title: T87

status: Public on Apr 17 2015

city: West Point

first: Michael

last: Nebozhyn

address: Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4

department: GpGx/Computational System biology

institute: Merck, Inc

description:
ACRG Gastric cohort: microarray profiles from 300 gastric tumors and 100 patient matched normal tissue from gastric cancer patients
Nugen amplification protocol

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45oC with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: The data were analyzed by RMA with Affymetrix Power Tools package using Affymetrix default analysis settings.

source_name: Tumor from patient 87

label_protocol: standard Affymetrix protocol

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: Gastric tumor

tag: patient


title: BALB/cA FAE_rep.1

status: Public on Apr 18 2015

type: RNA

city: New York

first: Gaku

last: Nakato

state: NY

address: 701W 168th street HHMC

department: Microbiology & Immunology

country: USA

institute: Columbia University Medical Center

description:
Mouse miRNA Microarray Release 12.0, 8x15K Catalog # G4471A-021828
microRNA expression

hyb_protocol: Use 100 ng of total RNA to labeling by Agilent miRNA Complete Labeling Reagent and Hyb Kit (Agilent) according to the manufacturer’s instructions. The labeled miRNAs were hybridized with a probe array for 20 hours at 55ºC.

scan_protocol: Slides were scanned after washing on the Agilent Scanner (G2505B)

data_processing:
Agilent Feature Extraction Software.  Data analysis was further performed with Genespring software version 11.0  (Agilent Technologies).
Expression data were considered significant when they differed by at least two-fold between FAE and VE.

molecule: total RNA

organism: Mus musculus

source_name: Murine Follicle-associated epithelium

label_protocol: Agilent miRNA Microarray System Protocol

extract_protocol: Total RNA Extraction from intestinal epithelium using mirVana.

treatment_protocol: Peyer’s patch was dissected from the small intestine and soaked in Hank's Balanced Salt Solution (HBSS) (GIBCO). The tissue was treated with 30 mM EDTA in HBSS for 20min at room temperature to collect murin FAE and VE. Murine FAE and IFE were collected with a fine 29G needle under stereomicroscope.

tag: gender

value: Female

tag: age

value: 10 weeks

tag: organism part

value: Peyer's patch

tag: cell type

value: Follicle associated epithelium

tag: strain

value: BALB/cA

tag: microbial condition

value: SPF


title: T9

state: PA

label: biotin

organism: Homo sapiens

source_name: Tumor from patient 9

tag: tissue


title: T89

source_name: Tumor from patient 89


title: Pericarps of BBA type NIL stages at 7 days after heading

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

description: BBA type NIL 7d

hyb_protocol: 825 ng of cRNAs were hybridized using Agilent's Gene Expression Hybridization Kit following the manufacturer's instructions at NIAS RGRC Laboratory.

scan_protocol: This slides were scanned in Agilent Microarray Scanner G2505C

data_processing:
The scanned images were quantified using Agilent's Feature Extraction Software (version 10.5.1.1)
The signal values were defined after background correction, mutiplicative detrending and dye normalization. Each expression data was subjected to 75 percentile normalization.

organism: Oryza sativa

source_name: Koshihikari_7 days after heading_pericarps

label_protocol: 400 ng of total RNAs were reverse-transcribed and labelled using Agilent's Quick Amp Labeling Kit following the manufacturer's instructions. Labelled cRNAs were purified with the Qiagen RNeasy Mini Kit.

growth_protocol: The rice plants were grown at growth chamber.

extract_protocol: Total RNAs were extracted using Qiagen RNeasy Mini Kit following manufacturer's instructions.

treatment_protocol: No paticular treatment.

tag: background

value: Koshihikari

tag: developmental stage

value: 7 days after heading

value: pericarps

source_name: BBA type NIL_7 days after heading_pericarps

tag: variety

value: BBA type NIL


title: T96

source_name: Tumor from patient 96


title: T95

source_name: Tumor from patient 95


title: T82

source_name: Tumor from patient 82


title: T90

source_name: Tumor from patient 90


title: T94

source_name: Tumor from patient 94


title: T97

source_name: Tumor from patient 97


title: T93

source_name: Tumor from patient 93


title: T88

source_name: Tumor from patient 88


title: T86

source_name: Tumor from patient 86


title: T80

source_name: Tumor from patient 80


title: Pericarps of BAB type NIL stages at 7 days after heading

description: BAB type NIL 7d

source_name: BAB type NIL_7 days after heading_pericarps

value: BAB type NIL


title: T91

source_name: Tumor from patient 91


title: T84

source_name: Tumor from patient 84


title: T81

source_name: Tumor from patient 81


title: T83

source_name: Tumor from patient 83


title: T75

source_name: Tumor from patient 75


title: T61

source_name: Tumor from patient 61


title: T68

source_name: Tumor from patient 68


title: T55

source_name: Tumor from patient 55


title: T58

source_name: Tumor from patient 58


title: T53

source_name: Tumor from patient 53


title: T78

source_name: Tumor from patient 78


title: T54

source_name: Tumor from patient 54


title: T60

source_name: Tumor from patient 60


title: T79

source_name: Tumor from patient 79


title: T62

source_name: Tumor from patient 62


title: zebrafish neurons regenerated, bio rep 1

city: Pitsburgh

first: Katarina

last: Vajn

address: 200 Lothrop St

institute: University of Pittsburgh

description: gene expression from cerebrospinal neurons that regenerated their axons

hyb_protocol: After labeling, 25 µg of cDNA were hybridized for 18 hours at 45°C to Genechip Zebrafish Genome Array. Genechips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip scanner 3000 with 7G upgrade

data_processing: The .cel files were obtained with Affymetrix® GeneChip® Command Console® Software (AGCC). Data was analyzed in GeneSpring GX 12.6.1 (Agilent Technologies, Santa Clara, CA). Robust Multi-array Average (RMA) (Irizarry, 2003.) summarization algorithm (with Quantile Normalization and Median Polish probe summarization procedure) and baseline transformation (baseline to median of all 9 samples) was run on data using logarithmic scale. Probe sets were filtered by expression values based on percentiles (20th to 100th). For comparison of the 3 groups, ANOVA with Tukey HSD post-hoc test was done to identify statistically significant (p-value cutoff 0.05) differentially expressed transcripts. Statistical test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated with GeneSpring GX 12.6.1.

organism: Danio rerio

label_protocol: The amplified SPIA cDNA (5µg) was  labeled using Encore Biotin Module V2 (cat.no. 4200-12, NuGEN Technologies, Inc., San Carlos, CA).

extract_protocol: The total RNA isolated using miRNeasy Micro Kit (cat.no. 217084, Qiagen Germantown, MD). The total RNA was then amplified using Ovation® Pico WTA System V2 (cat.no. 3302-12, NuGEN Technologies, Inc., San Carlos, CA)

value: brain

tag: treatment

value: spinal cord transection

tag: sample type

value: regenerated their axons


title: T77

source_name: Tumor from patient 77


title: zebrafish neurons regenerated, bio rep 3

source_name: cerebrospinal neurons that regenerated their axons


title: T57

source_name: Tumor from patient 57


title: T63

source_name: Tumor from patient 63


title: T56

source_name: Tumor from patient 56


title: T52

source_name: Tumor from patient 52


title: T85

source_name: Tumor from patient 85


title: zebrafish neurons non-regenerated, bio rep 3

description: gene expression from cerebrospinal neurons that did not regenerate their axons

value: did not regenerate their axons


title: T51

source_name: Tumor from patient 51


title: T50

source_name: Tumor from patient 50


title: T49

source_name: Tumor from patient 49


title: zebrafish neurons regenerated, bio rep 2


title: zebrafish neurons non-regenerated, bio rep 2

source_name: cerebrospinal neurons that did not regenerate their axons


title: T47

source_name: Tumor from patient 47


title: zebrafish neurons control, biological rep 3

description: gene expression from cerebrospinal neurons isolated from unlesioned zebrafish

