P5 Cochlea DAPT GFP+ 2

source_name: Purified LFng-GFP+ cells from P5 mouse cochlea cultured for 24 hours in DAPT

treatment_protocol: For Notch inhibition experiments, cultures were treated with 10µM DAPT (Gamma secretase inhibitor IX, Calbiochem EMD) or 0.04% v/v DMSO (vehicle control; Thermo Fisher Scientific) for 24 hours


title: P5 Cochlea DAPT GFP+ 1


title: LNCaP DHT treated 3 h

value: LNCaP

value: 3 h


title: H3 ChIP-seq, Epididymal white adipose tissue


title: P0 Cochlea DAPT GFP- 2

source_name: Purified LFng-GFP- cells from P0 mouse cochlea cultured for 24 hours in DAPT

value: P0  cochlea


title: P5 Cochlea DAPT GFP- 1


title: P0 Cochlea DAPT GFP+ 2

source_name: Purified LFng-GFP+ cells from P0 mouse cochlea cultured for 24 hours in DAPT


title: P0 Cochlea DAPT GFP+ 1

source_name: Purified LFng-GFP+ cells from P0  mouse cochlea cultured for 24 hours in DAPT


title: P5 Cochlea DMSO GFP- 2

source_name: Purified LFng-GFP- cells from P5 mouse cochlea cultured for 24 hours in DMSO

value: DMSO


title: P5 Cochlea DMSO GFP- 1


title: P1 Cochlea GFP- 1


title: P0 Cochlea DMSO GFP+ 2

source_name: Purified LFng-GFP+ cells from P0 mouse cochlea cultured for 24 hours in DMSO


title: P0 Cochlea DMSO GFP- 1

source_name: Purified LFng-GFP- cells from P0 mouse cochlea cultured for 24 hours in DMSO


title: P5 Cochlea DMSO GFP+ 1

source_name: Purified LFng-GFP+ cells from P5 mouse cochlea cultured for 24 hours in DMSO


title: FSL1

source_name: ventral dentate gyrus


title: P5 Cochlea DMSO GFP+ 2


title: P0 Cochlea DMSO GFP+ 1


title: 1_cEedKO_6w_1

first: Martijn

last: Koppens

address: Plesmanlaan 121

department: Molecular Genetics

institute: NKI-AVL

data_processing:
The reads were sequenced using a stranded protocol and aligned against the mouse genome, build 38, using Tophat 2.0.12 with bowtie 0.12.9/1.1
The parameters used are --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count. Genes that have no expression across all samples are removed from the dataset.
Prior to analysis the provided processed data files were only normalized for sequencing depth, using the DESeq2 package, and normalized for batch effects (ex: sequencing run) if necessary using ComBat, as described in the paper.
Genome_build: Mus_musculus.GRCm38.dna.primary_assembly
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples; format: 2 tab-separated text files corresponding to the two sequencing runs, 385 and 440

source_name: cEedKO_6w_small intestinal crypts

extract_protocol:
RNA was harvested from samples using TRIzol and further purified using the Qiagen MinElute Cleanup Kit.
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc., San Diego, RS-122-2101/2) according to the manufacturer's instructions (Illumina, Part # 15031047 Rev. E).

treatment_protocol: After treating 6 weeks old mice with beta-naphthoflavone for 6 weeks, crypts were isolated from the small intestine by scraping off villi and EDTA chelation, after which they were washed. Crypts were then lysed in TRIzol.

tag: strain background

value: C57BL/6-FVB mixed

tag: genotype/variation

value: Eed-/-

tag: treated with

value: beta-naphthoflavone for 6 weeks

tag: tissue/cell type

value: small intestinal crypts

tag: run id

value: Run 385


title: FDC-P1 RUNX-ERt2_IgG_ChIPSeq

city: Hamburg

first: Kira

last: Behrens

address: Martinistrasse 52

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

data_processing:
Basecalls performed using  RTA 1.13.48.0 (for HiSeq2000) or RTA 1.17.20.0 (for HiSeq2500)
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.8 with the following configurations: --threads 6 --best --strata –m 1
peaks were called using MACS version 1.4.1 using default setting
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS14

source_name: FDC-P1 wt

growth_protocol: FDCP1 and FDCP1_RUNX1-ERt2 cells were cultured in DMEM 10%FCS + IL3

