title: CES_ZV Sample 473

description: bigWig

data_processing:
Base calls performed with Illumina RTA 1.18.64.
Sequence reads were mapped to the human genome using STAR version 2.3.0 (Dobin et al, 2013) with the parameters: --genomeLoad LoadAndRemove --alignIntronMax 500000 --alignMatesGapMax 500000 --outSAMunmapped Within --outFilterMultimapNmax 1 --outFilterMismatchNmax 3 --outFilterMismatchNoverLmax 0.3 --sjdbOverhang 50 -- chimSegmentMin 15 --chimScoreMin 1 --chimScoreJunctionNonGTAG 0 -- chimJunctionOverhangMin 15.
The mapped reads were quantified using HTSeq-count from the HTSeq framework version 0.6.0 using the intersection_nonempty option in a stranded fashion according to the gencode17 annotation (Anders et al, 2015).
hs37d5
bigWig files were generated using bamCoverage (deepTools). Coverage tracks were normalized to 1x.

extract_protocol:
Small and large RNA fractions were isolated with the miRNeasy Mini Kit (Qiagen), RNA was digested by DNase I (Promega) for 30 min at 37°C, depleted from rRNA with RiboZero Gold.
Directional cDNA synthesis and sequencing library preparation was conducted according to the NEBNext Ultra Directional RNA Library Prep Kit (NEB).


title: CES_FG_WGBS Sample 478

status: Public on May 22 2019

type: SRA

city: Heidelberg

first: Karsten

last: Rippe

state: Germany

address: Im Neuenheimer Feld 267-BQ24

department: Division of Chromatin Networks

country: Germany

institute: DKFZ

description: bigBed

library_source: genomic

data_processing:
Base calls performed with Illumina RTA 1.18.64.
In addition to the default pipeline of MethylCtools, an updated version of BWA-MEM (v0.7.12-r1039) was used to align reads to the human reference genome.
Whole-genome bisulfite sequencing data were processed with MethylCtools as previously described in detail (Hovestadt et al, 2014).
DNA methylation levels (beta-values) were calculated for more than 23 million CpG sites covered with at least five reads and supported to be a correct CpG by the sequencing data in individual samples (>75% of reads) (Hovestadt et al, 2014).
hs37d5
bigBed file containing the Beta values for the CpG sites.

molecule: genomic DNA

organism: Homo sapiens

source_name: CD19+ B-cells from peripheral blood of CLL patient

extract_protocol:
DNA was extracted with the Allprep DNA/RNA Mini Kit (Qiagen), spiked with unmethylated lambda DNA (Promega) and sonicated to achieve an average size of 250-300 bp. Bisulfite conversion was done using the EZ DNA Methylation kit (Zymo).
Strand-specific WGBS-seq libraries were prepared as described previously (Kretzmer et al, 2015).

tag: disease

value: CLL

tag: donor

value: FG

tag: treatment


title: CES_EM_WGBS Sample 477

description: bigBed

source_name: Non-malignant B cells of healthy donors

value: Non-malignant

value: EM


title: CES_GN_WGBS Sample 479

description: bigBed

value: GN


title: Naive_0A

type: RNA

city: Birmingham

first: Frances

last: Lund

state: AL

address: 1720 2nd Avenue South

department: Microbiology

country: USA

institute: University of Alabama at Birmingham

description: Gene expression data from B cells before culture with T cells, time 0

hyb_protocol: Labeled cRNA was fragmented to an average size of 35 to 200 bases by incubation at 94 degrees C for 35 min. Hybridization (16 hr), washing, and staining of the Affymetrix GeneChip® Mouse Genome U430 Plus 2.0 Array was conducted according to manufacturer specifications in the Affymetrix Fluidics station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: The signal value of each probe set (gene) was calculated using the Microarray Suite 5 (MAS5) algorithm and normalized using global scaling which set the average signal intensity of an array to 750.  MAS5 values were log2-transformed and a p value for each probe set was calculated using an unpaired t-test. Positive FDR and q values were computed using Matlab (The Mathworks Inc., Natick MA) based on the method of Storey (2002).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Naïve B cell, culture day 0

label_protocol: Biotin-labeled cRNA was generated using the Affymetrix one-cycle cDNA synthesis and IVT kit according to manufacturers specifications from 5ug total RNA

growth_protocol: Be1 and Be2 cells were generated by co-culturing splenic B cells with mitomycin C-treated ovalbumin-specific Th1 or Th2 polarized CD4+ T cells (OTII cells) in the presence of IL-2 (20 units/ml), anti-IgM F(ab')2 (40 μg/ml), and OT-II peptide (5 μM) for 1, 2, 3, or 4 days.

extract_protocol: Be1 and Be2 cells were sort purified and washed with PBS prior to lysis. RNA was isolated using the Qiagen RNeasy mini kit followed by DNase I digestion. The quality of the RNA was evaluated by electrophoresis prior to submission.  RINs are not available.

tag: cell type

value: B cell

tag: b cell source tissue

value: Spleen

tag: co-culture

value: none (naïve)

tag: time point (day)


title: CES_IO_WGBS Sample 480

description: bigBed

value: IO


title: CES_PP_WGBS Sample 482

description: bigBed

value: PP


title: CES_YF Sample 471

description: bigWig

library_source: transcriptomic

value: YF


title: CES_ZV Sample 472

description: bigWig

value: ZV


title: CES_AY_WGBS Sample 474

description: bigBed

value: AY


title: CES_BK_WGBS Sample 475

description: bigBed

value: BK


title: CES_YF Sample 470

description: bigWig


title: CES_XP Sample 469

description: bigWig

value: XP


title: CES_XP Sample 468

description: bigWig


title: CES_WS Sample 467

description: bigWig

value: WS


title: CES_WS Sample 466

description: bigWig


title: CES_VL Sample 465

description: bigWig

value: VL


title: CES_TH Sample 462

description: bigWig

value: CLL

value: TH


title: CES_TB Sample 461

description: bigWig

value: TB


title: CES_VL Sample 464

description: bigWig

value: Non-malignant


title: CES_TH Sample 463

description: bigWig


title: CES_TB Sample 460

description: bigWig


title: CES_RP Sample 459

description: bigWig

value: RP


title: CES_PP Sample 451

description: bigWig


title: CES_RC Sample 457

description: bigWig

value: RC


title: CES_PP Sample 450

description: bigWig


title: CES_QU Sample 454

description: bigWig

value: QU


title: CES_QP Sample 452

description: bigWig

value: QP


title: CES_QP Sample 453

description: bigWig


title: CES_OZ Sample 449

description: bigWig

value: OZ


title: CES_NQ Sample 446

description: bigWig

value: NQ


title: CES_MA_2h_P Sample 444

description: bigWig

growth_protocol: Malignant and non-malignant B cells of each four individual CLL patients or healthy donors respectively were enriched for CD19-positive. 10,000 cells were seeded in serum-free medium and incubated for 30 min with DMSO as mock control or panobinostat.

value: MA

value: 2h Panobinostat


title: CES_MA_2h_P Sample 445

description: bigWig


title: CES_MA_24h_N Sample 441

description: bigWig

value: 24h control for Panobinostat


title: CES_NQ Sample 447

description: bigWig


title: CES_MA_24h_N Sample 440

description: bigWig


title: CES_LM_2h_P Sample 437

description: bigWig

value: LM


title: CES_LM Sample 439

description: bigWig


title: CES_LM_2h_P Sample 436

description: bigWig


title: CES_LM Sample 438

description: bigWig


title: CES_LM_2h_N Sample 435

description: bigWig

value: 2h control for Panobinostat


title: CES_RP Sample 458

description: bigWig


title: CES_LM_24h_N Sample 430

description: bigWig


title: CES_LM_24h_N Sample 431

description: bigWig


title: CES_RC Sample 456

description: bigWig


title: CES_LM_24h_P Sample 433

description: bigWig

value: 24h Panobinostat


title: CES_LM_24h_P Sample 432

description: bigWig


title: CES_OZ Sample 448

description: bigWig


title: CES_QU Sample 455

description: bigWig


title: CES_MA_24h_P Sample 443

description: bigWig


title: CES_KL Sample 428

description: bigWig

value: KL


title: CES_JK Sample 427

description: bigWig

value: CLL

value: JK


title: CES_MA_24h_P Sample 442

description: bigWig


title: Naive_0D

description: Gene expression data from B cells before culture with T cells, time 3

source_name: Naïve B cell, culture day 3

value: B cell

value: Spleen

value: none (naïve)


title: CES_KL Sample 429

description: bigWig


title: CES_JK_2h_P Sample 424

description: bigWig


title: CES_JK_2h_N Sample 423

description: bigWig


title: CES_JK Sample 426

description: bigWig


title: CES_JK_24h_N Sample 419

description: bigWig


title: CES_JK_24h_P Sample 421

description: bigWig


title: CES_JK_24h_P Sample 420

description: bigWig


title: CES_JK_2h_N Sample 422

description: bigWig


title: CES_IO Sample 416

description: bigWig

value: IO


title: CES_HA Sample 415

description: bigWig

value: HA


title: CES_HA Sample 414

description: bigWig


title: CES_LM_2h_N Sample 434

description: bigWig


title: CES_HA_2h_P Sample 413

description: bigWig


title: CES_HA_2h_P Sample 412

description: bigWig


title: CES_HA_24h_P Sample 409

description: bigWig


title: CES_HA_24h_N Sample 406

description: bigWig


title: CES_HA_2h_N Sample 410

description: bigWig


title: CES_GN Sample 405

description: bigWig

value: Non-malignant

value: GN


title: CES_HA_24h_P Sample 408

description: bigWig


title: CES_HA_24h_N Sample 407

description: bigWig


title: CES_HA_2h_N Sample 411

description: bigWig


title: CES_DT Sample 399

description: bigWig

value: DT


title: CES_EM Sample 401

description: bigWig

value: EM


title: CES_EM Sample 400

description: bigWig


title: CES_DT Sample 398

description: bigWig


title: CES_CX Sample 397

description: bigWig

value: CX


title: CES_JK_2h_P Sample 425

description: bigWig

value: 2h Panobinostat


title: CES_FG Sample 402

description: bigWig

value: FG


title: CES_JK_24h_N Sample 418

description: bigWig

value: 24h control for Panobinostat


title: CES_IO Sample 417

description: bigWig


title: CES_FG Sample 403

description: bigWig


title: CES_GN Sample 404

description: bigWig


title: CES_ZV_H3K9me3 Sample 393

description: bigWig

data_processing:
Base calls performed with Illumina RTA 1.18.64.
Reads were aligned using bowtie (options --best --strata -v 1 -m 1).
SICER was used to determine enriched regions, peaks, with histone H3 serving again as a control.
hs37d5
bigWig files were generated using bamCoverage (deepTools). Coverage tracks were normalized to 1x.

extract_protocol:
Patient derived cells were cross-linked with 1 % methanol-free formaldehyde for 10 min. After quenching with glycine, cells were washed three times with PBS and the cell pellet was frozen in liquid nitrogen. For analysis, the cell pellet was thawn and treated with 4U MNase per 1x106 cells for 15 min. MNase was stopped with 10x covaris buffer and the chromatin was sheared for an additional 15 min with the S2 covaris device and the soluble chromatin was then recovered and subjected to a background-minimizing pre-clearing step with an unspecific IgG antibody. For each ChIP-assay an equivalent of 3x106 cells were used with the antibodies. After the IP, chromatin was digested with RNaseA and proteinase K.
The purified DNA was cloned into illumina sequencing libraries with the NEBNext Ultra library preparation kit (NEB).

value: ZV

tag: chip antibody

value: Rabbit polyclonal H3K9me3 (Abcam, ab8898)


title: CES_ZV_H3K36me3 Sample 389

description: bigWig

value: CLL


title: CES_ZV_H3K4me1 Sample 390

description: bigWig

data_processing:
Base calls performed with Illumina RTA 1.18.64.
Reads were aligned using bowtie (options --best --strata -v 1 -m 1).
Peaks were called with MACS using H3 as a background control.
hs37d5
bigWig files were generated using bamCoverage (deepTools). Coverage tracks were normalized to 1x.

value: Rabbit polyclonal H3K4me1 (Abcam, ab8895)


title: CES_BK Sample 394

description: bigWig

value: BK


title: CES_ZV_H3K27me3 Sample 388

description: bigWig

value: Mouse monoclonal H3K27me3 (Abcam, ab6002)


title: CES_ZV_H3K9ac Sample 392

description: bigWig

value: Rabbit polyclonal H3K9ac (Active Motif, 39917)


title: CES_ZV_H3K4me3 Sample 391

description: bigWig

value: Rabbit polyclonal H3K4me3 (Abcam, ab8580)


title: CES_ZV_H3K27ac Sample 387

description: bigWig

value: Rabbit polyclonal H3K27ac (Abcam, ab4729)


title: CES_BK Sample 395

description: bigWig

value: Non-malignant


title: CES_YF_H3K4me3 Sample 383

description: bigWig

value: YF


title: CES_YF_H3K27ac Sample 379

description: bigWig


title: CES_YF_H3K36me3 Sample 381

description: bigWig


title: CES_YF_H3K27me3 Sample 380

description: bigWig


title: CES_YF_H3 Sample 378

description: bigWig

data_processing:
Base calls performed with Illumina RTA 1.18.64.
Reads were aligned using bowtie (options --best --strata -v 1 -m 1).
NucTools was used to generate genome-wide nucleosome occupancy landscapes, extract individual genomic regions and calculate the nucleosome repeat length, as described previously
hs37d5
bigWig files were generated using bamCoverage (deepTools). Coverage tracks were normalized to 1x.