value: unlesioned

value: control


title: zebrafish neurons control, biological rep 2

source_name: cerebrospinal neurons isolated from unlesioned zebrafish


title: T3

source_name: Tumor from patient 3

value: Gastric tumor


title: T42

source_name: Tumor from patient 42


title: zebrafish neurons non-regenerated, bio rep 1


title: T38

source_name: Tumor from patient 38


title: zebrafish neurons control, biological rep 1


title: T34

source_name: Tumor from patient 34


title: T45

source_name: Tumor from patient 45


title: T35

source_name: Tumor from patient 35


title: T32

source_name: Tumor from patient 32


title: T41

source_name: Tumor from patient 41


title: T4

source_name: Tumor from patient 4


title: T36

source_name: Tumor from patient 36


title: T39

source_name: Tumor from patient 39


title: T287

source_name: Tumor from patient 287


title: T301

source_name: Tumor from patient 301


title: T318

source_name: Tumor from patient 318


title: T299

source_name: Tumor from patient 299


title: T31

source_name: Tumor from patient 31


title: T282

source_name: Tumor from patient 282


title: T319

source_name: Tumor from patient 319


title: T29

source_name: Tumor from patient 29


title: T23

source_name: Tumor from patient 23


title: T26

source_name: Tumor from patient 26


title: T28

source_name: Tumor from patient 28


title: T311

source_name: Tumor from patient 311


title: T33

source_name: Tumor from patient 33


title: T30

source_name: Tumor from patient 30


title: T25

source_name: Tumor from patient 25


title: T288

source_name: Tumor from patient 288


title: T238

source_name: Tumor from patient 238


title: T226

source_name: Tumor from patient 226


title: T24

source_name: Tumor from patient 24


title: T246

source_name: Tumor from patient 246


title: T241

source_name: Tumor from patient 241


title: T240

source_name: Tumor from patient 240


title: T213

source_name: Tumor from patient 213


title: T205

source_name: Tumor from patient 205


title: T225

source_name: Tumor from patient 225


title: T237

source_name: Tumor from patient 237


title: T22

source_name: Tumor from patient 22


title: T201

source_name: Tumor from patient 201


title: T64

source_name: Tumor from patient 64


title: T236

source_name: Tumor from patient 236


title: T227

source_name: Tumor from patient 227


title: T190

source_name: Tumor from patient 190


title: T1

source_name: Tumor from patient 1


title: T21

source_name: Tumor from patient 21


title: T192

source_name: Tumor from patient 192


title: T206

source_name: Tumor from patient 206


title: T188

source_name: Tumor from patient 188


title: T18

source_name: Tumor from patient 18


title: T209

source_name: Tumor from patient 209


title: T212

source_name: Tumor from patient 212


title: T20

source_name: Tumor from patient 20


title: T204

source_name: Tumor from patient 204


title: T186

source_name: Tumor from patient 186


title: T19

source_name: Tumor from patient 19


title: T193

source_name: Tumor from patient 193


title: T202

source_name: Tumor from patient 202


title: T185

source_name: Tumor from patient 185


title: T180

source_name: Tumor from patient 180


title: T197

source_name: Tumor from patient 197


title: T182

source_name: Tumor from patient 182


title: T189

source_name: Tumor from patient 189


title: T172

source_name: Tumor from patient 172


title: T177

source_name: Tumor from patient 177


title: T173

source_name: Tumor from patient 173


title: T187

source_name: Tumor from patient 187


title: T175

source_name: Tumor from patient 175


title: T16

source_name: Tumor from patient 16


title: T171

source_name: Tumor from patient 171


title: T156

source_name: Tumor from patient 156


title: T155

source_name: Tumor from patient 155


title: T17

source_name: Tumor from patient 17


title: T154

source_name: Tumor from patient 154


title: T148

source_name: Tumor from patient 148


title: T146

source_name: Tumor from patient 146


title: T157

source_name: Tumor from patient 157


title: T151

source_name: Tumor from patient 151


title: T152

source_name: Tumor from patient 152


title: T14

source_name: Tumor from patient 14


title: T145

source_name: Tumor from patient 145


title: T143

source_name: Tumor from patient 143


title: T144

source_name: Tumor from patient 144


title: T150

source_name: Tumor from patient 150


title: T140

source_name: Tumor from patient 140


title: T139

source_name: Tumor from patient 139


title: T137

source_name: Tumor from patient 137


title: T136

source_name: Tumor from patient 136


title: T138

source_name: Tumor from patient 138


title: T129

source_name: Tumor from patient 129


title: T128

source_name: Tumor from patient 128


title: T134

source_name: Tumor from patient 134


title: T12

source_name: Tumor from patient 12


title: T141

source_name: Tumor from patient 141


title: T132

source_name: Tumor from patient 132


title: T142

source_name: Tumor from patient 142


title: T133

source_name: Tumor from patient 133


title: T106

source_name: Tumor from patient 106


title: T121

source_name: Tumor from patient 121


title: T135

source_name: Tumor from patient 135


title: T113

source_name: Tumor from patient 113


title: T117

source_name: Tumor from patient 117


title: T116

source_name: Tumor from patient 116


title: T11

source_name: Tumor from patient 11


title: T114

source_name: Tumor from patient 114


title: T115

source_name: Tumor from patient 115


title: T124

source_name: Tumor from patient 124


title: T118

source_name: Tumor from patient 118


title: T101

source_name: Tumor from patient 101


title: T105

source_name: Tumor from patient 105


title: T596

source_name: Tumor from patient 596


title: T595

source_name: Tumor from patient 595


title: T207

source_name: Tumor from patient 207


title: T603

source_name: Tumor from patient 603


title: T112

source_name: Tumor from patient 112


title: T561

source_name: Tumor from patient 561


title: T584

source_name: Tumor from patient 584


title: T571

source_name: Tumor from patient 571


title: T592

source_name: Tumor from patient 592


title: T589

source_name: Tumor from patient 589


title: T547

source_name: Tumor from patient 547


title: T554

source_name: Tumor from patient 554


title: T566

source_name: Tumor from patient 566


title: T586

source_name: Tumor from patient 586


title: T228

source_name: Tumor from patient 228


title: T557

source_name: Tumor from patient 557


title: T540

source_name: Tumor from patient 540


title: T541

source_name: Tumor from patient 541


title: T560

source_name: Tumor from patient 560


title: T551

source_name: Tumor from patient 551


title: T556

source_name: Tumor from patient 556


title: T538

source_name: Tumor from patient 538


title: T559

source_name: Tumor from patient 559


title: T542

source_name: Tumor from patient 542


title: T532

source_name: Tumor from patient 532


title: T550

source_name: Tumor from patient 550


title: T544

source_name: Tumor from patient 544


title: T529

source_name: Tumor from patient 529


title: T533

source_name: Tumor from patient 533


title: T525

source_name: Tumor from patient 525


title: T523

source_name: Tumor from patient 523


title: T528

source_name: Tumor from patient 528


title: T524

source_name: Tumor from patient 524


title: T553

source_name: Tumor from patient 553


title: T534

source_name: Tumor from patient 534


title: T522

source_name: Tumor from patient 522


title: T519

source_name: Tumor from patient 519


title: T514

source_name: Tumor from patient 514


title: T520

source_name: Tumor from patient 520


title: T517

source_name: Tumor from patient 517


title: T516

source_name: Tumor from patient 516


title: T518

source_name: Tumor from patient 518


title: T502

source_name: Tumor from patient 502


title: T489

source_name: Tumor from patient 489


title: T505

source_name: Tumor from patient 505


title: T510

source_name: Tumor from patient 510


title: T501

source_name: Tumor from patient 501


title: T493

source_name: Tumor from patient 493


title: T488

source_name: Tumor from patient 488


title: T485

source_name: Tumor from patient 485


title: T503

source_name: Tumor from patient 503


title: T476

source_name: Tumor from patient 476


title: T480

source_name: Tumor from patient 480


title: T588

source_name: Tumor from patient 588


title: T460

source_name: Tumor from patient 460


title: T482

source_name: Tumor from patient 482


title: T457

source_name: Tumor from patient 457


title: T459

source_name: Tumor from patient 459


title: T448

source_name: Tumor from patient 448


title: T450

source_name: Tumor from patient 450


title: T465

source_name: Tumor from patient 465


title: T455

source_name: Tumor from patient 455


title: T445

source_name: Tumor from patient 445


title: T483

source_name: Tumor from patient 483


title: T451

source_name: Tumor from patient 451


title: T477

source_name: Tumor from patient 477


title: T469

source_name: Tumor from patient 469


title: T441

source_name: Tumor from patient 441


title: T433

source_name: Tumor from patient 433


title: T471

source_name: Tumor from patient 471


title: T437

source_name: Tumor from patient 437


title: T442

source_name: Tumor from patient 442


title: T456

source_name: Tumor from patient 456


title: T438

source_name: Tumor from patient 438


title: T446

source_name: Tumor from patient 446


title: T431

source_name: Tumor from patient 431


title: T432

source_name: Tumor from patient 432


title: T447

source_name: Tumor from patient 447


title: T430

source_name: Tumor from patient 430


title: T444

source_name: Tumor from patient 444


title: T428

source_name: Tumor from patient 428


title: T470

source_name: Tumor from patient 470


title: T427

source_name: Tumor from patient 427


title: T426

source_name: Tumor from patient 426


title: T425

source_name: Tumor from patient 425


title: T443

source_name: Tumor from patient 443


title: T440

source_name: Tumor from patient 440


title: T424

source_name: Tumor from patient 424


title: T420

source_name: Tumor from patient 420


title: T421

source_name: Tumor from patient 421


title: T419

source_name: Tumor from patient 419


title: T414

source_name: Tumor from patient 414


title: T423

source_name: Tumor from patient 423


title: T422

source_name: Tumor from patient 422


title: T415

source_name: Tumor from patient 415


title: T402

source_name: Tumor from patient 402


title: T405

source_name: Tumor from patient 405


title: T416

source_name: Tumor from patient 416


title: mouse embryo_E8.5_SE_rep3

city: Isumi

first: Chiharu

last: Kimura-Yoshida

state: Osaka

address: 840 Murodo-cho

department: Department of Molecular Embryology

institute: Osaka Medical Center and Research Institute for Maternal and Child Health

description: SAMPLE 6

hyb_protocol: Performed according to the manufacturer's (Illumina) recommendations

scan_protocol: GeneChips were scanned using illuminaBeadReader

data_processing: Raw data were analyzed using illuminBeadsStudio software. Average Sample intensities are scaled by a factor equal to the ratio of average intensity of virtual sample to the average intensity of the given sample. Background is subtracted prior to the scaling. Average normalization adjusts for differences in overall intensity between arrays and chips. Sample intensities are scaled by a factor so that the average signal of all samples becomes equal to the global average of all sample signals. Background subtraction is done prior to scaling, so half of the unexpressed targets are expected to have negative signals.  (refered by BeadStudio Gene Expression Module User Guide (illumina))

source_name: mouse embryo, E8.5, SE, forebrain level

label_protocol: Samples were labeled with biotin using Illumina TotalPrep RNA Amplification Kit

extract_protocol: Wild-type embryos were dissected in PBS with calcium and magnesium. The embryos were then incubated in pancreatin/trypsin in calcium- and magnesium-free PBS for dissection. The surface ectoderm and neural ectoderm at the forebrain level, which does not include cephalic mesenchymal cells, were isolated using tungsten needles.

value: surface ectoderm, forebrain level


title: mouse embryo_E8.5_NE_rep3

description: SAMPLE 3

source_name: mouse embryo, E8.5, NE, forebrain level

value: neural ectoderm, forebrain level


title: T394

source_name: Tumor from patient 394


title: T395

source_name: Tumor from patient 395


title: mouse embryo_E8.5_SE_rep1

description: SAMPLE 4


title: T396

source_name: Tumor from patient 396


title: T397

source_name: Tumor from patient 397


title: T401

source_name: Tumor from patient 401


title: T385

source_name: Tumor from patient 385


title: mouse embryo_E8.5_NE_rep2

description: SAMPLE 2


title: T388

source_name: Tumor from patient 388


title: T375

source_name: Tumor from patient 375


title: T377

source_name: Tumor from patient 377


title: mouse embryo_E8.5_NE_rep1

description: SAMPLE 1


title: T374

source_name: Tumor from patient 374


title: T376

source_name: Tumor from patient 376


title: T372

source_name: Tumor from patient 372


title: T369

source_name: Tumor from patient 369


title: BLT1+/+ with CS bilogical replicate 3

city: Louisville

first: Venkatakrishna

middle: R

last: Jala

state: KY

address: 505 S Hancock Street # 323

department: Dept. Microbiology and Immunology

institute: University of Louisville

description: Lungs from BLT1+/+ mice instilled with CS for 2 days

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Affymetrix Mouse GeneArray 1.0 ST v1 arrays according to the GeneChip WT Terminal Labeling and Hybridization User Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 3.2 (Affymetrix)

data_processing: The CEL files were imported into Partek software Version 6.6 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization on a gene level. A one-way ANOVA was set up to compare various subtypes.

source_name: Lungs

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix' GeneChip® WT  Reagent Kit from 250 ng total RNA

growth_protocol: BLT1+/+, BLT1-/-, BLT1+/+KRasLA1 and BLT1-/-KRasLA1 in C57BL/6 background mice (10-12  weeks of age) were maintained in Specific Pathogen Free conditions.

extract_protocol: RNA from total lungs were isolated using Qiagen RNeasy Mini kit.

