title: scTrioSeq2Met_CRC13_LN3_485

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_NC_442

status: Public on Nov 29 2018

type: SRA

city: Beijing

first: Yu

last: Hou

state: Beijing

address: No.5 Yiheyuan Street

department: School of life sciences

country: China

institute: Peking University

description: single cell DNA methylome seq

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
The raw sequencing reads were trimmed to remove sequencing adapters, amplification primers, and low-quality bases in read ends.
For the data from scRNA-seq performed according to Tang protocol (Tang et al., 2009), trimmed clean reads were aligned to human reference genome (hg19) using STAR (v2.5.0) 2-pass mapping steps. For the data from scRNA-seq performed according to the multiplexed scRNA-seq method, the analyses were done as the previous paper (Dong et al., 2018).
For bisulfite sequencing data, trimmed clean reads were mapped to human reference genome (hg19) using Bismark (v0.7.6)
Genome_build: hg19
Supplementary_files_format_and_content: The FPKM.txt files include the FPKM values of RefSeq genes. The TPM.txt files include the TPM values of RefSeq genes. The SingleC files include the DNA methylation level of each singleC sites.

molecule: genomic DNA

organism: Homo sapiens

source_name: CRC

growth_protocol: The HEp-2 (ATCC CCL-23) cell line were cultured in RPMI 1640 with 10% FBS, and digested with trypsin before single cell picking.

extract_protocol:
The single viable cells were individually picked into 200-uL tubes containing lysis buffer. For scTrio-seq2, we used magnetic beads (Invitrogen, cat. #65011) to separate the nucleus and RNA of one single cell. We added 0.2 ?L magnetic beads to each single-cell lysis buffer. Then the single cells were lysed and vortexed for 1 min to release RNA. The lysis products were then centrifuged at 1,000 × g for 5 min at 4°C, and placed on the magnetic rack for 5 min. The magnetic beads can aggregate on the surface of the nucleus to maintain the nucleus in the pellet, while the RNA was released in the supernatants. The supernatants containing RNA were transferred to a new tube for transcriptome sequencing. The remaining beads containing a single nucleus were re-suspended with lysis buffer of scBS-seq for DNA methylation sequencing
For single-cell whole-genome bisulfite sequencing, the scBS-seq libraries were constructed according to the published protocol as described in 2017 (Clark et al., 2017). For CRC01 and CRC02, the transcriptome sequencing libraries were constructed according to Tang protocol (Tang et al., 2009); for the remaining patients, the transcriptome sequencing libraries were constructed according to a multiplexed scRNA-seq method, in which the poly T primers were combined with barcodes and unique molecule identifiers (UMIs) (Dong et al., 2018).

treatment_protocol: Informed consent was obtained from all patients preoperatively. Multi-regional sampling tissues were collected. For each tumor, 3-6 regions, including both surface and center areas, were sampled. Except for the MP of CRC01 which was sampled after six cycles of chemotherapy, other tumors were all sampled before treatment. Patient-derived tumors and adjacent normal tissue were collected and processed immediately after surgical resection. The dissected tissues were then mechanically dissociated and enzymatically digested to single-cell suspension using collagenase type II (Invitrogen, cat. #17101015) and collagenase type IV (Invitrogen, cat. #17104019). For 5 patients (CRC11, CRC12, CRC13, CRC14, and CRC15), leukocytes were depleted by magnetic-activated cell sorting (MACS) (CD45 Microbeads, Miltenyi Biotec, cat. #130-045-801) or fluorescence-activated cell sorting (FACS) (BV421 Mouse Anti-Human CD45, BD Horizon, cat. #563879).