value: Rabbit polyclonal H3 (Abcam, ab1791)


title: CES_YF_H3K4me1 Sample 382

description: bigWig


title: CES_CX Sample 396

description: bigWig


title: CES_YF_H3K9ac Sample 384

description: bigWig


title: CES_XP_H3K9ac Sample 376

description: bigWig

value: XP


title: CES_XP_H3K4me3 Sample 375

description: bigWig


title: CES_XP_H3K27ac Sample 371

description: bigWig


title: CES_XP_H3K4me1 Sample 374

description: bigWig


title: CES_XP_H3K27me3 Sample 372

description: bigWig


title: CES_XP_H3K36me3 Sample 373

description: bigWig


title: CES_WW_H3K9me3 Sample 369

description: bigWig

value: WW


title: CES_WW_H3K9ac Sample 368

description: bigWig


title: CES_WW_H3K4me3 Sample 367

description: bigWig


title: CES_WW_H3K4me1 Sample 366

description: bigWig


title: CES_XP_H3 Sample 370

description: bigWig


title: CES_WW_H3K27me3 Sample 364

description: bigWig


title: CES_WW_H3K27ac Sample 363

description: bigWig


title: CES_WW_H3K36me3 Sample 365

description: bigWig


title: CES_WW_H3 Sample 362

description: bigWig


title: CES_WS_H3K9me3 Sample 361

description: bigWig

value: WS


title: CES_WS_H3K4me3 Sample 359

description: bigWig


title: CES_WS_H3K9ac Sample 360

description: bigWig


title: CES_WS_H3K27ac Sample 355

description: bigWig


title: CES_WS_H3K36me3 Sample 357

description: bigWig


title: CES_ZV_H3 Sample 386

description: bigWig


title: CES_XP_H3K9me3 Sample 377

description: bigWig


title: CES_VL_H3K9me3 Sample 353

description: bigWig

value: VL


title: CES_WS_H3 Sample 354

description: bigWig


title: CES_VL_H3K4me3 Sample 351

description: bigWig


title: CES_VL_H3K36me3 Sample 349

description: bigWig


title: CES_VL_H3K4me1 Sample 350

description: bigWig


title: CES_TH_H3K9ac Sample 344

description: bigWig

value: TH


title: CES_VL_H3K27ac Sample 347

description: bigWig


title: CES_TH_H3K4me3 Sample 343

description: bigWig


title: CES_VL_H3K27me3 Sample 348

description: bigWig


title: CES_TH_H3K9me3 Sample 345

description: bigWig


title: CES_VL_H3K9ac Sample 352

description: bigWig


title: CES_VL_H3 Sample 346

description: bigWig


title: CES_WS_H3K4me1 Sample 358

description: bigWig


title: CES_WS_H3K27me3 Sample 356

description: bigWig


title: CES_TH_H3K36me3 Sample 341

description: bigWig


title: CES_TB_H3K4me3 Sample 335

description: bigWig

value: TB


title: CES_TB_H3K9ac Sample 336

description: bigWig


title: CES_TH_H3K27me3 Sample 340

description: bigWig


title: CES_TH_H3K27ac Sample 339

description: bigWig


title: CES_TB_H3K9me3 Sample 337

description: bigWig

value: Rabbit polyclonal H3K9me3 (Abcam, ab8898)


title: CES_TB_H3K4me1 Sample 334

description: bigWig

value: CLL


title: CES_TH_H3 Sample 338

description: bigWig


title: CES_TB_H3K36me3 Sample 333

description: bigWig


title: CES_TB_H3K27me3 Sample 332

description: bigWig


title: CES_RP_H3K9me3 Sample 329

description: bigWig

value: RP


title: CES_RP_H3K9ac Sample 328

description: bigWig


title: CES_RP_H3K4me3 Sample 327

description: bigWig


title: CES_TB_H3K27ac Sample 331

description: bigWig


title: CES_RP_H3K4me1 Sample 326

description: bigWig

value: Rabbit polyclonal H3K4me1 (Abcam, ab8895)


title: CES_RP_H3K27ac Sample 323

description: bigWig


title: CES_TH_H3K4me1 Sample 342

description: bigWig


title: CES_RP_H3K36me3 Sample 325

description: bigWig


title: CES_RP_H3K27me3 Sample 324

description: bigWig

value: Mouse monoclonal H3K27me3 (Abcam, ab6002)


title: CES_RC_H3K9me3 Sample 321

description: bigWig

value: RC


title: CES_RP_H3 Sample 322

description: bigWig


title: CES_RC_H3K27me3 Sample 316

description: bigWig


title: CES_RC_H3K9ac Sample 320

description: bigWig

value: Rabbit polyclonal H3K9ac (Active Motif, 39917)


title: CES_RC_H3K4me1 Sample 318

description: bigWig


title: CES_RC_H3K4me3 Sample 319

description: bigWig

value: Rabbit polyclonal H3K4me3 (Abcam, ab8580)


title: CES_RC_H3K27ac Sample 315

description: bigWig

value: Rabbit polyclonal H3K27ac (Abcam, ab4729)


title: CES_RC_H3 Sample 314

description: bigWig


title: CES_RC_H3K36me3 Sample 317

description: bigWig


title: CES_QU_H3K9ac Sample 312

description: bigWig

value: QU


title: CES_QU_H3K9me3 Sample 313

description: bigWig


title: CES_QU_H3K4me3 Sample 311

description: bigWig


title: CES_QU_H3K27me3 Sample 308

description: bigWig


title: CES_QU_H3K4me1 Sample 310

description: bigWig


title: CES_QU_H3K36me3 Sample 309

description: bigWig


title: CES_TB_H3 Sample 330

description: bigWig

value: Rabbit polyclonal H3 (Abcam, ab1791)


title: CES_QU_H3K27ac Sample 307

description: bigWig


title: CES_QP_H3K27me3 Sample 300

description: bigWig

value: QP


title: CES_QP_H3K9me3 Sample 305

description: bigWig


title: CES_QP_H3K4me1 Sample 302

description: bigWig


title: CES_QP_H3K4me3 Sample 303

description: bigWig


title: CES_QP_H3K27ac Sample 299

description: bigWig


title: CES_QU_H3 Sample 306

description: bigWig


title: CES_QP_H3K36me3 Sample 301

description: bigWig


title: CES_QP_H3K9ac Sample 304

description: bigWig


title: CES_QP_H3 Sample 298

description: bigWig


title: CES_PP_H3K9me3 Sample 297

description: bigWig

value: PP


title: CES_PP_H3K9ac Sample 296

description: bigWig


title: CES_PP_H3K27me3 Sample 292

description: bigWig


title: CES_PP_H3K4me3 Sample 295

description: bigWig


title: CES_PP_H3K36me3 Sample 293

description: bigWig


title: CES_PP_H3K4me1 Sample 294

description: bigWig


title: CES_PP_H3 Sample 290

description: bigWig


title: CES_OZ_H3K4me3 Sample 287

description: bigWig

value: OZ


title: CES_PP_H3K27ac Sample 291

description: bigWig


title: CES_OZ_H3K9me3 Sample 289

description: bigWig


title: CES_OZ_H3K9ac Sample 288

description: bigWig


title: CES_OZ_H3K4me1 Sample 286

description: bigWig


title: CES_OZ_H3K27me3 Sample 284

description: bigWig


title: CES_OZ_H3K27ac Sample 283

description: bigWig


title: CES_NQ_H3K9ac Sample 280

description: bigWig

value: NQ


title: CES_NQ_H3K9me3 Sample 281

description: bigWig


title: CES_OZ_H3 Sample 282

description: bigWig


title: CES_NQ_H3K4me1 Sample 278

description: bigWig


title: CES_NQ_H3K4me3 Sample 279

description: bigWig


title: CES_NQ_H3K27me3 Sample 276

description: bigWig


title: CES_NQ_H3K36me3 Sample 277

description: bigWig


title: CES_MA_H3K9me3 Sample 273

description: bigWig

value: Non-malignant

value: MA


title: CES_MA_H3K9ac Sample 272

description: bigWig


title: CES_NQ_H3 Sample 274

description: bigWig


title: CES_NQ_H3K27ac Sample 275

description: bigWig


title: CES_MA_H3K4me1 Sample 270

description: bigWig


title: CES_MA_H3K27me3 Sample 268

description: bigWig


title: CES_MA_H3K27ac Sample 267

description: bigWig


title: CES_MA_2h_P_H3K4me3 Sample 263

description: bigWig

value: 2h Panobinostat


title: CES_MA_2h_P_H3K4me1 Sample 262

description: bigWig


title: CES_MA_2h_P_H3K36me3 Sample 261

description: bigWig

value: Rabbit polyclonal H3K36me3 (Abcam, ab9050)


title: CES_MA_2h_P_H3K27me3 Sample 260

description: bigWig


title: CES_MA_H3K4me3 Sample 271

description: bigWig


title: CES_MA_2h_P_H3K27ac Sample 259

description: bigWig


title: CES_MA_2h_P_H3K9ac Sample 264

description: bigWig


title: CES_MA_2h_P_H3K9me3 Sample 265

description: bigWig

value: Rabbit polyclonal H3K9me3 (Abcam, ab8898)


title: CES_OZ_H3K36me3 Sample 285

description: bigWig

value: CLL


title: CES_MA_2h_N_H3K9ac Sample 256

description: bigWig

value: 2h control for Panobinostat


title: CES_MA_2h_N_H3K4me3 Sample 255

description: bigWig


title: CES_MA_2h_P_H3 Sample 258

description: bigWig


title: CES_MA_24h_P_H3K9me3 Sample 249

description: bigWig

value: 24h Panobinostat


title: CES_MA_2h_N_H3 Sample 250

description: bigWig


title: CES_MA_2h_N_H3K4me1 Sample 254

description: bigWig

value: Rabbit polyclonal H3K4me1 (Abcam, ab8895)


title: CES_MA_24h_P_H3K9ac Sample 248

description: bigWig

value: Rabbit polyclonal H3K9ac (Active Motif, 39917)


title: CES_MA_H3K36me3 Sample 269

description: bigWig


title: CES_MA_24h_P_H3K4me3 Sample 247

description: bigWig

value: Rabbit polyclonal H3K4me3 (Abcam, ab8580)


title: CES_MA_24h_P_H3K36me3 Sample 245

description: bigWig


title: CES_MA_24h_P_H3K4me1 Sample 246

description: bigWig


title: CES_MA_24h_P_H3 Sample 242

description: bigWig


title: CES_MA_24h_P_H3K27me3 Sample 244

description: bigWig

value: Mouse monoclonal H3K27me3 (Abcam, ab6002)


title: CES_MA_H3 Sample 266

description: bigWig

value: Rabbit polyclonal H3 (Abcam, ab1791)


title: CES_MA_24h_N_H3K9me3 Sample 241

description: bigWig

value: 24h control for Panobinostat


title: CES_MA_2h_N_H3K9me3 Sample 257

description: bigWig


title: CES_YF_H3K9me3 Sample 385

description: bigWig

value: YF


title: CES_MA_24h_N_H3K9ac Sample 240

description: bigWig


title: CES_MA_2h_N_H3K27me3 Sample 252

description: bigWig


title: CES_MA_2h_N_H3K36me3 Sample 253

description: bigWig


title: CES_MA_24h_N_H3K4me3 Sample 239

description: bigWig


title: CES_MA_24h_N_H3K4me1 Sample 238

description: bigWig


title: CES_LM_H3K4me3 Sample 231

description: bigWig

value: LM


title: CES_MA_24h_N_H3K27ac Sample 235

description: bigWig

value: Rabbit polyclonal H3K27ac (Abcam, ab4729)


title: CES_MA_24h_N_H3K36me3 Sample 237

description: bigWig

value: Non-malignant


title: CES_MA_24h_N_H3K27me3 Sample 236

description: bigWig

value: MA


title: CES_LM_H3K9ac Sample 232

description: bigWig


title: CES_LM_H3K27me3 Sample 228

description: bigWig


title: CES_MA_2h_N_H3K27ac Sample 251

description: bigWig


title: CES_LM_H3K36me3 Sample 229

description: bigWig


title: CES_LM_H3K27ac Sample 227

description: bigWig


title: CES_LM_2h_P_H3K9ac Sample 224

description: bigWig

value: 2h Panobinostat


title: CES_LM_2h_P_H3K9me3 Sample 225

description: bigWig


title: CES_LM_H3 Sample 226

description: bigWig


title: CES_LM_2h_P_H3K4me3 Sample 223

description: bigWig


title: CES_MA_24h_P_H3K27ac Sample 243

description: bigWig


title: CES_LM_2h_P_H3K4me1 Sample 222

description: bigWig


title: CES_LM_2h_P_H3K27me3 Sample 220

description: bigWig


title: CES_LM_2h_P_H3K27ac Sample 219

description: bigWig


title: CES_LM_2h_P_H3 Sample 218

description: bigWig


title: CES_LM_2h_N_H3K9me3 Sample 217

description: bigWig


title: CES_MA_24h_N_H3 Sample 234

description: bigWig


title: CES_LM_H3K9me3 Sample 233

description: bigWig


title: CES_LM_2h_N_H3K4me3 Sample 215

description: bigWig


title: CES_LM_2h_N_H3K9ac Sample 216

description: bigWig


title: CES_LM_2h_N_H3K4me1 Sample 214

description: bigWig


title: CES_LM_H3K4me1 Sample 230

description: bigWig


title: CES_LM_2h_N_H3K36me3 Sample 213

description: bigWig

value: Rabbit polyclonal H3K36me3 (Abcam, ab9050)