treatment_protocol: Mice were intra-trachial instilled with CS or control phosphate buffer saline (PBS)

tag: genotype/variation

value: 10-12 weeks of age


title: BLT1+/+ with PBS (Pooled)

description: Lungs from BLT1+/+ mice instilled with PBS for 2 days (pooled 3 mice)


title: BLT1+/+ with CS bilogical replicate 2


title: T355

source_name: Tumor from patient 355


title: BLT1+/+ with CS bilogical replicate 1


title: T361

source_name: Tumor from patient 361


title: BLT1+/+KRasLA1 with PBS (Pooled)

description: Lungs from BLT1+/+KRasLa1 mice instilled with PBS for 60 days(pooled 3 mice)


title: T363

source_name: Tumor from patient 363


title: T343

source_name: Tumor from patient 343


title: T339

source_name: Tumor from patient 339


title: BLT1+/+KRasLA1 with CS biological replicate 3

description: Lungs from BLT1+/+KRasLa1 mice instilled with CS for 60 days


title: T341

source_name: Tumor from patient 341


title: BLT1+/+KRasLA1 with CS biological replicate 1


title: T330

source_name: Tumor from patient 330


title: T336

source_name: Tumor from patient 336


title: BLT1-/-KRasLA1 with PBS (Pooled)

description: Lungs from BLT1-/-KRasLa1 mice instilled with PBS for 60 days (pooled 3 mice)


title: T333

source_name: Tumor from patient 333


title: T329

source_name: Tumor from patient 329


title: T331

source_name: Tumor from patient 331


title: T346

source_name: Tumor from patient 346


title: T337

source_name: Tumor from patient 337


title: T328

source_name: Tumor from patient 328


title: BLT1-/-KRasLA1 with CS biological replicate 3

description: Lungs from BLT1-/-KRasLa1 mice instilled with CS for 60 days


title: T327

source_name: Tumor from patient 327


title: BLT1-/- with CS biological replicate 3

description: Lungs from BLT1-/- mice instilled with CS for 2 days


title: BLT1-/-KRasLA1 with CS biological replicate 2


title: BLT1-/-KRasLA1 with CS biological replicate 1


title: BLT1-/- with CS biological replicate 1


title: BLT1-/- with CS biological replicate 2


title: T324

source_name: Tumor from patient 324


title: T326

source_name: Tumor from patient 326


title: T338

source_name: Tumor from patient 338


title: BLT1-/- with PBS (pooled)

description: Lungs from BLT1-/- mice instilled with PBS for 2 days (pooled 3 mice)

source_name: Lungs


title: T321

source_name: Tumor from patient 321


title: T323

source_name: Tumor from patient 323


title: T275

source_name: Tumor from patient 275


title: T325

source_name: Tumor from patient 325


title: ob/Fsp-497

city: Beijing

first: Linkang

last: Zhou

state: Beijing

address: Haidian District

country: China

institute: Tsinghua Unversity

description: Gene expression data from GWAT of 4 months old ob/ob/Fsp27-/- male mice

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Array (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)， using the Genechip2 Scanner 3000 7G.

data_processing: Quality control and statistical analyses of all the 6 Mouse Gene 1.0 ST microarray data was conducted using R/Bioconductor. Methods like scatterplot, distribution histograms, boxplots, and unsupervised Principle Component Analysis (PCA) were employed to visualize the data before and after preprocessing procedures. All arrays were consistent and comparable for further analyses, and we performed background adjustment, quantile normalisation and summarisation of transcript-level intensity for all arrays using the Robust Multi-array Average (RMA) algorithm, followed by two rounds of probeset filtering. First, control probesets were removed, and 28,858 main probesets out of all 35,556 were retained. Then, the Detection Above Background (DABG) p-values for probesets were calculated using the xps package, and only the significant ones (p < 0.05) were considered as “present”. We only retained probesetsflagged as present in at least one sample for each type of tissue, and used the package LIMMA to identify probesets that were differentially expressed between the ob/ob/Fsp27-/- and ob/ob mice . The Benjamini and Hochberg method was used to estimate the false discovery rate (FDR) and correct for multiple hypotheses testing. Annotation was taken, and genes that changed by log fold of at least 0.5 between ob/ob/Fsp27-/- and ob/ob mice and with a FDR < 0.05 were considered significant. The up- and down-regulated genes were further mapped to biological pathways using PathVisio with Wiki Pathways content, and the results were sorted by Z-score, which is the standard statistical test under the hypergeometric distribution .

source_name: fat

label_protocol: Single-stranded cDNA was  fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Mice were maintained at chow diet. GWAT was obtained at 4 months old under normal diet.

extract_protocol: RNA was isolated from GWAT with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. All samples were treated with Rnase-free DnaseI (Qiagen) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the Expression Kit (Ambion) according to the manufacturer’s instructions.

value: male

value: 4 mo

value: gonadal white adipose tissue

value: ob/ob/Fsp27-/-, leptin and Fsp27 double deficient


title: ob/Fsp-493


title: T268

source_name: Tumor from patient 268


title: T269

source_name: Tumor from patient 269


title: T256

source_name: Tumor from patient 256


title: ob-541

description: Gene expression data from GWAT of 4 months old ob/ob male mice

value: ob/ob, leptin deficient


title: ob/Fsp-495


title: mouse embryo_E8.5_SE_rep2

description: SAMPLE 5

source_name: mouse embryo, E8.5, SE, forebrain level


title: ob-478


title: T263

source_name: Tumor from patient 263


title: T270

source_name: Tumor from patient 270


title: T255

source_name: Tumor from patient 255


title: ob-539


title: T322

source_name: Tumor from patient 322


title: T253

source_name: Tumor from patient 253


title: T244

source_name: Tumor from patient 244


title: 4121T3_CBD

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

hyb_protocol: The Affymetrix Genechip WT Terminal Labeling and Hybridization protocol was used

scan_protocol: Chips were scanned using the Affymetrix 7G Plus scanner and Command Console Software

data_processing: Data was processed by importing CEL files into Partek Software and RMA normalization was performed

label: Biotin

source_name: Glioma stem cells treated with CBD

label_protocol: The Ambion WT Expression Kit with accompanying protocol was used to label the samples

growth_protocol: Glioma stem cells were grown as neurospheres in Neural Basal Media supplemented with N2, EGF and FGF (2ug/ml). Prior to CBD treatment, growth factors were withdrawn for 12h

extract_protocol: RNA was extracted using Qiagen RNAeasy kit according to the manufacturer instructions

treatment_protocol: CBD dissolved in ethanol was used at 2uM. Vehicle ethanol alone was used to treat the control cultures. Compounds were left on cells until RNA was harvested, 48h later.

value: glioblastoma

tag: grade

value: grade IV


title: T399

source_name: Tumor from patient 399


title: CC4121_CBD


title: T169

source_name: Tumor from patient 169


title: Infant_Cdexposed_10

type: genomic

city: Chapel Hill

first: Saideep

middle: Rao

last: Gona

state: NC

address: 135 Dauer Dr

department: Environmental Sciences and Engineering

institute: University of North Carolina at Chapel Hill

description: Abundance data for methylated gene regions in fetal cord blood

hyb_protocol: Samples were hybridized to Affymetrix Human Promoter 1.0R Array according to Affymetrix

scan_protocol: The tiling arrays were scanned using Affymetrix Scanner 3000 7G Plus with Autoloader according to manufacturer's instruction.

data_processing: Raw data are provided as .cel files. CpG summarized data were RMA normalized.  Abundance average values are provided in the file "normalized_signal_matrix.txt" available on the series level.

molecule: genomic DNA

source_name: Infant cord blood_exposed_to_Cd

label_protocol: Enriched DNA was first amplified using the WGA3 kit (Sigma) according to manufacturer instructions with the following modification: 10 mM dATP, 10 mM dCTP, 10 mM dGTP, 8 mM dTTP, and 2 mM dUTP with remaining  labeling steps according to Affymetrix specifications.

extract_protocol: DNA was extracted using Qiagen’s PAXgene Blood DNA kit according to manufacturer’s protocol.

value: Blood

value: At birth


title: Infant_Cdexposed_9


title: Infant_Cdunexposed_7

source_name: Infant cord blood_not_exposed_to_Cd


title: Infant_Cdunexposed_6


title: Infant_Cdexposed_7


title: Infant_Cdexposed_8


title: Infant_Cdexposed_6


title: 4121T3_Veh

source_name: Glioma stem cells treated with vehicle


title: Infant_Cdexposed_3


title: T235

source_name: Tumor from patient 235


title: CC4121_Veh


title: 0609_CBD


title: 0609_Veh


title: T165

source_name: Tumor from patient 165


title: Infant_Cdexposed_2


title: T164

source_name: Tumor from patient 164


title: T109

source_name: Tumor from patient 109


title: Infant_Cdunexposed_4


title: T108

source_name: Tumor from patient 108


title: T168

source_name: Tumor from patient 168


title: T160

source_name: Tumor from patient 160


title: BLT1+/+KRasLA1 with CS biological replicate 2

source_name: Lungs


title: Infant_Cdunexposed_3


title: Infant_Cdunexposed_2


title: T413

source_name: Tumor from patient 413


title: Infant_Cdunexposed_1


title: Mother_Cdexposed_10

description: Abundance data for methylated gene regions in maternal veinous blood

source_name: Maternal veinous blood_exposed_to_Cd

value: At time of delivery


title: Mother_Cdexposed_9


title: Infant_Cdexposed_1


title: Mother_Cdunexposed_6


title: T107

description:
ACRG Gastric cohort: microarray profiles from 300 gastric tumors and 100 patient matched normal tissue from gastric cancer patients
Nugen amplification protocol

source_name: Tumor from patient 107


title: Mother_Cdexposed_4


title: Mother_Cdexposed_3


title: Mother_Cdunexposed_5


title: Mother_Cdexposed_2


title: Mother_Cdunexposed_4


title: Infant_Cdexposed_5


title: Mother_Cdunexposed_3


title: Mother_Cdunexposed_2


title: Mother_Cdunexposed_1


title: Mother_Cdunexposed_7


title: Mother_Cdexposed_7


title: Mother_Cdexposed_8


title: Mother_Cdexposed_6


title: Mother_Cdexposed_1


title: Internal Organs Control Rep4

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

description: Mock infected fish internal organs biological replicate 4

hyb_protocol: The slides were pre-treated with 1% BSA fraction V, 5 X SSC, 0.1% SDS for 30 min. at 50 ºC and washed with 2 X SSC (3 min) and 0.2 X SSC (3 min) and hybridized overnight in cocktail containing 1.3 X Denhardt's, 3 X SSC, 0.3% SDS, 2.1 ug/ul polyadenylate and 1 ug/ul yeast tRNA.

scan_protocol: Signal was captured and processed using an Agilent scanner (G2565B, Agilent Technologies). The scanner images were segmented by the Agilent Feature Extraction Software (v9.5) with the protocol GE1-v5_95.

data_processing: The gProccesedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent feature extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information

source_name: head kidney and spleen of 3 mock-infected zebrafish  rep 4

label_protocol: RNA were labeled with Cy3 (Amersham Pharmacia) by using SuperScript III reverse transcriptase (InVitroGen) and oligo(dT) primer, and the resulting cDNA was purified with Microcon YM30 (Millipore)

growth_protocol: Adult wild type zebrafish were obtained from a local pet shop and maintained in a 30 l aquarium provided with biological filter, 23ºC, pH 8.

extract_protocol: RNA was extracted using the RNAeasyPlus kit (Qiagen, Hilden, Germany).

treatment_protocol: For each viral infection experiment, groups of zebrafish were moved to 2 l aquaria provided with biological filters. Zebrafish were infected by bath immersion with a final dose of 106 pfu/ml  for 90 minutes.   Mock-infected zebrafish were incubated with cell culture medium.

tag: line

value: Wild type

tag: development stage

value: Adult

value: internal organs

value: mock infected


title: Internal Organs Control Rep2

description: Mock infected fish internal organs biological replicate 2

source_name: head kidney and spleen of 3 mock-infected zebrafish  rep 2


title: Internal Organs Control Rep3

description: Mock infected fish internal organs biological replicate 3

source_name: head kidney and spleen of 3 mock-infected zebrafish  rep 3


title: Internal Organs Control Rep1

description: Mock infected fish internal organs biological replicate 1

source_name: head kidney and spleen of 3 mock-infected zebrafish  rep 1


title: Control 5

city: Changsha

first: Fengzhen

last: Huang

address: 87# Xiangya Road Changsha, Hunan 410008P.R.China

institute: Xiangya Hospital, Central South University

description:
Age-, gender-matched control 5 of 5.
Total RNA from 5mL peripheral blood using Trizol.

