title: genomic DNA from 201172220003_R04C01

description:
201172220003_R04C01_Grn.idat
201172220003_R04C01_Red.idat
Sample 85
whole blood sample


title: genomic DNA from 201172540032_R03C01

status: Public on Nov 17 2017

type: genomic

city: New Haven

first: Ke

last: Xu

address: 300 George St.

department: department of psychiatry

country: USA

institute: Yale University

description:
201172540032_R03C01_Grn.idat
201172540032_R03C01_Red.idat
Sample 83
whole blood sample

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

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

data_processing:
GenomeStudio V2011.1
MatrixProcessed.txt contains ssNoob normalized Average Beta; the signals of common probes between 450k and EPIC were provided.
MethylatedSignal.txt contains Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: DNAs were extracted from whole blood using the standard protocol.

tag: age

tag: Sex

value: Male

tag: race

value: Other

tag: hiv

tag: idu

tag: smoking

tag: artadherence

tag: tissue

value: whole blood


title: genomic DNA from 201172550022_R03C01

description:
201172550022_R03C01_Grn.idat
201172550022_R03C01_Red.idat
Sample 82
whole blood sample

value: White


title: genomic DNA from 201172540034_R04C01

description:
201172540034_R04C01_Grn.idat
201172540034_R04C01_Red.idat
Sample 87
whole blood sample


title: genomic DNA from 201172220024_R02C01

description:
201172220024_R02C01_Grn.idat
201172220024_R02C01_Red.idat
Sample 78
whole blood sample


title: genomic DNA from 201172520035_R02C01

description:
201172520035_R02C01_Grn.idat
201172520035_R02C01_Red.idat
Sample 80
whole blood sample


title: genomic DNA from 201172540034_R02C01

description:
201172540034_R02C01_Grn.idat
201172540034_R02C01_Red.idat
Sample 79
whole blood sample


title: genomic DNA from 201172520035_R04C01

description:
201172520035_R04C01_Grn.idat
201172520035_R04C01_Red.idat
Sample 88
whole blood sample


title: genomic DNA from 201172550005_R08C01

description:
201172550005_R08C01_Grn.idat
201172550005_R08C01_Red.idat
Sample 73
whole blood sample


title: genomic DNA from 201172550022_R05C01

description:
201172550022_R05C01_Grn.idat
201172550022_R05C01_Red.idat
Sample 93
whole blood sample


title: genomic DNA from 201172220006_R06C01

description:
201172220006_R06C01_Grn.idat
201172220006_R06C01_Red.idat
Sample 100
whole blood sample


title: genomic DNA from 201194010088_R08C01

description:
201194010088_R08C01_Grn.idat
201194010088_R08C01_Red.idat
Sample 71
whole blood sample


title: genomic DNA from 201172220001_R03C01

description:
201172220001_R03C01_Grn.idat
201172220001_R03C01_Red.idat
Sample 81
whole blood sample


title: genomic DNA from 201172550016_R04C01

description:
201172550016_R04C01_Grn.idat
201172550016_R04C01_Red.idat
Sample 86
whole blood sample


title: genomic DNA from 201172220003_R01C01

description:
201172220003_R01C01_Grn.idat
201172220003_R01C01_Red.idat
Sample 74
whole blood sample


title: genomic DNA from 201172550016_R01C01

description:
201172550016_R01C01_Grn.idat
201172550016_R01C01_Red.idat
Sample 75
whole blood sample


title: genomic DNA from 201172220003_R05C01

description:
201172220003_R05C01_Grn.idat
201172220003_R05C01_Red.idat
Sample 91
whole blood sample


title: genomic DNA from 201172520050_R08C01

description:
201172520050_R08C01_Grn.idat
201172520050_R08C01_Red.idat
Sample 69
whole blood sample


title: genomic DNA from 201172220001_R02C01

description:
201172220001_R02C01_Grn.idat
201172220001_R02C01_Red.idat
Sample 76
whole blood sample


title: genomic DNA from 201194000183_R08C01

description:
201194000183_R08C01_Grn.idat
201194000183_R08C01_Red.idat
Sample 72
whole blood sample


title: genomic DNA from 201172550016_R02C01

description:
201172550016_R02C01_Grn.idat
201172550016_R02C01_Red.idat
Sample 77
whole blood sample


title: genomic DNA from 201172550055_R08C01

description:
201172550055_R08C01_Grn.idat
201172550055_R08C01_Red.idat
Sample 70
whole blood sample


title: genomic DNA from 201172520058_R07C01

description:
201172520058_R07C01_Grn.idat
201172520058_R07C01_Red.idat
Sample 65
whole blood sample


title: genomic DNA from 201172520050_R07C01

description:
201172520050_R07C01_Grn.idat
201172520050_R07C01_Red.idat
Sample 64
whole blood sample


title: genomic DNA from 201172520049_R08C01

description:
201172520049_R08C01_Grn.idat
201172520049_R08C01_Red.idat
Sample 68
whole blood sample


title: genomic DNA from 201172540041_R07C01

description:
201172540041_R07C01_Grn.idat
201172540041_R07C01_Red.idat
Sample 62
whole blood sample


title: genomic DNA from 201172520049_R07C01

description:
201172520049_R07C01_Grn.idat
201172520049_R07C01_Red.idat
Sample 63
whole blood sample


title: genomic DNA from 201172520035_R03C01

description:
201172520035_R03C01_Grn.idat
201172520035_R03C01_Red.idat
Sample 84
whole blood sample


title: genomic DNA from 201172220054_R06C01

description:
201172220054_R06C01_Grn.idat
201172220054_R06C01_Red.idat
Sample 58
whole blood sample


title: genomic DNA from 201172550005_R06C01

description:
201172550005_R06C01_Grn.idat
201172550005_R06C01_Red.idat
Sample 61
whole blood sample


title: genomic DNA from 201194010088_R06C01

description:
201194010088_R06C01_Grn.idat
201194010088_R06C01_Red.idat
Sample 60
whole blood sample


title: genomic DNA from 201172520049_R06C01

description:
201172520049_R06C01_Grn.idat
201172520049_R06C01_Red.idat
Sample 56
whole blood sample


title: genomic DNA from 201172540053_R06C01

description:
201172540053_R06C01_Grn.idat
201172540053_R06C01_Red.idat
Sample 57
whole blood sample


title: genomic DNA from 201172550055_R06C01

description:
201172550055_R06C01_Grn.idat
201172550055_R06C01_Red.idat
Sample 59
whole blood sample


title: genomic DNA from 201194000210_R05C01

description:
201194000210_R05C01_Grn.idat
201194000210_R05C01_Red.idat
Sample 55
whole blood sample


title: genomic DNA from 201194010088_R05C01

description:
201194010088_R05C01_Grn.idat
201194010088_R05C01_Red.idat
Sample 54
whole blood sample


title: genomic DNA from 201172220054_R05C01

description:
201172220054_R05C01_Grn.idat
201172220054_R05C01_Red.idat
Sample 52
whole blood sample


title: genomic DNA from 201172520058_R05C01

description:
201172520058_R05C01_Grn.idat
201172520058_R05C01_Red.idat
Sample 53
whole blood sample


title: genomic DNA from 201172540053_R05C01

description:
201172540053_R05C01_Grn.idat
201172540053_R05C01_Red.idat
Sample 51
whole blood sample


title: genomic DNA from 201172550005_R07C01

description:
201172550005_R07C01_Grn.idat
201172550005_R07C01_Red.idat
Sample 66
whole blood sample


title: genomic DNA from 201172220054_R04C01

description:
201172220054_R04C01_Grn.idat
201172220054_R04C01_Red.idat
Sample 45
whole blood sample


title: genomic DNA from 201172220041_R04C01

description:
201172220041_R04C01_Grn.idat
201172220041_R04C01_Red.idat
Sample 49
whole blood sample


title: genomic DNA from 201172520050_R05C01

description:
201172520050_R05C01_Grn.idat
201172520050_R05C01_Red.idat
Sample 50
whole blood sample


title: genomic DNA from 201172220041_R07C01

description:
201172220041_R07C01_Grn.idat
201172220041_R07C01_Red.idat
Sample 67
whole blood sample


title: genomic DNA from 201172520058_R04C01

description:
201172520058_R04C01_Grn.idat
201172520058_R04C01_Red.idat
Sample 46
whole blood sample


title: genomic DNA from 201194000210_R04C01

description:
201194000210_R04C01_Grn.idat
201194000210_R04C01_Red.idat
Sample 48
whole blood sample


title: genomic DNA from 201194000210_R01C01

description:
201194000210_R01C01_Grn.idat
201194000210_R01C01_Red.idat
Sample 35
whole blood sample


title: genomic DNA from 201172520058_R01C01

description:
201172520058_R01C01_Grn.idat
201172520058_R01C01_Red.idat
Sample 34
whole blood sample


title: genomic DNA from 201172550055_R02C01

description:
201172550055_R02C01_Grn.idat
201172550055_R02C01_Red.idat
Sample 38
whole blood sample


title: genomic DNA from 201194010088_R02C01

description:
201194010088_R02C01_Grn.idat
201194010088_R02C01_Red.idat
Sample 39
whole blood sample


title: genomic DNA from 201172220054_R03C01

description:
201172220054_R03C01_Grn.idat
201172220054_R03C01_Red.idat
Sample 42
whole blood sample

value: Black


title: genomic DNA from 201172220041_R02C01

description:
201172220041_R02C01_Grn.idat
201172220041_R02C01_Red.idat
Sample 41
whole blood sample


title: genomic DNA from 201172550005_R01C01

description:
201172550005_R01C01_Grn.idat
201172550005_R01C01_Red.idat
Sample 36
whole blood sample


title: genomic DNA from 201194000183_R02C01

description:
201194000183_R02C01_Grn.idat
201194000183_R02C01_Red.idat
Sample 40
whole blood sample


title: genomic DNA from 201172220020_R08C01

description:
201172220020_R08C01_Grn.idat
201172220020_R08C01_Red.idat
Sample 31
whole blood sample


title: genomic DNA from 201172540041_R01C01

description:
201172540041_R01C01_Grn.idat
201172540041_R01C01_Red.idat
Sample 33
whole blood sample


title: genomic DNA from 201172550039_R08C01

description:
201172550039_R08C01_Grn.idat
201172550039_R08C01_Red.idat
Sample 32
whole blood sample


title: genomic DNA from 201172220016_R08C01

description:
201172220016_R08C01_Grn.idat
201172220016_R08C01_Red.idat
Sample 30
whole blood sample


title: genomic DNA from 201172220008_R08C01

description:
201172220008_R08C01_Grn.idat
201172220008_R08C01_Red.idat
Sample 28
whole blood sample


title: genomic DNA from 201172220013_R08C01

description:
201172220013_R08C01_Grn.idat
201172220013_R08C01_Red.idat
Sample 29
whole blood sample


title: genomic DNA from 201172530005_R08C01

description:
201172530005_R08C01_Grn.idat
201172530005_R08C01_Red.idat
Sample 27
whole blood sample


title: genomic DNA from 201172550039_R07C01

description:
201172550039_R07C01_Grn.idat
201172550039_R07C01_Red.idat
Sample 26
whole blood sample


title: genomic DNA from 201194000183_R04C01

description:
201194000183_R04C01_Grn.idat
201194000183_R04C01_Red.idat
Sample 47
whole blood sample


title: genomic DNA from 201172220023_R07C01

description:
201172220023_R07C01_Grn.idat
201172220023_R07C01_Red.idat
Sample 24
whole blood sample


title: genomic DNA from 201172520050_R04C01

description:
201172520050_R04C01_Grn.idat
201172520050_R04C01_Red.idat
Sample 44
whole blood sample


title: genomic DNA from 201172550039_R05C01

description:
201172550039_R05C01_Grn.idat
201172550039_R05C01_Red.idat
Sample 20
whole blood sample


title: genomic DNA from 201172220013_R07C01

description:
201172220013_R07C01_Grn.idat
201172220013_R07C01_Red.idat
Sample 23
whole blood sample


