title: CP-CML_310

description: Sample 310


title: CP-CML_302

status: Public on Jun 30 2014

type: genomic

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

country: France

institute: Centre hospitalier de Versailles

description: Sample 302

hyb_protocol: Array were prepared for hybridization in the capillary flow-through chamber. Samples were applied to BeadChips and incubated overnight. After hybridization, allelic specificity was conferred by enzymatic base extension. Products were subsequently fluorescently stained.

scan_protocol: Illumina  iScan System

data_processing: GenomeStudio Genotyping (GT) Module

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: chronic phase chronic myeloid leukemia (CP-CML)

label_protocol: Cy3 and Cy5; according to standard protocol

extract_protocol: DNA sample were isothermally amplified. Amplified product were then fragmented by a controlled enzymatic process.

tag: disease state

value: Chronic phase

tag: gender

value: male

tag: imatinib dose (mg/day)

tag: sokal score

value: Int

tag: molecular response

tag: tissue

value: peripheral blood

tag: cell type

value: Leucocyte


title: CP-CML_300

description: Sample 300


title: 10656_case_4hrs_BCG_stimulated

type: RNA

city: London

first: Helen

middle: Alison

last: Fletcher

address: Keppel Street

department: IID

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86701.gif

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Illumina BeadStudio

molecule: total RNA

source_name: PBMC isolated from BCG vaccinated_case. Stimulation time and condition: 4 hrs BCG stimulated.

label_protocol: not provided

extract_protocol: not provided

value: pbmc isolated from bcg vaccinated_case

tag: stimulation time and condition

value: 4 hrs BCG stimulated


title: 16890_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86784.gif


title: CP-CML_303

description: Sample 303


title: CP-CML_301

description: Sample 301


title: CP-CML_299

description: Sample 299


title: CP-CML_297

description: Sample 297

value: female

value: High


title: CP-CML_298

description: Sample 298


title: chHES-10-initial, biological rep3

city: changsha

first: Ge

last: Lin

state: hunan

address: xiangya road

department: Institute of Reproductive & Stem Cell Engineering

country: China

institute: Central South University

description:
10-P4
P4-P9 represents the initial passaged hESCs, P20-P44 represents the low-passaged hESCs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Gcos1.4GeneChip Operating Software using Affymetrix default analysis settings.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

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

treatment_protocol: hESCs cultured in Standard human embryonic stem cell media amd RNA was isolated

value: Human embryonic stem cell line

tag: cell line

tag: passage


title: 13472_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86742.gif

source_name: PBMC isolated from BCG vaccinated_control. Stimulation time and condition: 12 hrs BCG stimulated.

value: pbmc isolated from bcg vaccinated_control

value: 12 hrs BCG stimulated


title: chHES-175-low, biological rep3

description:
175-P23
P4-P9 represents the initial passaged hESCs, P20-P41 represents the low-passaged hESCs

growth_protocol: Standard human embryonic stem cell media


title: 18195_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86734.gif


title: 15651_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86836.gif

source_name: PBMC isolated from BCG vaccinated_case. Stimulation time and condition: 4 hrs unstimulated.

value: 4 hrs unstimulated


title: chHES-8-initial, biological rep3

description:
8-P4
P4-P9 represents the initial passaged hESCs, P20-P42 represents the low-passaged hESCs


title: chHES-8-low, biological rep3

description:
8-P25
P4-P9 represents the initial passaged hESCs, P20-P43 represents the low-passaged hESCs


title: 19382_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86722.gif


title: CP-CML_340

description: Sample 340


title: CP-CML_295

description: Sample 295


title: 15417_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86874.gif


title: CP-CML_296

description: Sample 296

value: Low


title: chHES-10-low, biological rep3

description:
10-P27
P4-P9 represents the initial passaged hESCs, P20-P45 represents the low-passaged hESCs


title: CP-CML_294

description: Sample 294


title: CP-CML_292

description: Sample 292


title: CP-CML_293

description: Sample 293


title: CP-CML_290

description: Sample 290


title: CP-CML_291

description: Sample 291


title: 17448_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86816.gif

source_name: PBMC isolated from BCG vaccinated_control. Stimulation time and condition: 4 hrs unstimulated.


title: chHES-137-low, biological rep3

description:
137-P30
P4-P9 represents the initial passaged hESCs, P20-P39 represents the low-passaged hESCs


title: chHES-175-initial, biological rep3

description:
175-P6
P4-P9 represents the initial passaged hESCs, P20-P40 represents the low-passaged hESCs


title: 19382_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86724.gif

source_name: PBMC isolated from BCG vaccinated_case. Stimulation time and condition: 12 hrs unstimulated.