hyb_protocol: Pre-hybridization: 1)  Assembled  CustomArray™ microarray with Hybridization Cap and Clips. 2) Fill the hybridization chambers with nuclease-free water. Avoid introducing air bubbles into the chambers. Cover the solution portals with adhesive tape to evaporation. 3) Incubate at 65°C for 10min. 4) Remove the microarray from the incubator and bring to room temperature. Remove the adhesive tape and aspirate the water out of the hybridization chambers. 5) Fill the hybridization chambers with Pre-hybridization Solution. Mix gently by pipetting. A small air bubble can be introduced to improve the mixing process if the arrays are rotated. Wipe the surface clean with a lint-free tissue and cover the solution portals with adhesive tape. 6) Load the microarray onto the rotisserie in the hybridization oven and incubate at 37°C for 60 min with gentle rotation.  Hybridization: 1) Prepare the hybridization solution with labeled microRNA target. 2) Denature the hybridization solution at 95°C for 3 minutes, and then cool for 20 seconds on ice. Remove the hybridization solution from ice and keep it at room temperature. 3) Spin down the hybridization solution in a microcentrifuge for 5 seconds at maximum speed. 4) Remove the adhesive tape and pipet the pre-hybridization solution out of the hybridization chambers. 5) Fill the hybridization chambers with the hybridization solution and mix gently with repeated pipetting. A small air bubble wil form, and it will improve the mixing process if the arrays are rotated in the hybridization rotisserie oven. 6) Carefully wipe excess solution from the surface of the hybridization cap with a lint-free tissue, and cover the solution portals with adhesive tape. 7) Load the microarray onto the rotisserie in the hybridization oven and incubate at 37°C for 16 hours with gentle rotation.  Hybridization washing: 1) Remove the microarray from the hybridization oven. Remove the adhesive tape and pipet the hybridization solution out of the chambers. 2) Using the Wash solution 1, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperature. Remove the Wash solution 1 from the hybridization chambers. 3) Using the Wash solution 2, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperature. Remove the Wash solution 2 from the hybridization chambers. 4) Using the Wash solution 3, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperature. Remove the Wash solution 3 from the hybridization chambers. 5) Repeat step one more time for a total of two washings with the Wash solution 3.

scan_protocol: Imaging is done by laser scanner GenePix 4000B (Molecular Device). Remove the microarray from the clamp and place it horizontally. Cover the semiconductor microarray surface with the imaging solution. Using a fresh lifterslip cover it, taking care not to introduce air bubbles. Load the microarray into the scanner to scan.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. After normalizing with quantile normalization method (Bioinformatics, 19 (2):185-193), the p-values are calculated with Rank Product Method. For advanced data analysis, all biological replicates were pooled and calculated to identify differentially expressed genes based on the fold change. Standard selection criteria to identify differentially expressed genes are established at P < 0. 05. The correlation of expression profiles between biological replicates and treatment conditions was demonstrated by unsupervised hierarchical clustering analysis. The log2 scale of the expression signal values was plotted.

source_name: Peripheral blood, control

label_protocol:
1. Reverse Transcription to Synthesize First Strand cDNA is primed with the T7 Oligo(dT) Primer to synthesize cDNA containing a T7 promoter sequence.
2. Second Strand cDNA Synthesis converts the single-stranded cDNA into a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA.
3. cDNA Purification removes RNA, primers, enzymes, and salts that would inhibit in vitro transcription.
4. In Vitro Transcription to Synthesize Amino Allyl-Modified aRNA with aaUTP generates multiple copies of amino allyl-modified aRNA from the double-stranded cDNA templates; this is the amplification step.
5. aRNA Purification removes unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the aRNA and to facilitate NHS ester coupling or subsequent enzymatic reactions.
6. aRNA:Dye Coupling Reaction takes place between the amino allyl-modified UTP residues on the aRNA and amine reactive Cy5 dyes.
7. Dye Labeled aRNA Purification removes free dye and exchanges the buffer with Nuclease-free Water.

extract_protocol:
1. For proper amount of cells or homogenized tissue, add 1mL of TRIzol reagent and mix by briefly vortex. Stand for 5 mins at room temperature. If a lot of insoluble material exists after homogenization and room-temperature incubation, remove by centrifugation at 12, 000Xg for 10 mins at 4ºC. Transfer the supernatant to a fresh tube.
2. Add 200ul chloroform for 1ml mixture and vortex for 15 sec. Then stand for 5 mins at room temperature.
3. Centrifuge the mixture for 15 min at ≥12000xg at 4ºC.
4. Transfer the aqueous phase (the upper layer containing RNA) to a fresh tube.
5. Add equal volume of 100% Isopropanol to the aqueous phase, mix by inverting the tube several times.
6. Incubate at ‐20ºC for ≥30 min.
7. Centrifuge at 13000 rpm for 15 min at 4ºC.
8. Wash the pellet with 80% EtOH, invert the tube several times. Centrifuge at 7500 rpm for 5 min at -4ºC.
9. Carefully discard the supernatant without touching the pellet, dry the pellet at room temperature.
10. Dissolve the pellet with 20‐30ul DEPC-treated H2O, based on the size of the pellet. RNA solution should be stored at -80ºC.

tag: disease state

value: control

value: peripheral blood

value: 5 years


title: Mother_Cdexposed_5


title: Internal Organs +VHSV Rep3

description: VHSV infected fish internal organs biological replicate 3

source_name: head kidney and spleen of 3 zebrafish infected with VHSV rep 3

value: VHSV at 106 pfu/ml for 90 minutes


title: Control 3

description:
Age-, gender-matched control 3 of 5.
Total RNA from 5mL peripheral blood using Trizol.

tag: gender

value: male

value: 2 years


title: Fins Control Rep4

description: Mock infected fish fins biological replicate 4

source_name: fins of 3 control  mock-infected zebrafish rep4

value: fins


title: Internal Organs +VHSV Rep2

description: VHSV infected fish internal organs biological replicate 2

source_name: head kidney and spleen of 3 zebrafish infected with VHSV rep 2


title: Internal Organs +VHSV Rep1

description: VHSV infected fish internal organs biological replicate 1

source_name: head kidney and spleen of 3 zebrafish infected with VHSV rep 1


title: Fins Control Rep3

description: Mock infected fish fins biological replicate 3

source_name: fins of 3 control  mock-infected zebrafish rep3


title: Fins Control Rep2

description: Mock infected fish fins biological replicate 2

source_name: fins of 3 control  mock-infected zebrafish rep2


title: Control 1

description:
Age-, gender-matched control 1 of 5.
Total RNA from 5mL peripheral blood using Trizol.

tag: age

value: 7 years


title: Patient 5

description:
ASD patient 5 of 5.
Total RNA from 5mL peripheral blood using Trizol.

source_name: Peripheral blood, ASD patient

value: autism spectrum disorder (ASD)


title: Internal Organs +VHSV Rep4

description: VHSV infected fish internal organs biological replicate 4

source_name: head kidney and spleen of 3 zebrafish infected with VHSV rep 4


title: Fins +VHSV Rep4

description: VHSV infected fish fins biological replicate 4

source_name: fins of 3 zebrafish infected with VHSV rep4


title: Fins Control Rep1

description: Mock infected fish fins biological replicate 1

source_name: fins of 3 control  mock-infected zebrafish rep1


title: Patient 2

description:
ASD patient 2 of 5.
Total RNA from 5mL peripheral blood using Trizol.

value: female

value: 6 years


title: Control 4

description:
Age-, gender-matched control 4 of 5.
Total RNA from 5mL peripheral blood using Trizol.

value: 3 years


title: Patient 1

description:
ASD patient 1 of 5.
Total RNA from 5mL peripheral blood using Trizol.


title: Patient 3

description:
ASD patient 3 of 5.
Total RNA from 5mL peripheral blood using Trizol.


title: Fins +VHSV Rep3

description: VHSV infected fish fins biological replicate 3

source_name: fins of 3 zebrafish infected with VHSV rep3


title: CoA patient 3634

status: Public on Apr 16 2015

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

description: Hybridized to SNP 6.0

hyb_protocol: as per manufacturer (Affymetrix)

scan_protocol: washed by Affymetrix Fluidics Station 450, scanned with Affymetrix GeneChip Scanner 3000

data_processing:
CEL files generated by Affymetrix GeneChip Command Console (AGCC) v3, then processed by birdsuite 1.5.5
probeset summaries from apt-probeset-summarize; algorithm options: quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true

source_name: CoA patient 3634

label_protocol: as per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral venous blood lymphocytes by QIAamp DNA Blood Kit (Qiagen).

tag: family

value: family 3

value: affected

value: peripheral venous blood lymphocyte


title: CoA patient 3677

description: Hybridized to SNP 6.0

source_name: CoA patient 3677

value: unaffected

tag: cell type


title: CoA patient 3680

description: Hybridized to SNP 6.0

source_name: CoA patient 3680


title: CoA patient 3683

description: Hybridized to SNP 6.0

source_name: CoA patient 3683


title: Fins +VHSV Rep1

description: VHSV infected fish fins biological replicate 1

source_name: fins of 3 zebrafish infected with VHSV rep1

value: Wild type

value: Adult


title: CoA patient 3658

description: Hybridized to SNP 6.0

source_name: CoA patient 3658

value: family 2


title: Fins +VHSV Rep2

description: VHSV infected fish fins biological replicate 2

source_name: fins of 3 zebrafish infected with VHSV rep2


title: Control 2

description:
Age-, gender-matched control 2 of 5.
Total RNA from 5mL peripheral blood using Trizol.

source_name: Peripheral blood, control

value: control

value: peripheral blood


title: CoA patient 3674

description: Hybridized to SNP 6.0

source_name: CoA patient 3674

value: male


title: CoA patient 3661

description: Hybridized to SNP 6.0

source_name: CoA patient 3661


title: CoA patient 3670

description: Hybridized to SNP 6.0

source_name: CoA patient 3670


title: CoA patient 3671

description: Hybridized to SNP 6.0

source_name: CoA patient 3671


title: CoA patient 3631

description: Hybridized to SNP 6.0

source_name: CoA patient 3631

value: family 1


title: CoA patient 3695

description: Hybridized to SNP 6.0

source_name: CoA patient 3695


title: CoA patient 3628

description: Hybridized to SNP 6.0

source_name: CoA patient 3628


title: CoA patient 88

description: Hybridized to SNP 6.0

source_name: CoA patient 88

value: familial coarctation of the aorta (CoA)


title: CoA patient 87

description: Hybridized to SNP 6.0

source_name: CoA patient 87


title: Patient 4

description:
ASD patient 4 of 5.
Total RNA from 5mL peripheral blood using Trizol.