title: CES_LM_2h_N_H3K27me3 Sample 212

description: bigWig


title: CES_LM_24h_P_H3K9me3 Sample 209

description: bigWig

value: Rabbit polyclonal H3K9me3 (Abcam, ab8898)


title: CES_LM_24h_P_H3K9ac Sample 208

description: bigWig

value: CLL


title: CES_LM_2h_N_H3K27ac Sample 211

description: bigWig

value: 2h control for Panobinostat


title: CES_LM_2h_N_H3 Sample 210

description: bigWig


title: CES_LM_24h_P_H3K4me1 Sample 206

description: bigWig

value: 24h Panobinostat


title: CES_LM_24h_P_H3K4me3 Sample 207

description: bigWig


title: CES_LM_24h_P_H3K27ac Sample 203

description: bigWig


title: CES_LM_24h_P_H3K36me3 Sample 205

description: bigWig


title: CES_LM_24h_P_H3 Sample 202

description: bigWig


title: CES_LM_24h_N_H3K4me3 Sample 199

description: bigWig


title: CES_LM_2h_P_H3K36me3 Sample 221

description: bigWig


title: CES_LM_24h_N_H3K9me3 Sample 201

description: bigWig


title: CES_LM_24h_N_H3K9ac Sample 200

description: bigWig


title: CES_LM_24h_N_H3K4me1 Sample 198

description: bigWig

value: Rabbit polyclonal H3K4me1 (Abcam, ab8895)


title: CES_LM_24h_P_H3K27me3 Sample 204

description: bigWig


title: CES_LM_24h_N_H3K36me3 Sample 197

description: bigWig


title: CES_LM_24h_N_H3K27me3 Sample 196

description: bigWig


title: CES_KL_H3K9me3 Sample 193

description: bigWig

value: KL


title: CES_LM_24h_N_H3K27ac Sample 195

description: bigWig


title: CES_LM_24h_N_H3 Sample 194

description: bigWig


title: CES_KL_H3K4me3 Sample 191

description: bigWig

value: Rabbit polyclonal H3K4me3 (Abcam, ab8580)


title: CES_KL_H3K27me3 Sample 188

description: bigWig

value: Mouse monoclonal H3K27me3 (Abcam, ab6002)


title: CES_KL_H3K36me3 Sample 189

description: bigWig


title: CES_KL_H3K9ac Sample 192

description: bigWig

value: Rabbit polyclonal H3K9ac (Active Motif, 39917)


title: CES_KL_H3K4me1 Sample 190

description: bigWig


title: CES_KL_H3K27ac Sample 187

description: bigWig


title: CES_JK_H3K9me3 Sample 185

description: bigWig

value: JK


title: CES_JK_H3K9ac Sample 184

description: bigWig


title: CES_JK_H3K4me3 Sample 183

description: bigWig


title: CES_JK_H3K36me3 Sample 181

description: bigWig


title: CES_JK_H3K4me1 Sample 182

description: bigWig


title: CES_JK_H3K27me3 Sample 180

description: bigWig


title: CES_JK_H3K27ac Sample 179

description: bigWig


title: CES_JK_2h_P_H3K9me3 Sample 177

description: bigWig


title: CES_JK_H3 Sample 178

description: bigWig

value: Rabbit polyclonal H3 (Abcam, ab1791)


title: CES_JK_2h_P_H3K4me3 Sample 175

description: bigWig


title: CES_JK_2h_P_H3K4me1 Sample 174

description: bigWig


title: CES_JK_2h_P_H3K27ac Sample 171

description: bigWig


title: CES_JK_2h_P_H3K9ac Sample 176

description: bigWig


title: CES_JK_2h_P_H3K36me3 Sample 173

description: bigWig


title: CES_JK_2h_N_H3K36me3 Sample 165

description: bigWig


title: CES_JK_2h_N_H3K4me1 Sample 166

description: bigWig


title: CES_JK_2h_N_H3K9me3 Sample 169

description: bigWig


title: CES_KL_H3 Sample 186

description: bigWig


title: CES_JK_2h_N_H3K4me3 Sample 167

description: bigWig


title: CES_JK_2h_P_H3 Sample 170

description: bigWig


title: CES_JK_2h_N_H3K27ac Sample 163

description: bigWig


title: CES_JK_2h_N_H3K9ac Sample 168

description: bigWig


title: CES_JK_24h_P_H3K9ac Sample 160

description: bigWig


title: CES_JK_2h_N_H3 Sample 162

description: bigWig


title: CES_JK_24h_P_H3K36me3 Sample 157

description: bigWig


title: CES_JK_24h_P_H3K4me3 Sample 159

description: bigWig


title: CES_JK_2h_N_H3K27me3 Sample 164

description: bigWig


title: CES_JK_24h_P_H3K27ac Sample 155

description: bigWig


title: CES_JK_24h_P_H3K27me3 Sample 156

description: bigWig


title: CES_JK_24h_P_H3K4me1 Sample 158

description: bigWig


title: CES_JK_24h_P_H3 Sample 154

description: bigWig


title: CES_JK_2h_P_H3K27me3 Sample 172

description: bigWig


title: CES_JK_24h_N_H3K9ac Sample 152

description: bigWig

value: 24h control for Panobinostat


title: CES_JK_24h_N_H3K9me3 Sample 153

description: bigWig


title: CES_JK_24h_N_H3K4me3 Sample 151

description: bigWig


title: CES_JK_24h_N_H3K4me1 Sample 150

description: bigWig


title: CES_JK_24h_N_H3K36me3 Sample 149

description: bigWig


title: CES_JK_24h_N_H3 Sample 146

description: bigWig


title: CES_JK_24h_N_H3K27me3 Sample 148

description: bigWig


title: CES_JK_24h_N_H3K27ac Sample 147

description: bigWig

value: Rabbit polyclonal H3K27ac (Abcam, ab4729)


title: CES_JK_24h_P_H3K9me3 Sample 161

description: bigWig


title: CES_IO_H3K9me3 Sample 145

description: bigWig

value: IO


title: CES_IO_H3K9ac Sample 144

description: bigWig


title: CES_IO_H3K4me1 Sample 142

description: bigWig


title: CES_IO_H3K27me3 Sample 140

description: bigWig


title: CES_IO_H3K36me3 Sample 141

description: bigWig


title: CES_HA_H3K9ac Sample 136

description: bigWig

value: HA


title: CES_HA_H3K9me3 Sample 137

description: bigWig


title: CES_HA_H3K4me1 Sample 134

description: bigWig


title: CES_IO_H3K27ac Sample 139

description: bigWig


title: CES_HA_H3K36me3 Sample 133

description: bigWig


title: CES_HA_H3 Sample 130

description: bigWig


title: CES_HA_H3K27me3 Sample 132

description: bigWig


title: CES_HA_2h_P_H3K9ac Sample 128

description: bigWig

value: 2h Panobinostat


title: CES_HA_H3K4me3 Sample 135

description: bigWig


title: CES_HA_2h_P_H3K9me3 Sample 129

description: bigWig


title: CES_HA_2h_P_H3K36me3 Sample 125

description: bigWig

value: Rabbit polyclonal H3K36me3 (Abcam, ab9050)


title: CES_HA_2h_P_H3K4me1 Sample 126

description: bigWig


title: CES_HA_H3K27ac Sample 131

description: bigWig


title: CES_HA_2h_P_H3 Sample 122

description: bigWig


title: CES_HA_2h_N_H3K9me3 Sample 121

description: bigWig

value: Rabbit polyclonal H3K9me3 (Abcam, ab8898)


title: CES_HA_2h_N_H3K4me3 Sample 119

description: bigWig

value: CLL


title: CES_HA_2h_N_H3K9ac Sample 120

description: bigWig

value: 2h control for Panobinostat


title: CES_IO_H3K4me3 Sample 143

description: bigWig


title: CES_HA_2h_N_H3K36me3 Sample 117

description: bigWig


title: CES_HA_2h_N_H3K27me3 Sample 116

description: bigWig


title: CES_IO_H3 Sample 138

description: bigWig


title: CES_HA_2h_N_H3K27ac Sample 115

description: bigWig


title: CES_HA_24h_P_H3K9me3 Sample 113

description: bigWig

value: 24h Panobinostat


title: CES_HA_2h_N_H3 Sample 114

description: bigWig


title: CES_HA_24h_P_H3K4me1 Sample 110

description: bigWig

value: Rabbit polyclonal H3K4me1 (Abcam, ab8895)


title: CES_HA_24h_P_H3K4me3 Sample 111

description: bigWig


title: CES_HA_24h_P_H3K9ac Sample 112

description: bigWig


title: CES_HA_2h_P_H3K27me3 Sample 124

description: bigWig


title: CES_HA_2h_P_H3K27ac Sample 123

description: bigWig


title: CES_HA_24h_N_H3K9ac Sample 104

description: bigWig


title: CES_HA_24h_N_H3K9me3 Sample 105

description: bigWig


title: CES_HA_24h_P_H3K36me3 Sample 109

description: bigWig


title: CES_HA_24h_P_H3 Sample 106

description: bigWig


title: CES_HA_24h_P_H3K27me3 Sample 108

description: bigWig


title: CES_HA_24h_P_H3K27ac Sample 107

description: bigWig


title: CES_HA_24h_N_H3K4me3 Sample 103

description: bigWig


title: CES_HA_24h_N_H3K27me3 Sample 100

description: bigWig


title: CES_HA_24h_N_H3K27ac Sample 99

description: bigWig


title: CES_HA_24h_N_H3K36me3 Sample 101

description: bigWig


title: CES_HA_24h_N_H3 Sample 98

description: bigWig


title: CES_HA_2h_P_H3K4me3 Sample 127

description: bigWig


title: CES_HA_2h_N_H3K4me1 Sample 118

description: bigWig


title: CES_GN_H3K36me3 Sample 93

description: bigWig

value: Non-malignant

value: GN


title: CES_GN_H3K27me3 Sample 92

description: bigWig

value: Mouse monoclonal H3K27me3 (Abcam, ab6002)


title: CES_GN_H3K27ac Sample 91

description: bigWig


title: CES_GN_H3K9ac Sample 96

description: bigWig

value: Rabbit polyclonal H3K9ac (Active Motif, 39917)


title: CES_GN_H3K4me3 Sample 95

description: bigWig

value: Rabbit polyclonal H3K4me3 (Abcam, ab8580)


title: CES_GN_H3 Sample 90

description: bigWig

value: Rabbit polyclonal H3 (Abcam, ab1791)


title: CES_FG_H3K9me3 Sample 89

description: bigWig

value: FG


title: CES_FG_H3K9ac Sample 88

description: bigWig


title: CES_FG_H3K4me1 Sample 86

description: bigWig


title: CES_FG_H3K36me3 Sample 85

description: bigWig


title: CES_FG_H3K4me3 Sample 87

description: bigWig


title: CES_HA_24h_N_H3K4me1 Sample 102

description: bigWig

value: 24h control for Panobinostat


title: CES_FG_H3 Sample 82

description: bigWig


title: CES_EM_H3K4me3 Sample 79

description: bigWig

value: EM


title: CES_GN_H3K9me3 Sample 97

description: bigWig


title: CES_EM_H3K9me3 Sample 81

description: bigWig


title: CES_EM_H3K27ac Sample 75

description: bigWig

value: Rabbit polyclonal H3K27ac (Abcam, ab4729)


title: CES_EM_H3 Sample 74

description: bigWig


title: CES_DT_H3K9ac Sample 72

description: bigWig

value: DT


title: CES_DT_H3K4me3 Sample 71

description: bigWig


title: CES_DT_H3K9me3 Sample 73

description: bigWig


title: CES_EM_H3K27me3 Sample 76

description: bigWig


title: CES_EM_H3K9ac Sample 80

description: bigWig


title: CES_EM_H3K36me3 Sample 77

description: bigWig


title: CES_FG_H3K27ac Sample 83

description: bigWig


title: CES_DT_H3K36me3 Sample 69

description: bigWig


title: CES_DT_H3K4me1 Sample 70

description: bigWig


title: CES_DT_H3K27me3 Sample 68

description: bigWig


title: CES_DT_H3 Sample 66

description: bigWig


title: CES_CX_H3K9me3 Sample 65

description: bigWig

value: CX


title: CES_GN_H3K4me1 Sample 94

description: bigWig


title: CES_CX_H3K9ac Sample 64

description: bigWig


title: CES_CX_H3K4me3 Sample 63

description: bigWig


title: CES_CX_H3K4me1 Sample 62

description: bigWig


title: CES_CX_H3K27me3 Sample 60

description: bigWig


title: CES_CX_H3K27ac Sample 59

description: bigWig


title: CES_FG_H3K27me3 Sample 84

description: bigWig


title: CES_CX_H3 Sample 58

description: bigWig


title: CES_EM_H3K4me1 Sample 78

description: bigWig


title: CES_DT_H3K27ac Sample 67

description: bigWig


title: CES_BK_H3K4me1 Sample 54

description: bigWig

value: BK


title: CES_BK_H3K4me3 Sample 55

description: bigWig


title: CES_BK_H3K27me3 Sample 52

description: bigWig


title: CES_BK_H3K36me3 Sample 53

description: bigWig


title: CES_BK_H3K9ac Sample 56

description: bigWig


title: CES_BK_H3K27ac Sample 51

description: bigWig


title: CES_WW_TechRep2_ATACseq Sample 45

description: bigWig

data_processing:
Base calls performed with Illumina RTA 1.18.64.
Reads were trimmed using Trimmomatic version 0.36 (Bolger et al, 2014). Trimmed reads were mapped to the human genome (hs37d5) using bowtie2 (Langmead et al, 2009) with the options “--very- sensitive -X 2000”.
After removing reads overlapping ENCODE blacklist regions, duplicated reads were discarded using rmdup of SAMtools version 1.3 (Li et al, 2009). Only reads not mapping to the mitochondrial genome were kept.
For further analysis and calculation of coverage tracks all reads were shifted to be centered on the cutting position of the transposase and extended to a total of 29 bp to represent the region occupied by the transposase (Adey et al, 2010).
hs37d5
bigWig files were generated using bamCoverage (deepTools). Coverage tracks were normalized to 1x.