value: 12 hrs unstimulated


title: CP-CML_288

description: Sample 288


title: chHES-137-initial, biological rep3

description:
137-P3
P4-P9 represents the initial passaged hESCs, P20-P38 represents the low-passaged hESCs


title: chHES-51-low, biological rep3

description:
51-P25
P4-P9 represents the initial passaged hESCs, P20-P37 represents the low-passaged hESCs


title: CP-CML_287

description: Sample 287


title: CP-CML_286

description: Sample 286


title: CP-CML_283

description: Sample 283


title: CP-CML_289

description: Sample 289


title: CP-CML_284

description: Sample 284


title: CP-CML_282

description: Sample 282


title: chHES-51-initial, biological rep3

description:
51-P6
P4-P9 represents the initial passaged hESCs, P20-P36 represents the low-passaged hESCs


title: CP-CML_285

description: Sample 285


title: 21457_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86752.gif


title: chHES-45-low, biological rep3

description:
45-P27
P4-P9 represents the initial passaged hESCs, P20-P35 represents the low-passaged hESCs


title: 22168_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86660.gif


title: CP-CML_281

description: Sample 281


title: CP-CML_280

description: Sample 280


title: 18224_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86730.gif


title: chHES-26-low, biological rep3

description:
26-P26
P4-P9 represents the initial passaged hESCs, P20-P33 represents the low-passaged hESCs


title: CP-CML_279

description: Sample 279


title: chHES-45-initial, biological rep3

description:
45-P6
P4-P9 represents the initial passaged hESCs, P20-P34 represents the low-passaged hESCs


title: 14379_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86837.gif

source_name: PBMC isolated from BCG vaccinated_control. Stimulation time and condition: 4 hrs BCG stimulated.


title: CP-CML_278

description: Sample 278


title: chHES-26-initial, biological rep3

description:
26-P5
P4-P9 represents the initial passaged hESCs, P20-P32 represents the low-passaged hESCs


title: CP-CML_277

description: Sample 277


title: 12748_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86802.gif


title: chHES-22-low, biological rep3

description:
22-P23
P4-P9 represents the initial passaged hESCs, P20-P31 represents the low-passaged hESCs


title: CP-CML_276

description: Sample 276


title: CP-CML_274

description: Sample 274


title: CP-CML_275

description: Sample 275


title: chHES-22-initial, biological rep3

description:
22-P5
P4-P9 represents the initial passaged hESCs, P20-P30 represents the low-passaged hESCs


title: 15421_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86814.gif


title: CP-CML_267

description: Sample 267


title: CP-CML_268

description: Sample 268


title: chHES-10-low,biological rep2

description: P4-P9 represents the initial passaged hESCs, P20-P30 represents the low-passaged hESCs

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


title: CP-CML_269

description: Sample 269


title: 13236_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86790.gif


title: 12776_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86798.gif


title: CP-CML_266

description: Sample 266


title: chHES-10-initial,biological rep1


title: 19508_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86668.gif


title: CP-CML_271

description: Sample 271


title: CP-CML_273

description: Sample 273


title: CP-CML_270

description: Sample 270


title: chHES-10-low  biological rep1


title: chHES-127-low,biological rep2


title: CP-CML_272

description: Sample 272


title: CP-CML_265

description: Sample 265


title: 22482_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86691.gif


title: CP-CML_264

description: Sample 264


title: 13468_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86720.gif


title: 13572_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86682.gif


title: 13472_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86748.gif


title: chHES-127-low  biological rep1


title: 18224_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86732.gif


title: chHES-10-initial,biological rep2


title: 15651_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86773.gif

source_name: PBMC isolated from BCG vaccinated_case. Stimulation time and condition: 12 hrs BCG stimulated.


title: CP-CML_261

description: Sample 261


title: chHES-127-initial,biological rep2


title: CP-CML_262

description: Sample 262


title: CP-CML_255

description: Sample 255


title: CP-CML_263

description: Sample 263


title: CP-CML_258

description: Sample 258


title: CP-CML_253

description: Sample 253


title: 18195_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86736.gif


title: 15421_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86815.gif


title: 18195_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86735.gif


title: chHES-88-low  biological rep1


title: CP-CML_254

description: Sample 254


title: chHES-88-initial,biological rep2


title: 22208_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86775.gif


title: CP-CML_259

description: Sample 259


title: CP-CML_260

description: Sample 260


title: CP-CML_251

description: Sample 251


title: CP-CML_247

description: Sample 247


title: CP-CML_256

description: Sample 256


title: CP-CML_257

description: Sample 257


title: CP-CML_252

description: Sample 252


title: CP-CML_248

description: Sample 248


title: 16032_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86689.gif


title: CP-CML_250

description: Sample 250


title: CP-CML_249

description: Sample 249


title: 14379_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86834.gif

source_name: PBMC isolated from BCG vaccinated_control. Stimulation time and condition: 12 hrs unstimulated.


title: chHES-63-initial,biological rep2


title: chHES-88-low,biological rep2


title: CP-CML_245

description: Sample 245


title: 19002_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86756.gif


title: chHES-88-initial,biological rep1

description: P4-P9 represents the initial passaged hESCs, P20-P30 represents the low-passaged hESCs