source_name: Peripheral blood, ASD patient


title: CoA patient 84

description: Hybridized to SNP 6.0

source_name: CoA patient 84


title: CoA patient 3692

description: Hybridized to SNP 6.0

source_name: CoA patient 3692


title: CoA patient 82

description: Hybridized to SNP 6.0

source_name: CoA patient 82


title: CoA patient 83

description: Hybridized to SNP 6.0

source_name: CoA patient 83


title: CoA patient 81

description: Hybridized to SNP 6.0

source_name: CoA patient 81


title: CoA patient 80

description: Hybridized to SNP 6.0

source_name: CoA patient 80


title: CoA patient 78

description: Hybridized to SNP 6.0

source_name: CoA patient 78


title: CoA patient 77

description: Hybridized to SNP 6.0

source_name: CoA patient 77


title: CoA patient 76

description: Hybridized to SNP 6.0

source_name: CoA patient 76


title: CoA patient 71

description: Hybridized to SNP 6.0

source_name: CoA patient 71


title: CoA patient 72

description: Hybridized to SNP 6.0

source_name: CoA patient 72


title: CoA patient 67

description: Hybridized to SNP 6.0

source_name: CoA patient 67


title: CoA patient 66

description: Hybridized to SNP 6.0

source_name: CoA patient 66


title: CoA patient 74

description: Hybridized to SNP 6.0

source_name: CoA patient 74


title: CoA patient 68

description: Hybridized to SNP 6.0

source_name: CoA patient 68


title: CoA patient 69

description: Hybridized to SNP 6.0

source_name: CoA patient 69


title: CoA patient 70

description: Hybridized to SNP 6.0

source_name: CoA patient 70


title: CoA patient 65

description: Hybridized to SNP 6.0

source_name: CoA patient 65


title: CoA patient 64

description: Hybridized to SNP 6.0

source_name: CoA patient 64


title: CoA patient 62

description: Hybridized to SNP 6.0

source_name: CoA patient 62


title: CoA patient 60

description: Hybridized to SNP 6.0

source_name: CoA patient 60


title: CoA patient 58

description: Hybridized to SNP 6.0

source_name: CoA patient 58


title: CoA patient 59

description: Hybridized to SNP 6.0

source_name: CoA patient 59


title: CoA patient 57

description: Hybridized to SNP 6.0

source_name: CoA patient 57


title: CoA patient 55

description: Hybridized to SNP 6.0

source_name: CoA patient 55


title: CoA patient 56

description: Hybridized to SNP 6.0

source_name: CoA patient 56


title: CoA patient 61

description: Hybridized to SNP 6.0

source_name: CoA patient 61


title: CoA patient 53

description: Hybridized to SNP 6.0

source_name: CoA patient 53


title: CoA patient 52

description: Hybridized to SNP 6.0

source_name: CoA patient 52


title: CoA patient 51

description: Hybridized to SNP 6.0

source_name: CoA patient 51


title: Infant_Cdexposed_4

description: Abundance data for methylated gene regions in fetal cord blood

source_name: Infant cord blood_exposed_to_Cd

value: Blood

value: At birth


title: CoA patient 48

description: Hybridized to SNP 6.0

source_name: CoA patient 48


title: CoA patient 75

description: Hybridized to SNP 6.0

source_name: CoA patient 75


title: CoA patient 47

description: Hybridized to SNP 6.0

source_name: CoA patient 47

value: female


title: CoA patient 46

description: Hybridized to SNP 6.0

source_name: CoA patient 46


title: CoA patient 44

description: Hybridized to SNP 6.0

source_name: CoA patient 44


title: CoA patient 45

description: Hybridized to SNP 6.0

source_name: CoA patient 45


title: CoA patient 63

description: Hybridized to SNP 6.0

source_name: CoA patient 63


title: CoA patient 40

description: Hybridized to SNP 6.0

source_name: CoA patient 40


title: CoA patient 39

description: Hybridized to SNP 6.0

source_name: CoA patient 39


title: CoA patient 38

description: Hybridized to SNP 6.0

source_name: CoA patient 38


title: CoA patient 41

description: Hybridized to SNP 6.0

source_name: CoA patient 41


title: CoA patient 35

description: Hybridized to SNP 6.0

source_name: CoA patient 35


title: CoA patient 34

description: Hybridized to SNP 6.0

source_name: CoA patient 34


title: CoA patient 33

description: Hybridized to SNP 6.0

source_name: CoA patient 33


title: CoA patient 37

description: Hybridized to SNP 6.0

source_name: CoA patient 37


title: CoA patient 32

description: Hybridized to SNP 6.0

source_name: CoA patient 32


title: CoA patient 31

description: Hybridized to SNP 6.0

source_name: CoA patient 31


title: CoA patient 30

description: Hybridized to SNP 6.0

source_name: CoA patient 30


title: CoA patient 23

description: Hybridized to SNP 6.0

source_name: CoA patient 23


title: CoA patient 22

description: Hybridized to SNP 6.0

source_name: CoA patient 22


title: CoA patient 24

description: Hybridized to SNP 6.0

source_name: CoA patient 24


title: CoA patient 19

description: Hybridized to SNP 6.0

source_name: CoA patient 19


title: CoA patient 28

description: Hybridized to SNP 6.0

source_name: CoA patient 28


title: CoA patient 18

description: Hybridized to SNP 6.0

source_name: CoA patient 18


title: CoA patient 15

description: Hybridized to SNP 6.0

source_name: CoA patient 15


title: CoA patient 17

description: Hybridized to SNP 6.0

source_name: CoA patient 17


title: CoA patient 14

description: Hybridized to SNP 6.0

source_name: CoA patient 14


title: CoA patient 16

description: Hybridized to SNP 6.0

source_name: CoA patient 16


title: CoA patient 13

description: Hybridized to SNP 6.0

source_name: CoA patient 13


title: CoA patient 11

description: Hybridized to SNP 6.0

source_name: CoA patient 11


title: CoA patient 10

description: Hybridized to SNP 6.0

source_name: CoA patient 10


title: CoA patient 04

description: Hybridized to SNP 6.0

source_name: CoA patient 04


title: CoA patient 05

description: Hybridized to SNP 6.0

source_name: CoA patient 05


title: CoA patient 08

description: Hybridized to SNP 6.0

source_name: CoA patient 08


title: CoA patient 03

description: Hybridized to SNP 6.0

source_name: CoA patient 03


title: CoA patient 02

description: Hybridized to SNP 6.0

source_name: CoA patient 02


title: CoA patient 07

description: Hybridized to SNP 6.0

source_name: CoA patient 07


title: CoA patient 01

description: Hybridized to SNP 6.0

source_name: CoA patient 01


title: Infant_Cdunexposed_5

source_name: Infant cord blood_not_exposed_to_Cd


title: CoA patient 49

description: Hybridized to SNP 6.0

source_name: CoA patient 49


title: adipose-TDF-6-5

city: Birmingham

first: Mohsen

last: Shahmanesh

address: Vincent Drive

department: School of Clinical and Experimental Medicine, College of Medical and Dental Sciences

country: United Kingdom

institute: University of Birmingham

description:
251485055924_1_4
crest fat biopsy

hyb_protocol: cRNA was fragmented to uniform size and verified on the Bioanalyzer. Agilent Whole Genome arrays were hybridized with the cRNA target

scan_protocol: Slides were washed and scanned on an Agilent G2505C Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.31 (Agilent) using default parameters (protocol GE1_107_Sep09  and Grid: 014850_D_F_20080701) to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cy3 labeling

extract_protocol: Qiagen Rneasy Lipid Tissue Mini Kit

tag: subject id

tag: age (yrs)

tag: ethnicity

value: black

tag: weight (kg)

tag: bmi

tag: treated with

value: TDF/emtricitabine+ efavirenz

tag: time point

value: 6 month after treatment

value: adipose


title: adipose-TDF-6-10

description:
251485055936_1_4
crest fat biopsy

tag: tissue


title: IP Pomc-Cre:RiboTag mouse_rep1

city: Bellaterra

first: Elisenda

last: Sanz

state: Barcelona

address: M1/113 Facultat de Medicina

department: Institut de Neurociencies

institute: Universitat Autonoma de Barcelona

description:
9254035037_F
replicate 1

hyb_protocol: Biotinilated cDNA was hybridized at 48ºC to MouseRef-8 v2 expression beadchips (Illumina) for 16h before washing and analyzing according to manufacturer’s directions.

scan_protocol: Signal was detected using a Beadarray Reader (Illumina)

data_processing: Data was analyzed for differential expression using the GenomeStudio data analysis software (Illumina). Average normalization, the Illumina custom error model and multiple testing corrections using Benjamini and Hochberg False discovery rate were applied to the analysis. Only transcripts with a differential score >13 were considered.

source_name: Immunoprecipitated polysome RNA, Pomc-Cre mice crossed to RiboTag mouse

label_protocol: RNA was amplified using the Ovation SL WTA system (Nugen) prior to biotinilation according to the EncoreIL biotinilation kit (Nugen).

extract_protocol: RNA was extracted using the RNeasy micro kit (Qiagen)

value: Pomc-derived lineage


title: adipose-TDF-6-6

description:
251485055925_1_3
crest fat biopsy


title: IP Pomc-cre AAV-DIO-RiboTag_rep2

description:
9254035037_D
replicate 2

source_name: Immunoprecipitated polysome RNA, Pomc-Cre mice injected with RiboTag viral vector

value: adult POMC neuron


title: adipose-TDF-6-2

description:
251485055920_1_4
crest fat biopsy


title: shFOXM1+EZH2 OE

city: Columbus

first: Ichiro

last: Nakano

state: OH

address: 400w 12th, wisemanhall

institute: Ohio State University

hyb_protocol: Labeled targets were hybridized to Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA 2.0) for 16 h at 45°C and washed according to Affymetrix standard protocols.

scan_protocol: The Genechips were scanned with an Affymetrix G7 scanner.

data_processing: For gene expression analysis, arrays were normalized using RMA as implemented in Partek Genomics Suite 6.6 (Partek Incorporated, St Louis MO).

source_name: GBM patient derived GSCs

label_protocol: A 100 ng aliquot of total RNA from four independent incubations was amplified using the GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) following the manufacturer’s instructions and then 5.5 ug of cDNA was fragmented and terminally labeled.

growth_protocol: All cells were cultured using DMEM/F12(Lonza) supplemented with B27(Invitrogen), epidermal growth factor (EGF, 20 ng/ml; R&D Systems), basic fibroblast growth factor (bFGF, 20 ng/ml; R&D Systems), Heparin(5mg/ml; Sigma) in suspension.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen), including DNase I treatment before the final elution to eliminate any DNA contamination, following the manufacturer’s directions.

treatment_protocol: Transfection of non-target control vector or vector expression shFoxm1, shMELK, and EZH2

value: glioma stem cells

tag: cell line

tag: transfection

value: pLKO 1.0- shFoxm1+ EZH2 Overexpression vector


title: IP Pomc-Cre:RiboTag mouse_rep2

description:
9254035037_H
replicate 2


title: adipose-TDF-6-9

description:
251485055934_1_4
crest fat biopsy

value: white


title: adipose-TDF-6-3

description:
251485055921_1_2
crest fat biopsy


title: shMELK

value: pLKO 1.0- shMELK


title: adipose-TDF-6-7

description:
251485055927_1_2
crest fat biopsy


title: adipose-TDF-6-1

description:
251485055831_1_3
crest fat biopsy

value: other


title: shNT

value: pLKO 1.0- shNon-targeting vector


title: Patient 4 (6M)

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description:
Gene Expression data from Patient after 6 Months Treatment with Placebo along with other Cardiac Medications after randomization at baseline
PBMCs were isolated from whole blood of the study subjects by the method of Boyum by density gradient centrifugation

hyb_protocol: Following fragmentation, 12 ug of cRNA was hybridized for 16 hrs at 45°C on GeneChip®HT 3' IVT.

scan_protocol: The arrays were washed and stained after 16 hours of hybridization in Fluidic station 450 using appropriate Fluidic Script followed by the scanning of the Array to generate CEL files.    Wash and Stain the arrays after 16 hours of hybridization in Fluidic station 450 by using appropriate Fluidic Script followed by the scanning of the Array to generate cell files.

data_processing:
Raw gene expression data was analyzed using the GeneSpringGx 12.0 software (Agilent® Technologies, Santa Clara, CA)
Genes that showed more than 2-fold difference between the treated and untreated subjects and with a p-value of <0.05 were considered as differentially expressed.