extract_protocol: Nuclei from formaldehyde fixed cells were isolated with Nuclei EZ lysis buffer (Sigma-Aldrich) then washed once in ATAC-seq lysis buffer and incubated with Tn5 for 30 min at 37°C. Tn5 was stopped with EDTA. Previously fixed samples were reverse cross-linked with 300 mM NaCl for two hours at 65°C and DNA was purified with Ampure beads. After barcodes were added by PCR, the libraries were purified with Ampure beads.

value: CLL

value: WW


title: CES_WW_TechRep1_ATACseq Sample 44

description: bigWig


title: CAST APP/PS1 Male Rep4

city: Farmington

first: Asli

last: Uyar

state: CT

address: 10 Discovery Dr

department: Computational Sciences

institute: The Jackson Laboratory

data_processing:
Sequenced reads were quality trimmed and filtered using Trimmomatic tool and reads passing the quality filtering were mapped to the mouse mm10 reference genome using ‘STAR’ aligner. Custom genomes were generated for CAST, PWK and WSB strains by incorporating REL-1505 variants into the reference genome.
HTSeq Python package was used to calculate raw read counts per transcript.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw read counts values for each Sample.

source_name: Whole brain

extract_protocol:
Left brain hemispheres (n=93) were snap frozen at harvest. RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher).
RNA libraries were prepared for sequencing using the KAPA mRNA HyperPrep Kit (KAPA Biosystems), according to the manufacturer’s instructions.

tag: strain/background

value: CAST

tag: genotype/variation

tag: Sex

value: Male

tag: age

value: 8 months

tag: tissue

value: Left brain hemisphere


title: CAST APP/PS1 Male Rep6


title: CAST APP/PS1 Male Rep3


title: CAST APP/PS1 Male Rep2


title: CES_VL_TechRep1_ATACseq Sample 40

description: bigWig

value: Non-malignant

value: VL


title: CES_VL_TechRep2_ATACseq Sample 41

description: bigWig


title: CES_UP_TechRep2_ATACseq Sample 39

description: bigWig

source_name: Non-malignant B cells of healthy donor

extract_protocol: Viable frozen cells were incubated with Tn5 for 30 min at 37°C in the presence of 0.1 % Igepal CA-630 (Sigma-Aldrich). Tn5 was stopped with EDTA. After barcodes were added by PCR, the libraries were purified with Ampure beads.

value: UP


title: CAST APP/PS1 Male Rep1


title: CAST WT Male Rep6

value: WT


title: CES_CX_H3K36me3 Sample 61

description: bigWig


title: CES_CX_TechRep2_ATACseq Sample 2

description: bigWig


title: CES_BK_H3 Sample 50

description: bigWig

value: Rabbit polyclonal H3 (Abcam, ab1791)


title: CES_CX_TechRep1_ATACseq Sample 1

description: bigWig


title: CAST WT Male Rep4


title: CAST WT Male Rep3


title: SH-SY5Y_untreated_SmcHD1 ChIP-seq

city: Burnaby

first: Shabnam

last: Massah

state: British Columbia

address: 8888 University Drive

country: Canada

institute: Simon Fraser University

description: Pooled twenty replicates

data_processing:
MACS2 paried peak calling software was used for identification of SmcHD1 peaks
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: MACS2-paired analysis to obtain the BED.txt files

source_name: SH-SY5Y neuroblastoma

growth_protocol: SH-SY5Y cells were cultured in DMEM which was supplemented with 10% fetal bovine serum. The cells were maintained ina humidified atmospheere which contained 5% CO2 at 37 degree.

extract_protocol:
The cells were fixed using 1% formaldehyde. Upon cell cysis, the chromatin was sheared by sonication and SmcHD1 bound chromatin was isolated using anti-SmcHD1 antiserum.
The DNA libraries were prepared according the Illumina's suggested protocol.

treatment_protocol: the SH-SY5Y cells were treated with 8uM 5azaC for 72 hours. The cells were treated with 5azaC every 24 hours .

tag: cell line

tag: cell line source tissue

value: bone marrow

value: neurobalstoma cells

tag: passage

value: anti-SmcHD1 antiserum


title: SH-SY5Y_5azaC_SmcHD1 ChIP-seq

description: Pooled twenty replicates

source_name: SH-SY5Y neuroblastoma-5azaC treated

tag: treated with

value: DNA demethylating agent 5azaC for 72 hrs


title: P2 GFP+ rep2 ATAC-Seq

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

description:
Bulk ATAC-sequencing
counts10k.tsv
countsgene.tsv

data_processing:
Bowtie2 alignment onto the mm10 genome assembly
RNA-Seq reads were aligned to the mouse transcriptome (mm10 by UCSC) by Hisat2, and differentially expressed genes (DEGs) were identified by Cuffdiff2 with difault parameters.
Bowtie2 was adapted for ATAC-Seq reads alignment on the mouse genome (mm9).Duplicate reads were removed using Picard tools (version 2.10.7). Improper mapped reads were removed using samtools (version 1.5). Read counts for each gene were retrieved using featureCounts program (version 1.5.3).  Read counts overlapping 200 bp interval extending out 5kb on either side of the transcription start site were generated with custom scripts using bedtools (version 2.26.0)
Genome_build: mm10 for RNA-Seq, mm9 for ATAC-Seq

source_name: retinal cells

extract_protocol:
Open chromatin extraction, tagmentation and profiling (ATAC-Seq) performed based on Buenrostro et al. (2013); RNA extraction performed with Qiagen RNAeasy Mini kit;
RNA-Seq; ATAC-Seq; Libraries prepared  according to the Manufacturer's protocols:  TruSeq total RNA Sample preparation kit and Nextera DNA sample preparation kit, Illumina® respectively.

value: retinal progenitor cells (RPCs)

tag: developmental time point

value: post-natal day 2

tag: strain


title: CAST WT Male Rep2


title: CAST WT Male Rep1


title: CAST APP/PS1 Female Rep6

value: Female


title: P0 GFP+ rep2 ATAC-Seq

value: post-natal day 0


title: CAST APP/PS1 Female Rep5

value: CAST


title: CES_GT_TechRep1_ATACseq Sample 5

description: bigWig

extract_protocol: Nuclei from viable frozen cells were isolated with Nuclei EZ lysis buffer (Sigma-Aldrich) then washed once in ATAC-seq lysis buffer and incubated with Tn5 for 30 min at 37°C . Tn5 was stopped with EDTA. After barcodes were added by PCR, the libraries were purified with Ampure beads.

tag: disease

tag: donor

value: GT

tag: treatment


title: CAST APP/PS1 Male Rep5

value: Male

value: 8 months


title: P0 GFP+ rep1 ATAC-Seq

tag: cell type


title: E18 GFP+ rep2 ATAC-Seq

value: embryonic day 18


title: CAST APP/PS1 Female Rep3

value: Left brain hemisphere


title: E16.5 GFP+ rep2 ATAC-Seq

value: embryonic day 16.5


title: E16.5 GFP+ rep1 ATAC-Seq


title: E18 GFP+ rep1 ATAC-Seq


title: CAST WT Male Rep5

value: WT


title: CES_UP_TechRep1_ATACseq Sample 38

description: bigWig

value: Non-malignant

value: UP


title: CAST APP/PS1 Female Rep4


title: CAST WT Female Rep6


title: CAST APP/PS1 Female Rep1


title: E14 GFP+ rep2 ATAC-Seq

value: embryonic day 14


title: E12.5 GFP+ rep2 ATAC-Seq

value: embryonic day 12.5


title: CAST WT Female Rep4


title: CAST WT Female Rep3


title: CAST WT Female Rep5


title: E12.5 GFP+ rep1 ATAC-Seq


title: CAST WT Female Rep2


title: E10 GFP+ rep1 ATAC-Seq

value: embryonic day 10/11


title: CAST WT Female Rep1


title: CES_BK_H3K9me3 Sample 57

description: bigWig

value: BK

value: Rabbit polyclonal H3K9me3 (Abcam, ab8898)


title: P2 GFP-  rep1 RNA-Seq

description:
Bulk RNA-sequencing
RNAseq_diff.tsv

molecule: polyA RNA

value: post-mitotic retinal cells

value: post-natal day 2


title: PWK APP/PS1 Male Rep6

value: PWK


title: P2 GFP-  rep2 RNA-Seq

description:
Bulk RNA-sequencing
RNAseq_diff.tsv


title: P2 GFP+  rep2 RNA-Seq

description:
Bulk RNA-sequencing
RNAseq_diff.tsv

value: retinal progenitor cells (RPCs)


title: PWK APP/PS1 Male Rep5

value: Male


title: P2 GFP+  rep1 RNA-Seq

description:
Bulk RNA-sequencing
RNAseq_diff.tsv


title: PWK APP/PS1 Male Rep4

value: 8 months


title: PWK APP/PS1 Male Rep3


title: PWK APP/PS1 Male Rep2


title: PWK APP/PS1 Male Rep1


title: PWK WT Male Rep6


title: E18 GFP+ rep2 RNA-Seq

description:
Bulk RNA-sequencing
RNAseq_diff.tsv

value: embryonic day 18


title: E18 GFP-  rep1 RNA-Seq

description:
Bulk RNA-sequencing
RNAseq_diff.tsv


title: E18 GFP-  rep2 RNA-Seq

description:
Bulk RNA-sequencing
RNAseq_diff.tsv


title: E18 GFP+ rep1 RNA-Seq

description:
Bulk RNA-sequencing
RNAseq_diff.tsv


title: PWK WT Male Rep5

value: Left brain hemisphere


title: PWK WT Male Rep4


title: E14 GFP+ rep1 ATAC-Seq


title: E14 GFP+ rep2 RNA-Seq

description:
Bulk RNA-sequencing
RNAseq_diff.tsv


title: PWK WT Male Rep3


title: E14 GFP-  rep2 RNA-Seq

description:
Bulk RNA-sequencing
RNAseq_diff.tsv


title: E14 GFP-  rep1 RNA-Seq

description:
Bulk RNA-sequencing
RNAseq_diff.tsv


title: PWK WT Male Rep2


title: PWK APP/PS1 Female Rep6

value: Female


title: E14 GFP+ rep1 RNA-Seq

description:
Bulk RNA-sequencing
RNAseq_diff.tsv


title: PWK WT Male Rep1

value: WT


title: HP_Exposure_2_Treg_Lung

city: Zuerich

first: Lennart

last: Opitz

address: Winterthurerstr. 190

country: Switzerland

institute: FGCZ Zuerich

description: TReg of lungs expression of PBS treated Mice, Biological Replicate 2

data_processing:
The single-end reads that passed Illumina filters were quality filtered and trimmed using Trimmomatic (v0.36).
Read alignment was perfomed using the STAR-aligner (v.2.5.4b) against GRCm38.p5.
Gene quantification was performed using the FeatureCount-function in the R-package Rsubreads (v1.30.3)
Genome_build: GRCm38.p5, Ensembl gene model release 91
Supplementary_files_format_and_content: tab-delimeted txt-files including the raw counts based on Rsubread for each sample

source_name: Treg cells

extract_protocol:
Lung regulatory T-cells were sorted on a FACS Aria II of perinatal PBS and H. pylori extract exposed offspring and RNA was isolated using the RNeasy Micro Kit (Qiagen).
smart-seq2 protocol (Picelli et al., 2014)

treatment_protocol: Mice were treated with an H. pylori extract during pregnancy and lactation.