title: CP-CML_244

description: Sample 244


title: chHES-63-low  biological rep1


title: CP-CML_246

description: Sample 246


title: chHES-63-low,biological rep2


title: 21257_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86780.gif


title: 14116_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86665.gif


title: CP-CML_240

description: Sample 240


title: CP-CML_242

description: Sample 242


title: CP-CML_241

description: Sample 241


title: CP-CML_239

description: Sample 239


title: chHES-35-low,biological rep2


title: CP-CML_234

description: Sample 234


title: CP-CML_243

description: Sample 243


title: chHES-35-low  biological rep1


title: chHES-63-initial,biological rep1


title: CP-CML_237

description: Sample 237


title: 13236_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86787.gif


title: chHES-35-initial,biological rep1


title: CP-CML_235

description: Sample 235


title: chHES-35-initial,biological rep2


title: CP-CML_238

description: Sample 238


title: 15651_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86771.gif


title: CP-CML_233

description: Sample 233


title: CP-CML_232

description: Sample 232


title: CP-CML_236

description: Sample 236


title: CP-CML_231

description: Sample 231


title: 17417_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86821.gif


title: CP-CML_229

description: Sample 229


title: chHES-8-low  biological rep1


title: CP-CML_228

description: Sample 228


title: 13082_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86712.gif


title: CP-CML_225

description: Sample 225


title: CP-CML_226

description: Sample 226


title: CP-CML_227

description: Sample 227


title: CP-CML_224

description: Sample 224


title: 14116_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86663.gif


title: 22168_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86662.gif


title: CP-CML_230

description: Sample 230


title: CP-CML_223

description: Sample 223


title: chHES-8-low,biological rep2


title: chHES-8-initial,biological rep2


title: 21457_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86751.gif


title: 17039_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86762.gif


title: chHES-8-initial,biological rep1


title: chHES-175-low,biological rep2


title: 17417_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86823.gif


title: 21257_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86777.gif


title: CP-CML_220

description: Sample 220


title: CP-CML_221

description: Sample 221


title: CP-CML_222

description: Sample 222


title: CP-CML_219

description: Sample 219


title: CP-CML_218

description: Sample 218


title: CP-CML_217

description: Sample 217


title: chHES-175-initial,biological rep1


title: chHES-175-initial,biological rep2


title: 12776_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86793.gif


title: chHES-175-low  biological rep1


title: chHES-137-low  biological rep1


title: CP-CML_213

description: Sample 213


title: CP-CML_214

description: Sample 214


title: CP-CML_212

description: Sample 212


title: CP-CML_215

description: Sample 215


title: 16890_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86786.gif


title: 15203_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86686.gif


title: chHES-127-initial,biological rep1


title: CP-CML_216

description: Sample 216


title: chHES-51-low  biological rep1


title: chHES-137-initial,biological rep2


title: 13301_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86704.gif


title: CP-CML_208

description: Sample 208


title: CP-CML_206

description: Sample 206


title: chHES-51-low,biological rep2

description: P4-P9 represents the initial passaged hESCs, P20-P30 represents the low-passaged hESCs


title: CP-CML_207

description: Sample 207


title: CP-CML_209

description: Sample 209


title: CP-CML_210

description: Sample 210


title: CP-CML_211

description: Sample 211


title: 19933_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86767.gif


title: chHES-137-low,biological rep2


title: CP-CML_205

description: Sample 205


title: CP-CML_202

description: Sample 202


title: CP-CML_203

description: Sample 203


title: 13229_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86718.gif


title: 17771_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86671.gif


title: CP-CML_201

description: Sample 201


title: 14528_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86738.gif


title: CP-CML_204

description: Sample 204


title: 15193_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86827.gif


title: chHES-51-initial,biological rep1


title: 19508_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86669.gif


title: CP-CML_200

description: Sample 200


title: 15193_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86825.gif


title: chHES-45-low, biological rep2


title: chHES-51-initial,biological rep2


title: chHES-45-low, biological rep1


title: chHES-137-initial,biological rep1


title: CP-CML_195

description: Sample 195


title: CP-CML_194

description: Sample 194


title: CP-CML_196

description: Sample 196


title: CP-CML_197

description: Sample 197


title: CP-CML_199

description: Sample 199


title: 19933_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86770.gif


title: CP-CML_193

description: Sample 193


title: CP-CML_198

description: Sample 198


title: CP-CML_192

description: Sample 192


title: CP-CML_191

description: Sample 191


title: chHES-45-initial, biological rep1


title: chHES-26-low, biological rep2


title: chHES-45-initial, biological rep2


title: CP-CML_188

description: Sample 188


title: chHES-26-low, biological rep1


title: 13472_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86741.gif


title: CP-CML_189

description: Sample 189


title: 12776_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86792.gif


title: CP-CML_186

description: Sample 186


title: 19382_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86725.gif


title: CP-CML_187

description: Sample 187


title: 13082_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86714.gif


title: CP-CML_185

description: Sample 185


title: CP-CML_182

description: Sample 182


title: CP-CML_180

description: Sample 180


title: 13236_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86788.gif


title: CP-CML_183

description: Sample 183


title: CP-CML_184

description: Sample 184


title: chHES-22-low, biological rep2


title: chHES-22-low, biological rep1


title: CP-CML_181

description: Sample 181


title: 21457_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86750.gif


title: chHES-22-initial, biological rep1


title: 15193_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86824.gif


title: chHES-26-initial, biological rep2


title: CP-CML_179

description: Sample 179


title: chHES-26-initial, biological rep1


title: CP-CML_176

description: Sample 176


title: chHES-22-initial, biological rep2


title: CP-CML_178

description: Sample 178


title: 13572_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86676.gif


title: 17039_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86763.gif


title: 15203_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86684.gif


title: CP-CML_177

description: Sample 177


title: TRT_57_EM

city: Sacramento

first: Yingfang

last: Tian

state: CA

country: USA

institute: University of California at Davis

description:
TS diagnosis: Tourette diagnosis was based on Statistical Manual of Mental Disorders Fourth Edition, Text Revision DSM-IV-TR criteria. Tic severity was assessed based on direct child and parent interview using the Yale Global Tic Severity Scale (YGTSS).
ADHD syptoms assesment: The Conners Parent Rating Scale–Revised Short Form (CPRS-R:S) was used to assess ADHD symptoms using continuous, standardized age and gender adjusted CPRS-T scores. A higher score indicates more severe behavior. No clinical diagnosis of ADHD was made in the study.