extract_protocol:
ChIP was performed using the EZ-ChIP Kit (Upstate/Millipore) on murine FDCP1 cells. After chromatin-crosslinking with 1% formaldehyde, cells were lysed and nuclei were isolated by centrifugation. Chromatin was extracted from the isolated nuclei and fragmented by sonication to an average length of 200–500 bp. Material from 1x10e7 cells was pre-cleared with protein-G agarose beads to reduce non-specific background. Chromatin immunoprecipitation was performed with either rabbit anti-Runx1 antibody, generated against a C-terminal peptide,2 or rabbit IgG (Abcam). Bound protein-DNA complexes were captured with Protein G Sepharose 4 Fast Flow (GE Healthcare) and chromatin eluted according to the manufacturer’s protocol.
Purified DNA from chromatin immunoprecipitations (10-50 ng) was adapter-ligated using the Illumina-compatible NEXTflexTM ChIP Seq-Kit (Bioo Scientific) for DNA inserts >70 bps. DNA fragments between 200-400 bp were isolated using PippinPrep (Sage Science) and quantified and sized on a microfluidics-based Bioanalyzer 2100 using a High Sensitivity DNA Kit (Agilent)

treatment_protocol: FDCP1_RUNX1-ERt2 were treated with 1 µM 4-OHT for 48h prior to assay

tag: infection

value: GFP

tag: chip antibody

value: Rabbit IgG (ab37415, Abcam)


title: 1_cEedKO_6w_2


title: 1_cWT_6w_2

source_name: cWT_6w_small intestinal crypts

value: WT


title: 1_oEedKO_10dBNF_2

treatment_protocol: Organoids were grown from either isolated AhCre or AhCre;Eedf/f crypts and treated with bNF for 10 days, after which the organoids were removed from Matrigel with ice-cold medium, washed, and lysed in TRIzol.

value: beta-naphthoflavone for 10 days

value: small intestinal organoids


title: P0 Cochlea DAPT GFP- 1

value: LFng-GFP BAC Transgenic Mouse (B6;FVB-Tg(Lfng-EGFP)HM340Gsat/Mmucd)


title: 1_cWT_6w_1


title: 1_oEedKO_10dBNF_1


title: ChIP-Seq WCE_new_Mecp2_KO

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

description: novel mechanism by which MeCP2 regulates gene expression by facilitating FoxO deacetylation by HDAC3.

data_processing:
ChIP-Seq data analysis: Sequencing reads were mapped to mouse genome assembly (mm9) using BWA aligner (samse option). Duplicate reads were removed by samtools. Bed alignment files were generated using bedtools. Peak calling was also performed using dfilter.
Genome_build: mm9
Supplementary_files_format_and_content: wig files (trace)

source_name: hippocampus

growth_protocol: Hippocampus was dissected at postnatal day 45

extract_protocol:
For ChIPseq, frozen tissue was fixed with 2mM disuccinimidyl glutarate in PBS for 35 min, 1 % formaldehyde for 10 min, and quenched with 125 mM glycine. Fixed homogenate was washed twice, douce-homogenized, and resuspend in Lysis Buffer (1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8.0, 0.5 % sarcosyl) and chromatin sheared using a BioruptorPlus (Diagenode Inc, NJ) set to high for 40 cycles of 30 sec on, 30 sec off. About 3 µg chromatin was precleared and ChIP was performed using 5 µg HDAC3 antibody (Abcam, ab7030) overnight, followed by enrichment using protein A sepharose beads for 4 hours. Beads were washed 4 times with RIPA buffer and once with TE, then eluted and reverse-cross linked in TE plus 1 % SDS at 65oC. Chromatin was subjected to RNase and proteinase K treatment, followed by DNA purification by phenol chloroform extraction and ethanol precipitation. DNA pellets were resuspended in 10 mM Tris.
ChIPseq libraries were prepared and sequenced as previously described (Gjorneska et al. Nature 2015).

treatment_protocol: Wildtype and Mecp2 KO mice obtained from The Jackson Laboratory (B6.129P2(C)-Mecp2tm1.1Bird/J)

tag: genotype

value: Mecp2 KO

tag: age

value: WCE


title: FDC-P1 RUNX-ERt2_Runx1_ChIPSeq

value: Runx1, rabbit (Aziz-Aloya R, 1998)


title: ChIP-Seq WCE_new_WT

value: Wildtype


title: ChIP-Seq HDAC3_new_WT

value: HDAC3 Abcam ab7030


title: ChIP-Seq HDAC3_new_Mecp2_KO