tag: disease

value: Carcinoma


title: scTrioSeq2Met_CRC13_LN3_488

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_487

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_NC_455

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_483

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_NC_451

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_480

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_482

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_479

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_503

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_478

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_475

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_471

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_472

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_508

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_473

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_470

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_468

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_396

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_465

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_467

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_474

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_393

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN3_466

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_395

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_381

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_384

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_377

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_378

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_383

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_379

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_374

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_373

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_371

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_375

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_372

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_370

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_369

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_367

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_360

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_368

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_359

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_362

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_394

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_361

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_356

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_355

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_357

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_354

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_353

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_376

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_351

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_350

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_422

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_424

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_420

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_416

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_414

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_421

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_415

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_411

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_413

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_358

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_419

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_409

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_410

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_408

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_406

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_405

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN2_352

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_404

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_407

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_402

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_748

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_747

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_742

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_418

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_741

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_740

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_737

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_412

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_739

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_735

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_732

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_733

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_731

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_728

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_734

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_726

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_727

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_403

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_724

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_723

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_721

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_719

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC13_LN1_401

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_720

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_746

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_725

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_718

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_717

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_711

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_710

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_707

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_708

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_713

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_706

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_715

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_714

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_705

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_701

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_703

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_796

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_702

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_722

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_795

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_794

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_704

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_730

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_793

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_792

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_791

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_790

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_789

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_786

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_788

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_785

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_787

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_712

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT4_716

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_782

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_778

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_776

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_773

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_774

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_765

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_761

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_762

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_768

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_760

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_767

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_781

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_758

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_779

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_764

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_759

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_755

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_754

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_756

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_771

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_753

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_751

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_750

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_528

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_525

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_749

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_775

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_780

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_508

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_506

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_783

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_504

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_495

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_494

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_486

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_488

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_485

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_481

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_537

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_536

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_475

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_541

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_471

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_540

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_472

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_534

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_533

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_467

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_469

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_466

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_463

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_470

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_464

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_465

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_468

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_460

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT2_480

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_459

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_461

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_542

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_457

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_456

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_455

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_453

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_458

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_452

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_451

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_450

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_449

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_446

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_445

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_444

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_442

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_440

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_441

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_439

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_443

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_438

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_435

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_434

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_433

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_437

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_432

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_431

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_429

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_430

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_428

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_427

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_421

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_423

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_422

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_447

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_419

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_418

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_417

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_416

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_415

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_413

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_412

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_414

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_407

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_409

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_408

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_410

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_406

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_405

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_404

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_402

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_396

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_395

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_393

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_391

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_390

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_420

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT1_425

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_387

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_388

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_NC_389

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_383

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_382

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_385

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_379

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_381

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_380

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_386

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_375

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_376

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_374

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_377

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_372

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_371

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_367

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_368

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_370

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_365

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_366

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_363

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_361

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_362

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_360

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_364

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_359

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_378

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_356

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_355

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_358

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_357

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_354

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_353

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_351

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_352

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_350

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_369

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_373

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_348

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_345

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_344

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_343

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_342

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_346

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_340

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_338

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_333

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_334

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_335

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_332

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_326

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_328

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_327

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_329

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_347

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_349

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_323

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_324

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_321

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_PT3_757

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_318

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_319

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_316

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_317

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_315

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_314

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_339

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_336

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_310

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_311

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_313

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_309

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_307

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_330

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_306

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_325

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_308

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_304

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT4_747

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_303

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_320

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT4_746

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT4_745

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT4_743

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT4_734

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_302

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT4_740

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC11_LN1_301

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_146

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT4_738

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_144

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_143

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT4_739

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_141

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT4_733

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_140

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_138

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_142

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_137

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_139

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_135

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_133

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_136

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_129

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_130

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_128

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_125

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_123

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_122

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_126

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_145

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_124

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_121

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_120

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_119

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_115

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_114

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_118

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_112

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_132

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_110

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_111

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_109

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_108

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT2_235

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_107

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_106

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT1_191

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT1_189

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_127

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT1_156

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT1_160

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT1_155

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT1_175

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT1_150

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT1_149

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_NC_206

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_NC_204

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_NC_202

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_113

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_080

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_NC_201

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_PT3_117

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_073

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_070

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_067

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_064

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_065

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_061

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_063

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_062

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_059

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_057

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_056

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_054

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_055

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_053

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_052

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_NC_205

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_051

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_049

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_050

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_047

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_048

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_046

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_042

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_044

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_041

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_066

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_037

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_035

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_033

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_060

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN3_058

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_031

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_032

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_028

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_026

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_025

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_024

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_023

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_021

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_019

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_043

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_016

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_038

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_017

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_039

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_012

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_022

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_014

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_011

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_015

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_018

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_029

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_007

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_008

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_004

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_005

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_013

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_006

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_731

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_730

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_020

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_729

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_728

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_725

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_724

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_721

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_717

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_714

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_003

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_712

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_709

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_722

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_702

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT4_517

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_701

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT4_531

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT4_515

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_720

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT4_526

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_726

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT4_516

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_563

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_564

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT4_509

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT3_742

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_711

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_562

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT3_755

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_703

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_561

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT5_716

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_559

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_NC_203

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_552

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_548

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_551

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_549

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_546

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_544

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_533

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_543

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_317

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_537

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_541

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_312

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_313

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_307

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_311

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_315

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT1_596

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_310

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_540

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_305

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_304

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_301

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_303

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_297

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC10_LN1_030

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN2_492

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_PT2_534

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN2_486

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN2_491

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN2_480

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN2_483

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN2_481

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN2_477

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN2_484

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_NC_306

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN2_465

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN2_469

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_403

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_402

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_377

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN2_476

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_381

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_401

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_364

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_358

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN2_468

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_363

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_380

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_361

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_378

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_360

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_362

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_357

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_356

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_355

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_354

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_353

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_351

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_349

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC04_LN1_352

description: single cell DNA methylome seq


title: OSUCLL_ATACseq

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

data_processing:
Alignment to hg19: (H3k27ac ChIP-seq) Bowtie2 v2.3.0, default settings with parameters -p 4 -k 1; (ATAC-seq) Bowtie2 v2.3.0, default settings with parameters -p 4 -k 1; (mRNA-seq) HiSat with default parameters
Peak calling: (H3K27ac ChIP-seq) MACS v1.4 with p value cutoff 1e-6; (ATAC-seq) ZINBA v2.03.1 with read extension=200 winSize=300 offset=75
mRNA transcript abundance: Cuffquant
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files contain aligned read density generated by Bowtie2; .xlsx file contains normalized transcript abundance values (FPKM)

source_name: OSU-CLL

growth_protocol: Cells were grown in RPMI media supplemented with 10% fetal bovine serum.

extract_protocol:
Transposed chromatin was column-purified following transposition of permeabilized cells.
Transposed DNA was amplified with Nextera-compatible primers as described in Buenrostro et al, Nature Methods 2013.

tag: cell type

value: CLL cell line


title: CII_input_ChIPseq

source_name: CII

extract_protocol:
Lysates were clarified from sonicated nuclei and samples taken before immunoprecipitation.
Immunoprecipitated genomic DNA was prepared for Illumina sequencing using the ThruPLEX DNA-seq kit (Rubicon Genomics).

tag: chip antibody


title: CII_H3K27ac_ChIPseq

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Immunoprecipitated genomic DNA was prepared for Illumina sequencing using the ThruPLEX DNA-seq kit (Rubicon Genomics).

value: H3K27ac abcam ab4729


title: MEC2_ATACseq


title: MEC1_ATACseq


title: MEC2_input_ChIPseq


title: MEC1_input_ChIPseq


title: OSUCLL_H3K27ac_ChIPseq


title: rps28b 4474-mRNA RPKM

city: Berkeley

first: Gloria

last: Brar

address: 626 Barker Hall

department: MCB

institute: UC Berkeley

description:
mRNA
rps28b 4474-mRNA from total RNA-seq
TotRNA-seq RPL RPS

library_source: transcriptomic

data_processing:
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint reads were assigned to one genomic position based on a-site analysis of fragment length distribution
Genome_build: sk1_revised_100331 (published in Brar et. al, Science, 2012)
Supplementary_files_format_and_content: txt matrix files of RPKM measurements using standard SGD genome annotations
Supplementary_files_format_and_content: TotRNA-seq RPL RPS: mRNA abundance measurements
Supplementary_files_format_and_content: Rib prof RPL RPS: fp abundance measurements

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Strains were grown in YEPD(2%) at 30C, with shaking.

extract_protocol:
For ribosome profiling, cells were flash frozen and mixermilled at -80 together with ribosome profiling lysis buffer, extract was clarified with a low and high speed spin, all as described in Ingolia et. al, Science, 2009. For mRNA, cells were flash frozen and lysed using hot acid phenol and SDS as described in Ingolia et al., Science, 2009
As described in Ingolia et al, Science 2009

treatment_protocol: Cells were harvested in exponential growth phase (OD600=0.6)

tag: strain


title: rps0b 4651-mRNA RPKM

description:
mRNA
rps0b 4651-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: OSUCLL_input_ChIPseq


title: MEC1_H3K27ac_ChIPseq


title: MEC2_H3K27ac_ChIPseq


title: rpl40a/+ rpl40b/+ 3654v-mRNA RPKM

description:
mRNA
rpl40a/+ rpl40b/+ 3654v-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: rpl26b 2374-mRNA RPKM

description:
mRNA
rpl26b 2374-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: rpl26a3851-mRNA RPKM

description:
mRNA
rpl26a3851-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: rpl41a 7467-mRNA RPKM

description:
mRNA
rpl41a 7467-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: scTrioSeq2Met_CRC04_LN1_350

description: single cell DNA methylome seq


title: rpl38 3853v-mRNA RPKM

description:
mRNA
rpl38 3853v-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: rps25a rps25b 7463-fp RPKM

description:
ribosome footprints
rps25a rps25b 7463- ribosome footprints
Rib prof RPL RPS


title: rps22a 4659-fp RPKM

description:
ribosome footprints
rps22a 4659- ribosome footprints
Rib prof RPL RPS


title: rps29b 4480v-fp RPKM

description:
ribosome footprints
rps29b 4480v- ribosome footprints
Rib prof RPL RPS


title: rps22a/+ rps22b/+ 4665-fp RPKM

description:
ribosome footprints
rps22a/+ rps22b/+ 4665- ribosome footprints
Rib prof RPL RPS


title: rps25b 4658v-fp RPKM

description:
ribosome footprints
rps25b 4658v- ribosome footprints
Rib prof RPL RPS


title: rps28a 4472v-fp RPKM

description:
ribosome footprints
rps28a 4472v- ribosome footprints
Rib prof RPL RPS