source_name: Patient 4 (6M) after 6 Months treatment with Placebo along with Cardiac Medications

label_protocol: Biotinylated cRNA samples were prepared according to the standard Affymetrix protocol from 250ng total RNA (GeneChip®HT 3' IVT Express Kit, Affymetrix, USA).

growth_protocol: PBMCs were isolated from 2 randomly selected patients in the each sub-group i.e. Terminalia arjuna or Placebo at 3 and 6 Months respectively to understand specificity, efficacy and mode of action of T.arjuna.

extract_protocol: RNA was isolated from samples with an RNeasy Mini Kit (Catalog No. 74104, QIAGEN, US) using silica column Method, as per manufacturer's protocol.

treatment_protocol: PBMCs were isolated from whole blood of the study subjects by density gradient centrifugation method of Boyum , using Histopaque-1077 (Cat no.10771; Sigma, USA).

tag: diagnosis

value: coronary artery disease (CAD)

value: PBMCs


title: adipose-TDF-6-8

description:
251485055927_1_4
crest fat biopsy

value: male


title: adipose-TDF-18.24-3

description:
251485055921_1_3
crest fat biopsy

value: 18-24 month after treatment


title: adipose-TDF-6-11

description:
251485055939_1_2
crest fat biopsy


title: adipose-TDF-18.24-9

description:
251485062450_1_2
crest fat biopsy


title: adipose-TDF-6-4

description:
251485055922_1_4
crest fat biopsy

value: female


title: adipose-TDF-18.24-7

description:
251485055939_1_3
crest fat biopsy


title: shMELK+EZH2 OE

value: pLKO 1.0- shMELK+EZH2 overexpression vector


title: shFOXM1

value: pLKO 1.0- shFoxm1


title: IP Pomc-cre AAV-DIO-RiboTag_rep1

description:
9254035037_B
replicate 1


title: adipose-TDF-18.24-4

description:
251485055925_1_1
crest fat biopsy

value: black

value: TDF/emtricitabine+ efavirenz


title: adipose-TDF-18.24-5

description:
251485055925_1_4
crest fat biopsy

value: adipose


title: adipose-TDF-18.24-2

description:
251485055831_1_4
crest fat biopsy


title: adipose-TDF-18.24-8

description:
251485062448_1_1
crest fat biopsy


title: adipose-TDF-18.24-6

description:
251485055938_1_2
crest fat biopsy


title: adipose-TDF-0-16

description:
251485062450_1_3
crest fat biopsy

value: treatment naïve


title: adipose-TDF-0-12

description:
251485055937_1_1
crest fat biopsy


title: adipose-TDF-18.24-1

description:
251485055831_1_1
crest fat biopsy


title: adipose-TDF-6-12

description:
251485062450_1_1
crest fat biopsy

value: 6 month after treatment


title: 72h incubation, biological rep3

city: Wageningen

first: Maria

middle: Cecilia

last: Costa

state: The Netherlands

address: Droevendaalsesteeg, 1

department: Plant Physiology

country: Netherlands

institute: Wageningen University

description: Gene expression data from germinated Arabidopsis seeds at the stage of radicle protrusion incubated in ABA for 72h

hyb_protocol: Following fragmentation, 2.5 ug of ss-cDNA were hybridized on the Affymetrix ARAGene 1.1ST Array plates. Plates were washed and stained by the GeneTitan machine using the Affymetrix HWS Kit for the GeneTitan.

scan_protocol: Plates were scanned using the Affymetrix GeneTitan scanner operated by the software program Affymetrix GeneChip Command Console.

data_processing: The Robust Multichip Analysis (RMA-Sketch for gene level analysis) algorithm was used for the summarization. Signal intensities were extracted and analysed using the Bioconductor packages of R. The data was normalized using the RMA algorithm with the TAIRG v17 cdf file.

organism: Arabidopsis thaliana

source_name: Germinated seeds at the stage of radicle protrusion incubated in ABA for 72h

label_protocol: Biotin-labeled cDNA was prepared using the Affymetrix NuGEN Ovation PicoSL WTA and Biotin Module from 50ng total RNA according to the manufacturer's specifications.

growth_protocol: Seeds were cold stratified for 72 h at 4˚C in 9 cm Petri dishes on two layers of blue filter paper and 10 ml of distilled water. After stratification, seeds were transferred to germination cabinets with constant white light at 22 ˚C.

extract_protocol: Total RNA was extracted following the hot borate protocol modified from Wan and Wilkins (1994) (Maia et al, Plos ONE 2011)

treatment_protocol: Germinated seeds at the stage of radicle protrusion were incubated in 6-cm Petri dishes containing 1.3 ml of an ABA solution (10µM) on two sheets of white filter paper, in the dark, at 20˚C.

tag: ecotype

tag: plant organ

value: seeds at the stage of radical protrusion


title: Patient 3 (6M)

source_name: Patient 3 (6M) after 6 Months treatment with Placebo along with Cardiac Medications


title: adipose-TDF-0-11

description:
251485055936_1_3
crest fat biopsy

tag: gender


title: Patient 1 (6M)

description:
Gene Expression data from Patient after 6 Months Treatment with Arjuna along with other Cardiac Medications after randomization at baseline
PBMCs were isolated from whole blood of the study subjects by the method of Boyum by density gradient centrifugation

source_name: Patient 1 (6M) after 6 Months Treatment with Arjuna along with Cardiac Medications


title: adipose-TDF-0-15

description:
251485062449_1_4
crest fat biopsy


title: Patient 4 (3M)

description:
Gene Expression data from Patient after 3 Months Treatment with Placebo along with other Cardiac Medications after randomization at baseline
PBMCs were isolated from whole blood of the study subjects by the method of Boyum by density gradient centrifugation

source_name: Patient 4 (3M)  after 3 Months treatment with Placebo along with Cardiac Medications


title: adipose-TDF-0-10

description:
251485055934_1_3
crest fat biopsy

value: white


title: Patient 3 (3M)

source_name: Patient 3 (3M) after 3 Months treatment with Placebo along with other Cardiac Medications


title: adipose-TDF-0-14

description:
251485055939_1_1
crest fat biopsy


title: 72h incubation, biological rep1


title: adipose-TDF-0-9

description:
251485055927_1_3
crest fat biopsy


title: adipose-TDF-0-7

description:
251485055925_1_2
crest fat biopsy


title: Patient 2 (6M)

source_name: Patient 2 (6M) after 6 Months Treatment with Arjuna along with Cardiac Medications


title: adipose-TDF-0-13

description:
251485055938_1_1
crest fat biopsy


title: adipose-TDF-0-8

description:
251485055926_1_1
crest fat biopsy


title: 72h incubation, biological rep2


title: 24h incubation, biological rep3

description: Gene expression data from germinated Arabidopsis seeds at the stage of radicle protrusion incubated in ABA for 24h

source_name: Germinated seeds at the stage of radicle protrusion incubated in ABA for 24h


title: Patient 2 (3M)

description:
Gene Expression data from Patient after 3 Months Treatment with Arjuna along with other Cardiac Medications after randomization at baseline
PBMCs were isolated from whole blood of the study subjects by the method of Boyum by density gradient centrifugation

source_name: Patient 2 (3M) after 3 Months Treatment with Arjuna along with other Cardiac Medications


title: adipose-TDF-0-5

description:
251485055924_1_2
crest fat biopsy


title: adipose-TDF-0-6

description:
251485055924_1_3
crest fat biopsy


title: adipose-TDF-0-4

description:
251485055922_1_3
crest fat biopsy


title: 24h incubation, biological rep1


title: Patient 1 (3M)

source_name: Patient 1 (3M)  after 3 Months Treatment with Arjuna along with other Cardiac Medications


title: adipose-TDF-0-2

description:
251485055920_1_3
crest fat biopsy


title: adipose-CNTRL-0-13

description:
251485062274_1_2
crest fat biopsy

value: HIV Negative Control

value: Control


title: adipose-CNTRL-0-15

description:
251485062274_1_4
crest fat biopsy


title: Patient 1 (Baseline)

description:
Gene Expression data from Patient having disease more than 3 months prior to their enrolment and using any combination of cardiac-related medications including ASA, ACEIs, ARBs, β-blockers and statins
PBMCs Isolated from Blood of Patient 1 having disease more than 3 months prior to their enrolment and using any combination of cardiac-related medications including ASA, ACEIs, ARBs, β-blockers and statins

data_processing:
Raw gene expression data was analyzed using the GeneSpringGx 12.0 software (Agilent® Technologies, SantaClara, CA)
Genes that showed more than 2-fold difference between the treated and untreated subjects and with a p-value of <0.05 were considered as differentially expressed. Significant gene ontology categories and pathways that harbor these differentially regulated genes were reported for further biological analysis and interpretation.

growth_protocol: PBMCs were isolated from 2 healthy controls and 4 randomly selected patients for Global Gene expression profiling to screen for the gene signatures for identifying candidate genes as future therapeutic targets.


title: Patient 4 (Baseline)

description:
Gene Expression data from Patient having disease more than 3 months prior to their enrolment and using any combination of cardiac-related medications including ASA, ACEIs, ARBs, β-blockers and statins
PBMCs Isolated from Blood of Patient 4 having disease more than 3 months prior to their enrolment and using any combination of cardiac-related medications including ASA, ACEIs, ARBs, β-blockers and statins


title: 12h incubation, biological rep2

description: Gene expression data from germinated Arabidopsis seeds at the stage of radicle protrusion incubated in ABA for 12h

source_name: Germinated seeds at the stage of radicle protrusion incubated in ABA for 12h


title: 12h incubation, biological rep3


title: adipose-TDF-0-3

description:
251485055921_1_1
crest fat biopsy


title: adipose-CNTRL-0-10

description:
251485062273_1_3
crest fat biopsy


title: adipose-CNTRL-0-14

description:
251485062274_1_3
crest fat biopsy


title: adipose-CNTRL-0-12

description:
251485062274_1_1
crest fat biopsy


title: adipose-CNTRL-0-9

description:
251485062273_1_2
crest fat biopsy


title: Normal Healthy Control, Rep 2

description:
Gene Expression data from Normal Healthy Controls
PBMCs Isolated from Blood of Normal Healthy Control

source_name: Normal Healthy Control, Rep 2

value: healthy


title: Patient 3 (Baseline)

description:
Gene Expression data from Patient having disease more than 3 months prior to their enrolment and using any combination of cardiac-related medications including ASA, ACEIs, ARBs, β-blockers and statins
PBMCs Isolated from Blood of Patient 3 having disease more than 3 months prior to their enrolment and using any combination of cardiac-related medications including ASA, ACEIs, ARBs, β-blockers and statins

value: coronary artery disease (CAD)


title: Patient 2 (Baseline)

description:
Gene Expression data from Patient having disease more than 3 months prior to their enrolment and using any combination of cardiac-related medications including ASA, ACEIs, ARBs, β-blockers and statins
PBMCs Isolated from Blood of Patient 2 having disease more than 3 months prior to their enrolment and using any combination of cardiac-related medications including ASA, ACEIs, ARBs, β-blockers and statins

value: PBMCs


title: 12h incubation, biological rep1


title: 2h incubation, biological rep1

description: Gene expression data from germinated Arabidopsis seeds at the stage of radicle protrusion incubated in ABA for 2h

source_name: Germinated seeds at the stage of radicle protrusion incubated in ABA for 2h


title: adipose-CNTRL-0-11

description:
251485062273_1_4
crest fat biopsy


title: adipose-CNTRL-0-8

description:
251485062273_1_1
crest fat biopsy


title: adipose-TDF-0-1

description:
251485055831_1_2
crest fat biopsy

value: other


title: adipose-CNTRL-0-7

description:
251485062272_1_3
crest fat biopsy


title: 2h incubation, biological rep2


title: 24h incubation, biological rep2


title: Normal Healthy Control, Rep 1

source_name: Normal Healthy Control, Rep 1


title: 2h incubation, biological rep3


title: adipose-CNTRL-0-1

description:
251485062271_1_1
crest fat biopsy

value: male


title: adipose-AZT-6-9

description:
251485062448_1_3
crest fat biopsy

value: AZT/lamivudine+efavirenz


title: adipose-CNTRL-0-3

description:
251485062271_1_3
crest fat biopsy


title: adipose-CNTRL-0-4

description:
251485062271_1_4
crest fat biopsy


title: adipose-AZT-6-8

description:
251485055937_1_3
crest fat biopsy

value: female


title: Wild type 42h II

city: Peoria

first: Z Lewis

last: Liu

state: IL

address: 1815 N University

institute: USDA-ARS

description: treated with 20 mM furfrual and 20 mM HMF

hyb_protocol: Based on Hegde et al (2000) with modifications using HS 4800 Hybridization station

scan_protocol: GenePix 4000B using control genes or normalization based on Liu and Slininger (2007)

data_processing: Median foreground signal intensity subtracted by background signal intensity was used. After outlier removal, the nonparametric loess regression (R function loess()) was applied to estimate the log2 ratio of 2 channels.