value: 12.5 weeks

value: Treg cells


title: HP_Exposure_1_Treg_Lung

description: TReg of lungs expression of PBS treated Mice, Biological Replicate 1


title: P2 GFP+ rep1 ATAC-Seq


title: PBS_2_Treg_Lung


title: PWK APP/PS1 Female Rep4


title: PWK APP/PS1 Female Rep3


title: PWK APP/PS1 Female Rep5


title: PWK APP/PS1 Female Rep2


title: 3082 [RNA-seq]

city: Montreal

first: Pierre

last: Paradis

state: QC

address: 3755 ch. de la Côte-Sainte-Catherine

institute: Lady Davis Institute for medical research, Jewish General Hospital, McGill University

data_processing:
Bcl2fastq-1.8.4 (Illumina) was used for base-calling,  adapter trimming, sample identification by barcode and bcl-to-fastq conversion
FastQC was used for sequence quality control. Only samples with >25 base quality at every position were included in the data analysis.
Sequences were mapped to the mouse mm10 genome using STAR 2.3.1.
HTSeq-count 0.5.3p3 was used for RNA gene annotation and counting.
Differential expression analysis was done in R 3.2.3 (https://www.r-project.org) using package EdgeR 3.6.8. A trimmed mean of M-values (TMM) method in the EdgeR protocol was used for sequence read normalization. Only genes with expression level over 1 read per million mapped reads in more than 8 (# of each group) samples were analyzed.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file containing normalized expression levels

source_name: Mesenteric arteries

extract_protocol:
The mesenteric arteries (MAs) were dissected from surrounding tissues, perivascular fat and veins in RNAlater (ThermoFisher Scientific, Waltham, MA). The dissected MAs were homogenized in 1 mL of mirVana miRNA lysis/binding buffer  (ThermoFisher Scientific) for 1 min at maximum speed with a Polytron PT 1600 E homogenizer (KINEMATICA AG, Luzern, Switzerland) and processed for total RNA extraction using the mirVana miRNA isolation kit. Contaminating DNA was removed with the TURBO DNA-free kit according to the manufacturer’s protocol (ThermoFisher Scientific). The concentration and purity of the RNA were assessed with a NanoDrop ND-100 spectrophotometer (ThermoFisher Scientific). RNA quality was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).
Five hundred ng of total RNA (n = 6 per group) was used for total RNA library construction using the TruSeq stranded total RNA sample preparation kit (Illumina) according to the manufacturer's protocol.

treatment_protocol: Ten to 12-week-old male C57BL/6J (Harlan laboratories, Indianapolis, IN) mice (n = 10 per group) were infused or not SC with Ang II (1000 ng/kg/min) for 7 or 14 days.

value: 14-day Ang II


title: PBS_1_Treg_Lung


title: PWK WT Female Rep5


title: 2631 [RNA-seq]


title: PWK WT Female Rep4


title: PBS_3_Treg_Lung

description: TReg of lungs expression of PBS treated Mice, Biological Replicate 3


title: 3081 [RNA-seq]


title: 2625 [RNA-seq]


title: 2621 [RNA-seq]


title: PWK APP/PS1 Female Rep1


title: 2831 [RNA-seq]

value: 14-day Sham


title: PWK WT Female Rep3


title: 2640 [RNA-seq]


title: WSB APP/PS1 Male Rep6

value: WSB


title: PWK WT Female Rep1


title: 2702 [RNA-seq]


title: 2639 [RNA-seq]


title: PWK WT Female Rep2


title: WSB APP/PS1 Male Rep3


title: WSB APP/PS1 Male Rep5


title: WSB APP/PS1 Male Rep4


title: 2886 [RNA-seq]

value: 7-day Ang II


title: 2630 [RNA-seq]


title: 2883 [RNA-seq]


title: WSB APP/PS1 Male Rep1


title: WSB WT Male Rep5


title: 2821 [RNA-seq]


title: 2706 [RNA-seq]


title: WSB WT Male Rep3


title: 2708 [RNA-seq]


title: 2828 [RNA-seq]

value: 7-day Sham


title: WSB WT Male Rep1


title: 2822 [RNA-seq]


title: 2712 [RNA-seq]


title: WSB APP/PS1 Female Rep4


title: WSB WT Male Rep2


title: WSB APP/PS1 Female Rep5


title: 2711 [RNA-seq]


title: WSB APP/PS1 Female Rep3


title: WSB APP/PS1 Female Rep2


title: 3082 [miRNA-seq]

data_processing:
Bcl2fastq-1.8.4 (Illumina) was used for base-calling,  adapter trimming, sample identification by barcode and bcl-to-fastq conversion
FastQC was used for sequence quality control. Only samples with >25 base quality at every position were included in the data analysis.
Sequences were mapped to the mouse mm10 genome using STAR 2.3.1.
miRDeep2 2.0.0.5 was used for Gene annotation, assembly and counting
Differential expression analysis was done in R 3.2.3 (https://www.r-project.org) using package EdgeR 3.6.8. A trimmed mean of M-values (TMM) method in the EdgeR protocol was used for sequence read normalization. Only genes with expression level over 1 read per million mapped reads in more than 8 (# of each group) samples were analyzed.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file containing normalized expression levels

extract_protocol:
The mesenteric arteries (MAs) were dissected from surrounding tissues, perivascular fat and veins in RNAlater (ThermoFisher Scientific, Waltham, MA). The dissected MAs were homogenized in 1 mL of mirVana miRNA lysis/binding buffer  (ThermoFisher Scientific) for 1 min at maximum speed with a Polytron PT 1600 E homogenizer (KINEMATICA AG, Luzern, Switzerland) and processed for total RNA extraction using the mirVana miRNA isolation kit. Contaminating DNA was removed with the TURBO DNA-free kit according to the manufacturer’s protocol (ThermoFisher Scientific). The concentration and purity of the RNA were assessed with a NanoDrop ND-100 spectrophotometer (ThermoFisher Scientific). RNA quality was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).
One μg of total RNA (n = 8 per group) was used for small RNA library construction using the TruSeq small RNA sample preparation kit (Illumina, San Diego, CA) according to the manufacturer's protocol.

treatment_protocol: Ten to 12-week-old male C57BL/6J WT (Harlan laboratories, Indianapolis, IN) mice (n = 10 per group) were infused or not SC with Ang II (1000 ng/kg/min) for 7 or 14 days.


title: WSB APP/PS1 Female Rep1


title: WSB APP/PS1 Female Rep6


title: 2624 [RNA-seq]


title: 3081 [miRNA-seq]


title: WSB APP/PS1 Male Rep2


title: WSB WT Female Rep5


title: WSB WT Male Rep6


title: 2636 [miRNA-seq]


title: 2626 [miRNA-seq]


title: 2631 [miRNA-seq]


title: 2709 [RNA-seq]


title: 2625 [miRNA-seq]


title: 2707 [RNA-seq]


title: WSB WT Female Rep2


title: 2705 [RNA-seq]


title: 2621 [miRNA-seq]


title: WSB WT Female Rep1


title: 2831 [miRNA-seq]


title: B6 APP/PS1 Male Rep5


title: B6 APP/PS1 Male Rep6


title: B6 APP/PS1 Male Rep4


title: 2702 [miRNA-seq]


title: B6 APP/PS1 Male Rep3


title: 2637 [miRNA-seq]


title: B6 APP/PS1 Male Rep2


title: 2819 [miRNA-seq]


title: 2630 [miRNA-seq]


title: B6 APP/PS1 Male Rep1


title: 2639 [miRNA-seq]


title: WSB WT Female Rep4


title: B6 WT Male Rep4


title: B6 WT Male Rep6


title: 2886 [miRNA-seq]


title: 2624 [miRNA-seq]


title: B6 WT Male Rep3


title: 2883 [miRNA-seq]


title: B6 WT Male Rep5


title: 2821 [miRNA-seq]


title: 2640 [miRNA-seq]


title: B6 WT Male Rep2


title: 2711 [miRNA-seq]


title: B6 APP/PS1 Female Rep4


title: B6 APP/PS1 Female Rep3


title: B6 WT Male Rep1


title: B6 APP/PS1 Female Rep2


title: 2622 [miRNA-seq]


title: B6 WT Female Rep5


title: B6 WT Female Rep6


title: 2703 [miRNA-seq]


title: 2708 [miRNA-seq]


title: 2830 [miRNA-seq]


title: 2828 [miRNA-seq]


title: 2824 [miRNA-seq]


title: 2822 [miRNA-seq]


title: B6 WT Female Rep2


title: B6 WT Female Rep4


title: 2712 [miRNA-seq]


title: 2706 [miRNA-seq]


title: B6 WT Female Rep1


title: 2709 [miRNA-seq]


title: CES_ZV_EBF1

data_processing:
Base calls performed with Illumina RTA 2.7.7.
Reads were aligned using bowtie (options --best --strata -v 1 -m 1).
Peaks were called with MACS with standard settings.
genome_build: hs37d5
supplementary_files_format_and_content: bigWig files were generated using bamCoverage (deepTools). Coverage tracks were normalized to 1x.
Supplementary_files_format_and_content: bw

extract_protocol: Patient derived cells were cross-linked with 1 % methanol-free formaldehyde for 10 min. After quenching with glycine, cells were washed three times with PBS and the cell pellet was frozen in liquid nitrogen. For analysis, the cell pellet was thawn and treated with 4U MNase per 1x106 cells for 15 min. MNase was stopped with 10x covaris buffer and the chromatin was sheared for an additional 15 min with the S2 covaris device and the soluble chromatin was then recovered and subjected to a background-minimizing pre-clearing step with an unspecific IgG antibody. For each ChIP-assay an equivalent of 3x106 cells were used with the antibodies. After the IP, chromatin was digested with RNaseA and proteinase K. The purified DNA was cloned into illumina sequencing libraries with the NEBNext Ultra library preparation kit (NEB).

value: CD19+ B-cells from peripheral blood

value: CLL

value: ZV

value: SAB2501166 Sigma goat Lot#7809C2G2


title: B6 APP/PS1 Female Rep1


title: 2707 [miRNA-seq]


title: CES_WW_EBF1

value: WW


title: B6 WT Female Rep3

value: 8 months


title: 2704 [miRNA-seq]


title: 2705 [miRNA-seq]


title: CES_QU_EBF1

value: QU


title: CES_IO_EBF1

value: IO


title: CES_KE_EBF1

value: Non-malignant B cells

value: Non-malignant

value: KE


title: CES_IY_EBF1

value: IY


title: CES_KL_EBF1

value: KL


title: CES_QR_EBF1

value: QR


title: CES_GD_EBF1

value: GD


title: CES_QU_CTCF

value: 61311 Active Motif rabbit Lot#31917004


title: CES_FG_EBF1

value: FG


title: CES_QR_CTCF


title: CES_WW_CTCF

value: CD19+ B-cells from peripheral blood


title: CES_QP_CTCF

value: CLL

value: QP


title: WSB WT Female Rep3

value: WSB

value: WT

value: Female

value: Left brain hemisphere


title: CES_PP_EBF1

value: PP

value: SAB2501166 Sigma goat Lot#7809C2G2


title: CES_QP_EBF1


title: HV_012

city: Homburg Saar

first: Masood

last: Abu-Halima

address: Kirrberger St 60

department: Human Genetics

institute: Univeristy of Saarland

hyb_protocol: standard Agilent protocol

scan_protocol: Arrays were washed and then scanned using a DNA Microarray Scanner (Agilent). Feature extraction software was utilized to extract gene expression data (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label: Cyanine 3-PCP

source_name: Blood

label_protocol: 100 ng total RNA from each sample was processed using the miRNA Complete Labeling and Hyb Kit (Agilent) to generate fluorescently labeled miRNA. The labeled RNA was then applied to the microarray slide per the manufacturer's instructions and hybridized in a rotating oven for 20 hours at 55°C and 20 rpm.

extract_protocol: Total RNA including miRNAs of all MFS patients and HV controls was isolated with the PAXgene miRNA blood kit using the QIAcube™ automated isolation instrument

treatment_protocol: Freshly drawn peripheral blood collected in PAXgene tubes from healthy volunteers and patients with confirmed Marfan syndrome

tag: condition

value: Healthy Control


title: HV_007


title: Jam2-HSC #6

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

hyb_protocol: 3.8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Mouse Gene 2.0 ST arrays for 16 h at 45° C in a GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: The data was read using the R oligo package and was rma normalized. A paired t.test was applied to find significant differences between Jam2- and Jam2+ samples.

label_protocol: Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the dUTP residues followed by a terminal labeling with biotin.

extract_protocol: Total RNA was isolated from both, Jam2+ and Jam2- HSCs, using RNeasy Micro Kit (Qiagen) in accordance with the manufacturer's protocol.