title: WT2 4484-2-fp RPKM

description:
ribosome footprints
WT2 4484-2- ribosome footprints
Rib prof RPL RPS


title: rps22a 4662v-fp RPKM

description:
ribosome footprints
rps22a 4662v- ribosome footprints
Rib prof RPL RPS


title: WT1 4484-1-fp RPKM

description:
ribosome footprints
WT1 4484-1- ribosome footprints
Rib prof RPL RPS


title: rpl24a 7469-fp RPKM

description:
ribosome footprints
rpl24a 7469- ribosome footprints
Rib prof RPL RPS


title: rpl40a 7889-fp RPKM

description:
ribosome footprints
rpl40a 7889- ribosome footprints
Rib prof RPL RPS


title: rpl24b 7465-fp RPKM

description:
ribosome footprints
rpl24b 7465- ribosome footprints
Rib prof RPL RPS


title: rpl26a rpl26b 5048-fp RPKM

description:
ribosome footprints
rpl26a rpl26b 5048- ribosome footprints
Rib prof RPL RPS


title: rpl26a/+ rpl26b/+ 4654v-fp RPKM

description:
ribosome footprints
rpl26a/+ rpl26b/+ 4654v- ribosome footprints
Rib prof RPL RPS


title: rpl7a 7962-fp RPKM

description:
ribosome footprints
rpl7a 7962- ribosome footprints
Rib prof RPL RPS


title: rpl7a/+ rpl7b/+  2435-fp RPKM

description:
ribosome footprints
rpl7a/+ rpl7b/+  2435- ribosome footprints
Rib prof RPL RPS


title: CII_ATACseq


title: rpl40b 2700-fp RPKM

description:
ribosome footprints
rpl40b 2700- ribosome footprints
Rib prof RPL RPS


title: scTrioSeq2Met_CRC04_LN2_485

description: single cell DNA methylome seq


title: Indolent Disease Rai 0/I UM CLL-29

type: RNA

city: Rochester

first: Renee

last: Tschumper

state: MN

address: 200 1st St SW

department: Immunology Research

institute: Mayo Clinic

hyb_protocol: Hybridization was done in an Agilent SureHyb Hybridization Chamber

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner

data_processing: Data was extracted using Agilent Feature Extraciton software. Raw signal intensities were normalized in quantile method by GeneSpring GX v12.1, and low intensity LncRNAs were filtered .LncRNAs that at least 12 out of 84 samples have flags in Present or Marginal were chosen for further analysis.

source_name: CLL Sample

label_protocol: Arraystar Flash FNA labeling kit was used for sample labeling

growth_protocol: Freshly isolated cells and RNA

extract_protocol: Total RNA was isolated by the Trizol method following manufacturers protocols

tag: tissue

value: PBMCs

tag: collection time frame

value: within 2 months of diagnosis

tag: time to first treatment

value: TTT 5 years or more  after diagnosis (ID)


title: Indolent Disease Rai 0/I UM CLL-25


title: Indolent Disease Rai 0/I UM CLL-18


title: Indolent Disease Rai 0/I UM CLL-21


title: Indolent Disease Rai 0/I UM CLL-22


title: Indolent Disease Rai 0/I UM CLL-23


title: Indolent Disease Rai 0/I UM CLL-26


title: Indolent Disease Rai 0/I UM CLL-15


title: Indolent Disease Rai 0/I UM CLL-24


title: Indolent Disease Rai 0/I UM CLL-28


title: Indolent Disease Rai 0/I UM CLL-14


title: Indolent Disease Rai 0/I UM CLL-20


title: Indolent Disease Rai 0/I UM CLL-13


title: Indolent Disease Rai 0/I UM CLL-10


title: Indolent Disease Rai 0/I UM CLL-16


title: Indolent Disease Rai 0/I UM CLL-12


title: Indolent Disease Rai 0/I UM CLL-27


title: Indolent Disease Rai 0/I UM CLL-11


title: Indolent Disease Rai 0/I UM CLL-9


title: Indolent Disease Rai 0/I UM CLL-17


title: Indolent Disease Rai 0/I UM CLL-19


title: Indolent Disease Rai 0/I UM CLL-8


title: Indolent Disease Rai 0/I UM CLL-3


title: Indolent Disease Rai 0/I UM CLL-6


title: Indolent Disease Rai 0/I UM CLL-4


title: Indolent Disease Rai 0/I UM CLL-1


title: Indolent Disease Rai 0/I UM CLL-5


title: Indolent Disease Rai 0/I UM CLL-7


title: Progressive Disease Rai 0/I UM CLL-34

value: TTT less than 2 years after diagnosis (PD)


title: Progressive Disease Rai 0/I UM CLL-30


title: Progressive Disease Rai 0/I UM CLL-31


title: Progressive Disease Rai 0/I UM CLL-28


title: Progressive Disease Rai 0/I UM CLL-27


title: Progressive Disease Rai 0/I UM CLL-25


title: Progressive Disease Rai 0/I UM CLL-32


title: Progressive Disease Rai 0/I UM CLL-29


title: Progressive Disease Rai 0/I UM CLL-23


title: Progressive Disease Rai 0/I UM CLL-24


title: Progressive Disease Rai 0/I UM CLL-21


title: Progressive Disease Rai 0/I UM CLL-22


title: Progressive Disease Rai 0/I UM CLL-26


title: scTrioSeq2Met_CRC10_LN1_010

description: single cell DNA methylome seq


title: Progressive Disease Rai 0/I UM CLL-33


title: Progressive Disease Rai 0/I UM CLL-20


title: Progressive Disease Rai 0/I UM CLL-19


title: Progressive Disease Rai 0/I UM CLL-17


title: Progressive Disease Rai 0/I UM CLL-18


title: genomic DNA from melanoma [10]

type: genomic

city: Kobe

first: Susumu

last: Fujiwara

state: Hyogo

address: 7-5-1, Kusunoki-cho, Chuo-ku

department: dermatology

country: Japan

institute: Kobe univ

description: SAMPLE 10

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software

label: Cy5 and Cy3

source_name: melanoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using Qiagen AllPrep DNA/RNA Micro Kit according to standard instructions

tag: source lesion

value: shoulder

value: melanoma

tag: disease state

value: malignant

tag: name of article


title: genomic DNA from melanoma [15]

description: SAMPLE 15

source_name: melanocyte

value: vagina


title: Progressive Disease Rai 0/I UM CLL-16


title: Progressive Disease Rai 0/I UM CLL-15


title: Progressive Disease Rai 0/I UM CLL-12


title: Progressive Disease Rai 0/I UM CLL-14


title: genomic DNA from melanocyte [16]

description: SAMPLE 16

label: Cy5 and Cy4

value: abdominal skin

value: melanocyte

value: normal


title: genomic DNA from melanoma [9]

description: SAMPLE 9

value: cell line G361


title: Progressive Disease Rai 0/I UM CLL-13


title: genomic DNA from melanoma [18]

description: SAMPLE 18

value: inguinal LN


title: Progressive Disease Rai 0/I UM CLL-10


title: genomic DNA from melanoma[17]

description: SAMPLE 17

label: Cy5 and Cy5

value: lower leg


title: Progressive Disease Rai 0/I UM CLL-9


title: Indolent Disease Rai 0/I UM CLL-2


title: genomic DNA from melanocyte [11]

description: SAMPLE 11


title: IA34

status: Public on Nov 26 2018

city: Utrecht

first: Ynte

last: Ruigrok

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

data_processing:
Mapping with STAR 2.3.1, allowing for two mismatches.
SAMtools 0.1.185 was used to sort the aligned reads.
Gene level quantification was performed with HTSeq-0.5.4 using -- mode=union -- stranded=no, using Ensembl version 71 as gene annotation database
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: raw counts txt files containing readcounts were generated using HTSeq-0.5.4 and Ensembl version 71 on RNA-seq data

molecule: polyA RNA

source_name: Unruptured intracranial aneurysm

extract_protocol:
Frozen in liquid nitrogen, RNA extraction.
Illumina TruSeq DNA library protocol.