title: genomic DNA from 201172220023_R05C01

description:
201172220023_R05C01_Grn.idat
201172220023_R05C01_Red.idat
Sample 18
whole blood sample


title: genomic DNA from 201194010088_R03C01

description:
201194010088_R03C01_Grn.idat
201194010088_R03C01_Red.idat
Sample 43
whole blood sample


title: genomic DNA from 201172550038_R07C01

description:
201172550038_R07C01_Grn.idat
201172550038_R07C01_Red.idat
Sample 25
whole blood sample


title: genomic DNA from 201172220023_R06C01

description:
201172220023_R06C01_Grn.idat
201172220023_R06C01_Red.idat
Sample 22
whole blood sample


title: genomic DNA from 201194000021_R06C01

description:
201194000021_R06C01_Grn.idat
201194000021_R06C01_Red.idat
Sample 21
whole blood sample


title: genomic DNA from 201172220023_R04C01

description:
201172220023_R04C01_Grn.idat
201172220023_R04C01_Red.idat
Sample 15
whole blood sample


title: genomic DNA from 201172550038_R05C01

description:
201172550038_R05C01_Grn.idat
201172550038_R05C01_Red.idat
Sample 19
whole blood sample


title: genomic DNA from 201172220013_R04C01

description:
201172220013_R04C01_Grn.idat
201172220013_R04C01_Red.idat
Sample 13
whole blood sample


title: genomic DNA from 201172220016_R04C01

description:
201172220016_R04C01_Grn.idat
201172220016_R04C01_Red.idat
Sample 14
whole blood sample


title: genomic DNA from 201172220023_R03C01

description:
201172220023_R03C01_Grn.idat
201172220023_R03C01_Red.idat
Sample 10
whole blood sample


title: genomic DNA from 201172520050_R02C01

description:
201172520050_R02C01_Grn.idat
201172520050_R02C01_Red.idat
Sample 37
whole blood sample


title: genomic DNA from 201172220009_R03C01

description:
201172220009_R03C01_Grn.idat
201172220009_R03C01_Red.idat
Sample 9
whole blood sample


title: genomic DNA from 201172520001_R05C01

description:
201172520001_R05C01_Grn.idat
201172520001_R05C01_Red.idat
Sample 17
whole blood sample


title: genomic DNA from 201172530005_R02C01

description:
201172530005_R02C01_Grn.idat
201172530005_R02C01_Red.idat
Sample 8
whole blood sample


title: genomic DNA from 201172550039_R04C01

description:
201172550039_R04C01_Grn.idat
201172550039_R04C01_Red.idat
Sample 16
whole blood sample


title: genomic DNA from 201172550039_R01C01

description:
201172550039_R01C01_Grn.idat
201172550039_R01C01_Red.idat
Sample 7
whole blood sample


title: genomic DNA from 201172520001_R04C01

description:
201172520001_R04C01_Grn.idat
201172520001_R04C01_Red.idat
Sample 12
whole blood sample


title: genomic DNA from 201172220020_R01C01

description:
201172220020_R01C01_Grn.idat
201172220020_R01C01_Red.idat
Sample 6
whole blood sample


title: genomic DNA from 201172220008_R01C01

description:
201172220008_R01C01_Grn.idat
201172220008_R01C01_Red.idat
Sample 3
whole blood sample


title: genomic DNA from 201172530005_R01C01

description:
201172530005_R01C01_Grn.idat
201172530005_R01C01_Red.idat
Sample 2
whole blood sample


title: genomic DNA from 201172220009_R01C01

description:
201172220009_R01C01_Grn.idat
201172220009_R01C01_Red.idat
Sample 4
whole blood sample


title: 9741950076_R02C02

description: Sample 384

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

data_processing: GenomeStudio V2011.1

source_name: genomic DNA from 9741950076_R02C02

value: African American

tag: nk

tag: bcell

tag: mono

tag: gran


title: 9741950050_R04C01

description: Sample 378

source_name: genomic DNA from 9741950050_R04C01


title: 9741950050_R03C01

description: Sample 377

source_name: genomic DNA from 9741950050_R03C01


title: 9741950076_R03C02

description: Sample 385

source_name: genomic DNA from 9741950076_R03C02


title: 9741950076_R02C01

description: Sample 383

source_name: genomic DNA from 9741950076_R02C01


title: genomic DNA from 201172220016_R01C01

description:
201172220016_R01C01_Grn.idat
201172220016_R01C01_Red.idat
Sample 5
whole blood sample


title: genomic DNA from 201172550039_R03C01

description:
201172550039_R03C01_Grn.idat
201172550039_R03C01_Red.idat
Sample 11
whole blood sample