organism: Saccharomyces cerevisiae

source_name: Wild type

label_protocol: started with 15 ug total RNA, indirect dUTP Cy3 and Cy5 labeling, and examined with s-Gel and NonoDrop

growth_protocol: Cells cultured on YM medium at 30C with agitation

extract_protocol: hot phenol method and purified with Rneasy mini kit

treatment_protocol: furfural and HMF added at a final concentration of 20 mM each after 6h pre-incubation

tag: strain

tag: genotype

value: wild type

source_name: Toerance

value: tolerant


title: Tolerant 28h


title: 0h incubation, biological rep3

description: Gene expression data from germinated Arabidopsis seeds at the stage of radicle protrusion incubated in ABA for 0h

source_name: Germinated seeds at the stage of radicle protrusion incubated in ABA for 0h


title: Tolerant 42h II


title: 0h incubation, biological rep1


title: adipose-AZT-6-2

description:
251485055919_1_4
crest fat biopsy

value: black


title: adipose-AZT-6-3

description:
251485055922_1_1
crest fat biopsy

value: adipose


title: adipose-CNTRL-0-2

description:
251485062271_1_2
crest fat biopsy


title: adipose-AZT-6-6

description:
251485055934_1_2
crest fat biopsy


title: adipose-AZT-6-7

description:
251485055936_1_2
crest fat biopsy


title: Wild type 28h


title: 0h incubation, biological rep2


title: adipose-CNTRL-0-6

description:
251485062272_1_2
crest fat biopsy


title: adipose-AZT-6-1

description:
251485055919_1_2
crest fat biopsy


title: adipose-AZT-6-5

description:
251485055926_1_3
crest fat biopsy


title: adipose-AZT-6-4

description:
251485055923_1_1
crest fat biopsy


title: Wild type 24h


title: Tolerant 24h


title: adipose-CNTRL-0-5

description:
251485062272_1_1
crest fat biopsy


title: Wild type 42h I


title: Copy number profiling of the HER2-Negative of patient 13

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

hyb_protocol: Denatured DNA samples were applied to the microarray under a coverslip and hybridised at 37 °C for 18 h. After hybridisation, the coverslips were removed by washing slides in 2× SSC/1% SDS for 15 min at 45 °C. Slides were then washed in 50% deionised formamide/2× SSC for 15 min at 45 °C, followed by 2× SSC/1% SDS for 30 min at 45 °C and twice in 0.2× SSC for 15 min at room temperature [28, 29]. After washing, the arrays were dried by centrifugation at 2000 r.p.m. for 2 min.

scan_protocol: Slides were accned using an Axon 4000B scanner and images were processed using Genepix Pro Image analysis software.

data_processing: Log2 ratios were normalised for spatial and intensity dependent biases using a two-dimensional loess regression followed by a BAC-dependent bias correction. A categorical analysis was applied to the BACs after classifying them as representing gain, loss, or no-change according to their smoothed Log2 ratio values.

label_protocol: Reference (normal DNA extracted from blood lymphocytes pooled from 24 females) and tumour DNA samples (300ng aliquots) were labelled with Cy3- or Cy5-conjugated dCTP  respectively (Amersham Biosciences, Buckinghamshire, UK) using random primed BioPrime DNA labelling (Invitrogen Life Technologies) according to the manufacturer's protocol, modified to incorporate 1.0 mM Cy dye, 0.6 mM dCTP and 1.2 mM dATP, dGTP and dTTP. After labelling at 37 °C for 16 h, non-incorporated reaction constituents were removed by MinElute Reaction Cleanup (Qiagen Ltd, Crawley, UK). Labelled reference and tumour DNA were co-ethanol precipitated with 100 µg human Cot-1 DNA (Invitrogen Life Technologies) and re-suspended in 45 µl hybridisation buffer (50% deionised formamide, 10% w/v dextran sulphate, 2× SSC, 2% SDS, 20 µg yeast tRNA). Labelled DNA was denatured at 70 °C for 15 min, followed by a 30 min incubation at 37 °C to allow blocking of repetitive sequences by human Cot-1 DNA.

extract_protocol: DNA was extracted using the DNeasy Blood and Tissue Kit.

tag: patient

value: Negative

value: breast cancer

source_name: Pooled normal reference

value: blood

tag: cell type

value: lymphocytes


title: Copy number profiling of the HER2-Positive of patient 12

value: Positive


title: Tolerant 42h I


title: Copy number profiling of the HER2-Negative of patient 12


title: adipose-AZT-18.24-2

description:
251485055923_1_2
crest fat biopsy

tag: subject id

tag: age (yrs)

value: 18-24 month after treatment


title: adipose-AZT-18.24-7

description:
251485062448_1_4
crest fat biopsy

tag: ethnicity

tag: weight (kg)


title: Tolerant 18h


title: adipose-AZT-0-12

description:
251485055938_1_3
crest fat biopsy

tag: bmi

tag: treated with

value: treatment naïve


title: Copy number profiling of the HER2-Negative of patient 11

tag: tissue


title: adipose-AZT-0-15

description:
251485062449_1_2
crest fat biopsy

tag: time point


title: adipose-AZT-18.24-1

description:
251485055920_1_1
crest fat biopsy


title: Copy number profiling of the HER2-Negative of patient 10


title: adipose-AZT-18.24-3

description:
251485055924_1_1
crest fat biopsy


title: adipose-AZT-18.24-6

description:
251485055938_1_4
crest fat biopsy


title: Copy number profiling of the HER2-Positive of patient 13


title: Copy number profiling of the HER2-Positive of patient 11


title: adipose-AZT-18.24-4

description:
251485055926_1_4
crest fat biopsy


title: adipose-AZT-0-14

description:
251485062448_1_2
crest fat biopsy


title: adipose-AZT-0-11

description:
251485055937_1_2
crest fat biopsy


title: adipose-AZT-0-8

description:
251485055927_1_1
crest fat biopsy

value: white


title: Wild type 18h


title: adipose-AZT-0-10

description:
251485055936_1_1
crest fat biopsy


title: Copy number profiling of the HER2-Negative of patient 8


title: Copy number profiling of the HER2-Positive of patient 10


title: adipose-AZT-0-9

description:
251485055934_1_1
crest fat biopsy


title: adipose-AZT-18.24-5

description:
251485055937_1_4
crest fat biopsy


title: Copy number profiling of the HER2-Positive of patient 8


title: adipose-AZT-0-6

description:
251485055923_1_4
crest fat biopsy


title: adipose-AZT-0-13

description:
251485055939_1_4
crest fat biopsy


title: adipose-AZT-0-7

description:
251485055926_1_2
crest fat biopsy


title: adipose-AZT-0-3

description:
251485055920_1_2
crest fat biopsy


title: adipose-AZT-0-4

description:
251485055921_1_4
crest fat biopsy


title: Copy number profiling of the HER2-Positive of patient 5


title: adipose-ABC-6-7

description:
251485062269_1_3
crest fat biopsy

value: ABC/lamivudine+efavirenz

value: 6 month after treatment


title: Copy number profiling of the HER2-Positive of patient 9


title: Copy number profiling of the HER2-Negative of patient 9


title: adipose-AZT-0-5

description:
251485055923_1_3
crest fat biopsy

value: male


title: Copy number profiling of the HER2-Negative of patient 5


title: adipose-ABC-6-9

description:
251485062454_1_4
crest fat biopsy


title: Copy number profiling of the HER2-Positive of patient 6


title: Copy number profiling of the HER2-Negative of patient 6


title: adipose-AZT-0-2

description:
251485055919_1_3
crest fat biopsy

value: AZT/lamivudine+efavirenz


title: Copy number profiling of the Distant metastasis of patient 4

value: Distant metastasis

value: female


title: Copy number profiling of the HER2-Negative of patient 4


title: adipose-ABC-6-5

description:
251485062268_1_3
crest fat biopsy


title: adipose-ABC-6-3

description:
251485062265_1_4
crest fat biopsy


title: adipose-ABC-6-6

description:
251485062269_1_1
crest fat biopsy


title: adipose-ABC-6-8

description:
251485062454_1_2
crest fat biopsy


title: adipose-AZT-0-1

description:
251485055919_1_1
crest fat biopsy


title: Copy number profiling of the HER2-Positive of patient 3


title: adipose-ABC-18.24-10

description:
251485062454_1_3
crest fat biopsy


title: adipose-ABC-6-4

description:
251485062268_1_2
crest fat biopsy


title: adipose-ABC-6-2

description:
251485062265_1_2
crest fat biopsy


title: Copy number profiling of the HER2-Negative of patient 3


title: Copy number profiling of the HER2-Negative of patient 2


title: Copy number profiling of the HER2-Positive of patient 4


title: adipose-ABC-18.24-9

description:
251485062270_1_4
crest fat biopsy


title: adipose-ABC-6-1

description:
251485062265_1_1
crest fat biopsy


title: adipose-ABC-18.24-5

description:
251485062269_1_4
crest fat biopsy


title: adipose-ABC-18.24-7

description:
251485062270_1_2
crest fat biopsy


title: adipose-ABC-18.24-8

description:
251485062270_1_3
crest fat biopsy


title: adipose-ABC-18.24-4

description:
251485062269_1_2
crest fat biopsy


title: Copy number profiling of the HER2-Negative of patient 1


title: adipose-ABC-18.24-6

description:
251485062270_1_1
crest fat biopsy


title: adipose-ABC-18.24-3

description:
251485062268_1_4
crest fat biopsy


title: Copy number profiling of the HER2-Positive of patient 1


title: VDR-null duodenum 2

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

hyb_protocol: Following fragmentation, 3.0 μg of cDNAs were hybridized for 16 hours at 45oC, 60 rpm on GeneChip® Mouse Gene 2.0 ST arrays . The chips were then washed and stained in the GeneChip® Fluidics Station 450.