tag: Sex

value: Female

tag: age

tag: aneurysm location

value: ICA

tag: tissue/status

value: Unruptured intracranial aneurysm


title: genomic DNA from melanoma [13]

description: SAMPLE 13

value: cheek


title: Progressive Disease Rai 0/I UM CLL-11

value: PBMCs

value: within 2 months of diagnosis


title: genomic DNA from melanoma [19]

description: SAMPLE 19

value: cell line HM2KO


title: T0-LPS_3

status: Public on Nov 17 2018

city: New York

first: David

middle: G

last: Thomas

state: NY

department: Medicine

institute: Columbia University

data_processing:
Nextseq 500 lanes were merged using gunzip/cat
Adaptor contamination was removed using cutadapt
Reads were aligned to mouse genome mm10 using Bowtie2
PCR duplicates were removed using samtools rmdup
Quadruplicate samples for each condition were used for peak calling by MACS2 (Zhang et al. 2008) with the parameters –q 0.001 –nomodel –shift 88 –extsize 177 to set an FDR threshold of 0.1% and account for average insert size
To limit ATAC peak identification to transposase-accessible enhancers and exclude other accessible loci, ATAC peaks were filtered according to correspondence with H3K27ac- or H3K4me2-marked macrophage enhancers in resting or stimulated primary macrophages identified by Oishi et al (Oishi et al. 2017)
Enhancer overlap, overlap between conditions, and nearest gene annotation were performed using bedtools (Quinlan and Hall 2010)
Genome_build: mm10
Supplementary_files_format_and_content: bed file with peaks called in each condition

organism: Mus musculus

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow cells were differentiated into macrophages by culture in DMEM 10% FBS, 1% pen-strep supplemented with 20% L-cell conditioned medium. After 7 days, macrophages were fully differentiated and subjected to a one-day serum deprivation in DMEM, 1% pen-strep supplemented with 4% L-cell conditioned medium to normalize exposure to serum-derived lipoproteins.

extract_protocol:
Samples were prepared for ATAC-Seq essentially as described in Buenrostro et al., 2013. Macrophages were washed twice in cold PBS, scraped in cold PBS, and counted using a hemocytometer. Based on this count, 50,000 cells were aliquoted and pelleted by centrifugation. Cell pellets were washed once with 50 uL cold PBS on ice before lysis in 50 uL hypotonic lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) over the course of a 10 minute spin at 4°C.
Pelleted nuclei were resuspended in 50 uL transposition reaction mix with 3 uL Nextera transposase per sample (Illumina). The reaction was stopped with 0.1% SDS and transposase-accessible DNA was isolated using AMPure XP beads (Beckman-Coulter). Accessible DNA was amplified by PCR for 5 cycles, assessed for yield by qPCR as described (Buenrostro et al. 2013) and amplified for an additional 7 cycles.

treatment_protocol: On day 8, macrophages were treated with LXR agonist T0901317 (Selleckchem) or GW3965 (Selleckchem) at a concentration of 500 nM or DMSO vehicle alone at a 1:10,000 dilution in serum-free medium with 4% L-cell conditioned medium for 3 hours. After this treatment period, macrophages were harvested directly for unstimulated chromatin assays or stimulated with 10 ng/mL LPS (Cell Signaling) added directly to agonist-containing medium for 2 hours before sample collection.

value: Bone marrow-derived macrophages

tag: treatment


title: genomic DNA from melanocyte [12]

description: SAMPLE 12

value: shoulder


title: T0-LPS_4


title: Progressive Disease Rai 0/I UM CLL-6

value: TTT less than 2 years after diagnosis (PD)


title: T0-LPS_2


title: Progressive Disease Rai 0/I UM CLL-5


title: Progressive Disease Rai 0/I UM CLL-1


title: Progressive Disease Rai 0/I UM CLL-7


title: Progressive Disease Rai 0/I UM CLL-4


title: Progressive Disease Rai 0/I UM CLL-2


title: genomic DNA from melanoma [8]

description: SAMPLE 8

value: cell line SK-mel-28

value: melanoma

value: malignant


title: LPS_4

value: DMSO+LPS


title: LPS_3


title: genomic DNA from melanoma [4]

description: SAMPLE 4

value: sole


title: Progressive Disease Rai 0/I UM CLL-3


title: genomic DNA from melanocyte [7]

description: SAMPLE 7

value: unknown

value: melanocyte

value: normal


title: LPS_1


title: genomic DNA from melanocyte [6]

description: SAMPLE 6


title: T0_2


title: Progressive Disease Rai 0/I UM CLL-8


title: Veh_3

value: DMSO


title: genomic DNA from melanocyte [3]

description: SAMPLE 3

value: abdominal skin


title: genomic DNA from melanocyte [5]

description: SAMPLE 5


title: genomic DNA from melanoma [14]

description: SAMPLE 14

value: cell line DEOC-1


title: LPS_2


title: Veh_2


title: T0_4


title: T0_1


title: Veh_1 [RNA-Seq]

data_processing:
Nextseq 500 lanes were merged using gunzip/cat
Adaptor contamination was removed using cutadapt
Reads were aligned to mouse genome mm10 using HISAT2
Feature assignment was performed using Subread-featureCounts
Statistical comparison of read counts was performed using DESeq2
Differentially expressed gene lists were prepared by filtering for q<0.1 (10% FDR)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with counts for each gene; comma-delimited text file with differentially expressed gene lists

extract_protocol:
For RNA-Seq, macrophages were washed twice with cold PBS and lysed in TRIzol reagent (Thermo). RNA was isolated from the aqueous phase using RNeasy kits (Qiagen).
RNA with RIN > 8 was subjected to poly-dT pulldown using magnetic beads (NEB) before preparation for RNA-Seq using RNA Ultra kits (NEB).