title: 9741950050_R05C02

description: Sample 380

source_name: genomic DNA from 9741950050_R05C02


title: 9741950050_R06C01

description: Sample 381

source_name: genomic DNA from 9741950050_R06C01


title: 9741950050_R02C02

description: Sample 376

source_name: genomic DNA from 9741950050_R02C02


title: 9741950032_R03C02

description: Sample 372

source_name: genomic DNA from 9741950032_R03C02


title: 9741950032_R05C01

description: Sample 373

source_name: genomic DNA from 9741950032_R05C01


title: 9741950032_R01C02

description: Sample 370

source_name: genomic DNA from 9741950032_R01C02


title: 9741950032_R02C01

description: Sample 371

source_name: genomic DNA from 9741950032_R02C01


title: 9741950016_R03C02

description: Sample 368

source_name: genomic DNA from 9741950016_R03C02


title: 9741950050_R01C02

description: Sample 374

source_name: genomic DNA from 9741950050_R01C02


title: 9741950050_R02C01

description: Sample 375

source_name: genomic DNA from 9741950050_R02C01


title: 9741950016_R06C01

description: Sample 369

source_name: genomic DNA from 9741950016_R06C01


title: 9741950050_R05C01

description: Sample 379

source_name: genomic DNA from 9741950050_R05C01


title: 9741950076_R01C02

description: Sample 382

source_name: genomic DNA from 9741950076_R01C02


title: 9741950076_R04C02

description: Sample 386

source_name: genomic DNA from 9741950076_R04C02


title: 9741950016_R03C01

description: Sample 367

source_name: genomic DNA from 9741950016_R03C01


title: 9741950016_R01C02

description: Sample 365

source_name: genomic DNA from 9741950016_R01C02


title: 9741950016_R01C01

description: Sample 364

source_name: genomic DNA from 9741950016_R01C01


title: 9701417141_R04C02

description: Sample 363

source_name: genomic DNA from 9701417141_R04C02


title: 9701417139_R06C01

description: Sample 360

source_name: genomic DNA from 9701417139_R06C01


title: 9701417141_R02C01

description: Sample 361

source_name: genomic DNA from 9701417141_R02C01


title: 9701417141_R03C01

description: Sample 362

source_name: genomic DNA from 9701417141_R03C01


title: 9741950016_R02C01

description: Sample 366

source_name: genomic DNA from 9741950016_R02C01


title: 9701417112_R02C02

description: Sample 345

source_name: genomic DNA from 9701417112_R02C02


title: 9701417123_R03C02

description: Sample 357

source_name: genomic DNA from 9701417123_R03C02


title: 9701417115_R04C02

description: Sample 350

source_name: genomic DNA from 9701417115_R04C02


title: 9701417107_R06C02

description: Sample 344

source_name: genomic DNA from 9701417107_R06C02


title: 9701417112_R03C02

description: Sample 347

source_name: genomic DNA from 9701417112_R03C02


title: 9701417123_R03C01

description: Sample 356

source_name: genomic DNA from 9701417123_R03C01


title: 9701417107_R03C02

description: Sample 341

source_name: genomic DNA from 9701417107_R03C02


title: 9701417123_R02C02

description: Sample 355

source_name: genomic DNA from 9701417123_R02C02


title: 9701417107_R06C01

description: Sample 343

source_name: genomic DNA from 9701417107_R06C01


title: 9701417115_R05C01

description: Sample 351

source_name: genomic DNA from 9701417115_R05C01


title: 9701417139_R02C02

description: Sample 359

source_name: genomic DNA from 9701417139_R02C02


title: 9701417112_R03C01

description: Sample 346

source_name: genomic DNA from 9701417112_R03C01


title: 9701417093_R02C02

description: Sample 335

source_name: genomic DNA from 9701417093_R02C02


title: 9701417086_R06C02

description: Sample 334

source_name: genomic DNA from 9701417086_R06C02


title: 9701417115_R06C02

description: Sample 353

source_name: genomic DNA from 9701417115_R06C02


title: 9701417115_R04C01

description: Sample 349

source_name: genomic DNA from 9701417115_R04C01


title: 9701417139_R01C02

description: Sample 358

source_name: genomic DNA from 9701417139_R01C02


title: 9701417086_R02C01

description: Sample 331

source_name: genomic DNA from 9701417086_R02C01


title: 9701417112_R04C01

description: Sample 348

source_name: genomic DNA from 9701417112_R04C01


title: 9701417107_R01C01

description: Sample 338

source_name: genomic DNA from 9701417107_R01C01


title: 9701417115_R06C01

description: Sample 352

source_name: genomic DNA from 9701417115_R06C01


title: 9701417123_R01C02

description: Sample 354

source_name: genomic DNA from 9701417123_R01C02


title: 9701417107_R02C02

description: Sample 340

source_name: genomic DNA from 9701417107_R02C02


title: 9701417107_R01C02

description: Sample 339

source_name: genomic DNA from 9701417107_R01C02


title: 9701417093_R06C02

description: Sample 337

source_name: genomic DNA from 9701417093_R06C02


title: 9701417093_R04C01

description: Sample 336

source_name: genomic DNA from 9701417093_R04C01


title: 9701417107_R05C02

description: Sample 342

source_name: genomic DNA from 9701417107_R05C02


title: 9701417086_R05C01

description: Sample 332

source_name: genomic DNA from 9701417086_R05C01


title: 9701417086_R05C02

description: Sample 333

source_name: genomic DNA from 9701417086_R05C02


title: 9701417086_R01C01

description: Sample 330

source_name: genomic DNA from 9701417086_R01C01


title: 9701417085_R04C02

description: Sample 328

source_name: genomic DNA from 9701417085_R04C02


title: 9701417085_R04C01

description: Sample 327

source_name: genomic DNA from 9701417085_R04C01


title: 9701417085_R05C02

description: Sample 329

source_name: genomic DNA from 9701417085_R05C02


title: 9701417081_R05C02

description: Sample 323

source_name: genomic DNA from 9701417081_R05C02


title: 9701417081_R02C01

description: Sample 320

source_name: genomic DNA from 9701417081_R02C01


title: 9701417085_R03C02

description: Sample 326

source_name: genomic DNA from 9701417085_R03C02


title: 9701417057_R01C01

description: Sample 314

source_name: genomic DNA from 9701417057_R01C01


title: 9701417048_R06C01

description: Sample 307

source_name: genomic DNA from 9701417048_R06C01


title: 9701417081_R04C01

description: Sample 321

source_name: genomic DNA from 9701417081_R04C01


title: 9701417057_R06C02

description: Sample 318

source_name: genomic DNA from 9701417057_R06C02


title: 9701417081_R06C01

description: Sample 324

source_name: genomic DNA from 9701417081_R06C01


title: 9701417053_R03C01

description: Sample 310

source_name: genomic DNA from 9701417053_R03C01


title: 9701417057_R02C02

description: Sample 315

source_name: genomic DNA from 9701417057_R02C02


title: 9701417047_R01C02

description: Sample 302

source_name: genomic DNA from 9701417047_R01C02


title: 9701417048_R05C01

description: Sample 306

source_name: genomic DNA from 9701417048_R05C01


title: 9701417057_R04C02

description: Sample 317

source_name: genomic DNA from 9701417057_R04C02


title: 9701417048_R02C01

description: Sample 303

source_name: genomic DNA from 9701417048_R02C01


title: 9701417053_R04C02

description: Sample 311

source_name: genomic DNA from 9701417053_R04C02


title: 9701417053_R05C02

description: Sample 313

source_name: genomic DNA from 9701417053_R05C02


title: 9701417081_R01C01

description: Sample 319

source_name: genomic DNA from 9701417081_R01C01


title: 9701417048_R03C01

description: Sample 305

source_name: genomic DNA from 9701417048_R03C01


title: 9701417048_R06C02

description: Sample 308

source_name: genomic DNA from 9701417048_R06C02


title: 9701417053_R02C02

description: Sample 309

source_name: genomic DNA from 9701417053_R02C02


title: 9701417057_R04C01

description: Sample 316

source_name: genomic DNA from 9701417057_R04C01


title: 9701417081_R04C02

description: Sample 322

source_name: genomic DNA from 9701417081_R04C02


title: 9701417085_R02C01

description: Sample 325

source_name: genomic DNA from 9701417085_R02C01


title: 9701417035_R05C02

description: Sample 300

source_name: genomic DNA from 9701417035_R05C02


title: 9701417048_R02C02

description: Sample 304

source_name: genomic DNA from 9701417048_R02C02


title: 9701417047_R01C01

description: Sample 301

source_name: genomic DNA from 9701417047_R01C01


title: 9701417035_R03C01

description: Sample 299

source_name: genomic DNA from 9701417035_R03C01


title: 9701417053_R05C01

description: Sample 312

source_name: genomic DNA from 9701417053_R05C01


title: 9701417035_R02C02

description: Sample 298

source_name: genomic DNA from 9701417035_R02C02


title: 9701417035_R02C01

description: Sample 297

source_name: genomic DNA from 9701417035_R02C01


title: 9701417031_R05C02

description: Sample 294

source_name: genomic DNA from 9701417031_R05C02


title: 9701417031_R06C01

description: Sample 295

source_name: genomic DNA from 9701417031_R06C01


title: 9701417035_R01C01

description: Sample 296

source_name: genomic DNA from 9701417035_R01C01


title: 9701417031_R04C01

description: Sample 293

source_name: genomic DNA from 9701417031_R04C01


title: 9407210093_R03C01

description: Sample 285

source_name: genomic DNA from 9407210093_R03C01


title: 9407210093_R01C02

description: Sample 284

source_name: genomic DNA from 9407210093_R01C02


title: 9701417031_R02C01

description: Sample 291

source_name: genomic DNA from 9701417031_R02C01


title: 9701417031_R02C02

description: Sample 292

source_name: genomic DNA from 9701417031_R02C02


title: 9407210074_R04C02

description: Sample 283

source_name: genomic DNA from 9407210074_R04C02


title: 9407210107_R06C01

description: Sample 289

source_name: genomic DNA from 9407210107_R06C01


title: 9407210107_R04C01

description: Sample 288

source_name: genomic DNA from 9407210107_R04C01


title: 9701417031_R01C01

description: Sample 290

source_name: genomic DNA from 9701417031_R01C01


title: 9407210093_R06C01

description: Sample 287

source_name: genomic DNA from 9407210093_R06C01


title: 9407210074_R03C02

description: Sample 281

source_name: genomic DNA from 9407210074_R03C02


title: 9407210073_R03C02

description: Sample 277

source_name: genomic DNA from 9407210073_R03C02


title: 9407210063_R06C02

description: Sample 275

source_name: genomic DNA from 9407210063_R06C02


title: 9407210065_R03C01

description: Sample 276

source_name: genomic DNA from 9407210065_R03C01


title: 9407210063_R01C02

description: Sample 274

source_name: genomic DNA from 9407210063_R01C02


title: 9407210061_R03C02

description: Sample 273

source_name: genomic DNA from 9407210061_R03C02


title: 9407210061_R02C02

description: Sample 272

source_name: genomic DNA from 9407210061_R02C02


title: 9407210061_R02C01

description: Sample 271

source_name: genomic DNA from 9407210061_R02C01


title: 9407210029_R05C02

description: Sample 269

source_name: genomic DNA from 9407210029_R05C02


title: 9407210061_R01C02

description: Sample 270

source_name: genomic DNA from 9407210061_R01C02


title: 9407210029_R04C02

description: Sample 268

source_name: genomic DNA from 9407210029_R04C02


title: 9407210029_R03C01

description: Sample 267

source_name: genomic DNA from 9407210029_R03C01


title: 9407210093_R05C02

description: Sample 286

source_name: genomic DNA from 9407210093_R05C02


title: 9407210074_R04C01

description: Sample 282

source_name: genomic DNA from 9407210074_R04C01


title: 9407210073_R06C02

description: Sample 280

source_name: genomic DNA from 9407210073_R06C02


title: 9407210073_R05C02

description: Sample 279

source_name: genomic DNA from 9407210073_R05C02


title: 9407210073_R04C01

description: Sample 278

source_name: genomic DNA from 9407210073_R04C01


title: 9407210016_R01C01

description: Sample 261

source_name: genomic DNA from 9407210016_R01C01


title: 9407201144_R05C02

description: Sample 259

source_name: genomic DNA from 9407201144_R05C02


title: 9407210016_R06C01

description: Sample 264

source_name: genomic DNA from 9407210016_R06C01


title: 9407210016_R03C02

description: Sample 263

source_name: genomic DNA from 9407210016_R03C02


title: 9407201127_R05C01

description: Sample 256

source_name: genomic DNA from 9407201127_R05C01


title: 9407210016_R01C02

description: Sample 262

source_name: genomic DNA from 9407210016_R01C02


title: 9407201144_R06C02

description: Sample 260

source_name: genomic DNA from 9407201144_R06C02


title: 9407210016_R06C02

description: Sample 265

source_name: genomic DNA from 9407210016_R06C02


title: 9407201127_R01C01

description: Sample 252

source_name: genomic DNA from 9407201127_R01C01


title: 9407201127_R02C01

description: Sample 254

source_name: genomic DNA from 9407201127_R02C01


title: 9407201127_R01C02

description: Sample 253

source_name: genomic DNA from 9407201127_R01C02


title: 9407201144_R04C02

description: Sample 258

source_name: genomic DNA from 9407201144_R04C02


title: 9407201144_R01C02

description: Sample 257

source_name: genomic DNA from 9407201144_R01C02


title: 9407201108_R06C02

description: Sample 251

source_name: genomic DNA from 9407201108_R06C02


title: 9407201108_R04C02

description: Sample 249

source_name: genomic DNA from 9407201108_R04C02


title: 9407201108_R03C02

description: Sample 248

source_name: genomic DNA from 9407201108_R03C02


title: 9407201108_R02C01

description: Sample 247

source_name: genomic DNA from 9407201108_R02C01


title: 9407201108_R01C01

description: Sample 246

source_name: genomic DNA from 9407201108_R01C01


title: 200090280075_R06C02

description: Sample 245


title: 200090280075_R06C01

description: Sample 244


title: 9407210029_R02C02

description: Sample 266

source_name: genomic DNA from 9407210029_R02C02


title: 200090280075_R04C02

description: Sample 242


title: 200090280075_R05C01

description: Sample 243


title: 200090280075_R04C01

description: Sample 241


title: 200090280075_R01C02

description: Sample 238


title: 9407201127_R04C01

description: Sample 255

source_name: genomic DNA from 9407201127_R04C01


title: 200090280075_R03C02

description: Sample 240


title: 200090280075_R02C01

description: Sample 239


title: 200090280073_R06C02

description: Sample 237


title: 200090280073_R05C01

description: Sample 234


title: 200090280073_R05C02

description: Sample 235


title: 200090280073_R03C02

description: Sample 231


title: 200090280073_R04C01

description: Sample 232


title: 9407201108_R05C01

description: Sample 250

source_name: genomic DNA from 9407201108_R05C01


title: 200090280073_R04C02

description: Sample 233


title: 200090280073_R01C01

description: Sample 228


title: 200109350073_R04C01

description: Sample 223


title: 200109350073_R06C01

description: Sample 226


title: 200109350073_R03C02

description: Sample 222


title: 200109350073_R05C02

description: Sample 225


title: 200109350073_R05C01

description: Sample 224


title: 200090280073_R01C02

description: Sample 229


title: 200109350007_R06C02

description: Sample 219


title: 200109350073_R02C02

description: Sample 220


title: 200109350007_R05C01

description: Sample 218


title: 200109350073_R06C02

description: Sample 227


title: 200109350073_R03C01

description: Sample 221


title: 200109350007_R04C01

description: Sample 217


title: 200109350007_R03C01

description: Sample 216


title: 200109350007_R01C02

description: Sample 213


title: 200109350007_R02C02

description: Sample 215


title: 200090280073_R06C01

description: Sample 236


title: 101279510019_R06C01

description: Sample 210


title: 200090280073_R03C01

description: Sample 230


title: 200109350007_R01C01

description: Sample 212


title: 101279510019_R06C02

description: Sample 211


title: 101279510019_R05C02

description: Sample 209


title: 101279510019_R04C01

description: Sample 207


title: 101279510019_R03C01

description: Sample 205


title: 101279510019_R02C01

description: Sample 203


title: 101279510019_R02C02

description: Sample 204


title: 101279510019_R04C02

description: Sample 208


title: 101279510019_R01C02

description: Sample 202


title: 101279430036_R06C02