hyb_protocol: 4.4ug of fragmented and labeled cDNA was Hybridized Affymetrix Human U133 Plus 2.0 arrays for 18 hours according to Nugen's protocol  (Nugen, San Carlos, CA).The arrays were washed and processed on a Fluidics Station 450.

scan_protocol: GeneChips were scanned  on the Genechip Scanner 3000

data_processing: The data were analyzed with Partek Genomics Suite 6.4 (Partek Inc., St. Louis, MO, USA). Probe summarization and probe-set normalization were performed using Robust Multi-Chip Average (RMA), which included background correction, quantile normalization, log2-transformation and median polish probe set summarization.

source_name: Blood of the patient with Tourette

label_protocol: 50 ng of total RNA was used as input into Nugen's Ovation Whole Blood Solution (NuGEN, San Carlos,CA) which allows for an optimized amplification of whole blood RNA and the fragmentation and labeling of the amplified cDNA. The RNA was processed according to manufacturer's protocol.

extract_protocol: Total RNA was isolated using the PAXgene Blood RNA Kit (Qiagen) according to the manufacturer’s protocol.

tag: disorder

value: Tourette Syndrome

value: blood

tag: inattention

tag: hyperactive/impulsivity

tag: ygtss

tag: age


title: 17417_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86820.gif


title: CP-CML_173

description: Sample 173

value: Chronic phase


title: CP-CML_174

description: Sample 174

value: male


title: CP-CML_175

description: Sample 175


title: CP-CML_169

description: Sample 169


title: CP-CML_172

description: Sample 172


title: CP-CML_170

description: Sample 170


title: CP-CML_171

description: Sample 171


title: TRT_56_SH


title: CP-CML_168

description: Sample 168


title: 20426_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86680.gif


title: 22482_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86693.gif


title: CP-CML_166

description: Sample 166


title: 17771_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86673.gif


title: TRT_53_AM


title: TRT_51_CS


title: CP-CML_167

description: Sample 167


title: CP-CML_163

description: Sample 163


title: CP-CML_164

description: Sample 164


title: TRT_50_KC


title: CP-CML_165

description: Sample 165

value: Int


title: CP-CML_162

description: Sample 162

value: peripheral blood


title: CP-CML_161

description: Sample 161

value: Leucocyte


title: 16015_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86743.gif

value: pbmc isolated from bcg vaccinated_case


title: TRT_41_DR


title: TRT_48_MW


title: 18224_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86729.gif

value: 4 hrs BCG stimulated


title: TRT_43_EA

value: female


title: 13572_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86675.gif


title: TRT_40_RS


title: CP-CML_160

description: Sample 160

value: High


title: CP-CML_157

description: Sample 157


title: CP-CML_156

description: Sample 156


title: CP-CML_158

description: Sample 158


title: CP-CML_155

description: Sample 155


title: TRT_31_MW


title: CP-CML_159

description: Sample 159


title: 12406_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86795.gif


title: CP-CML_152

description: Sample 152


title: CP-CML_153

description: Sample 153


title: 13228_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86811.gif


title: 16032_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86688.gif


title: 17448_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86817.gif


title: CP-CML_154

description: Sample 154


title: TRT_23_HW


title: CP-CML_150

description: Sample 150


title: 14106_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86727.gif


title: TRT_27_SL


title: CP-CML_149

description: Sample 149


title: TRT_18_JM


title: 13187_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86708.gif


title: TRT_20_ZD


title: CP-CML_148

description: Sample 148


title: 14379_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86766.gif


title: TRT_14_AP


title: CP-CML_147

description: Sample 147


title: 19002_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86753.gif


title: CP-CML_190

description: Sample 190


title: CP-CML_146

description: Sample 146


title: CP-CML_145

description: Sample 145


title: CP-CML_144

description: Sample 144


title: TRT_13_DM


title: TRT_17_GT


title: CP-CML_143

description: Sample 143


title: CP-CML_140

description: Sample 140


title: 17039_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86765.gif


title: TRT_11_NN

description:
TS diagnosis: Tourette diagnosis was based on Statistical Manual of Mental Disorders Fourth Edition, Text Revision DSM-IV-TR criteria. Tic severity was assessed based on direct child and parent interview using the Yale Global Tic Severity Scale (YGTSS).
ADHD syptoms assesment: The Conners Parent Rating Scale–Revised Short Form (CPRS-R:S) was used to assess ADHD symptoms using continuous, standardized age and gender adjusted CPRS-T scores. A higher score indicates more severe behavior. No clinical diagnosis of ADHD was made in the study.