title: T0-LPS_2 [RNA-Seq]


title: Veh_3 [RNA-Seq]


title: LPS_2 [RNA-Seq]

description:
Veh_LPS_FDR10.csv
LPS_T0.LPS_FDR10.csv


title: T0-LPS_3 [RNA-Seq]


title: Veh_2 [RNA-Seq]


title: T0-LPS_1 [RNA-Seq]


title: LPS_3 [RNA-Seq]

description:
Veh_LPS_FDR10.csv
LPS_T0.LPS_FDR10.csv


title: RPE FANCD2 LOW HU REP2

status: Public on Nov 01 2018

first: Duncan

last: Smith

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

data_processing:
Library strategy: Replication mapping.
SE fastq files were aligned to the hg19 genome with bowtie2.  samtools was used to convert from sam to bam file and keep only reads with > 30 MAPQ score.  PCR duplicates were removed with the Picard MarkDuplicates command.  Resulting bam file was converted to bedGraph file reporting genome coverage for W and C strands, e.g. “genomeCoverageBed -ibam infile.bam -bg -strand + > outfile_W.bedGraph”.  A custom python script was then used to average W/C totals over each 1kb region for chroms 1-22.  TSS and TTS locations were obtained from the UCSC genome browser.  Gene lists were filtered to include only chr1-22 and protein coding (RefSeq ID starts with NM), and duplicates were dropped based on gene symbol, keeping only the first version of the gene listed (in the case of multiple annotated TSS/TTS sites for a gene).
Supplementary_files_format_and_content: txt files representing the density of Okazaki fragment 5' ends on the Watson or Crick strand across the genome (1kb bins); csv files representing the density of Okazaki fragment 5' ends around the initiation and termination sites of annotated genes

source_name: hTERT immortalized RPE-1 cells

growth_protocol: RPE-1 cells were grown and prepared as stated in Chen et al., Mol Cell, 2015; DOI: 10.1016/j.molcel.2015.02.031

extract_protocol:
RPE-1 cells were pulsed with EdU (20 mM) for 2 min in untreated condition or 4 min in HU-treated samples and Okazaki fragments were isolated according to the protocol of Petryk et al., Nature Communications, 7, 10208; DOI: 10.1038/ncomms10208
Libraries were prepared and sequenced essentially following the protocol of Petryk et al., Nature Communications, 7, 10208; DOI: 10.1038/ncomms10208; Purified Okazaki fragments were ligated directly to double-stranded adaptors with polar single-stranded overhangs, amplified by PCR, and sequenced

treatment_protocol: RPE-1 cells were treated with low dose HU (0.2 mM)  as stated in Chen et al., Mol Cell, 2015; DOI: 10.1016/j.molcel.2015.02.031

tag: cell line

tag: sirna

value: FANCD2 siRNA


title: RPE FANCD2 LOW HU REP1


title: RPE FANCI LOW HU REP1

value: FANCI siRNA


title: Veh_1


title: RPE FANCI LOW HU REP2


title: RPE CONTROL LOW HU REP2

value: control siRNA


title: RPE CONTROL REP2

data_processing:
Library strategy: Replication mapping.
SE fastq files were aligned to the hg19 genome with bowtie2.  samtools was used to convert from sam to bam file and keep only reads with > 30 MAPQ score.  PCR duplicates were removed with the Picard MarkDuplicates command.  Resulting bam file was converted to bedGraph file reporting genome coverage for W and C strands, e.g. “genomeCoverageBed -ibam infile.bam -bg -strand + > outfile_W.bedGraph”.  A custom python script was then used to average W/C totals over each 1kb region for chroms 1-22.  TSS and TTS locations were obtained from the UCSC genome browser.  Gene lists were filtered to include only chr1-22 and protein coding (RefSeq ID starts with NM), and duplicates were dropped based on gene symbol, keeping only the first version of the gene listed (in the case of multiple annotated TSS/TTS sites for a gene).
Supplementary_files_format_and_content: txt files representing the density of Okazaki fragment 5' ends on the Watson or Crick strand across the genome (1kb bins); csv files representing the density of Okazaki fragment 5' ends around the initiation and termination sites of annotated genes.


title: RPE CONTROL REP1

data_processing:
Library strategy: Replication mapping.
SE fastq files were aligned to the hg19 genome with bowtie2.  samtools was used to convert from sam to bam file and keep only reads with > 30 MAPQ score.  PCR duplicates were removed with the Picard MarkDuplicates command.  Resulting bam file was converted to bedGraph file reporting genome coverage for W and C strands, e.g. “genomeCoverageBed -ibam infile.bam -bg -strand + > outfile_W.bedGraph”.  A custom python script was then used to average W/C totals over each 1kb region for chroms 1-22.
TSS and TTS locations were obtained from the UCSC genome browser.  Gene lists were filtered to include only chr1-22 and protein coding (RefSeq ID starts with NM), and duplicates were dropped based on gene symbol, keeping only the first version of the gene listed (in the case of multiple annotated TSS/TTS sites for a gene).
Supplementary_files_format_and_content: txt files representing the density of Okazaki fragment 5' ends on the Watson or Crick strand across the genome (1kb bins); csv files representing the density of Okazaki fragment 5' ends around the initiation and termination sites of annotated genes.


title: Veh_4

value: Bone marrow-derived macrophages


title: genomic DNA from melanoma [2]

description: SAMPLE 2

value: cheek


title: LPS_1 [RNA-Seq]

description:
Veh_LPS_FDR10.csv
LPS_T0.LPS_FDR10.csv


title: VISp_Vipr2-IRES2-Cre/wt;Pvalb-T2A-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1

status: Public on Oct 31 2018

city: Seattle

first: Allen

last: Institute

state: WA

address: 615 Westlake Ave N

institute: The Allen Institute for Brain Science

description:
processed data file:
cells_exon_counts.csv.gz
cells_intron_counts.csv.gz

data_processing:
50-base pair paired-end reads were aligned to GRCm38 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 01/18/2016 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/). Sequence alignment was performed using STAR v2.5.3 (Dobin et al., 2013) in twopassMode. PCR duplicates were masked and removed using STAR option “bamRemoveDuplicates”. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) sumarizeOverlaps function using “IntersectionNotEmpty”.
Cells with fewer than 2,000 detected genes (count > 0) and less than 30% of reads mapped to the transcriptome were removed. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. For each class, we selected highly specific genes that are only present in this class against all other classes, and computed the eigengene (the first principle component based on the given gene set). Eigengenes for all classes were normalized in the range of 0 and 1, and we removed any cells that scored > 0.2 in more than one class.
We mapped all non-genome-mapped reads to sequences in Extended Data Table 6 (Tasic et al., 2018). To avoid ambiguous counting due to stretches of sequence identity, we designated unique regions within these sequences to count mRNAs of interest. We counted only reads for which at least one of the paired ends had an overlap with the unique regions of at least 10 bp.
Genome_build: mm10
Supplementary_files_format_and_content:
cells_*_counts.csv.gz: matrix file of exon or intron counts of non-control samples
controls_*_counts.csv.gz: matrix file of exon or intron counts of control samples

growth_protocol: All procedures were carried out in accordance with Institutional Animal Care and Use Committee protocols 1508, 1510, and 1511 at the Allen Institute for Brain Science. Animals were provided food and water ad libitum and were maintained on a regular 12-h day/night cycle at no more than five adult animals per cage. Animals were maintained on the C57BL/6J background, and newly received or generated transgenic lines were backcrossed to C57BL/6J. Experimental animals were heterozygous for the recombinase transgenes and the reporter transgenes. Standard tamoxifen treatment for CreER lines included a single dose of tamoxifen (40 μl of 50 mg ml−1) dissolved in corn oil and administered via oral gavage at postnatal day (P)10–14. Tamoxifen treatment for Nkx2.1-CreERT2;Ai14 was performed at embryonic day (E)17 (oral gavage of the dam at 1 mg per 10 g of body weight), pups were delivered by cesarean section at E19 and then fostered. Cux2-CreERT2;Ai14 mice received tamoxifen treatment at P35 ± 5 for five consecutive days. Trimethoprim was administered to animals containing Ctgf-2A-dgCre by oral gavage at P40 ± 5 for three consecutive days (0.015 ml per g of body weight using 20 mg ml−1 trimethoprim solution). Ndnf-IRES2-dgCre animals did not receive trimethoprim induction, since the baseline dgCre activity (without trimethoprim) was sufficient to label the cells with the Ai14 reporter (Tasic et al., 2016). We excluded any animals with anophthalmia or microphthalmia.