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G. Raw data were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.0

data_processing:
CEL files were processed to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

label_protocol: Biotinylated cDNA targets were prepared from 150 ng of total RNA using  Ambion WT Expression Kit (Cat # 4411974) and  Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: strain background

tag: genotype/variation

value: VDR-null

tag: age

value: 10 week-old

value: duodenum


title: wild-type duodenum 1

source_name: Wild type_duodenum

value: wild type


title: VDR-null duodenum 3


title: wild-type duodenum 2


title: LaminC G489V_larvae, biological rep 1

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

description: Gene expression data from 3rd instar larvae

hyb_protocol: The resulting biotin-labeled cDNA was mixed with Affymetrix hybridization buffer, placed onto Drosophila 2.0 arrays (Cat #900532), and incubated at 45º C for 18 h with 60 rpms rotation in an Affymetrix Model 640 Genechip Hybridization Oven.  Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc. Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) , and stained again with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), using the Affymetrix Model 450Fluidics Station (Affymetrix, Inc.) following the appropriate fluidics script protocol for the array

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4 and expression value estimates were generated using the microarray suite (MAS) v5.0 software.

data_processing: The .cel data was imported into Partek GS v6.12.1011. Values were normalized using the partek RMA workflow. Values are expressed as log2 normalized values

organism: Drosophila melanogaster

source_name: LaminC G489V_larvae

label_protocol: Fifty nanograms total RNA was converted to SPIA amplified cDNA using the Ovation RNA Amplification System, v2 (NuGEN Technologies, Cat. #3100) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column (QIAGEN Cat #28104) according to modifications from NuGEN.  3.75ug of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module,  (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol

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

treatment_protocol: Flies expressing UAS-LaminC transgenes were crossed to flies of the C57 muscle driver stock and cultured at 25 oC.

value: expressing LaminC G489V

tag: developmental stage

value: 3rd instar larvae

value: Larval muscle


title: LaminC DN_larvae, biological rep 2

source_name: LaminC DN_larvae

value: expressing LaminC DN


title: adipose-ABC-18.24-1

description:
251485062265_1_3
crest fat biopsy

value: black

tag: gender

value: 18-24 month after treatment

value: adipose


title: LaminC G489V_larvae, biological rep 2


title: LaminC G489V_larvae, biological rep 3


title: LaminC DN_larvae, biological rep 3


title: LaminC wildtype_larvae, biological rep 2

source_name: LaminC wildtype_larvae

value: expressing LaminC wildtype


title: LaminC DN_larvae, biological rep 1


title: LaminC wildtype_larvae, biological rep 3


title: wild-type duodenum 3


title: adipose-ABC-18.24-2

description:
251485062268_1_1
crest fat biopsy

value: ABC/lamivudine+efavirenz


title: Copy number profiling of the HER2-Positive of patient 2

value: Positive

value: breast cancer

value: blood

value: lymphocytes


title: LaminC wildtype_larvae, biological rep 1


title: Control 5

status: Public on Apr 15 2015

city: Kolkata

first: Soma

last: Banerjee

state: West Bengal

address: 244, A.J.C Bose Road

department: School of Digestive and Liver Diseases

institute: Institute of Post Graduate Medical Education and Research

description: microRNA expression profiling from liver tissue

hyb_protocol: According to Agilent

scan_protocol: Agilent Scanner (Agilent Technologies, Part Number: G2565CA)

data_processing:
Feature Extraction software v 10.7 of Agilent. Feature extracted data was analyzed using GeneSpring GX version 11.5 software from Agilent.
Raw intensity signals (RIS) of each miRNA were log transformed at base 2 (log2) and used for subsequent analysis. For intra-array normalization 75th percentile median shift of each log transformed RIS value was determined using the formula R=P/100(N+1) where R=rank, P=percentile, N=number of entities. By inter-array normalization differentially expressed miRNAs were identified by subtracting the median value of log2 transformed RIS of each miRNA of control group from that of HCC group. Using stringent criteria such as > 1.5 fold change in RIS value and detectable in all HCC specimens but at least in 6/8 controls were considered for two-tailed unpaired Student’s *t*-test to determine the significant alteration (p<0.05) in miRNA expression between two groups. miRNAs which were not detected in the microarray were represented as "null".

source_name: Liver tissue from biopsy

label_protocol: The miRNA labeling was performed using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Part Number: 5190-0456)

extract_protocol: Total RNA extrction from liver tissue by TRIzol  according to manufacturer protocol

value: liver

tag: etiology

value: HBV

tag: disease status

value: chronic hepatitis B (CHB) with no fibrosis

tag: Sex

value: Female


title: HCC 3

source_name: Explanted Liver tissue from HCC patient

value: hepatocellular carcinoma (HCC)

value: Male


title: Control 6


title: VDR-null duodenum 1

value: VDR-null

value: 10 week-old

value: duodenum


title: Control 1


title: Control 2


title: Control 7


title: Control 8


title: HCC 1


title: HCC 2


title: Control 3


title: HCC 4


title: Control 4


title: MDAMB231 HAH2#9_2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: SUV420H2 stably over-expressing MDA-MB-231 culture cells　（#9)

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Both cells were maintained in DMEM supplemented with 10% FCS

extract_protocol: RNA were extracted from cells using pure link RNA mini kit (Ambion)

treatment_protocol: human SUV420H2 was transfected in MDA-MB-231 cells and stably expressing cells were cloned  and termed H2#9

tag: cell line

value: breast cancer MDA-MB-231 cells

value: stably over-expressing SUV420H2


title: Patient 29 NCCRI_2012-054_58

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: responder_primary lung cancer

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Total RNA was extracted from human lungs using QIAzol and the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. The purity and concentration of all RNA samples were quantified using NanoDrop ND-1000 (Thermo Scientific). Detection of RNA from human lungs was performed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). Prior to the analysis, total RNA was prepared with the Agilent RNA 6000 Pico kit (Agilent Technologies) according to the manufacturer’s protocol. All clinical samples exhibited RNA Integrity Numbers > 6.0.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: Twenty-nine patients who received four or more courses of first-line platinum-based chemotherapy after postoperative recurrence were divided into two groups (responder (n=17) and non-responder group (n=12)).

tag: subject id

value: Patient 29

tag: therapeutic response

value: responder

value: primary lung cancer

tag: pathological type

value: adenocarcinoma (AD)

tag: pathological stage

value: IIIA


title: 24h - Vehicle Control (+S9) - Pooled Replicate

city: Ottawa

first: Julie

last: Buick

state: Ontario

address: 50 Colombine Driveway

department: Mechanistic Studies Division

country: Canada

institute: Health Canada

description:
Co-hybridized with negative vehicle control pool (DMSO -S9)
array 1_1: Cy3 VCP1 (+S9) and Cy5 VCP2 (-S9) array 2_1: Cy5 VCP1 (+S9) and Cy3 VCP2 (-S9)

hyb_protocol: Labelled cRNA samples (325 ng of cyanine-3 labelled cRNA and 325 ng of cyanine-5 labelled cRNA) were hybridized to Agilent SurePrint G3 Human GE 8x60K oligonucleotide microarrays (Agilent Catalogue No: G4851A, Agilent Microarray Design ID: 028004; Agilent Technologies, Mississauga, ON, Canada) at 65oC for 17 hours.

scan_protocol: Slides were washed according to the manufacturer’s specifications and scanned using an Agilent G2505C DNA Microarray Scanner at 3 μm resolution. Agilent Feature Extraction (version 11.0.1.1) was used for data extraction purposes from the generated image files and to generate QC reports for each array.

data_processing: The log2 of the ratio using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.  After normalization the log2 ratios for the dye swap were averaged yielding a ratio representing the treatment relative to the vehicle control.

source_name: TK6 lymphoblastoid cell line

label_protocol: Gene expression profiles were generated using a two-colour dye swap design [Kerr and Churchill, 2001]. Microarray analysis was conducted on one pooled replicate from each condition at 24h (n=3 per concentration and time point), along with the corresponding pooled vehicle and positive controls. Agilent Low-Input Quick Amp Labelling kits were used to ultimately generate cyanine-3 and cyanine-5 labelled cRNA from 100 ng of total RNA, according to the manufacturer’s instructions (Agilent Technologies, Mississauga, ON, Canada).

growth_protocol: TK6 cells, a human lymphoblastoid cell line, were obtained from American Type Culture Collection (ATCC# CRL-8015; ATCC, Manassas, VA, USA). TK6 cells were maintained as described elsewhere [Ellinger-Ziegelbauer et al., 2009]. Briefly, cells were cultured and maintained in RPMI 1640 medium containing 10% heat inactivated horse serum, in addition to 0.1% pluronics, sodium pyruvate and antibiotics (penicillin at 20 units/ml and streptomycin at 20 µg/ml) at 37 ± 1oC and 6 ± 1% CO2 in air. Immediately prior to chemical exposure, cells were seeded at a density of 4 (± 0.5) x 105 cells/ml in twelve-well plates with a final volume of 3 ml per well. Given that TK6 cells are not metabolically competent cells and that BaP requires metabolic activation to form reactive metabolites, all cellular exposures were conducted in the presence of 1% 5,6 benzoflavone-/phenobarbital-induced rat liver S9 (Moltox, Boone, NC, USA) with NADPH generating system cofactors. The in vitro cellular exposures were performed by Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, NC, USA), in addition to the associated cytotoxicity and genotoxicity testing.

extract_protocol: Following cellular exposures, total RNA was isolated from treated and control TK6 cells at the 24h time point. An RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate and purify total RNA using the spin technology protocol with an on-column DNase I digestion, following the manufacturer’s instructions. Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.6 to 10 and A260/280 absorbance ratios >2.0 were used for gene expression analysis.

treatment_protocol: TK6 cells were exposed to vehicle control (DMSO (±S9)), 10 μg/ml benzo[a]pyrene (-S9) and 7.5 mM dexamethasone (+S9) (n = 3 for each condition at 24h). Separate plates were used for exposures to negative and vehicle controls (NC (±S9), VC (±S9)). The time points was named as follows: 24h = four hours of exposure, media replaced and sampled 20 hours later. Benzo[a]pyrene was done in the absence of 1% BF/PB-induced rat liver S9 with NADPH generating system cofactors to verify that benzo[a]pyrene was not metabolically activated in the absence of S9, as TK6 cells do not have inherent metabolic capacity, in addition to its associated vehicle control). Dexamethasone was done in the presence of 1% BF/PB-induced rat liver S9 with NADPH generating system cofactors to test a higher concentraion of this non-genotoxic chemical, in addition to its associated vehicle control. Exponentially growing cells were exposed to each chemical for 4 ± 0.5 hours. At the end of the 4h exposure, the exposed and control TK6 cells for the 24h time point were removed by centrifugation and the cells were rinsed in PBS. The 24h samples were re-suspended in 3 ml of media and re-incubated for an additional 20 ± 0.5 before being harvested for RNA and cytotoxicity/MN assays. Cells dedicated for the purposes of RNA extraction were collected from each well (4 ± 0.5 x 106 cells), pelleted by centrifugation and flash frozen in liquid nitrogen. Cells were stored at -80oC until RNA extraction was performed.

value: TK6 lymphoblastoid

tag: time

value: 24h vehicle control with VCP1 (+S9)

tag: concentration

value: DMSO (+S9)

value: 24h vehicle control without VCP2 (-S9)

value: DMSO (-S9)


title: MDAMB231 HAH2#9_1