value: C57BL/6 SJL

tag: gender

value: male

value: Hematopoietic stem cells (HSCs:CD150+ CD48- c-kit+ Sca-I+ Lineage- cells)

value: without cell surface expression of Jam2


title: HV_006


title: Jam2+HSC #5

value: with cell surface expression of Jam2


title: Jam2-HSC #4


title: Jam2+HSC #4


title: CES_KE_CTCF

data_processing:
Base calls performed with Illumina RTA 1.18.64.
Reads were aligned using bowtie (options --best --strata -v 1 -m 1).
Peaks were called with MACS with standard settings.
genome_build: hs37d5
supplementary_files_format_and_content: bigWig files were generated using bamCoverage (deepTools). Coverage tracks were normalized to 1x.
Supplementary_files_format_and_content: bw

value: Non-malignant B cells

value: Non-malignant

value: KE

tag: chip antibody

value: 61311 Active Motif rabbit Lot#31917004


title: CES_LM_CTCF

value: CD19+ B-cells from peripheral blood

value: CLL

value: LM


title: Jam2-HSC #2


title: CES_IY_CTCF

value: IY


title: Jam2+HSC #6


title: Jam2-HSC #1


title: Jam2+HSC #2


title: Jam2-HSC #5


title: HV_008


title: CES_PP_CTCF


title: CES_IO_CTCF

value: IO


title: CES_KL_CTCF

value: KL


title: Jam2+HSC #1


title: CES_GD_CTCF

value: GD


title: HV_001

value: Healthy Control


title: CES_FG_CTCF

value: FG


title: CES_ZV_TechRep1_ATACseq Sample 48

description: bigWig

data_processing:
Base calls performed with Illumina RTA 2.7.7.
Reads were trimmed using Trimmomatic version 0.36 (Bolger et al, 2014). Trimmed reads were mapped to the human genome (hs37d5) using bowtie2 (Langmead et al, 2009) with the options “--very- sensitive -X 2000”.
After removing reads overlapping ENCODE blacklist regions, duplicated reads were discarded using rmdup of SAMtools version 1.3 (Li et al, 2009). Only reads not mapping to the mitochondrial genome were kept.
For further analysis and calculation of coverage tracks all reads were shifted to be centered on the cutting position of the transposase and extended to a total of 29 bp to represent the region occupied by the transposase (Adey et al, 2010).
hs37d5
bigWig files were generated using bamCoverage (deepTools). Coverage tracks were normalized to 1x.

value: ZV


title: MFS_012

value: Marfan syndrome


title: MFS_007


title: MFS_006


title: MFS_008


title: HV_003


title: HV_004


title: CES_XP_TechRep2_ATACseq Sample 47

description: bigWig

value: XP


title: rbpl-3 (RNA-seq)

city: Pullman

first: Li

last: Tian

state: WA

address: Clark hall, IBC, Washington State University

department: IBC

institute: Washington State University

data_processing:
RNA-seq reads were trimmed and mapped to the rice genome database (http://rice.plantbiology.msu.edu/index.shtml) using the CLC genomics workbench (Qiagen)
Genome_build: RGAP 7 rice genome database (http://rice.plantbiology.msu.edu/index.shtml)
Supplementary_files_format_and_content: tab-delimited file with data of RPKM, log2 fold change and P-value.

organism: Oryza sativa

source_name: Rice developing seeds

growth_protocol: Wild type and mutant lines were grown in walk-in growth chambers with a diurnal cycle of 12 h light/12 h dark at 27oC.

extract_protocol:
Total RNA samples of wild type, rbpl lines were extracted from the dehulled 10-14 days old developing seeds using Plant RNA Reagent (Invitrogen, www.invitrogen.com)
RNA-seq libraries were constructed using a NEBNext Ultra RNA Library Prep Kit for Illumina and sequenced by Novogene company (https://en.novogene.com).

value: Seed

tag: Stage

value: 10-14 days after flowering

tag: genotype

value: RBP-L knockdown line


title: MFS_003


title: MFS_004


title: MFS_001


title: CES_XP_TechRep1_ATACseq Sample 46

description: bigWig


title: CES_WS_TechRep2_ATACseq Sample 43

description: bigWig

value: Non-malignant

value: WS


title: rbpl-2 (RNA-seq)


title: CES_TC_TechRep1_ATACseq Sample 35

description: bigWig

value: TC


title: WT-2 (RNA-seq)

value: wild type, ZH11


title: rbpl-1 (RNA-seq)


title: WT-3 (RNA-seq)


title: WT-1 (RNA-seq)


title: CES_WS_TechRep1_ATACseq Sample 42

description: bigWig


title: CES_ZV_TechRep2_ATACseq Sample 49

description: bigWig

value: CLL


title: CES_TH_TechRep1_ATACseq Sample 36

description: bigWig

value: TH


title: CES_TH_TechRep2_ATACseq Sample 37

description: bigWig


title: CES_TB_TechRep1_ATACseq Sample 33

description: bigWig

value: TB


title: CES_SI_TechRep2_ATACseq Sample 32

description: bigWig

value: SI


title: CES_SI_TechRep1_ATACseq Sample 31

description: bigWig


title: Chd4_rep3

city: Denver

first: James

middle: R

last: Hagman

state: Colorado

address: 1400 Jackson St

department: Biomedical Research

institute: National Jewish Health

data_processing:
Sequence reads of 30 or more nt were mapped to the mm9 (NCBI build 37) assembly of the mouse genome with the STAR RNA-Seq aligner version 2.4.0a using gene annotation data from Ensembl version 67
For each gene in the Ensembl 67 annotation, reads were counted using the HTSeq software version 0.6.0
Statistical comparisons of the gene expression between the cell types were performed with the DESeq2 package version 1.4.5 for the R statistical software version 3.1.0.
Genome_build: mm9
Supplementary_files_format_and_content: gzipped tar ball of tab-separated text file with raw counts for genes.

source_name: pro-B cells

extract_protocol:
Pro-B cells (Lin–B220+CD43+CD24+BP1–IgM–) were isolated from the bone marrow of Chd4fl/flCd79a-Cre or wild-type littermate controls using the Synergy Sorter (iCyt). Pro-B cells were pooled from one to four mice of each genotype. RNA from these cells (~100,000-200,000 total cells per biological replicate) was isolated using the RNeasy Plus Mini kit and RNeasy MinElute kit (Qiagen), with on-column treatment with RNase-free DNaseI, according to manufacturer’s instructions.
mRNA was captured by two rounds of magnetic Oligo-dT beads.  Libraries were prepared with 100 ng of total RNA using the KAPA stranded mRNA-seq kit for the Illumina platform.

tag: age

value: 4-6 weeks

value: bone marrow

value: pro-B


title: Ctrl_rep1

tag: tissue

value: wild type


title: Ctrl_rep3


title: Ctrl_rep2


title: CES_RP_TechRep2_ATACseq Sample 30

description: bigWig

value: RP


title: P3MH-1

description: RNA sequencing

data_processing:
RNA-seq reads were trimmed and mapped to the rice genome database (http://rice.plantbiology.msu.edu/index.shtml) using the CLC genomics workbench (Qiagen)
Genome_build: mapped to rice genome database (http://rice.plantbiology.msu.edu/index.shtml)
Supplementary_files_format_and_content: Excel file includes RPKM values.

extract_protocol:
Total RNA samples of wild type, P1MH and P3MH mutants were extracted from the dehulled 10-14 days old developing seeds using Plant RNA Reagent (Invitrogen, www.invitrogen.com)
RNA-seq libraries were constructed using a ScriptSeqTM v2 RNA-Seq Library Preparation Kit (Illumina) following the manufacturer's instructions

value: RBP-P mutant A252T


title: P1MH-3

description: RNA sequencing

value: Seed

value: RBP-P mutant G401S


title: P3MH-2

description: RNA sequencing

value: 10-14 days after flowering


title: P1MH-2

description: RNA sequencing


title: P1MH-1

description: RNA sequencing


title: Chd4_rep2


title: Chd4_rep1


title: P3MH-3

description: RNA sequencing


title: CES_TB_TechRep2_ATACseq Sample 34

description: bigWig


title: WT-2

description: RNA sequencing


title: WT-1

description: RNA sequencing


title: CES_RC_TechRep2_ATACseq Sample 28

description: bigWig

value: RC


title: CES_RC_TechRep1_ATACseq Sample 27

description: bigWig


title: CES_QU_TechRep2_ATACseq Sample 26

description: bigWig

value: QU


title: CES_QP_TechRep2_ATACseq Sample 24

description: bigWig

value: QP


title: 4-3-15h

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
Run on NextSeq500 using v2 chemistry. RTA Version 2.4.6. BCL files were converted to fastq using bcl2fastq. Indexes were split using custom scripts allowing 1 mismatch
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The reads were aligned to the previously reported genome sequence for this strain (Love et al., 2016; PRJNA304977) using RSEM version 1.2.15 with bowtie2 version 2.2.3.
Alignment target was prepared with RSEM version 1.2.15 with bowtie2 version 2.2.3 and the command "rsem-prepare-reference --gtf phaffii_WT.c2.gtf --bowtie2 WT.v1.fa ./phaffii_WT". Input files are provided in Processed Data.
Genome_build: ASM170808v1
Supplementary_files_format_and_content: tab-delimited text files, one with FPKM values for each annotated gene and sample, one with RSEM expected counts for each annotated gene and sample, the WT Komagataella phaffii assembly and a gtf file reporting the gene annotations.

organism: Komagataella phaffii

source_name: Cultured Cells

growth_protocol: Cells were grown in 1 L shake flasks with 200mL working volume, shaken in an Innova 4230 shaking incubator. The shake rate was set to 300rpm and the temperature was controlled at 25°C.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit (cat. no. 74104) and genomic DNA clean-up was performed using NEB DNAse I kit (catalog number M0303S) and Beckman Coulter RNAClean XP beads (catalog number A63987).
Libraries were constructed using Neoprep and sequenced on the Illumina NextSeq platform to generate 75-nucleotide paired-end reads at a read depth of at least 9 million reads per sample.

tag: media formulation

value: d'Anjou


title: CES_QU_TechRep1_ATACseq Sample 25

description: bigWig

value: CLL


title: 4-5-15h

value: Generation 1


title: 4-1-15h

value: BMGY


title: 3-5-15h


title: WT-3

description: RNA sequencing


title: CES_PP_TechRep2_ATACseq Sample 22

description: bigWig

value: PP


title: WRKY26SI_replicate 2

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

country: Italy

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a ScanArray 4000XL (Perkin-Elmer) at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: Trangenic Shiraz; leaves; VvWRKY26 silenced line_replicate 2

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: Grapevine plants (Vitis vinifera cv. Shiraz, BVRC12 clone) were grown in Coombe Vineyard (University of Adelaide, Urrbrae, South Australia). For the genetic transformation embryogenic calli were collected from anthers during the 2009 season. For the microarray analysis performed on grapevine, three biological replicates of fully expanded leaves were collected from control and transgenic plants before the onset of the altered phenotype.

extract_protocol: Total RNA was isolated from ~100 mg of the ground grapevine leaves tissue using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich).

tag: cultivar

value: Shiraz

tag: genotype/valiation

value: RNA silencing of VvWRKY26

tag: vintage

value: leaves


title: 3-1-15h


title: 3-3-15h


title: CES_PP_TechRep1_ATACseq Sample 21

description: bigWig

extract_protocol: Nuclei from formaldehyde fixed cells were isolated with Nuclei EZ lysis buffer (Sigma-Aldrich) then washed once in ATAC-seq lysis buffer and incubated with Tn5 for 30 min at 37°C. Tn5 was stopped with EDTA. Previously fixed samples were reverse cross-linked with 300 mM NaCl for two hours at 65°C and DNA was purified with Ampure beads. After barcodes were added by PCR, the libraries were purified with Ampure beads.


title: CES_QP_TechRep1_ATACseq Sample 23

description: bigWig


title: CES_OZ_TechRep2_ATACseq Sample 20

description: bigWig

value: OZ


title: WRKY26SI_replicate 1

source_name: Trangenic Shiraz; leaves; VvWRKY26 silenced line_replicate 1


title: MYB5a/bSI_replicate 3

source_name: Trangenic Shiraz; leaves; VvMYB5a/VvMYB5b silenced line_replicate 3

value: RNA silencing of VvMYB5a and VvMYB5b


title: MYB5a/bSI_replicate 2

source_name: Trangenic Shiraz; leaves; VvMYB5a/VvMYB5b silenced line_replicate 2


title: 2-5-15h


title: WT_SI_replicate 3

source_name: Wild Type Shiraz; leaves; control of the silenced lines_Replicate 3

value: wild type


title: CES_OZ_TechRep1_ATACseq Sample 19

description: bigWig

source_name: CD19+ B-cells from peripheral blood of CLL patient


title: MYB5a/bSI_replicate 1

source_name: Trangenic Shiraz; leaves; VvMYB5a/VvMYB5b silenced line_replicate 1


title: WRKY26SI_replicate 3

source_name: Trangenic Shiraz; leaves; VvWRKY26 silenced line_replicate 3


title: 2-3-15h


title: WT_MYB5bOE_replicate 4

source_name: Wild Type Shiraz; leaves; control of the VvMYB5b overepression_Replicate 3


title: MYB5bOE_replicate 3

source_name: Trangenic Shiraz; leaves; VvMYB5b overexpressing line_replicate 3

value: VvMYB5b overexpression


title: WT_MYB5bOE_replicate 3

source_name: Wild Type Shiraz; leaves; control of the VvMYB5b overepression_Replicate 2


title: Retinoic acid+Poly I:C treatment

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform using PrimeView.cdf and PrimeView.na36.annot.csv annotation.  RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: dorsal hand

label_protocol: Biotinylated cRNAs were prepared with the Affymetrix GeneChip 3' IVT Plus Kit per manufacturer's instructions.