description: Sample 200


title: 101279430036_R06C01

description: Sample 199


title: 200109350007_R02C01

description: Sample 214


title: 101279430036_R04C01

description: Sample 195


title: 101279430036_R02C02

description: Sample 192


title: 101279430036_R05C02

description: Sample 198


title: 101279430036_R04C02

description: Sample 196


title: 101279430036_R03C02

description: Sample 194


title: 101279430036_R03C01

description: Sample 193


title: 101279430036_R01C01

description: Sample 189


title: 101279430036_R05C01

description: Sample 197


title: 101279430036_R01C02

description: Sample 190


title: 101279430035_R06C02

description: Sample 188


title: 101279510019_R01C01

description: Sample 201


title: 101279510019_R03C02

description: Sample 206


title: 101279430035_R05C02

description: Sample 186


title: 101279430035_R06C01

description: Sample 187


title: 101279430035_R05C01

description: Sample 185


title: 101279430035_R03C02

description: Sample 182


title: 101279430035_R04C01

description: Sample 183


title: 101279430035_R02C02

description: Sample 180


title: 101279430035_R03C01

description: Sample 181


title: 101279430035_R04C02

description: Sample 184


title: 101279430035_R02C01

description: Sample 179


title: 101279430033_R06C02

description: Sample 176


title: 101279430033_R05C01

description: Sample 174


title: 101279430035_R01C02

description: Sample 178


title: 101279430033_R05C02

description: Sample 175


title: 101279430035_R01C01

description: Sample 177


title: 101279430036_R02C01

description: Sample 191


title: 101279430033_R04C01

description: Sample 172


title: 101279430033_R03C01

description: Sample 171


title: 101279430033_R02C01

description: Sample 169


title: 101279430033_R04C02

description: Sample 173


title: 101279430033_R01C01

description: Sample 167


title: 101279430033_R02C02

description: Sample 170


title: 101279430032_R06C02

description: Sample 166


title: 101279430033_R01C02

description: Sample 168


title: 101279430032_R06C01

description: Sample 165


title: 101279430032_R03C02

description: Sample 161


title: 101279430032_R05C01

description: Sample 164


title: 101279430032_R02C01

description: Sample 159


title: 101279430032_R04C01

description: Sample 162


title: 101279430031_R06C02

description: Sample 156


title: 101279430032_R03C01

description: Sample 160


title: 101279430032_R01C01

description: Sample 157


title: 101279430032_R04C02

description: Sample 163


title: 101279430031_R06C01

description: Sample 155


title: 101279430031_R05C02

description: Sample 154


title: 101279430031_R04C02

description: Sample 153


title: 101279430031_R04C01

state: CT

address: 300 George St., Suite 901

department: Department of Psychiatry

description: Sample 152


title: 101279430031_R02C02

description: Sample 149


title: 101279430031_R01C01

description: Sample 146


title: 101279430031_R03C02

description: Sample 151


title: 101279430031_R02C01

description: Sample 148


title: 101279430031_R03C01

description: Sample 150


title: 101279430031_R01C02

description: Sample 147


title: 101279430027_R05C02

description: Sample 144


title: 101279430027_R06C02

description: Sample 145


title: 101279430032_R01C02

description: Sample 158


title: 101279430027_R05C01

description: Sample 143


title: 101279430027_R02C01

description: Sample 137


title: 101279430027_R03C02

description: Sample 140


title: 101279430027_R01C02

description: Sample 136


title: 101279430027_R04C02

description: Sample 142


title: 101279430027_R04C01

description: Sample 141


title: 101279430009_R05C01

description: Sample 133


title: 101279430027_R01C01

description: Sample 135


title: 101279430009_R06C01

description: Sample 134


title: 101279430009_R04C02

description: Sample 132


title: 101279430009_R03C02

description: Sample 131


title: 101274800047_R06C02

description: Sample 126


title: 101279430009_R01C02

description: Sample 128


title: 101279430009_R02C02

description: Sample 129


title: 101279430009_R03C01

description: Sample 130


title: 101274800047_R04C02

description: Sample 123


title: 101274800047_R06C01

description: Sample 125


title: 101274800047_R03C02

description: Sample 121


title: 101274800047_R05C02

description: Sample 124


title: 101274800047_R04C01

description: Sample 122


title: 101274800047_R02C01

description: Sample 118


title: 101274800047_R03C01

description: Sample 120


title: 101274800047_R01C02

description: Sample 117


title: 101274800047_R01C01

description: Sample 116


title: 101279430027_R02C02

description: Sample 138


title: 101274800046_R06C02

description: Sample 115


title: 101279430027_R03C01

description: Sample 139


title: 101274800046_R05C02

description: Sample 114


title: 101274800046_R05C01

description: Sample 113


title: 101274800046_R04C02

description: Sample 112


title: 101274800046_R04C01

description: Sample 111


title: 101274800046_R02C02

description: Sample 109


title: 101279430009_R01C01

description: Sample 127


title: 101274800046_R02C01

description: Sample 108


title: 101274800046_R03C01

description: Sample 110


title: 101274800046_R01C01

description: Sample 106


title: 101274800023_R05C02

description: Sample 103


title: 101274800023_R06C02

description: Sample 105


title: 101274800023_R04C02

description: Sample 101


title: 101274800023_R04C01

description: Sample 100


title: 101274800023_R03C02

description: Sample 99


title: 101274800023_R05C01

description: Sample 102


title: 101274800047_R02C02

description: Sample 119


title: 101274800023_R01C01

description: Sample 94


title: 101274800023_R02C01

description: Sample 96


title: 101231030075_R06C01

description: Sample 92


title: 101274800023_R03C01

description: Sample 98


title: 101231030075_R04C01

description: Sample 89


title: 101274800023_R02C02

description: Sample 97


title: 101231030075_R04C02

description: Sample 90


title: 101231030075_R03C02

description: Sample 88


title: 101274800023_R01C02

description: Sample 95


title: 101231030073_R05C02

description: Sample 82


title: 101231030075_R02C01

description: Sample 86


title: 101231030075_R03C01

description: Sample 87


title: 101231030073_R06C01

description: Sample 83


title: 101231030073_R01C02

description: Sample 76


title: 101274800046_R01C02

description: Sample 107


title: 101231030014_R06C01

description: Sample 74


title: 101231030073_R03C02

description: Sample 79


title: 101231030073_R04C02

description: Sample 81


title: 101231030073_R02C01

description: Sample 77


title: 101274800023_R06C01

description: Sample 104


title: 101231030073_R03C01

description: Sample 78


title: 101231030014_R04C02

description: Sample 72


title: 101231030075_R06C02

description: Sample 93


title: 101231030014_R06C02

description: Sample 75


title: 101231030075_R01C01

description: Sample 84


title: 101231030014_R03C02

description: Sample 71


title: 101231030014_R05C02

description: Sample 73


title: 101231030014_R02C01

description: Sample 69


title: 101231030075_R05C01

description: Sample 91


title: 101231030014_R01C01

description: Sample 68


title: 101231030073_R04C01

description: Sample 80


title: 101231030013_R06C02

description: Sample 67


title: 101231030013_R06C01

description: Sample 66


title: 101231030013_R04C02

description: Sample 63


title: 101231030013_R05C01

description: Sample 64


title: 101231030013_R05C02

description: Sample 65


title: 101231030013_R04C01

description: Sample 62


title: 101231030075_R01C02

description: Sample 85


title: 101231030013_R03C01

description: Sample 60


title: 101231030013_R03C02

description: Sample 61


title: 101231030013_R02C02

description: Sample 59


title: 101231030013_R02C01

description: Sample 58


title: 101231030014_R02C02

description: Sample 70


title: 101231000143_R06C02

description: Sample 56


title: 101231000143_R05C02

description: Sample 54


title: 101231000143_R05C01

description: Sample 53


title: 101231000143_R04C01

description: Sample 51


title: 101231030013_R01C02

description: Sample 57


title: 101231000143_R03C01

description: Sample 49


title: 101231000143_R03C02

description: Sample 50


title: 101231000133_R06C01

description: Sample 44


title: 101231000133_R05C02

description: Sample 43


title: 101231000143_R01C01

description: Sample 45


title: 101231000143_R02C02

description: Sample 48


title: 101231000143_R02C01

description: Sample 47


title: 101231000133_R04C02

description: Sample 41


title: 101231000143_R01C02

description: Sample 46


title: 101231000133_R05C01

description: Sample 42


title: 101231000133_R04C01

description: Sample 40


title: 101231000133_R02C01

description: Sample 36


title: 101231000133_R03C01

description: Sample 38


title: 101231000133_R02C02

description: Sample 37


title: 101231000133_R01C01

description: Sample 35


title: 101231000121_R06C02

description: Sample 34


title: 101231000133_R03C02

description: Sample 39


title: 101231000121_R05C02

description: Sample 33


title: 101231000121_R03C02

description: Sample 30


title: 101231000121_R04C02

description: Sample 31


title: 101231000121_R05C01

description: Sample 32


title: 101231000143_R04C02

description: Sample 52


title: 101231000143_R06C01

description: Sample 55


title: 101231000121_R03C01

description: Sample 29


title: 101231000120_R05C02

description: Sample 23


title: 101231000121_R01C01

description: Sample 26


title: 101231000121_R02C02

description: Sample 28


title: 101231000120_R06C02

description: Sample 25


title: 101231000120_R06C01

description: Sample 24


title: 101231000121_R01C02

description: Sample 27


title: 101231000120_R04C01

description: Sample 21


title: 101231000120_R02C01

description: Sample 18


title: 101231000120_R05C01

description: Sample 22


title: 101231000120_R03C02

description: Sample 20


title: 101231000120_R03C01

description: Sample 19


title: 101231000119_R06C02

description: Sample 17


title: 101231000119_R06C01

description: Sample 16


title: 101231000119_R05C02

description: Sample 15


title: 101231000119_R02C02

description: Sample 12


title: 101231000119_R04C01

description: Sample 14


title: 101231000119_R03C01

description: Sample 13


title: 101231000099_R06C02

description: Sample 9


title: 101231000119_R01C01

description: Sample 10


title: 101231000099_R04C02

description: Sample 7


title: 101231000099_R04C01

description: Sample 6


title: 101231000099_R06C01

description: Sample 8


title: 101231000099_R01C01

description: Sample 1


title: 101231000119_R01C02

description: Sample 11


title: 101231000099_R03C01

description: Sample 4


title: 101231000099_R01C02

description: Sample 2


title: 101231000099_R03C02

description: Sample 5


title: 101231000099_R02C02

description: Sample 3


title: U87MG_non-irradiated_3

type: RNA

city: Seoul

first: Yongjoon

last: Suh

address: Wangsimni-ro 222, Seongdong-gu

country: South Korea

institute: Hangyang University

hyb_protocol: Biotinylated cRNAs were hybridized with standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader following the standard Illumina scanning protocol.

data_processing: Standard Illumina GenomeStudio processing of images plus quantile normalization of all samples. Background subtracted.

label: biotin

molecule: total RNA

source_name: Human glioblastoma

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep™ RNA amplification kit for Illumina arrays.

growth_protocol: U87MG GBM cells were cultured in Dulbecco’s modified Eagle Medium (Invitrogen, Seoul, Korea) supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted manually using Trizol reagent. Quality control was performed by Qiagen Rotor Gene-Q

treatment_protocol: U87MG GBM cells were irradiated with 2 Gy once, twice (2 Gy/day for two days) or three times (2 Gy/day for three days). Each control counterparts (C1, C2 and C3) were cultured with same time periods.

tag: disease state

value: Glioblastoma

tag: treatment


title: U87MG_2Gyx3

value: three times (2 Gy/day for three days)


title: U87MG_2Gyx2

value: twice (2 Gy/day for two days)


title: U87MG_non-irradiated_2


title: U87MG_2Gyx1

value: 2 Gy once


title: U87MG_non-irradiated_1


title: VE9-0817

city: CUERNAVACA

first: ADRIAN

last: OCHOA-LEYVA

state: Morelos

address: Av. Universidad #2001, Col. Chamilpa

department: Microbiología Molecular

country: Mexico

institute: Instituto de Biotecnología, UNAM

description: Gene expression data from human leukocyte sample

hyb_protocol: The labeled cDNA fragments were hybridized for 16 hr at 45C on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data from RNA expression array experiments in the form of .cel files were analyzed using RMA normalization and log2 transformation.

source_name: Leukocyte

label_protocol: cDNA was fragmented and labeled with biotin according to the standard Affymetrix protocol from 1 ug total RNA (Whole-Transcript (WT) Sense Target Labeling Protocol).

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

tag: gender

value: Blood

tag: cell type

value: Leukocyte


title: VE9-0687


title: VE9-0515


title: VE9-0697

value: Female


title: VE9-1036


title: VE9-0748


title: VE9-0307


title: VE9-0567


title: VE9-1050


title: NI0627


title: VE9-0039


title: VE9-0291


title: VE9-0472


title: VE9-0432


title: VE9-0336


title: VE9-0739


title: Proliferating PSC27 cells at p9 sample 3

status: Public on Nov 16 2017

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505C (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software version 10.7.3.1 was used to grid and extract the data using the GE2_105_Jan09 protocol with default settings. We normalized the raw data within arrays using loess and normexp background correction with offset 50, removed control probes, averaged duplicate probes, and assigned a value of NA to spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers.  Data was further normalized using between-array quantile normalization.  All normalizations were performed using the Limma package in R.

label_protocol: Amplified amino-allyl cDNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl cDNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol:
ch1: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.
ch2: Total RNA was extracted using the Qiagen RNeasy Kit, (Qiagen Inc.) according to the manufacturer's protocol with on-column DNase digestion followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: male

tag: cell line

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Primary human prostate fibroblast cell line, designated PSC27, was a gift from Dr. Beatrice Knudsen. PSC27 cells were cultured in prostate stromal cell (PSC) complete medium.

tag: cell passage

value: passage 9

value: PSC27 prostate fibroblasts in standard (proliferation) culture conditions.


title: Quiescent PSC27 cells at p10 exposed to IR 10Gy sample 2

value: Quiescent PSC27 prostate fibroblasts exposed to a 10Gy ionizing radiation.


title: Quiescent PSC27 cells at p10 sample 1

description: Quiescent PSC27 cells at p10 sample 1

value: PSC27 prostate fibroblasts in culture conditions with serum-free growth medium deprived of mitogens, designated quiescence by serum-starvation.


title: Quiescent PSC27 cells at p10 exposed to IR 10Gy sample 1


title: Quiescent PSC27 cells at p10 exposed to IR 10Gy sample 3


title: Quiescent PSC27 cells at p10 sample 3

description: Quiescent PSC27 cells at p10 sample 3


title: Proliferating PSC27 cells at p9 sample 1


title: Quiescent PSC27 cells at p10 sample 2

description: Quiescent PSC27 cells at p10 sample 2


title: Proliferating PSC27 cells at p9 sample 2


title: Adrenal gland, biological replicate 1

status: Public on Nov 15 2017

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description:
Gene expression data from normal adrenal gland
A_WT_1