extract_protocol:
We isolated single cells as previously described (Hempel et al., 2007; Sugino et al., 2006; Tasic et al., 2016) with modifications. We mostly employed layer-enriching dissections, with focus on a single layer. Broader dissections (no layer enrichment or multiple layers combined) were employed for lines which label small numbers of cells, in order to facilitate isolation of sufficient number of cells. We updated our ACSF formulation to consist of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), thiourea (2 mM), and bubbled with carbogen gas (95% O2 and 5% CO2). For samples collected after 12/16/2016, the ACSF formulation also included trehalose (13.2 mM). Mice were anesthetized with isoflurane and perfused with cold carbogen-bubbled ACSF. The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-µm coronal sections on a compresstome (Precisionary). Enzymatic digestion, trituration into single cell suspension, and fluorescence-activated cell sorting (FACS) of single cells were carried out as previously described (Tasic et al., 2016). Cells were sorted into 8-well strips containing lysis buffer from SMART-Seq v4 kit with RNase inhibitor (0.17 U/µl), immediately frozen on dry ice, and stored at -80°C.
We used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat#634894) to reverse transcribe poly(A) RNA and amplify cDNA according to the manufacturer’s instructions. We performed reverse transcription and cDNA amplification for 18 PCR cycles in 8-well strips, in sets of 12-24 strips at a time. At least 1 control strip was used per amplification set, which contained 4 wells without cells and 4 wells with 10 pg control RNA. Control RNA was either Mouse Whole Brain Total RNA (Zyagen, MR-201) or control RNA provided in the SMART-Seq v4 kit. All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT DNA Library prep was performed according to manufactorer’s instructions except that the volumes of all reagents including cDNA input were decreased to 0.4× or 0.5× by volume. Details are available in Documentation on the Allen Institute data portal at: http://celltypes.brain-map.org/.

treatment_protocol: For retrogradely-labeled samples, we injected AAV2-retro-EF1a-Cre (Tervo et al., 2016), SADB-rabies-dGdL-Cre, or CAV-Cre (gift of Miguel Chillon Rodrigues, Universitat Autònoma de Barcelona) (Hnasko et al., 2006) into brains of heterozygous or homozygous Ai14 mice as previously described (Tasic et al., 2016). For ALM experiments, we also injected AAV2-retro-CAG-GFP or AAV2-retro-CAG-tdTomato (Tervo et al., 2016) into wild-type mice. For two VISp experiments, we injected into SCs by inserting the needle through the cerebellum at a 45°-angle in the posterior to anterior direction. TdT+ or GFP+ single cells were isolated from VISp or ALM, depending on the injection area.

value: No Injection

value: Primary Visual Cortex (VISp)


title: VISp_Vip-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: T0-LPS_1


title: VISp_Sst-IRES-Cre/wt;Pvalb-T2A-Dre/wt;Ai66(RCRL-tdT)/wt_No Injection_1


title: RPE CONTROL LOW HU REP1


title: VISp_Trib2-F2A-CreERT2/wt;Snap25-LSL-F2A-GFP/wt_No Injection_1


title: genomic DNA from melanocyte [1]

description: SAMPLE 1


title: VISp_Sst-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Slc32a1-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_3


title: VISp_Slc17a8-IRES2-Cre/wt;Slc32a1-IRES2-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1


title: VISp_Rorb-IRES2-FlpO/wt;Ai65F/wt_No Injection_1


title: VISp_Slc17a8-iCre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Snap25-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_6


title: VISp_Slc17a7-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_3


title: VISp_Snap25-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_5


title: VISp_Slc32a1-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_2


title: VISp_Pvalb-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_2


title: VISp_Nr5a1-Cre/wt;Ai11(RCL-FnGF-nT)/wt_No Injection_1


title: VISp_Nos1-CreERT2/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Nkx2-1-CreERT2/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Nr5a1-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Scnn1a-Tg3-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Slc17a6-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Rbp4-Cre_KL1/wt;Ai14(RCL-tdT)/wt_No Injection_2


title: VISp_Gad2-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_2


title: VISp_Chrna2-Cre_OE25/wt;Pvalb-T2A-Dre/wt;Ai66(RCRL-tdT)/wt_No Injection_1


title: VISp_Chrna2-Cre_OE25/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Gad2-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Ai14(RCL-tdT)/wt_Retrograde_2

value: Retrograde


title: VISp_Ai14(RCL-tdT)/Ai14(RCL-tdT)_Retrograde_1


title: VISp_Ai110(RCL-FnGF-nT)/wt_Retrograde_1


title: Control: 10pg Takara Control Total RNA_1

description:
processed data file:
controls_exon_counts.csv.gz
controls_intron_counts.csv.gz

source_name: Control: 10pg Takara Control Total RNA

tag: sample type

value: Control:10pg Takara Control Total RNA


title: VISp_Slc17a7-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_2


title: VISp_Sim1-Cre_KJ18/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Snap25-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_2


title: VISp_Snap25-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_3


title: Placebo Week12 [30_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]

status: Public on Oct 06 2018

first: Ana

last: Pavel

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

description:
Gene expression data from skin biopsy
Gene expression data from skin biopsy

hyb_protocol: Affymetrix Human U133Plus 2.0 gene arrays were used. Total RNA (50 ng) was reverse transcribed and amplified with Ovation Whole Blood Solution from NuGen (San Carlos, CA). The labeled target was fragmented and hybridized to probe gene arrays, using Encore Biotin Module from NuGen (San Carlos, CA). The chips were washed, stained with streptavidin-phycoerythrin, and scanned (HP GeneArray Scanner; Hewlett-Packard Company, Palo Alto, CA). On each chip, the human housekeeping genes β-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) served as controls. Suite 5.0 software normalized the expression level values using these controls.

scan_protocol: Hewlett-Packard GeneArray Scanner G2500A

data_processing: Expression values were obtained using the GCRMA algorithm. Batch effects were removed using ComBat from sva R package.

label: biotin

source_name: Skin biopsy

label_protocol: Ovation WB Reagent (Nugen)

extract_protocol: Skin biopsies from lesional and non-lesional skin at baseline, and week 12 were stored in RNAlater® (Invitrogen) until further processing. RNA was extracted (Covance Genomics Lab).