title: CP-CML_141

description: Sample 141


title: 13228_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86808.gif


title: 23033_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86760.gif


title: TRT_32_EB


title: 10656_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86700.gif


title: CP-CML_142

description: Sample 142


title: CP-CML_139

description: Sample 139


title: CP-CML_151

description: Sample 151


title: CP-CML_138

description: Sample 138


title: TRT_10_JH


title: TRT_12_CD


title: CP-CML_136

description: Sample 136


title: CP-CML_131

description: Sample 131


title: CP-CML_132

description: Sample 132


title: CP-CML_133

description: Sample 133


title: CP-CML_137

description: Sample 137


title: CP-CML_135

description: Sample 135


title: 16032_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86683.gif


title: 12406_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86797.gif


title: 13082_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86711.gif


title: 16365_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86805.gif


title: CP-CML_127

description: Sample 127


title: CP-CML_128

description: Sample 128


title: CP-CML_134

description: Sample 134


title: CP-CML_126

description: Sample 126


title: CP-CML_129

description: Sample 129


title: CP-CML_124

description: Sample 124


title: CP-CML_125

description: Sample 125


title: CP-CML_123

description: Sample 123


title: 15421_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86812.gif


title: CP-CML_122

description: Sample 122


title: 19382_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86723.gif


title: CP-CML_130

description: Sample 130


title: CP-CML_121

description: Sample 121


title: 15417_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86876.gif


title: 15421_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86813.gif


title: 23033_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86758.gif


title: 22482_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86698.gif


title: 14887_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86695.gif


title: CP-CML_117

description: Sample 117


title: CP-CML_119

description: Sample 119


title: CP-CML_118

description: Sample 118


title: shGFP_4th_day_LP6

city: Boston

first: Stefano

last: Sioletic

state: Ma

address: 450 Brookline Ave, Boston,

department: Medical Oncology

institute: Dana Farber Cancer Institute

hyb_protocol: Terminal Labeling and Hybridization (cat # 702880) onto Affymetrix Human Gene 1.0ST arrays.

scan_protocol: The arrays were washed and stained on Fluidics Stations 450 using the Affymetrix Hybe/Wash/Stain (cat # 900720). The arrays were scanned on GeneChip Scanner 3000 7G.

data_processing: Exon array data were processed using Affymetrix Expression Console software. Both exon-level and gene-level expression values were processed with Affymetrix core annotation by Expression Console for the downstream analyses. Gene-level expression was RMA normalized.

source_name: shGFP treated day 4 LP6 cell line

label_protocol: The ambion WT expression Kit (cat # 4425209) followed by labeling with Affymetrix GeneChip WT

growth_protocol: Cell lines were maintained in DMEM/F-12 supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol: RNA extraction and RT-PCR.  Total RNA was extracted using Trizol reagent (Invitrogen,Carlsbad, CA) according to the manufacturer's instructions. 1000 ng of total RNA was used for cDNA synthesis with the High Capacity cDNA Reverse Transcription kit (Applied Biosystems).

treatment_protocol: Lentivirus was produced by transient cotransfection of 293T cells using FUGENE, Δ 8.9 packaging plasmid and VSVg expression plasmid.  Media containing lentivirus was harvested 24 and 48 hours after transfection. Cells infected with lentivirus were selected with 2 ug/ml of puromycin to achieve stable knockdown.

value: dedifferentiated liposarcoma (DDLPS)

tag: jun status

value: Jun amplified LPS


title: CP-CML_120

description: Sample 120


title: shNT_4th_day_LP6

source_name: shNT treated day 4 LP6 cell line


title: shJun9_4th_day_LP6

source_name: shJun9 treated day 4 LP6 cell line


title: CP-CML_116

description: Sample 116


title: CP-CML_115

description: Sample 115


title: CP-CML_112

description: Sample 112


title: CP-CML_114

description: Sample 114


title: CP-CML_113

description: Sample 113


title: CP-CML_111

description: Sample 111


title: 13228_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86810.gif

value: pbmc isolated from bcg vaccinated_control


title: shJun12_4th_day_LP6

source_name: shJun12 treated day 4 LP6 cell line


title: CP-CML_108

description: Sample 108


title: CP-CML_106

description: Sample 106


title: CP-CML_110

description: Sample 110


title: CP-CML_107

description: Sample 107


title: shJun12_7th_day_141

source_name: shJun12 treated day 7 141 cell line

value: Non Jun amplified LPS


title: 22168_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86658.gif

value: 4 hrs unstimulated


title: shNT_7th_day_141

source_name: shNT treated day 7 141 cell line


title: shJun9_7th_day_141

source_name: shJun9 treated day 7 141 cell line


title: CP-CML_109

description: Sample 109

source_name: chronic phase chronic myeloid leukemia (CP-CML)


title: 12748_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86800.gif


title: 14528_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86737.gif


title: shJun12_4th_day_141

source_name: shJun12 treated day 4 141 cell line


title: 10656_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86702.gif

value: 12 hrs unstimulated


title: CP-CML_102

description: Sample 102


title: CP-CML_105

description: Sample 105


title: CP-CML_103

description: Sample 103

value: Low


title: CP-CML_104

description: Sample 104


title: shJun9_4th_day_141

source_name: shJun9 treated day 4 141 cell line


title: shGFP_7th_day_141

source_name: shGFP treated day 7 141 cell line


title: CP-CML_101

description: Sample 101


title: CP-CML_100

description: Sample 100


title: 19002_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86755.gif


title: CP-CML_99

description: Sample 99


title: shGFP_4th_day_141

source_name: shGFP treated day 4 141 cell line


title: CP-CML_96

description: Sample 96


title: 19508_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86667.gif

source_name: PBMC isolated from BCG vaccinated_control. Stimulation time and condition: 4 hrs unstimulated.