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary and quantile normalisation (Expression console v.1.3.0.187, Affymetrix)

organism: Rattus norvegicus

source_name: Normal adrenal gland, sample F11/450

label_protocol: Ovation PicoSL WTA System V2 in combination with the Encore Biotin Module (Nugen)

growth_protocol: Animals per housed under spf conditions

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: No treatment

tag: strain

value: Sprague–Dawley white eye/Wistar–Kyoto

tag: age

value: 24 months

tag: genotype/variation

value: wild type

value: normal adrenal gland


title: Adrenal gland, biological replicate 3

description:
Gene expression data from normal adrenal gland
A_WT_3

scan_protocol: According to the Affymetrix expression protocol

source_name: Normal adrenal gland, sample F10/2065

value: 12 months


title: Adrenal gland, biological replicate 4

description:
Gene expression data from normal adrenal gland
A_WT_4

source_name: Normal adrenal gland, sample M10/1940

value: Male


title: Adrenal lesion, heterozygous for Cdknb1 mutation, biological replicate 4

description:
Gene expression data from adrenal lesions
A_HT_4

source_name: Adrenal lesion, sample F12/416

value: 13 months

value: p27Kip1 (Cdknb1) mutant, heterozygous

value: adrenal lesions


title: Adrenal lesion, heterozygous for Cdknb1 mutation, biological replicate 3

description:
Gene expression data from adrenal lesions
A_HT_3

source_name: Adrenal lesion, sample M11/1006

value: 21 months


title: Adrenal lesion, heterozygous for Cdknb1 mutation, biological replicate 7

description:
Gene expression data from adrenal lesions
A_HT_7

source_name: Adrenal lesion, sample M12/420


title: Adrenal lesion, heterozygous for Cdknb1 mutation, biological replicate 1

description:
Gene expression data from adrenal lesions
A_HT_1

source_name: Adrenal lesion, sample F09/912

value: 23 months

value: Female


title: Adrenal lesion, heterozygous for Cdknb1 mutation, biological replicate 6

description:
Gene expression data from adrenal lesions
A_HT_6

source_name: Adrenal lesion, sample M12/418


title: Adrenal gland, biological replicate 2

description:
Gene expression data from normal adrenal gland
A_WT_2

source_name: Normal adrenal gland, sample M11/449


title: Adrenal lesion, heterozygous for Cdknb1 mutation, biological replicate 2

description:
Gene expression data from adrenal lesions
A_HT_2

source_name: Adrenal lesion, sample M07/929


title: Adrenal lesion, heterozygous for Cdknb1 mutation, biological replicate 5

description:
Gene expression data from adrenal lesions
A_HT_5

source_name: Adrenal lesion, sample F12/417


title: Pituitary lesion, heterozygous for Cdknb1 mutation, biological replicate 2

description: Gene expression data from pituitary lesions

data_processing: RMA probeset summary and quantile normalisation (Expression console)

source_name: Pituitary lesion, sample 08/665.2

label_protocol: GeneChip® Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix)

value: pituitary lesion


title: Pituitary lesion, heterozygous for Cdknb1 mutation, biological replicate 1

description: Gene expression data from normal pituitary

source_name: Pituitary lesion, sample 08/665.1

value: normal pituitary


title: Pituitary lesion, heterozygous for Cdknb1 mutation, biological replicate 8

source_name: Pituitary lesion, sample 08/772

value: 19 months


title: Pituitary lesion, heterozygous for Cdknb1 mutation, biological replicate 6

source_name: Pituitary lesion, sample 08/781.3

value: 10 months


title: Pituitary lesion, heterozygous for Cdknb1 mutation, biological replicate 5

source_name: Pituitary lesion, sample 08/781.2


title: Pituitary lesion, heterozygous for Cdknb1 mutation, biological replicate 7

source_name: Pituitary lesion, sample 08/775


title: Pituitary lesion, heterozygous for Cdknb1 mutation, biological replicate 3

source_name: Pituitary lesion, sample 08/665.5


title: Pituitary lesion, heterozygous for Cdknb1 mutation, biological replicate 4

source_name: Pituitary lesion, sample 08/792.2

value: 22 months


title: Breast_tumor_1203

city: Oslo

first: Thomas

last: Fleischer

address: Ullernchausséen 70

department: Department of Cancer Genetics, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

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

data_processing: Touleimat and Tost, Epigenomics 2012. Preprocessing and normalization involved steps of probe filtering, color bias correction, background subtraction and subset quantile normalization.

extract_protocol: genomic DNA from tumor tissue was isolated using the Maxwell ® 16 (Promega) instrument and the Maxwell R 16 tissue DNA Purification Kit (Progmega cat.nr.AS1030).

tag: er status

value: neg

value: Basal

tag: cohort


title: Breast_tumor_1098

value: pos

value: LumA


title: Breast_tumor_1270

value: LumB


title: Buffy coat_P50

city: Parkville

first: Alexandra

last: Sexton-Oates

state: VIC

address: 50 Flemington Rd

country: Australia

institute: Murdoch Children's Research Institute

data_processing: lumi, minfi, SWAN normalisation

source_name: genomic DNA from buffy coat sample P50

extract_protocol: genomic DNA was extracted and purified from buffy coat samples using Qiagen QIAamp DNA mini kit according to standard instructions, genomic DNA was extracted and purified from urine samples using Qiagen QIAamp viral RNA min kit according to standard instructions