value: lesional skin

tag: week

value: Placebo

tag: patient id


title: Normal2 [N8_HG U133 plus2_Hui_20160126_(HG-U133_Plus_2)]

value: Normal


title: Placebo Week0 [55_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: APRMST-40 Week0 [41_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]

value: non-lesional skin


title: Placebo Week12 [57_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: APRMST-30 Week0 [49_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: APRMST-30 Week12 [51_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: Placebo Week0 [56_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: APRMST-30 Week12 [48_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: APRMST-30 Week0 [46_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: APRMST-30 Week0 [50_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: Normal1 [N5_HG U133 plus2_Hui_20160126_(HG-U133_Plus_2)]


title: Placebo Week0 [28_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: APRMST-30 Week0 [47_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: Placebo Week12 [60_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: Placebo Week0 [59_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: Placebo Week0 [29_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: Placebo Week0 [58_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: APRMST-40 Week0 [40_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: VISp_Ai14(RCL-tdT)/wt_Retrograde_1


title: APRMST-30 Week12 [36_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)_2]


title: APRMST-30 Week0 [34_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: VISp_Pvalb-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Rbp4-Cre_KL1/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: Placebo Week12 [27-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: APRMST-40 Week0 [23-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: APRMST-40 Week12 [24-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: APRMST-30 Week0 [35_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: Placebo Week0 [19-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: APRMST-40 Week0 [17_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: APRMST-40 Week0 [22-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: APRMST-40 Week12 [18_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: Placebo Week0 [25-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: APRMST-40 Week0 [16_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: APRMST-40 Week12 [3-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: Placebo Week0 [26-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: APRMST-40 Week0 [1-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: Placebo Week0 [20-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: APRMST-40 Week0 [2-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: VISp_Snap25-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_4


title: T0_3

tag: cell type

tag: strain


title: Placebo Week0 [7-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]

tag: tissue


title: APRMST-30 Week12 [54_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: Placebo Week0 [8-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: Placebo Week12 [21-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: Cheese 5C

status: Public on Sep 11 2018

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Library strategy: DNA-seq
Barcodes from the raw data were identified and counted with MultiCodes.pl. The barcodes were correlated with their insertion sites using CombineBarSeq.pl. Both scripts are from Wetmore et al. 2015. DOI: 10.1128/mBio.00306-15
The 20 bp-barcode sequence is located beginning at nucleotide 36.
Genome_build: GenBank accession CP001340
Supplementary_files_format_and_content: Processed data shows the genome position, barcode sequence and number of hits for each insertion across all 30 fitness experiments.

organism: Caulobacter vibrioides

source_name: whole bacterial cells

growth_protocol: Barcoded transposon library caulo_47 (Hentchel et al. 2018; DOI: 10.1038/s41396-018-0295-6) was passaged in 12-well plates containing 1.5mL PYE and a sterile plug of cheesecloth.

extract_protocol:
Whole cells were used directly in PCR reaction described below
Adaptors were added directly by PCR amplifying the barcode region from the transposons according to Wetmore et al. 2015.; DOI: 10.1128/mBio.00306-15.

treatment_protocol: After 24 hours the spent medium was used to inoculate a fresh culture with a fresh piece of cheesecloth. Passaging was continued for a total of 5 passages.

tag: growth medium

value: PYE with cheesecloth plug

tag: passage


title: APRMST-40 Week0 [44_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: APRMST-30 Week0 [53_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: APRMST-40 Week0 [13_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: APRMST-40 Week12 [45_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: APRMST-40 Week0 [4_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: APRMST-40 Week0 [14_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: APRMST-40 Week12 [15_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: S2_BlueLight_rep2

status: Public on Sep 05 2018

first: Balazs

last: Balint

state: Csongrad

address: Vallalkozok street

country: Hungary

institute: Seqomics Ltd

data_processing:
CLC Bio, version: 9.5.4 was used for read trimming (Error probability threshold of 0.05, up to 2 ambiguois nucleotides per read were allowed).
Reads shorter than 36 nucleotides were removed.
CLC Bio, version: 9.5.4 was used for read mapping (read length fraction: 0.8, sequence identity fraction: 0.8, repeat reads were randomly mapped).
command “makeTagDirectory” from ChIP-Seq analysis package “Homer” V4.9 was used to create tag directory for each pulled sample as well as for the mock.
script “findPeaks” with parameter “-style factor” was executed from ChIP-Seq analysis package “Homer” V4.9 to find peaks.
Genome_build: Arabidopsis thaliana genome version TAIR10
Supplementary_files_format_and_content: Tab-separated text peak file from Homer.

organism: Arabidopsis thaliana

source_name: whole plant

growth_protocol: Surface sterilized seeds were sown on solidified Murashige and Skoog (MS) media supplemented with 0.5 % (w/v) sucrose.   White light during growth/entrainment was provided by LUMILUX XT T8 L 36 W/865 (Osram) fluorescent tubes at 70-100 μmol m−2 s−1 fluence rate,   whereas during free-run TUNSGRAM 15W F33-640 cool white tubes (General Electric) were operated at 15 μmol m−2 s−1 fluence rate.

extract_protocol:
Ten-day-old plants were fixed in 1 % (v/v) formaldehyde solution. Chromatin samples were sonicated on ice six times for 10 s using a   Vibra Cell sonicator (SONICS & MATERIALS Inc.,  Danbury, CT, USA)  at 10% power. Sonicated and diluted chromatin samples were pre-cleared by   20 µl (bed volume) of binding control agarose beads (Chromotek GmbH, Germany) for 1 h at 4oC. An aliquote of the pre-cleared chromatin solution   was saved for the input sample and the rest of the material was precipitated using 12.5 µl (bed volume) of GFP-Trap agarose beads (Chromotek GmbH, Germany)   for 16 h at 4oC. Precipitated chromatin was eluted from the beads, and along with the input sample, it was de-crosslinked and DNA was extracted using the NucleoSpin®   Gel and PCR Clean-up kit (Macherey-Nagel, 740609) with Buffer NTB (Macherey-Nagel, 740595). The mock sample was produced from the mix of the BL-treated triplicates by executing the same steps as above, but instead of GFP-Trap agarose beads, control agarose beads (i.e. without the immobilized anti-GFP antibody) were used for precipitation.
Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) along with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2, New England BioLabs) according to the manufacturer’s protocol, except the following modifications:   1) since the amount of input DNA was less than 5ng, we used a 25-fold adaptor dilution for adaptor ligation;   2) adaptor-ligated DNA was cleaned up using AmPureXP Beads (Backman Coulter) without size selection;   3) PCR amplification was performed with 16 PCR cycles.   Final libraries were quality checked using D1000 ScreenTape and Reagents on TapeStation 2200 (all from Agilent);   quantification was performed using Qubit dsDNA BR Assay kit (Thermo Fischer Scientific).

treatment_protocol: Plants entrained to 12:12 Light-Dark cycles were transferred to either blue (BL samples) or red light (RL samples) at 15 µmol m-2 s-1 fluence rate for 52 hours   before chromatin immunoprecipitation.