title: 20426_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86678.gif


title: 16365_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86806.gif

source_name: PBMC isolated from BCG vaccinated_case. Stimulation time and condition: 12 hrs unstimulated.


title: CP-CML_97

description: Sample 97


title: CP-CML_98

description: Sample 98


title: shNT_4th_day_141

source_name: shNT treated day 4 141 cell line


title: 19933_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86768.gif

source_name: PBMC isolated from BCG vaccinated_case. Stimulation time and condition: 4 hrs BCG stimulated.


title: shJun9_7th_day_LP6

source_name: shJun9 treated day 7 LP6 cell line


title: CP-CML_95

description: Sample 95


title: CP-CML_93

description: Sample 93


title: CP-CML_94

description: Sample 94


title: shNT_7th_day_LP6

source_name: shNT treated day 7 LP6 cell line


title: shJun12_7th_day_LP6

source_name: shJun12 treated day 7 LP6 cell line


title: CP-CML_89

description: Sample 89


title: CP-CML_87

description: Sample 87


title: CP-CML_92

description: Sample 92


title: shGFP_7th_day_LP6

source_name: shGFP treated day 7 LP6 cell line


title: 22208_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86776.gif

source_name: PBMC isolated from BCG vaccinated_control. Stimulation time and condition: 12 hrs BCG stimulated.

value: 12 hrs BCG stimulated


title: CP-CML_90

description: Sample 90

value: Chronic phase


title: CP-CML_86

description: Sample 86

value: male


title: 13468_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86716.gif


title: CP-CML_83

description: Sample 83


title: CP-CML_85

description: Sample 85

value: Int


title: 20691_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86830.gif

source_name: PBMC isolated from BCG vaccinated_control. Stimulation time and condition: 12 hrs unstimulated.


title: CP-CML_81

description: Sample 81

value: peripheral blood


title: CP-CML_82

description: Sample 82

value: Leucocyte


title: CP-CML_84

description: Sample 84


title: 20691_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86829.gif

source_name: PBMC isolated from BCG vaccinated_control. Stimulation time and condition: 4 hrs BCG stimulated.


title: 21257_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86778.gif


title: 16032_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86690.gif

value: pbmc isolated from bcg vaccinated_case


title: CP-CML_79

description: Sample 79


title: CP-CML_88

description: Sample 88


title: CP-CML_91

description: Sample 91


title: CP-CML_76

description: Sample 76


title: IPF patient P97

city: Reno

first: Tong

last: Zhou

state: NV

address: 1664 N Virginia St

institute: University of Nevada School of Medicine

description: Gene expression data from PBMC total RNA from IPF patient.

hyb_protocol: Samples were hybridized with Affymetrix GeneChip Human Exon 1.0 ST Arrays per manufacturer’s instructions.

scan_protocol: Array scanning was performed according to the manufacturer's instruction by the University of Chicago Functional Genomics Facility.

data_processing: The transcript expression data were summarized by RMA using the Affymetrix Power Tools v.1.12.0 and were later corrected for batch effect using the R COMBAT script.

source_name: IPF patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

tag: tissue peripheral blood mononuclear cells

value: Male

tag: ethnicity

tag: diagnosis

value: Idiopathic pulmonary fibrosis (IPF)

tag: forced vital capacity (fvc) percent predicted

tag: diffusing capacity of the lung for carbon monoxide (dlco) percent predicted


title: IPF patient P98

tag: gender

value: Female


title: 12748_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86803.gif

source_name: PBMC isolated from BCG vaccinated_case. Stimulation time and condition: 12 hrs BCG stimulated.

tag: tissue


title: CP-CML_78

description: Sample 78

source_name: chronic phase chronic myeloid leukemia (CP-CML)

tag: disease state

value: female

tag: imatinib dose (mg/day)