tag: Sex

value: male

tag: disease group

tag: diagnosis

value: Diabetic Chronic-Kidney Disease

value: blood


title: Buffy coat_P73

source_name: genomic DNA from buffy coat sample P73

tag: tissue


title: Breast_tumor_1329

value: Normal


title: Urine_P7

source_name: genomic DNA from urine sample P7

value: urine


title: Breast_tumor_1046


title: Breast_tumor_1071


title: Breast_tumor_1073


title: Breast_tumor_1153


title: Breast_tumor_1268


title: Breast_tumor_1112


title: Urine_P73

source_name: genomic DNA from urine sample P73


title: Breast_tumor_1276


title: Breast_tumor_1211


title: Breast_tumor_1017


title: Breast_tumor_1104


title: Breast_tumor_1278


title: Breast_tumor_1092


title: Breast_tumor_1084


title: Breast_tumor_1154


title: Buffy coat_P7

source_name: genomic DNA from buffy coat sample P7


title: Breast_tumor_1177


title: Breast_tumor_1049


title: Breast_tumor_1045


title: Breast_tumor_1143


title: Breast_tumor_1271


title: Buffy coat_P102

source_name: genomic DNA from buffy coat sample P102


title: Breast_tumor_1242


title: Breast_tumor_1303


title: Breast_tumor_1093


title: Breast_tumor_1168


title: Breast_tumor_1259


title: Breast_tumor_1314


title: Breast_tumor_1209


title: Breast_tumor_1220


title: Breast_tumor_1023


title: Breast_tumor_1190


title: Breast_tumor_1261


title: Breast_tumor_1214


title: Breast_tumor_1079


title: Breast_tumor_1004


title: Breast_tumor_1107


title: Breast_tumor_1122


title: Breast_tumor_1293


title: Breast_tumor_1068


title: Breast_tumor_1306


title: Breast_tumor_1254


title: Breast_tumor_1038


title: Breast_tumor_1172


title: Breast_tumor_1263


title: Breast_tumor_1282


title: Breast_tumor_1035


title: Breast_tumor_1180


title: Breast_tumor_1108


title: Breast_tumor_1260


title: Breast_tumor_1132


title: Breast_tumor_1101


title: Breast_tumor_1127


title: Breast_tumor_1151


title: Breast_tumor_1105


title: Breast_tumor_1224


title: Breast_tumor_1055


title: Breast_tumor_1148


title: Breast_tumor_1241


title: Breast_tumor_1065


title: Breast_tumor_1069


title: Breast_tumor_1231


title: Breast_tumor_1237


title: Breast_tumor_1256


title: Breast_tumor_1082


title: Breast_tumor_1244


title: Breast_tumor_1125


title: Breast_tumor_1042


title: Breast_tumor_1323


title: Breast_tumor_1284


title: Breast_tumor_1106


title: Breast_tumor_1115


title: Breast_tumor_1155


title: Breast_tumor_1113


title: Breast_tumor_1207


title: Breast_tumor_1064


title: Breast_tumor_1080


title: Breast_tumor_1083


title: Breast_tumor_1013


title: Breast_tumor_1325


title: Breast_tumor_1178


title: Breast_tumor_1085


title: Breast_tumor_1248


title: Breast_tumor_1228


title: Breast_tumor_1141


title: Breast_tumor_1200


title: Breast_tumor_1014


title: Breast_tumor_1007


title: Breast_tumor_1192


title: Breast_tumor_1205


title: Breast_tumor_1163


title: Breast_tumor_1296


title: Breast_tumor_1025


title: Breast_tumor_1036


title: Breast_tumor_1307


title: Breast_tumor_1189


title: Breast_tumor_1131


title: Breast_tumor_1197


title: Breast_tumor_1005


title: Breast_tumor_1034


title: Breast_tumor_1142


title: Breast_tumor_1077


title: Breast_tumor_1087


title: Breast_tumor_1103


title: Breast_tumor_1062


title: Breast_tumor_1330


title: Breast_tumor_1100


title: Breast_tumor_1240


title: Breast_tumor_1257


title: Breast_tumor_1279


title: Breast_tumor_1053


title: Breast_tumor_1202


title: Breast_tumor_1158


title: Breast_tumor_1234


title: Breast_tumor_1249


title: Breast_tumor_1198


title: Breast_tumor_1118


title: Breast_tumor_1236


title: Breast_tumor_1258


title: Breast_tumor_1215


title: Breast_tumor_1096


title: Breast_tumor_1060


title: Breast_tumor_1057


title: Breast_tumor_1156


title: Breast_tumor_1110


title: Breast_tumor_1264


title: Breast_tumor_1015


title: Breast_tumor_1150


title: Breast_tumor_1262


title: Breast_tumor_1028


title: Breast_tumor_1010


title: Breast_tumor_1041


title: Breast_tumor_1008


title: Breast_tumor_1020


title: Breast_tumor_1225


title: Breast_tumor_1285


title: Breast_tumor_1018


title: Breast_tumor_1109


title: Breast_tumor_1176


title: Breast_tumor_1187


title: Breast_tumor_1129


title: Breast_tumor_1039


title: Breast_tumor_1162


title: Breast_tumor_1194


title: Breast_tumor_1133


title: Breast_tumor_1199


title: Breast_tumor_1193


title: Breast_tumor_1128


title: Breast_tumor_1091


title: Breast_tumor_1009


title: Breast_tumor_1066


title: Breast_tumor_1171


title: Breast_tumor_1226


title: Breast_tumor_1266


title: Breast_tumor_1326


title: Breast_tumor_1165


title: Breast_tumor_1195


title: Breast_tumor_1170


title: Breast_tumor_1319


title: Breast_tumor_1019


title: Breast_tumor_1067


title: Breast_tumor_1052


title: Breast_tumor_1287


title: Breast_tumor_1031


title: Breast_tumor_1138


title: Breast_tumor_1030


title: Breast_tumor_1006


title: Breast_tumor_1159


title: Breast_tumor_1102


title: Breast_tumor_1117


title: Breast_tumor_1310


title: Breast_tumor_1245


title: Breast_tumor_1070


title: Breast_tumor_1136


title: Breast_tumor_1295


title: Breast_tumor_1322


title: Breast_tumor_1024


title: Breast_tumor_1027


title: Breast_tumor_1059


title: Breast_tumor_1033


title: Breast_tumor_1232


title: Breast_tumor_1137


title: Breast_tumor_1032


title: Breast_tumor_1054


title: Breast_tumor_1316


title: Breast_tumor_1208


title: Breast_tumor_1201


title: Breast_tumor_1299


title: Breast_tumor_1029


title: Breast_tumor_1088


title: Breast_tumor_1114


title: Breast_tumor_1267


title: Breast_tumor_1048


title: Breast_tumor_1075


title: Breast_tumor_1188


title: Breast_tumor_1233


title: Breast_tumor_1196


title: Breast_tumor_1311


title: Breast_tumor_1120


title: Breast_tumor_1317


title: Breast_tumor_1167


title: Breast_tumor_1312


title: Breast_tumor_1289


title: Breast_tumor_1123


title: Breast_tumor_1250


title: Breast_tumor_1247


title: Breast_tumor_1216


title: Breast_tumor_1086


title: Breast_tumor_1016


title: Breast_tumor_1181


title: Breast_tumor_1185


title: Breast_tumor_1318


title: Breast_tumor_1223


title: Breast_tumor_1134


title: Breast_tumor_1099


title: Breast_tumor_1076


title: Breast_tumor_1221


title: Breast_tumor_1324


title: Breast_tumor_1304


title: Breast_tumor_1301


title: Breast_tumor_1255


title: Breast_tumor_1166


title: Breast_tumor_1217


title: Breast_tumor_1089


title: Breast_tumor_1121


title: Breast_tumor_1164


title: Breast_tumor_1173


title: Breast_tumor_1078


title: Breast_tumor_1300


title: Breast_tumor_1050


title: Breast_tumor_1074


title: Breast_tumor_1229


title: Breast_tumor_1022


title: Breast_tumor_1145


title: Breast_tumor_1160


title: Breast_tumor_1235


title: Breast_tumor_1213


title: Breast_tumor_1021


title: Breast_tumor_1161


title: Breast_tumor_1238


title: Breast_tumor_1251


title: Breast_tumor_1191


title: Breast_tumor_1219


title: Breast_tumor_1090


title: Breast_tumor_1144


title: Breast_tumor_1040


title: Breast_tumor_1146


title: Breast_tumor_1269


title: Breast_tumor_1294


title: Breast_tumor_1313


title: Breast_tumor_1063


title: Breast_tumor_1286


title: Breast_tumor_1184


title: Breast_tumor_1058


title: Breast_tumor_1012


title: Breast_tumor_1283


title: Breast_tumor_1277


title: Breast_tumor_1130


title: Breast_tumor_1001


title: Breast_tumor_1139


title: Breast_tumor_1095


title: Breast_tumor_1056


title: Breast_tumor_1315


title: Breast_tumor_1321


title: Breast_tumor_1051


title: Breast_tumor_1292


title: Breast_tumor_1047


title: Breast_tumor_1186


title: Breast_tumor_1183


title: Breast_tumor_1327


title: LAU1314

type: SRA

city: Lausanne

first: David

last: Gfeller

address: Rue du Bugnon 25A

department: Department of Oncology UNIL CHUV; Ludwig Institute for Cancer Research Lausanne

country: Switzerland

institute: University of Lausanne

library_source: transcriptomic

data_processing:
Basecalling was performed using Illumina pipeline Casava 1.82
RNA-seq reads alignment to the human hg19 genome and gene expression quantification were performed with RSEM version 1.2.19, using Bowtie2 version 2.2.4 and Samtools version 1.2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Ensembl gene ID, transcript ID, gene length, effective length, expected counts, TPM counts and FPKM counts at the gene level

source_name: Iliac-obturator metastatic melanoma lymph node

extract_protocol:
Single cell suspension was obtained from lymph nodes using mechanical disruption and immediately cryopreserved in RPMI 1640 supplemented with 40% FCS and 10% DMSO. Dead cells were removed after thawing using a dead cell removal kit (Miltenyi) following the manufacturer's protocol. RNA was extracted using RNeasy Plus Mini kit from Qiagen and following the manufacturer's protocol and only samples with a RQN >= 7 as measured with a fragment analyser (Advanced Analytical) following the manufacturer's protocol were used for subsequential library construction.
The library was constructed using Truseq stranded RNA kit from Illumina following the manufacturer's protocol.

value: Male


title: Breast_tumor_1152

value: Female


title: Breast_tumor_1206


title: LAU355

source_name: Iliac-obturator lymph node

value: Iliac-obturator lymph node


title: Breast_tumor_1140


title: Breast_tumor_1328


title: Breast_tumor_1253


title: LAU1255

source_name: Axillary metastatic melanoma lymph node

value: Axillary metastatic melanoma lymph node


title: Breast_tumor_1290


title: LAU125

source_name: Iliac metastatic melanoma lymph node

value: Iliac metastatic melanoma lymph node


title: Breast_tumor_1182


title: Breast_tumor_1126


title: Breast_tumor_1124


title: Breast_tumor_1174


title: Breast_tumor_1288


title: Breast_tumor_1280


title: Breast_tumor_1072


title: Breast_tumor_1273


title: Breast_tumor_1111


title: Breast_tumor_1097


title: Breast_tumor_1011


title: aortic aneurysm 63

city: Shanghai

first: Jian

last: Dong

address: 168 Changhai Rd

department: Department of Vascular Surgery

country: China

institute: Changhai Hospital

description:
11653B_63-P1
microRNA profiling

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing:
Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data.
The signal value defaults to 0.1 if the probe were undetected, then the raw signal of detected probes are normalized by percentile 90 normalization.

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent miRNA microarray, according to manufacturer's protocol.

extract_protocol: Trizol

tag: condition

value: aortic aneurysm

value: plasma


title: Breast_tumor_1265


title: Breast_tumor_1274


title: aortic aneurysm 1

description:
11653B_1-P1
microRNA profiling


title: acute aortic dissection 15

description:
11653B_15-P1
microRNA profiling

value: acute aortic dissection


title: Breast_tumor_1218


title: Breast_tumor_1246


title: healthy 34

description:
11653B_H34-P1
microRNA profiling

value: healthy


title: healthy 9

description:
11653B_H9-P1
microRNA profiling


title: Breast_tumor_1002


title: Breast_tumor_1116


title: Breast_tumor_1204


title: aortic aneurysm 71

description:
11653B_71-P1
microRNA profiling


title: acute aortic dissection 59

description:
11653B_59-P1
microRNA profiling


title: Breast_tumor_1179


title: Breast_tumor_1003


title: acute aortic dissection 6

description:
11653B_6P1
microRNA profiling


title: Breast_tumor_1222


title: Breast_tumor_1243


title: healthy 3

description:
11653D_H3-P1
microRNA profiling


title: Breast_tumor_1119


title: Angiogenesis 3h Swap 2

city: San Juan

first: Humberto

last: Ortiz-Zuazaga

state: PR

address: PO BOX 23334

department: High Performance Computing facility

institute: University of Puerto Rico

description:
Sample name: 3h-swap2
24oct07_251535410112_S01-2_GE2-v5_95_Feb07_1_3.txt

hyb_protocol: The hybridization and washing protocol were done as recommended by the manufacturer (Two-Color Microarray-Based Gene Expression Analysis Protocol, Version 5.5, February 2007, from Agilent Technologies). Briefly, 300 ng of Cy-3 and Cy5-labeled cRNAs were combined with 10 X Blocking Agent, and 25 X Fragmentation Buffer at 60˚C for 30 min. The reaction was stopped with 2 X GEx Hybridization Buffer HI-RPM and hybridized to the oligo microarray for 17 hrs at 60˚C with continuing rotation (10 rpm). The reagents used for this step were from the Gene Expression Hybridization Kit. After hybridization, slides were washed during 1 min at RT using the GE Wash Solution 1, and 1 min at 37˚C with GE Wash Solution 2. Next, slides were washed for 1 min with acetonitrile (Sigma). A final washing was done using a Stabilization and Drying Solution for 30 sec.

scan_protocol: Data images were obtained by laser-based scanning using the Microarray Scanner and the Feature Extraction Software (v8.1) both from Agilent. Scanning parameters were as recommended by the manufacturer. Briefly, the resolution settings for scanning were 5 micrometers using minimum (10%) and maximum (100%) Photo Multiplier Tube detection sensitivities. An initial assessment of the array was performed using the information from the Quality Report extracted from the Feature Extraction Software (v8.1).

data_processing: The analysis of the microarray data consisted of the following steps: 1) within-array and 2) between-array normalization. Normalization of the data was as previously described (Smyth and Speed 2003). Briefly, in the “within-array normalization” analyses the M-values were normalized for each array separately using a global loess method without background correction, whereas in the “between-array normalization” analyses log-ratios were normalized to be comparable across arrays using the Aquantile method. Normalization success was determined using MA plot graphical representations. These MA-plots depict the log-ratio of Red versus Green (the M value in the y axis) against the overall intensity of each spot (the A value in the x axis). The log-ratio is represented by the M-value, M = log2(R) _ log2(G), and the overall intensity by the A-value, A = (log2(R) +log2(G))/2. In this experiment, RNA sources from different time points after Tunicamycin exposure were included (at 3 hrs and 32 hrs). Dye swapping was done to correct for differences in the incorporation of the dyes. The main comparisons were done for each time point against the control sample and the Tunicamycin treated sample.

organism: Bos taurus

source_name: Angiogenesis - 3h Control

label_protocol: Total RNA from control or experimental samples was linearly amplified and labeled using two different fluorescent dyes: cyanine 3-CTP (Cy-3), and cyanine 5-CTP (Cy-5, Amersham Biosciences) as described in the Agilent Low RNA Input Linear Amplification Kit. Briefly, in a first step, double stranded cDNA (dscDNA) was generated using the Moloney Murine Leukaemia virus reverse transcriptase (MMLV-RT). In the first reaction, 1 μg of total RNA was mixed with T7 promoter primers and the diluted Spike-in Mix (A or B), incubated at 65˚C during 10 min and placed on ice for 5 min. The denatured primers and total RNA were mixed with the following reagents: 5 X First Strand Buffer, 0.1 M DTT, 10 mM dNTP mix, MMLV-RT, and RNaseOUT. This reaction mix was incubated at 40˚C for 2 hrs, then at 65˚C for 15 min, and finally placed on ice for 5 min. Next, synthesis and labeling of cRNA was performed simultaneously mixing the prepared reaction (containing the dscDNA) with a transcription Master Mix: (4 X Transcription Buffer, 0.1 M DTT, NTP mix, 50% PEG, RNAseOUT, inorganic pyrophosphatase, T7 RNA polymerase, and Cy-3 or Cy-5 (10 mM, each). The reaction was incubated at 40˚C for 2 hrs. Amplified fluorescent cRNA probes were purified using the Qiagen's RNeasy-mini spin columns. Finally, fluorescently labeled cRNA samples were analyzed for yield and dye incorporation using the ND-1000 Spectrophotometer (NanoDrop Technologies, Rockland, DE). Only samples that presented a concentration of more than 8 pmol/mg (a measure representing efficient dye incorporation) were used for hybridization as recommended by the manufacturer.

extract_protocol: Total RNA was isolated as TRIzol method. RNA concentration and integrity were detected using the Agilent's 2100 Bioanalyzer with an RNA 6000 Nano LabChip® Kit. Confirmatory readings were performed using the ND-1000 Spectrophotometer (NanoDrop Technologies, Rockland, DE).