tag: ecotype

value: Wassilevskija (Ws) accession

value: whole plant

tag: hy5-ks50 status

value: T-DNA tagged insertion mutant

tag: hy5-yfp status

value: HY5-YFP fusion protein expressor

tag: light treatment

value: blue light treated


title: S7_RedLight_rep1

value: red light treated


title: S3_BlueLight_rep3


title: S9_RedLight_rep3


title: APRMST-40 Week0 [43_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: APRMST-40 Week0 [5_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: S8_RedLight_rep2


title: APRMST-40 Week12 [6_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: S13_Mock


title: S1_BlueLight_rep1


title: APRMST-30 Week0 [37_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: APRMST-30 Week0 [61_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: APRMST-30 Week0 [38_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]


title: APRMST-30 Week0 [31_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)_2]


title: APRMST-30 Week0 [62_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: APRMST-30 Week0 [52_HG-U133 plus 2.0_Hui_20160202_(HG-U133_Plus_2)]


title: PEO1_Adherent_1

status: Public on Jul 28 2018

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

description:
P1
Parental PEO1 cells

data_processing:
[Hisat2 (version 2.1.0)] Used to map reads to human genome GRCh37
[bedtools] Used to assemble transcripts
[edgeR] Used to identify differenentially expressed genes
[filtering] Genes with zero expression in all samples were excluded
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values

source_name: parental PEO1 cells

extract_protocol:
RNeasy kit (Qiagen)
RNAlibraries were prepared for sequencing using TruSEQ RNA Sample Prep v4 using standard Illumina protocols.

tag: phenotype

value: parental control


title: PEO1_Adherent_2

description:
P2
Parental PEO1 cells


title: Placebo Week0 [11-HGU133 Plus2.0_Hui_20160113_(HG-U133_Plus_2)]


title: Hashtag-ADT

status: Public on Jan 02 2018

first: Soumya

last: Badrinath

address: One Jimmy Fund Way

description: polyA ADT

data_processing:
Read 1 includes cell barcode, UMI; read 2 includes cDNA read.
10x data were processed using Drop-seq tools v1.12 (Macosko et al., 2015), specifying 50,000 cell barcodes to return
ADT data were mapped to a 12 bases or a 10 bases reference ADT list separately
HTO data were mapped to a 12 bases reference HTO list
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file for 10x data; comma-delimited file for ADT and HTO mapping

source_name: Peripheral blood mononuclear cells

extract_protocol:
For genotyping genomic DNA was purified using the All-prep kit (Qiagen, USA). For HTO and ADT we followed the protocol as described for CITE-seq (Stoeckius et al, 2017)
For genotyping the Infinium core exome 24 array (Illumina, USA) was used according to manufacturer instructions; ‘Stained’ and washed cells were loaded into 10x Genomics single cell 3’ system and processed according to manufacturer’s instructions, and the CITE-seq protocols (Stoeckius et al, 2017).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from Allcells (USA). For HTO and ADT cells were ‘stained’ with hashtagging antibodies and CITE-seq antibodies as described for CITE-seq (Stoeckius et al, 2017)

value: Peripheral blood mononuclear cells

tag: antibodies/tags

value: 12 bases tag:IgG_control, IgG2a_control, IgG1_control, IgG2a_2_control, IgG2b_control, IgM_control, IgG2b_2_control, IgG1_2_control; 10 bases tag:CD3, CD4, CD8, CD45RA, CCR7, HLA-DR, PD-1

tag: library type

value: 10x Genomics single cell 3' v2


title: APRMST-30 Week0 [32_HG_U133plus2.0_Hui_20150121_(HG-U133_Plus_2)]

tag: treatment


title: Hashtag-RNA

description: polyA RNA


title: Hashtag-HTO

description: polyA HTO

value: BatchA, BatchB, BatchC, BatchD, BatchE, BatchF, BatchG, BatchH


title: neural crest cells rep3

status: Public on Aug 31 2018

city: heidelberg

first: Lionel

last: Larribere

address: im neuenheimer Feld

country: Germany

institute: DKFZ

description:
D1NC_3
replicate 3
9347704022_L

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: healthy donor

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: mRNA was isolated with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Clean-up and DNase I treatment was included. Quality control was performed with Agilent Bioanalyzer.

value: neural crest

tag: biomaterial provider

value: generated at DKFZ


title: normal human melanocytes rep2

description:
NHM_2
replicate 2
9347704022_G

value: normal human melanocytes

value: isolated at DKFZ


title: normal human melanocytes rep3

description:
NHM_3
replicate 3
9347704022_H


title: neural crest cells rep1

description:
D1NC_1
replicate 1
8986302012_J


title: WT_rep_1

status: Public on Mar 30 2018

city: Pittsburgh

first: Satdarshan

last: Monga

state: PA

address: S-422 SBST, 200 Lothrop Street

department: Pathology

institute: University of Pittsburgh School of Medicine

description: Normal liver tissue extracted from wild type FVB mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G7.

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Wild type FVB mouse, biological replicate 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Six- to eight-week-old wild-type FVB/N mice (Charles River, Wilmington, MA) were used for this experiment. For hydrodynamic tail vein injection, YapS127A plasmid (10µg), ∆N90-β-catenin plasmid (10µg), and pCMV/SB (0.8µg) were diluted into 2ml 0.9% NaCl solution, sterile filtered with 0.2µm filters, and then injected into mouse lateral tail vein within 5–7 seconds as described in previous publications [Tao J, Calvisi D, Ranganathan S, et al. Gastroenterology, 2014 Sep; 147(3): 690–701]. Mice were sacrificed at 7-10.7 weeks post injection. WT mice were left untreated. Liver tissue was extracted and flash frozen for RNA isolation.

tag: strain background

value: FVB

value: Normal liver tissue

tag: age

value: 14 weeks (no treatment)


title: HB_tumor_9.7_weeks

description: Liver tissue extracted from FVB mice 9.7 weeks after hydrodynamic tail vein injection of Sleeping Beauty transposase and plasmids containing S127A YAP1 mutant gene and ΔN90 CTNNB1 mutant gene.

source_name: Hepatoblastoma tumor (9 weeks)

value: Liver tissue containing HB tumors

value: 9.7 weeks post plasmid injection


title: neural crest rep2

status: Public on Feb 16 2018

description: replicate 2

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: healthy donnor

extract_protocol: mRNA was isolated with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Clean-up and DNase I treatment was included. Quality control was performed with Agilent Bioanalyser.

tag: source


title: normal human melanocytes rep1

description:
NHM_1
replicate 1
8986302012_I

tag: cell type


title: WT_rep_2

source_name: Wild type FVB mouse, biological replicate 2

value: 15 weeks (no treatment)


title: neural crest rep3

description: replicate 3


title: BT20 Control

status: Public on May 02 2018

first: Michael

middle: K

last: Asiedu

address: 200 Fisrt ST SW

department: Surgery

institute: Mayo Foundation for Medical Education and Research

description:
Gene expression data from patient derived fibroblast cell lines
BT20 BT20 Control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 and performed by the Mayo Clinic Genomic Core

data_processing: The data were analyzed with using Partek Genomic Suite Ver. 6.6 (Partek Inc, St. Louis, MO) Partek Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: commercial cell lines

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was purified with the RNeasy Mini-kit (Qiagen, CA).

value: Cancer cell lines

tag: cell line