tag: sokal score

tag: molecular response

tag: cell type


title: CP-CML_77

description: Sample 77


title: 22208_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86835.gif

tag: stimulation time and condition


title: 23033_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86759.gif


title: 22208_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86774.gif


title: 23033_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86838.gif

value: 4 hrs BCG stimulated


title: IPF patient P95

value: Caucasian American


title: CP-CML_75

description: Sample 75


title: IPF patient P99


title: IPF patient P82


title: IPF patient P81


title: 20691_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86828.gif

value: pbmc isolated from bcg vaccinated_control


title: CP-CML_80

description: Sample 80


title: CP-CML_71

description: Sample 71

value: High


title: CP-CML_73

description: Sample 73


title: CP-CML_74

description: Sample 74


title: CP-CML_72

description: Sample 72


title: IPF patient P80


title: IPF patient P94


title: CP-CML_70

description: Sample 70


title: CP-CML_69

description: Sample 69


title: 15651_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86772.gif

value: 12 hrs unstimulated


title: CP-CML_65

description: Sample 65


title: IPF patient P79


title: CP-CML_66

description: Sample 66


title: CP-CML_64

description: Sample 64


title: CP-CML_67

description: Sample 67


title: IPF patient P78


title: IPF patient P74


title: CP-CML_68

description: Sample 68


title: CP-CML_62

description: Sample 62

value: Low


title: IPF patient P76


title: 12776_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86799.gif


title: CP-CML_63

description: Sample 63


title: 20426_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86681.gif

value: 12 hrs BCG stimulated


title: CP-CML_59

description: Sample 59

value: Chronic phase


title: CP-CML_60

description: Sample 60


title: IPF patient P73

value: African American


title: CP-CML_61

description: Sample 61

value: Int


title: 15203_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86687.gif


title: CP-CML_57

description: Sample 57

value: peripheral blood


title: 14887_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86694.gif

value: 4 hrs unstimulated


title: 22168_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86661.gif

value: pbmc isolated from bcg vaccinated_case


title: IPF patient P72

value: Male


title: 16890_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86785.gif


title: IPF patient P66

value: Idiopathic pulmonary fibrosis (IPF)


title: IPF patient P69


title: CP-CML_55

description: Sample 55

value: male

value: Leucocyte


title: CP-CML_54

description: Sample 54

value: female


title: CP-CML_56

description: Sample 56


title: IPF patient P65

value: Caucasian American


title: CP-CML_53

description: Sample 53


title: CP-CML_58

description: Sample 58


title: 14528_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86739.gif

value: pbmc isolated from bcg vaccinated_control


title: 13301_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86706.gif


title: CP-CML_51

description: Sample 51

value: High


title: IPF patient P63


title: IPF patient P64


title: CP-CML_48

description: Sample 48


title: 16015_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86744.gif

value: 4 hrs BCG stimulated


title: CP-CML_47

description: Sample 47


title: CP-CML_49

description: Sample 49

value: Low


title: CP-CML_52

description: Sample 52


title: CP-CML_46

description: Sample 46


title: 13301_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86705.gif


title: IPF patient P57

description: Gene expression data from PBMC total RNA from IPF patient.


title: CP-CML_50

description: Sample 50


title: 14116_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86666.gif

value: 12 hrs BCG stimulated


title: IPF patient P62


title: 18224_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86731.gif


title: CP-CML_44

description: Sample 44

value: Chronic phase


title: CP-CML_45

description: Sample 45


title: CP-CML_43

description: Sample 43


title: CP-CML_42

description: Sample 42


title: IPF patient P58


title: CP-CML_41

description: Sample 41


title: IPF patient P51


title: 21257_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86779.gif

value: 12 hrs unstimulated


title: CP-CML_40

description: Sample 40


title: 14106_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86721.gif


title: 14106_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86728.gif


title: 21457_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86749.gif


title: CP-CML_39

description: Sample 39


title: IPF patient P54


title: CP-CML_36

description: Sample 36


title: CP-CML_37

description: Sample 37

value: Int


title: CP-CML_34

description: Sample 34

value: peripheral blood


title: CP-CML_35

description: Sample 35


title: CP-CML_33

description: Sample 33


title: IPF patient P46


title: CP-CML_32

description: Sample 32


title: 15193_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86826.gif


title: IPF patient P45


title: CP-CML_38

description: Sample 38


title: 13082_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86713.gif


title: IPF patient P47

value: African American


title: IPF patient P49

value: Hispanic American


title: 17359_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86781.gif

source_name: PBMC isolated from BCG vaccinated_case. Stimulation time and condition: 4 hrs unstimulated.

value: pbmc isolated from bcg vaccinated_case

value: 4 hrs unstimulated


title: IPF patient P48

value: Male

value: Idiopathic pulmonary fibrosis (IPF)


title: 14528_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86740.gif


title: IPF patient P43

value: Female


title: 15203_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86685.gif


title: 17359_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86832.gif


title: IPF patient P44

value: Caucasian American


title: 17448_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86819.gif

value: pbmc isolated from bcg vaccinated_control


title: CP-CML_29

description: Sample 29

value: male

value: Leucocyte


title: IPF patient P41


title: 17417_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86822.gif


title: PFC 2012-03_control

city: Singapore

first: Wanwen

last: Lan

address: 9 Hospital Drive SON Blk C #02-03

country: Singapore

institute: Singapore Eye Research Institute

description: PFC Neg, PFC 2012-03 Neg

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 human GE 8x60K microarray  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent High Resolution Microarray scanner using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: PFCs_non-specific oligonucleotides for 24h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultured primary pterygium fibroblast cells are cultured in DMEM/F-12 with 10% FBS

extract_protocol: RNA was extracted using the RNAeasy mini kit (Qiagen) according to manufacturer's protocol

treatment_protocol: 100nM miR-215 mimic (Thermo Scientific) or random control oligonucleotides are added to cultured fibroblast cells for 24 hours

tag: cell culture id

value: Pterygium fibroblast cells (PFCs)