growth_protocol: Normal human epidermal keratinocytes (NHEKs) were harvested from adult dorsal hand skin and cultured in KGM-GOLD supplemented with ROCK inhibitor (10 uM; Y-27632) to passage 2 before use.

extract_protocol: Total RNA was isolated from cells using the RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Cells were plated onto 6-well plate with the number of 5x10^6 cells (Day 0). On Day 1, cells were treated with atRA (0.1 uM) incubated for 2 days. Then, Poly I:C (0.1 ug/ml) was treated into cells and incubated for 3 days. EtOH was used as a vehicle. At the end of experiment, cells were harvested for RNA isolation.

value: adult dorsal hand skin

value: normal human epidermal keratinocytes (NHEKs)

value: Retinoic acid and Poly I:C


title: CES_NQ_TechRep2_ATACseq Sample 18

description: bigWig

value: NQ


title: MYB5bOE_replicate 1

source_name: Trangenic Shiraz; leaves; VvMYB5b overexpressing line_replicate 1


title: WT_MYB5bOE_replicate 2

source_name: Wild Type Shiraz; leaves; control of the VvMYB5b overepression_Replicate 1


title: WT_SI_replicate 1

source_name: Wild Type Shiraz; leaves; control of the silenced lines_Replicate 1


title: WT_SI_replicate 2

source_name: Wild Type Shiraz; leaves; control of the silenced lines_Replicate 2


title: Poly I:C treatment

value: Poly I:C


title: 2-1-15h

source_name: Cultured Cells


title: 1-5-15h


title: CES_NQ_TechRep1_ATACseq Sample 17

description: bigWig


title: CES_MJ_TechRep1_ATACseq Sample 16

description: bigWig

source_name: Non-malignant B cells of healthy donor

extract_protocol: Viable frozen cells were incubated with Tn5 for 30 min at 37°C in the presence of 0.1 % Igepal CA-630 (Sigma-Aldrich). Tn5 was stopped with EDTA. After barcodes were added by PCR, the libraries were purified with Ampure beads.

value: Non-malignant

value: MJ


title: MYB5aOE_replicate 3

source_name: Trangenic Shiraz; leaves; VvMYB5a overexpressing line_replicate 3

value: VvMYB5a overexpression


title: MYB5bOE_replicate 2

source_name: Trangenic Shiraz; leaves; VvMYB5b overexpressing line_replicate 2


title: Retinoic acid treatment

value: Retinoic acid


title: CES_MA_TechRep2_ATACseq Sample 15

description: bigWig

source_name: Non-malignant B cells of healthy donors

value: MA


title: 1-1-15h

value: BMGY


title: MYB5aOE_replicate 2

source_name: Trangenic Shiraz; leaves; VvMYB5a overexpressing line_replicate 2

value: Shiraz


title: Control treatment

value: Control


title: CES_MA_TechRep1_ATACseq Sample 14

description: bigWig


title: MYB5aOE_replicate 1

source_name: Trangenic Shiraz; leaves; VvMYB5a overexpressing line_replicate 1

value: leaves


title: Control hESC H9 Schwann cells - biological repeat 2

first: Gabsang

last: Lee

address: 733 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

description:
gene expression data from hiPSCs differentiated into Schwann cells for 21 days
BMuk-IPS-Cntl24B-1a-HuPrView_(PrimeView).CEL

hyb_protocol: 18hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: Control hESC H9

label_protocol: NuGEN Ovation RNA amplification System v2 kit following manufacturer's protocol

growth_protocol: hiPSCs and hESCs were maintained on MEF feeder layers through weekly passaging for up to 50 passages.  Daily media change was performed with human ESC media.

extract_protocol: Trizol then QIAGEN RNeasy kit

treatment_protocol: Human pluripotent stem cells were plated and differentiated into putative Schwann cells. Briefly, colonies of pluripotent cells were rendered into single cells and plated on Geltrex, an artificial basement membrane-like matrix, in accordance with previous protocols9. They were then treated with a combination of small molecules to induce neuronal and Schwann cell differentiation. On day 0, to initiate differentiation, aspirate the medium and add KSR medium containing 10 μM SB-431542 and 500 nM LDN-193189. On day 2 change medium to KSR medium containing 10 μM SB-431542, 500 nM LDN-193189, 3 μM CHIR 99021, 10 μM DAPT. On day 4 change medium to KSR/NB (3:1) medium containing 3 μM CHIR 99021 and 10 μM DAPT (final concentrations are for the combined KSR/NB mixture). On day 6, change medium to KSR/NB (1:1) medium containing 3 μM CHIR 99021 and 10 μM DAPT. On day 8, change medium to KSR/NB (1:3) medium containing 3 μM CHIR 99021 and 10 μM DAPT. On day 10, 14, and 18 change medium to NB medium containing 200 μM dibutyrl cAMP and 200 μM sodium L-ascorbate. Maintain in this manner until day 21-23 of differentiation, when the cells are ready for purification.  Schwann cells were purified with Fluorescence Activated Cell Sorting (FACS) after 21-23 days of differentiation using a PE-conjugated antibody to the alpha4 integrin, CD49d (R&D Systems, FAB1354P), and then utilized for gene expression profiling.

tag: disease state

value: control

tag: fibroblast donor age

tag: cell line

value: hESC

tag: differentiated cell type

value: Schwann cell


title: 1-3-15h

tag: strain

value: d'Anjou


title: Control hiPSC 2623 Schwann cells - biological repeat 2

description:
gene expression data from hiPSCs differentiated into Schwann cells for 21 days
BMuk-IPS-Cntl23-1a-HuPrView_(PrimeView).CEL

source_name: Control hiPSC 2623

tag: cell type

value: hiPSC


title: GDT_Control_5h_Rep3

city: Bethesda

first: Cameron

last: Palmer

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

data_processing:
Illumina HiSeq2500 sequencing, 50bp reads.
Adapter removal with cutadapt v1.16
Alignment to Dictyostelium discoideum genome with hisat v2.1.0
Assignment of reads to gene features with Subread featureCounts v1.6.1
Signal detection via differential expression analysis between triplicate groups with DESeq2 1.18.1
Genome_build: ENSEMBL 2.7.33
Supplementary_files_format_and_content: Number of reads assigned to gene features, as computed by Subread featureCounts v1.6.1

organism: Dictyostelium discoideum

growth_protocol: Dictyostelium discoideum AX3 strain cells were grown axenically in HL5 medium with glucose (ForMedium) containing 100 μg/ml of ampicillin and 100 μg/ml streptomycin, at 22˚C in suspension culture, shaking at ~180 rpm, to a density of 1-1.5 x 106 cells/ml.

extract_protocol:
Total RNA from the growing or developing cells were isolated using the RNAeasy mini preparation kit [Qiagen; see Key Resource Table] and following the manufacturer’s protocol.
RNA integrity was checked by running a denaturing MOPS-formaldehyde gel and with the Agilent bioanalyzer. 4 µg of total RNA was used for poly(A) enrichment, followed by mRNA sequencing library preparations using the Truseq mRNA library preparation kit.

treatment_protocol: To examine Dictyostelium multicellular development in starvation condition, log phase growth cells (1-1.5×106 cells/ml) were adhered in six well plates (3.5 x 106 cells/well; or 0.4 x 106 cells/cm2), replenished with fresh full growth media or GDT-growth media (see below) and incubated for 2 hours. Followed by washing cells (2 times) with Developmental Buffer (DB; 5 mM Na2HPO4, 5 mM NaH2PO4, 1 mM CaCl2, 2 mM MgCl2, adjust to pH-6.6) to remove any sticking media components, filled wells with 2.0 ml of DB and monitored developmental progress at regular intervals during starvation. To examine growth-to-development transition induced by rapamycin without nutrient withdrawal, cells adhered in six well plates (see above), washed with GDT growth media (2 times), replenished with 2 ml of GDT media [50% Glc[—] (HL5 media without glucose, Formedium), 27 mM glucose, 1 mM MgCl2, 0.5 mM CaCl2, adjust to pH-6.6] media and incubated at 22°C for 2 hours, followed with rapamycin treatment to the GDT-media adapted cells for acquiring growth-to-development transition.

tag: growth medium

value: GDT (Growth-to-development transition)

tag: agent

tag: time point

value: 5 hours


title: GDT_Rapamycin_5h_Rep3

value: Rapamycin


title: Control hESC H9 Schwann cells - biological repeat 1

description:
gene expression data from hiPSCs differentiated into Schwann cells for 21 days
BMuk-IPS-Cntl24A-1a-HuPrView_(PrimeView).CEL


title: CES_LM_TechRep2_ATACseq Sample 13

description: bigWig

source_name: CD19+ B-cells from peripheral blood of CLL patient

tag: disease

value: CLL

tag: donor

value: LM

tag: treatment


title: CES_LM_TechRep1_ATACseq Sample 12

description: bigWig


title: GDT_Starvation_2h_Rep3

value: Starvation

value: 2 hours


title: CES_KL_TechRep2_ATACseq Sample 11

description: bigWig

value: KL


title: CES_KL_TechRep1_ATACseq Sample 10

description: bigWig


title: WT_MYB5aOE_replicate 2

source_name: Wild Type Shiraz; leaves; control of the VvMYB5a overepression_Replicate 2

value: wild type

tag: tissue


title: GDT_Starvation_5h_Rep3


title: CES_JK_TechRep2_ATACseq Sample 9

description: bigWig

value: JK


title: CMT1A hiPSC 5165 Schwann cells - biological repeat 1

description:
gene expression data from hiPSCs differentiated into Schwann cells for 21 days
BMuk-CMT1A-B52_5165-1a-PrimeView_(PrimeView).CEL

source_name: CMT1A hiPSC 5165


title: Control hiPSC 2623 Schwann cells - biological repeat 1

description:
gene expression data from hiPSCs differentiated into Schwann cells for 21 days
BMuk-IPS-Cntl22-1a-HuPrView_(PrimeView).CEL


title: GDT_Rapamycin_2h_Rep3


title: GDT_Control_2h_Rep3

value: Control


title: CES_JK_TechRep1_ATACseq Sample 8

description: bigWig


title: GDT_Starvation_30min_Rep3

value: 30 minutes


title: CES_IO_TechRep2_ATACseq Sample 7

description: bigWig

value: IO


title: GDT_Rapamycin_30min_Rep3


title: WT_MYB5aOE_replicate 3

source_name: Wild Type Shiraz; leaves; control of the VvMYB5a overepression_Replicate 3

value: Shiraz

value: leaves


title: CES_IO_TechRep1_ATACseq Sample 6

description: bigWig


title: CMT1A hiPSC 5148 Schwann cells - biological repeat 2

description:
gene expression data from hiPSCs differentiated into Schwann cells for 21 days
BMuk-CMT1A-B54_5148-1a-PrimeView_(PrimeView).CEL

source_name: CMT1A hiPSC 5148

value: Schwann cell


title: WT_MYB5aOE_replicate 1

source_name: Wild Type Shiraz; leaves; control of the VvMYB5a overepression_Replicate 1


title: GDT_Control_30min_Rep3


title: CES_FG_TechRep2_ATACseq Sample 4

description: bigWig

value: FG


title: UPEC_4H_C

city: Giessen

first: Melanie

last: Markmann

state: Hessen

address: Rudolf-Buchheim-Str. 7

department: Anaesthesiology

institute: University of Giessen

hyb_protocol: Extracted RNA was subjected to cRNA synthesis, cRNA fragmentation and finally hybridization on Rat Whole Genome Arrays using the CodeLink Expression Assay Kit (GE Healthcare, Chalfont St. Giles, Buckinghamshire, UK) according to the manufacturer's instructions.

scan_protocol: Samples were scanned using the GenePix® 4000 B scanner and the GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA)

data_processing: depletion of low signal values, outlier removal, quantile normalization, logarithization.  The file Data_Table_RatSertoli_HMDI_UPEC_log_normalized_Bhushan_2.xlsx includes the Codelink ID as gene identifier.

organism: Rattus norvegicus

label_protocol: Bioarrays were stained with Cy5™-streptavadin (GE Healthcare)

growth_protocol: Sertoli cells were isolated from 19-day-old Wistar rats as described and infected with either with bacteria from strain UPEC 536 (NCBI:NC_008253, CP000247) or the alpha-hemolysin (hlyA) double mutant (HDM) of this strain.

extract_protocol: RNA isolation was performed with miRNeasy Mini Kit QIAGEN Cat-No-217004 according to manufacturer’s instructions (“Purification of Total RNA, Including Small RNAs, from Animal Tissues”, miRNeasy Mini Handbook: pp 22-25).

treatment_protocol: Sertoli cells were treated as indicated conditions. RNA was isolated and subjected to cRNA synthesis, cRNA fragmentation and finally hybridization on CodeLink Human Whole Genome using the CodeLink Expression Assay Kit (GE Healthcare) according to manufacturer's instructions.