value: capillary endothelial cells

tag: time

value: 3h (nontransformed cell line)

tag: agent

value: control

value: Adrenal Medulla

value: Wild Type

source_name: Angiogenesis - 3h Tunicamycin

value: Tunicamycin


title: Breast_tumor_1026


title: Breast_tumor_1252


title: Breast_tumor_1135


title: healthy 50

description:
11653B_H50-P1
microRNA profiling


title: Breast_tumor_1275


title: Angiogenesis 3h Replicate 2

description:
Sample name: 3h-rep2
24oct07_251535410112_S01-2_GE2-v5_95_Feb07_1_1.txt


title: Breast_tumor_1061


title: Breast_tumor_1157


title: Angiogenesis 32h Swap 2

description:
Sample name: 32h-swap2
24oct07_251535410112_S01-2_GE2-v5_95_Feb07_1_4.txt

source_name: Angiogenesis - 32h Control

value: 32h (nontransformed cell line)

source_name: Angiogenesis - 32h Tunicamycin


title: Breast_tumor_1281


title: Breast_tumor_1037


title: acute aortic dissection 14

description:
11653B_14-P1
microRNA profiling


title: Breast_tumor_1149


title: Breast_tumor_1175


title: Breast_tumor_1291


title: Breast_tumor_1320


title: aortic aneurysm 98

description:
11653F_98-P1
microRNA profiling


title: Angiogenesis 32h Swap 1

description:
Sample name: 32h-swap1
24oct07_251535410111_S01-2_GE2-v4_95_Feb07_1_4.txt


title: Breast_tumor_1297


title: Angiogenesis 3h Swap 1

description:
Sample name: 3h-swap1
24oct07_251535410111_S01-2_GE2-v4_95_Feb07_1_3.txt


title: Angiogenesis 32h Replicate 1

description:
Sample name: 32h-rep1
24oct07_251535410111_S01-2_GE2-v4_95_Feb07_1_2.txt


title: aortic aneurysm 38

description:
11653B_38-P1
microRNA profiling


title: aortic aneurysm 87

description:
11653E_87-P1
microRNA profiling


title: aortic aneurysm 39

description:
11653E_39-P2
microRNA profiling


title: Breast_tumor_1043


title: aortic aneurysm 46

description:
11653E_46-P1
microRNA profiling


title: healthy 77

description:
11653E_H77-P1
microRNA profiling


title: Breast_tumor_1230

value: pos


title: MTA_3T3-L1_D9_Paral1-siRNA_Rep2

city: Lille

first: François

middle: Franck

last: FIRMIN

address: Boulevard du Professeur Jules Leclerc

department: Team 4

country: France

institute: Inserm U1011

description: RMA expression value derived from Expression Console software; probe analysis

hyb_protocol: Following fragmentation, 5,5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip Mouse Transcriptome Array 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: Total RNA (100-300ng) from 3T3-L1 cells was processed for labelling, purification and hybridized to Affymetrix Genechip Mouse Genome 430 2.0 or to Mouse Transcriptome Array 1.0 (MTA 1.0) according to the manufacturer's protocol. Raw data were pre-processed (Expression Console, v1.4.1. Affymetrix), using the GCCN and SST algorithms and RMA background correction for MTA arrays.

organism: Mus musculus

source_name: 3T3-L1 cells

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: 3T3-L1 cells were routinely grown at 37°C and 5% CO2 in Dulbecco’s Modified Eagle’s medium (DMEM)-high glucose (4.5g/L) containing 10% (v/v) Cosmic Calf Serum, 100U/mL penicillin and 100µg/mL streptomycin. Seeding densities were as follows: 5x104 cells/well (12-well cluster), 12.5x104 (6-well cluster) or 5x105 cells (P100 dish). Proliferation medium was renewed every other days.

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

treatment_protocol: Adipocyte differentiation was initiated 2 days after reaching confluence (Day 0, D0) by growing cells in DMEM supplemented with 10% Fetal Bovine Serum, 100U/mL penicillin and 100µg/mL streptomycin, 1µM dexamethasone (Sigma, Ref. D8893-1MG), 500µM 3-isobutyl-1-methylxanthine (IBMX, Sigma, Ref. I5879) and 1µg/mL bovine insulin (Sigma, Ref. I5500). Two days later (day 2, D2), medium was replaced by DMEM supplemented with 10% FBS, 1µg/mL bovine insulin and a mix of 100U/mL penicillin and 100µg/mL streptomycin (Life Technologies). Two days later (day 4, D4), medium was replaced by DMEM supplemented with 10% FBS and subsequently renewed every other day until day 9, D9. 3T3-L1 cells were transfected by siRNAs (100nM) using INTERFERin (Polyplus Transfection, Illkirch, France, Ref. 409-10). siRNAs were: control siRNA (Dharmacon, ON-TARGETplus non-targeting, ref. D-001810-10-10,) and Paral1-siRNA (Silencer Select ref. 101167, Ambion). Differentiated 3T3-L1 adipocytes were reverse-transfected as follows: cells were washed with 1x PBS, trypsinized and suspended (5x105 for 800µL) in DMEM supplemented with 10% FBS containing 100U/mL penicillin and 100µg/mL streptomycin. Cells in suspension were transfected by siRNA (100nM) with INTERFERin (Polyplus Transfection, Ref. 409-10) in 12-well plates according to the manufacturer’s instructions.

tag: days

tag: transfection

tag: experiment


title: Breast_tumor_1147

tag: gender


title: healthy 69

description:
11653E_H69-P1
microRNA profiling


title: healthy 63

description:
11653E_H63-P1
microRNA profiling


title: healthy 43

description:
11653F_H43-P1
microRNA profiling


title: Breast_tumor_1212

value: Normal


title: Breast_tumor_1298

value: Female

value: LumB


title: Breast_tumor_1081


title: acute aortic dissection 96

description:
11653E_96-P1
microRNA profiling


title: acute aortic dissection 92

description:
11653E_92-P1
microRNA profiling


title: MTA_3T3-L1_D9_Paral1-siRNA_Rep1

tag: cell line


title: acute aortic dissection 69

description:
11653E_69-P1
microRNA profiling


title: acute aortic dissection 30

description:
11653E_30-P1
microRNA profiling


title: Breast_tumor_1305


title: MTA_3T3-L1_D9_Ctrl-siRNA_Rep3

value: Ctrl-siRNA


title: Breast_tumor_1044

value: neg


title: MTA_3T3-L1_D9_Paral1-siRNA_Rep3


title: MTA_3T3-L1_D2_Paral1-siRNA_Rep2


title: MTA_3T3-L1_D2_Paral1-siRNA_Rep3


title: MTA_3T3-L1_D9_Ctrl-siRNA_Rep2


title: Breast_tumor_1272


title: Breast_tumor_1239


title: MTA_3T3-L1_D9_Ctrl-siRNA_Rep1


title: Breast_tumor_1302

value: LumA


title: Breast_tumor_1094


title: Breast_tumor_1308


title: parental T47D cell line 2

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

source_name: parental T47D cell line

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Cells were grown in DMEM 4,5g/L D-glucose medium supplemeted with 10% FBS, 50 U/ml penicilin, 50μg/ml streptomycin and 5% glutamine.

extract_protocol: Total RNA was isolated using the PureLink RNA mini kit (cat no 12183018A) according to manufacurer´s instruction

treatment_protocol: Treatment protocol described in Pavlovic et al JNCI 2015

tag: group

value: parental T47D cell line


title: SMC3i, Biological Replicate 2

city: La Jolla

first: George

last: Sen

state: CA

address: 9500 GIlman Drive

department: Dermatology/CMM

institute: UCSD

description: Cells transduced with retroviruses expressing SMC3 shRNAs

hyb_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)

scan_protocol: Affymetrix HG-U133 2.0 plus arrays were performed at the UCSD Genechip Microarray Core Facility.

data_processing: RMA

label: Biotin

source_name: SMC3 knockdown cells

growth_protocol: Human Primary Keratinocytes were grown in self-renewing condition using KSF-M (GIBCO-BRL) supplemented with epidermal growth factor (EGF) and bovine pituitary extract (BPE).

extract_protocol: Total RNA from cells was extracted using the RNeasy mini kit according to manufacturer's protocol.

treatment_protocol: Keratinocytes were transduced with retroviral vectors to knockdown SMC1A, SMC3, or scrambled control.

tag: cells

value: Human Primary Keratinocytes


title: Breast_tumor_1309


title: Breast_tumor_1227


title: Breast_tumor_1169


title: MTA_3T3-L1_D2_Paral1-siRNA_Rep1


title: MTA_3T3-L1_D2_Ctrl-siRNA_Rep1


title: parental T47D cell line 1


title: Breast_tumor_1210


title: MTA_3T3-L1_D2_Ctrl-siRNA_Rep3


title: Δset2:N+.2

status: Public on Nov 14 2017

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

hyb_protocol: 1.5 ug of Cy3-labeled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60 °C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. Upon completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Preprocessing steps including background correction, normalization and summarization of probe intensities were performed by employing the oligo R package (Carvalho 2010).

organism: Fusarium fujikuroi

source_name: Strain set2, 60mM Gln, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Strains were grown for 3 days in Darken medium and subsequently, an aliquot of 500 µL was transferred to liquid ICI medium with either 6 mM or 60 mM glutamine and grown for additional 3 days on a rotary shaker (180 rpm) at 28 °C.

extract_protocol: Total RNA was extracted using the TRI Reagent (Sigma-Aldrich, Steinheim, Germany) and DNA was removed using DNAse I (Roche Diagnostics, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).

treatment_protocol: The mycelium was harvested, shock frozen with liquid nitrogen and lyophilized.

tag: treatment

value: 60mM Gln


title: SMC3i, Biological Replicate 1

label_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)


title: MTA_3T3-L1_D2_Ctrl-siRNA_Rep2


title: bone metastatic subline T47D-5516 (DBM) 2

source_name: bone metastatic subline T47D-5516 (DBM)

value: bone metastatic subline T47D-5516 (DBM)


title: Control (CTL), Biological Replicate 1

description: Cells transduced with retroviruses expressing control shRNAs

source_name: Control Cells


title: SMC1Ai, Biological Replicate 2

description: Cells transduced with retroviruses expressing SMC1A shRNAs

source_name: SMC1A knockdown cells


title: Δset2:N+.1

source_name: Strain set2, 60mM Gln, replicate 1


title: bone metastatic subline T47D-5516 (DBM) 1


title: SMC1Ai, Biological Replicate 1


title: Δash1:N+.2

source_name: Strain ash1, 60mM Gln, replicate 2


title: wt2:N+.1

source_name: Strain wt2, 60mM Gln, replicate 1


title: Control (CTL), Biological Replicate 2


title: Δash1:N+.1

source_name: Strain ash1, 60mM Gln, replicate 1


title: Δset2:N-.2

source_name: Strain set2, 6mM Gln, replicate 2

value: 6mM Gln


title: wt2:N+.2

source_name: Strain wt2, 60mM Gln, replicate 2


title: Δash1:N-.2

source_name: Strain ash1, 6mM Gln, replicate 2


title: Δash1:N-.1

source_name: Strain ash1, 6mM Gln, replicate 1


title: Δset2:N-.1

source_name: Strain set2, 6mM Gln, replicate 1


title: wt2:N-.2

source_name: Strain wt2, 6mM Gln, replicate 2


title: wt2:N-.1

source_name: Strain wt2, 6mM Gln, replicate 1


status: Public on Nov 13 2017

city: Piracicaba

first: Luis

middle: Eduardo

last: Aranha Camargo

state: São Paulo

address: Av. Pádua Dias

department: Phytopathology

country: Brazil

institute: University of São Paulo

description: Chip Agilent, Sugarcane transcriptome - ch1: LxxI_60DAI; ch2: MI_60DAI_replicate2"

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings

data_processing: Raw and background corrected data

organism: Saccharum officinarum

label_protocol: CyScribe Post-Labelling Kit Protocol - GE Healthcare

growth_protocol: Single-bud stalk sections  of the variety SP80-3280  were cultivated in substrate  for 30 days and transferred to 22,5L  pots. Plants were grown in the greenhouse."

extract_protocol: Total RNA was extracted using TriZol reagent

treatment_protocol: Sugarcane plantlets inoculated 30 days after planting with Lxx (treatment LxxI_60DAI) . Leaf whorl tissue was collected 60 days after inoculation.

tag: cultivar

value: Saccharum hybrid cultivar mix

value: leaf whorl

tag: pool

value: 3 plants

tag: variety

tag: time point

value: 60 days after inoculation

value: Lxx CTCB07 strain inoculated plants

treatment_protocol: Sugarcane plantlets inoculated 30 days after planting with Lxx (treatment MI_60DAI) . Leaf whorl tissue was collected 60 days after inoculation.

value: Mocked inoculated plants


description: Chip Agilent, Sugarcane transcriptome - ch1: LxxI_30DAI; ch2: MI_30DAI_replicate2"

treatment_protocol: Sugarcane plantlets inoculated 30 days after planting with Lxx (treatment LxxI_30DAI) . Leaf whorl tissue was collected 30 days after inoculation.