value: sertoli cells

tag: background strain

value: Wistar

value: UPEC

tag: replicate


title: CMT1A hiPSC 5148 Schwann cells - biological repeat 3

description:
gene expression data from hiPSCs differentiated into Schwann cells for 21 days
BMuk-CMT1A-B52_5148-1a-PrimeView_(PrimeView).CEL

value: hiPSC


title: UPEC_4H_B


title: GDT_Control_0min_Rep3

value: GDT (Growth-to-development transition)

value: 0 minutes


title: CMT1A hiPSC 5148 Schwann cells - biological repeat 1

description:
gene expression data from hiPSCs differentiated into Schwann cells for 21 days
BMuk-CMT1A-B58_5148-1a-PrimeView_(PrimeView).CEL


title: HV_012

label: Cyanine 3-CTP

source_name: Blood

label_protocol: 100 ng total RNA from each sample was reversely transcribed, amplified and labeled using the LowInput QuickAmp Labeling Kit (Agilent). Quantification and specific activity of labeled complementary RNA (cRNA) was evaluated using the NanoDrop-2000 spectrophotometer (Thermo Scientific) to ensure that labeled cRNA was of sufficient quality for hybridization. A total of 600 ng of cRNA was then applied to the microarray slide per the manufacturer's instructions and hybridized in a rotating oven for 17 hours at 65°C and 10 rpm.

tag: condition

value: Healthy Control


title: CES_FG_TechRep1_ATACseq Sample 3

first: Karsten

last: Rippe

institute: DKFZ

description: bigWig

value: CLL


title: GDT_Starvation_5h_Rep2

value: Starvation

value: 5 hours


title: UPEC_2H_B


title: HV_008


title: HV_007


title: CES_RP_TechRep1_ATACseq Sample 29

description: bigWig

value: RP


title: UPEC_4H_A


title: GDT_Rapamycin_5h_Rep2

value: Rapamycin


title: KO spleen 3

city: Pittsburgh

first: Louise

last: D'Cruz

state: Pennsylvania

address: E1053 Biomedical Science Tower, 200 Lothrop Street

department: Immunolgy

institute: University of Pittsburgh

description: Sorting Protocol: A minimum of 500 cells were sorted from the indicated tissue using an BD Aria II FACS sorter

data_processing:
All alignment and analysis was processed using the CLC Genomics Suite software
Genome_build: mm9

source_name: sorted CD4+ CD25+ T cells from the spleen

extract_protocol:
mRNA was processed using the SMARTer-seq v4 Ultra Low input RNA kit from Takara according to the manufacturers instructions
Library was constructed using the Nextera DNA XT (low input) kit from Illumina

value: spleen

tag: genotype

value: Id2 CKO


title: UPEC_2H_C


title: UPEC_2H_A


title: GDT_Control_5h_Rep2

value: Control


title: HV_006


title: HV_004


title: HDM_4H_C

value: HDM


title: HDM_4H_B


title: HV_001


title: WT spleen 3

value: WT


title: HDM_4H_A

value: sertoli cells


title: MFS_012

value: Marfan syndrome


title: GDT_Rapamycin_2h_Rep2

value: 2 hours


title: GDT_Starvation_2h_Rep2


title: HDM_2H_C

value: Wistar


title: KO adipose 3

source_name: sorted CD4+ CD25+ T cells from the visceral adipose tissue

value: visceral adipose tissue


title: KO spleen 2


title: KO adipose 2


title: GDT_Control_2h_Rep2

value: GDT (Growth-to-development transition)


title: WT adipose 3


title: WT spleen 2


title: MFS_008


title: GDT_Starvation_30min_Rep2

value: 30 minutes


title: GDT_Rapamycin_30min_Rep2


title: CTRL_B


title: HDM_2H_A


title: MFS_006


title: HDM_2H_B


title: WT adipose 2


title: CTRL_C


title: MFS_004


title: CTRL_A


title: MFS_007


title: MFS_003


title: KO rep3

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: polysome mRNAs

data_processing:
Illumina bcl2fastq 1.8.4 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.0-alpha5. Before mapping, reads ≤40 bases were removed, and reads with  quality mean ≤30 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from Ensembl version 75) using the STAR mapper (version 2.4.0j, default parameters). Alignments from reads matching more than once on the genome were removed. Mus musculus GFF3 genome annotation from from Ensembl version mm10-ens75 was used to compute gene expression. All overlapping regions between alignments and referenced exons were counted with HTSeq-count 0.5.3.
Genome_build: mm10 version Ensembl 75
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

source_name: Hypocampus

extract_protocol:
BAC array purification
Ovation RNA-Seq system NuGEN

value: tg:Aldh1L1-RPL10aGFP/ Gfap Cre Cx43 fl/fl

tag: age

value: 6 weeks


title: GDT_Control_30min_Rep2


title: KO rep2

description: polysome mRNAs


title: GDT_Control_0min_Rep2

value: 0 minutes


title: KO rep1

description: polysome mRNAs


title: BCSCsGFP [ATAC-seq]

city: Hangzhou

first: sen

last: ye

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou, Zhejiang Province, P.R. China

country: China

institute: Zhejiang University

description:
ATAC-seq of overexpressed GFP in BCSCs
SETD4_vs_GFP_peak_compare_table.tsv

data_processing:
The library of each samples was sequenced on an Illumina Hiseq platform with a 150 bp paired-end module
Reads were aligned to the human genome using Bowtie2 (v2.2.9). Peaks were called for aligned reads using MACS2
Different enriched peaks were analyzed using differential peaks and notated using notate peaks.pl in the homer software.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files for each Sample.

source_name: MCF7 cell line

growth_protocol: BCSCsSETD4 or BCSCsGFP were plated at a density of 4000-8000 cells/well in the 6-well ultra-low-attachment plates and cultured in tumorspheres formation conditions (DMEM/F12 (Corning; 10-092-cv) supplemented with 10% serum replacement (SR; Thermo Fisher Scientific; 10828028), human recombinant epidermal growth factor (EGF 20 ng/ml), heparin sodium of 5 ng/ml (MedChemExpress; 9041-08-1), human recombinant basic fibroblast growth factor of bFGF (20 ng/ml) (PeproTech; 96-100-18B-500) at 37℃ in a humidified 5% CO2 incubator). The medium was replaced every 2 days. After culturing for two weeks, tumorspheres could be visualized using an inverted phase-contrast microscope.

extract_protocol:
Nuclei was extracted from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit.
The DNA samples were constructed for the library and sequenced on an Illumina Hiseq Hiseq platform.

treatment_protocol: SETD4 gene cloning: to obtain the full length ORF of human SETD4 gene, primers (GFP-SETD4F: GCCGCGATCGCCATGCAGAAAGGAAAAGG, GFP-SETD4R: CGTACGCGTTCAGGTAAAAGCTGTTTG) were designed and PCR was performed. Total RNA was extracted from Artemia by using TRIzol reagent (Invitrogen; 15596018), according to the manufacturer’s instructions, and then quantified by using a Genova UV-visible spectrophotometer at 260 nm. First-strand cDNA was synthesized from 1 ug of total RNA by using the SuperScript/First-Strand cDNA synthesis kit (Invitrogen; 11904018), according to the manufacturer’s protocol, and was used as a template for PCR. Victor and overexpression of SETD4 gene: Based on the sequence of the human SETD4 gene (NM_017438.4) in GenBank, the pLent-EF1a-SETD4-CMV-GFP-P2A-Puro overexpression plasmid (Vigene biosciences; LT88002) was synthesized and transfected with a viral packaging plasmid of 10 μg of plasmid containing the vector of SETD4, 10 μg of pMD2.G (Addgene; 12259) and 15 μg of psPAX2 (Addgene; 12260) by Lipo 3000 (Invitrogen; L3000015) into HEK293T cells overnight, and the viral supernatant was collected 48 hours later. The viral supernatant was filtered through a 0.45 μm filter, and the freshly sorted BCSCs were used for infection in the presence of 5 μg/ml Polybrene (Sigma-Aldrich; 107689-10G). Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) were performed in BCSCsSETD4 and BCSCsGFP.

tag: signature

value: H4K20me3 low


title: GDT_Starvation_5h_Rep1

value: Starvation

value: 5 hours


title: MFS_001


title: Littermates rep3

description: polysome mRNAs

value: tg:Aldh1L1-RPL10aGFP/ Cx43 fl/fl


title: HV_003

value: Healthy Control


title: BCSCsSETD4 [ATAC-seq]

description:
ATAC-seq of overexpressed SETD4 in BCSCs
SETD4_vs_GFP_peak_compare_table.tsv

tag: cell line

value: H4K20me3 high


title: GDT_Rapamycin_5h_Rep1

value: Rapamycin


title: CB primary cells normoxia

city: Heidelberg

first: Matias

last: Mosqueira

state: Baden-Wuttenberg

address: Im Neuenheimer Feld, 326 R414

department: Institute of Physiology and Pathop

institute: Heidelberg University Hospital

description:
This GEO Sample represents 3 replicates.
Nx
CB_Nx_1, CB_Nx_2, CB_Nx_3

hyb_protocol: Membranes were prehybridized in ExpressHyb hybridization buffer, containing the sheared salmon testes DNA for 30 min at 68 ºC in a rotating hybridization oven. The heat-denatured probe (95 ºC for 5 min) was hybridized overnight at 68 ºC with continuous agitation followed by three washing steps [twice at room temperature for 5 min with Sodium Chloride/ Sodium Citrate solution (1 X SSC = 150 mM NaCl/15 mM sodium citrate, pH 7.0), twice with 2 X SSC plus 1% SDS at 68 ºC for 30 min, and twice with 0.1 X SSC plus 0.5% SDS at room temperature for 30 min].

scan_protocol: The membranes were exposed on phosphoimager up to 3 hours at room temperature.

data_processing: Image acquisition and quantification of the average of three membranes under Nx and three under CH were performed using the software AtlasImage V2.0 (Clontech). The normalization was performed to each experiment using a coefficient of normalization (adding the averaging of the signal of all genes to the signal values for all the genes that are above the background signal). The parameters used for the data analysis were the ratio threshold (TR) and the difference threshold (TD). Here, we defined the criterion to classified as a significant change in gene expression for TR of 1.5 and TD of 1,000 pixels, respectively. The TR was defined as the ratio between the CH normalized and averaged of the adjusted intensity signal over the Nx normalized and averaged of the adjusted intensity signal of the same gene. TD was defined as the difference between CH normalized and averaged of the adjusted intensity signal minus the Nx normalized and averaged of the adjusted intensity signal of the same gene.

label: [α-32P] dCTP (3000 Ci/mmol)

source_name: carotid body primary cultured cells

label_protocol: Radiolabeled cDNA probes were synthesized from 6 μg of RNA amplified in the presence of dATP, dTTP, dGTP, [α-32P] dCTP (3000 Ci/mmol), poly T, Superscript II Reverse transcriptase (Invitrogen) and the purified (Atlas NucleoSpin Extraction Spin Columns, BD Biosciences Clontech).

growth_protocol: The experiments were performed on CB cultured cells from Sprague Dawley rats (ca. 100 g) anesthetized with sodium pentobarbital (40 mg/kg i.p.). The neck was opened and the carotid bifurcations were exposed. Sixteen CBs per primary culture were excised and placed in ice-chilled Ca2+ -Mg2+ -free Hank´s solution and then enzymatically dissociated under soft shaking with 0.1% collagenase and 150U/ml DNase at 37ºC for 1 h. The cells were centrifugated at 1500 rpm for 10 min and re-suspended in culture medium (HEPES-modified Ham´s F-12 nutrient mixture supplemented with 10% horse serum, 10% fetal bovine serum and 15 ng/ml nerve growth factor). The cells were plated into 35 mm Petri-dishes coated with poly-L-lysine (0.1mg/ml).

extract_protocol: Total RNA from CB cultured primary rat cells was isolated by adding 1.0 ml of Trizol (Invitrogen) following manufacturer's instructions.

treatment_protocol: The cells were maintained at 37ºC in water-saturated, 5% CO2 denominated in Nx conditions. A chronic hypoxic (CH) environment was generated in a 5-liters Billups-Rothenberg hypoxia chamber (Del Mar, CA, USA) (Allen et al., 2001) where cultured cells were maintained in the incubator at 37ºC after being flushed for 20 minutes with 5% CO2 - 95% N2. The gas mixture and the culture medium were changed every day.

tag: strain/background

value: Sprague Dawley

value: carotid body

tag: number of organ/ culture

value: Normoxia

tag: oxygen level

tag: days of culture

value: 7 days


title: CDG1_RNAseq

city: Guangzhou

first: Yang

middle: Qiu

last: Jiao

state: Guangdong

address: No.132, East Outer Ring Road

department: Academy of Life Science

institute: Sun Yat-Sen University

data_processing:
Data filtering1) Remove reads with adaptors;  2) Remove reads in which unknown bases are more than 10%;  3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we  define the low quality base to be the base whose sequencing quality is no more than 5).
ReCondition Specifity Analysisads Mapping We use Bowtie2 to map clean reads to reference gene and use HISAT to reference
Screening DEGs using Possion Distribution Method
Gene Quantification RSEM \[5\] is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model, including the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores, to determine which transcripts are isoforms of the same gene

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
RNSiso Plus Cat#9109 www.takara-bio.com for product information/protocols
1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase;6) Sequencing on BGISEQ-500 platform.

value: seedlings

value: 1 month old

tag: genotype/variation

value: CDG1 overexpression


title: MEKK1Km_RNAseq


title: WT_RNAseq

value: wild type


title: MEKK1KmCDG1_RNAseq

value: MEKK1Km; CDG1 overexpression


title: Littermates rep2

description: polysome mRNAs

tag: strain

value: 6 weeks