value: 30 days after inoculation

treatment_protocol: Sugarcane plantlets inoculated 30 days after planting with Lxx (treatment MI_30DAI) . Leaf whorl tissue was collected 30 days after inoculation.


title: Biopsy_ENR3_WK12_20cm

status: Public on Nov 11 2017

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis

hyb_protocol: Equal amount of Cy3 labeled target was hybridized to Sureprint G3 Human GE 8x60k array (Agilent) for 15 hours according to the manufacturers protocol

scan_protocol: Arrays were scanned using Agilent microarray scanner

data_processing: Raw signal intensities were extracted with feature extraction v11.5 software

source_name: intestinal mucosa pinch biopsy

label_protocol: Labeling was performed with Cy3 according to the manufacturer protoocl for one color microarray based gene expression analysis (Agilent)

extract_protocol: Pinch biopsies were obtained at colonoscopy using sterile cold biopsy forceps and snap-frozen for RNA extraction in Trizol reagent (Invitrogen). RNA was isolated using chloroform purification and isopropanol extraction and purified using QIAgen Rneasy Mini Kit.

value: intestinal mucosa

tag: research subject

tag: inflammatory state

value: Active

value: Placebo

value: week 12


title: Biopsy_ENR3_WK12_cecum

tag: tissue

value: Inactive


description: Chip Agilent, Sugarcane transcriptome - ch1: LxxI_60DAI; ch2: MI_60DAI_replicate1"

tag: condition

value: mocked inoculated plants


title: Biopsy_ENR3_WK0_30cm

value: week 0


description: Chip Agilent, Sugarcane transcriptome - ch1: LxxI_30DAI; ch2: MI_30DAI_replicate1"

value: mocked-inoculated plants


title: Biopsy_ENR3_WK12_30cm


title: Biopsy_ENR1_WK24_cecum

value: week 24


title: Biopsy_ENR3_WK0_cecum


title: Biopsy_ENR3_WK0_20cm


title: IECs of WT [Mouse430_2]

city: Beijing

first: Xicheng

last: Liu

address: 7 Science Park Rd., ZGC life science park

institute: National Institute of Biological Sciences, Beijing

description: Six- to eight-week-old sex-matched mice.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 430 2.0 Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000 7G. The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were analyzed with EC (Expression Console) using Affymetrix default analysis settings and RMA as normalization method.

source_name: Mouse IECs on day 12 of CAC model, WT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: Six- to eight-week-old sex-matched mice were intraperitoneally injected with 10 mg/kg of azoxymethane (AOM; Sigma). After 5 days, the mice were treated with 3.5% dextran sulfate sodium (DSS; MP Biomedicals, molecular weight 35-50 kDa) in drinking water for 5 days. On day 12, mice were sacrificed for the IECs isolation.

treatment_protocol: After removal of the Payer's patches and the adventitial fat, the colons were cut open longitudinally and washed with PBS. Colons were cut into 2-3 mm pieces and incubated in HBSS containing 5mM EDTA at 37°C, shaking for 20 min. The supernatant was collected and centrifuged. The pellet was washed in ice-cold PBS and maintained in RNA stabilization solution.

tag: strain/background

tag: model

value: colitis-associated colorectal cancer (CAC)

tag: genotype/variation

value: WT

tag: cell type

value: intestinal epithelial cells (IECs)

tag: age

value: 6-8 weeks


title: Biopsy_ENR1_WK24_10cm


title: IECs of Bmi1ΔIEC [Mouse430_2]

source_name: Mouse IECs on day 12 of CAC model, Bmi1ΔIEC


title: IECs of Mel18ΔIEC [Mouse430_2]

source_name: Mouse IECs on day 12 of CAC model, Mel18ΔIEC


title: Biopsy_ENR1_WK12_cecum

value: Trichuris suis ova


title: Biopsy_ENR1_WK24_20cm


title: Biopsy_ENR1_WK12_20cm


title: gPAK testicular teratocarcinoma #405

city: ITHACA

first: Robert

last: Weiss

state: NY

address: T2006C Veterinary Research Tower

institute: Cornell University

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (31 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 3.5 kb across the entire mouse genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: Arrays were processed using NimbleScan, which transformed image signal to digital signal, followed by using segMNT algorithm to analyze the normalized signal ratio.

source_name: Genomic DNA from gPAK testicular tumor #405

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Genomic DNA was isolated directly from testicular tumors or spleens via dounce homogenization in lysis buffer, phenol/chloroform extraction, and ethanol precipitation.

tag: genotype

value: Stra8-Cre+ Pten+/flox Kras+/LSL-G12D

value: Testicular teratocarcinoma

tag: strain

value: Mixed (FVB/129/B6)

source_name: Normal mouse spleen DNA

value: spleen


title: Biopsy_ENR1_WK12_10cm

value: intestinal mucosa

value: Active


title: IECs of Mel18ΔIEC [MoGene-1_0-st]

hyb_protocol: Following fragmentation, labeling product was hybridized for 16 hr at 45C on Mouse Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the Affymetrix scanner 3000 7G. The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

label_protocol: Labeling product was prepared according to the standard Affymetrix protocol from 200ng total RNA.


title: Biopsy_ENR1_Open_Label_20cm

value: Open Label


title: IECs of WT [MoGene-1_0-st]


title: Biopsy_ENR1_Open_Label_10cm

value: Inactive


title: IECs of DKO [MoGene-1_0-st]

source_name: Mouse IECs on day 12 of CAC model, DKO

value: Bmi1ΔIEC Mel18ΔIEC


title: gPAK testicular teratocarcinoma #492

source_name: Genomic DNA from gPAK testicular tumor #492


title: IECs of Bmi1ΔIEC [MoGene-1_0-st]


title: gPAK testicular teratocarcinoma #7403

source_name: Genomic DNA from gPAK testicular tumor #7403


title: control-160

data_processing:
Raw signal intensities were extracted with feature extraction v11.5 software
Expression intensities were background corrected using the normal plus exponential convolutional method, followed by between-array quantile normalization in limma (version 3.26.9), resulting in log2-transformed intensity values.

source_name: Intestinal mucosa pinch biopsy

tag: disease state

value: non-IBD control


title: control-91


title: control-87


title: IECs of DKO [Mouse430_2]


title: control-94


title: control-179


title: control-98


title: control-177


title: control-154


title: control-150


title: control-162


title: T47DBM vs T47D

hyb_protocol: Hybridization was performed in the Nimblegen Hybridization System according to manufacturer's instructions

scan_protocol: Arrays were scanned with the MS 200 Microarray Scanner and the MS 200 Data Collection Software. Import a scanned image and extract the data was performed using NimbleScan software

data_processing: VSN method as implemented in Bioconductor Ringo package

source_name: bone metastatic subline T47D-5516 (DBM)

label_protocol: 0,5 ug of each gDNA were labeled with Cy3 / Cy5 according to manufacturer's instructions

extract_protocol: Genomic DNA was extracted as described in Pavlovic et al JNCI 2015

tag: group

value: bone metastatic subline T47D-5516 (DBM)

source_name: parental T47D cell line

value: parental T47D cell line


title: control-88


title: control-86


title: control-149


title: control-167


title: control-93


title: gPAK testicular teratocarcinoma #7658

source_name: Genomic DNA from gPAK testicular tumor #7658


title: control-128


title: control-97


title: control-116


title: control-100


title: gPAK testicular teratocarcinoma #7818

source_name: Genomic DNA from gPAK testicular tumor #7818


title: control-113


title: control-107


title: control-101


title: control-103


title: control-117


title: pT47D vs T47D


title: 9N-UC-Normal-Ascending-26

tag: disease (uc = ulcerative colitis; cd = crohn's disease)

value: UC

tag: inflammation

value: Normal

tag: intestinal region

value: Ascending


title: control-111


title: gPAK testicular teratocarcinoma #69

source_name: Genomic DNA from gPAK testicular tumor #69


title: 8Ia-UC-Active-Sigmoid-25

value: Sigmoid


title: 7N-UC-Active-Sigmoid-24


title: 4I-CD-Active-Ileum-21

value: CD

value: Ileum


title: 4N-CD-Normal-Descending-21

value: Descending


title: 6N-CD-Normal-Transverse-23

value: Transverse


title: A012AAM-CD14-V1 vs. RF-href

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization [details provided in the Series supplementary file 'protocol_details.txt']

scan_protocol: scanning of slides using Agilent G256BA; features were extracted using Imagene software from Biodiscovery.

data_processing: [genes, no bg corr]: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve.

label_protocol: robot amplification and labeling v1.0 [details provided in the Series supplementary file 'protocol_details.txt']

extract_protocol: RNA extraction cellLine [details provided in the Series supplementary file 'protocol_details.txt']

tag: ra patient subgroup

value: GC Non-Responders

value: peripheral blood mononuclear cell (PBMC)

tag: cell subpopulation

value: CD14-positive cells

tag: sample group

source_name: reference sample

tag: sample type

value: Stratagene Universal Human Reference RNA

value: RF-HREF


title: 9I-UC-Active-Ascending-26

value: Active


title: 3Ib-CD-Active-Sigmoid-20


title: 8Ib-UC-Active-Ascending-25


title: 5I-CD-Active-Descending-22


title: 3Ia-CD-Active-Sigmoid-20


title: A012AAM-CD4-V1 vs. RF-href

value: CD4-positive cells


title: 2N-UC-Normal-Cecum-19

value: Cecum


title: 2I-UC-Normal-Rectum-19

value: Rectum


title: BM20990 vs MCF7


title: 26N-UC-Inactive-Transverse-17

value: UC

value: Inactive


title: A008AAI-CD4-V1 vs. RF-href


title: A011AAL-CD4-V1 vs. RF-href


title: A009AAJ-CD4-V1 vs. RF-href


title: A007AAH-CD4-V1 vs. RF-href


title: 27N-UC-Inactive-Transverse-18


title: A009AAJ-CD14-V1 vs. RF-href


title: control-148

value: non-IBD control


title: 27I-UC-Active-Sigmoid-18

value: Sigmoid


title: A008AAI-CD14-V1 vs. RF-href


title: A011AAL-CD14-V1 vs. RF-href


title: 24N-UC-Active-Sigmoid-15


title: 25N-CD-Normal-Sigmoid-16

value: CD

value: Normal


title: 24I-UC-Inactive-Ascending-15

value: Ascending


title: 23Na-CD-Normal-Ascending-14


title: 23Nb-CD-Normal-Descending-14

value: Descending


title: 22Na-CD-Normal-Sigmoid-13


title: A004AAE-CD4-V1 vs. RF-href

value: GC Responders


title: A006AAG-CD4-V1 vs. RF-href

value: GC Non-Responders

value: peripheral blood mononuclear cell (PBMC)


title: A006AAG-CD14-V1 vs. RF-href

value: CD14-positive cells

value: Stratagene Universal Human Reference RNA


title: A004AAE-CD14-V1 vs. RF-href

value: RF-HREF


title: 22Nb-CD-Normal-Ascending-13


title: A003AAD-CD14-V1 vs. RF-href


title: 1N-UC-Normal-Cecum-10


title: 26I-UC-Inactive-Rectum-17


title: A003AAD-CD4-V1 vs. RF-href

value: CD4-positive cells


title: A001BBB-CD4-V1 vs. RF-href


title: A001BBB-CD14-V1 vs. RF-href


title: A002AAC-CD4-V1 vs. RF-href


title: 21I-UC-Active-Transverse-12

value: Active

value: Transverse


title: A007AAH-CD14-V1 vs. RF-href


title: 20N-UC-Inactive-Sigmoid-11

value: UC


title: A002AAC-CD14-V1 vs. RF-href


title: 18N-CD-Inactive-Sigmoid-8

value: Inactive


title: 19N-UC-Normal-Transverse-9


title: 14N-CD-Normal-Ileum-5

value: Ileum


title: 1I-UC-Inactive-Sigmoid-10

value: Sigmoid


title: 14I-CD-Active-Ileum-5

value: CD


title: 12I-UC-Normal-Sigmoid-3

value: Normal


title: 13N-UC-Normal-Transverse-4


title: 10N-CD-Normal-Sigmoid-1