tag: treated with

value: Random oligonucleotides

tag: treatment time


title: CP-CML_31

description: Sample 31

value: Chronic phase

value: Low


title: CP-CML_30

description: Sample 30


title: PFC No.2_control

description: PFC Neg, PFC No 2 Neg

value: PFC no.2


title: CP-CML_28

description: Sample 28

value: Int

value: peripheral blood


title: PFC 2012-02_control

description: PFC Neg, PFC 2012-02 Neg


title: IPF patient P39

tag: age


title: IPF patient P40

tag: tissue peripheral blood mononuclear cells


title: CP-CML_26

description: Sample 26

value: female

value: High


title: CP-CML_27

description: Sample 27


title: IPF patient P38

tag: ethnicity


title: CP-CML_23

description: Sample 23


title: PFC No.2_miR215

description: PFC 24h, PFC No 2 24hr

source_name: PFCs_miR-215 for 24h

value: 100nM has-miR-215 mimic


title: 14887_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86696.gif

value: 12 hrs unstimulated


title: CP-CML_22

description: Sample 22


title: CP-CML_25

description: Sample 25


title: IPF patient P35

value: Male

value: Hispanic American

tag: diagnosis

value: Idiopathic pulmonary fibrosis (IPF)


title: CP-CML_24

description: Sample 24


title: 13229_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86719.gif

value: pbmc isolated from bcg vaccinated_control

value: 4 hrs BCG stimulated


title: RPI_24h_2 (miRNA)

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were log2 transformed and normalized using RSN normalization from lumi package in R.

source_name: TPC1 cell line, RPI-1 treated

label_protocol: Biotinylated cRNA were prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays.

extract_protocol: Total RNA with miRNA fraction was extracted from cell lines with miRNeasy mini kit (Qiagen) according to manufacturer's instructions.

tag: cell line

value: papillary thyroid carcinoma-derived cell line

tag: treatment

value: RTK inhibitor RPI-1


title: 16015_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86746.gif

value: pbmc isolated from bcg vaccinated_case

value: 12 hrs BCG stimulated


title: 17771_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86672.gif


title: 14116_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86664.gif


title: CP-CML_21

description: Sample 21

value: Chronic phase

tag: gender

value: Leucocyte


title: PFC 2012-03_miR215

description: PFC 24h, PFC 2012-03 24hr

value: Pterygium fibroblast cells (PFCs)


title: PFC 2012-01_control

description: PFC Neg, PFC 2012-01 Neg

value: Random oligonucleotides


title: PFC 2012-01_miR215

description: PFC 24h, PFC 2012-01 24hr


title: 12406_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86794.gif

tag: tissue

value: 4 hrs unstimulated


title: IPF patient P34

description: Gene expression data from PBMC total RNA from IPF patient.

value: Caucasian American

tag: forced vital capacity (fvc) percent predicted

tag: diffusing capacity of the lung for carbon monoxide (dlco) percent predicted


title: IPF patient P37


title: IPF patient P108


title: IPF patient P36


title: RPI_24h_1 (miRNA)


title: DMSO_24h_2 (miRNA)

source_name: TPC1 cell line, control

value: DMSO control


title: CP-CML_19

description: Sample 19

tag: disease state

value: male

tag: imatinib dose (mg/day)

tag: sokal score

value: High

value: peripheral blood


title: Thyrocyte+RET-PTC1

source_name: Thyrocytes + RET-PTC1

extract_protocol: Total RNA including miRNA fraction was extracted from cells with miRNeasy mini kit (Qiagen) according to manufacturer's instructions.

tag: cell type

value: thyrocytes

tag: ret/ptc1 oncogene expression

value: yes


title: DMSO_24h_1 (miRNA)


title: CP-CML_18

description: Sample 18

value: female

value: Low

tag: molecular response


title: 18195_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86733.gif

tag: stimulation time and condition


title: Primary Thyrocyte

source_name: Primary thyrocytes

value: no


title: CP-CML_17

description: Sample 17

value: Int


title: CP-CML_20

description: Sample 20


title: IPF patient P105

tag: age

value: Male

value: Idiopathic pulmonary fibrosis (IPF)


title: IPF patient P107

tag: tissue peripheral blood mononuclear cells


title: 8_SHAM 8

city: Glostrup

first: Ajoy

middle: Kumar

last: Samraj

address: NDR Ringvej 69

department: Department of clinical experimental medicine

country: Denmark

institute: Glostrup Hospital

description: Sacrifice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed using expression console software version 1.1.2 using default analysis settings and RMA as normalization method.

organism: Rattus norvegicus

source_name: SHAM operated

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

extract_protocol: Total RNA isolation kit (macherey-nagel)

tag: sample group

value: SHAM operated

value: Cerebral artery


title: CP-CML_16

description: Sample 16

value: Chronic phase

value: Leucocyte


title: Healthy control C64

description: Gene expression data from PBMC total RNA from healthy control.

source_name: Healthy control

tag: ethnicity

value: Caucasian American

tag: diagnosis

value: Healthy control


title: IPF patient P100


title: CP-CML_14

description: Sample 14

value: male


title: PFC 2012-02_miR215

description: PFC 24h, PFC 2012-02 24hr

tag: cell culture id

value: Pterygium fibroblast cells (PFCs)

tag: treated with

value: 100nM has-miR-215 mimic

tag: treatment time


title: Healthy control C63

tag: gender

tag: forced vital capacity (fvc) percent predicted


title: 7_SHAM 7

description: Sacrifice

tag: tissue


title: CP-CML_15

description: Sample 15

tag: disease state

tag: imatinib dose (mg/day)

value: peripheral blood


title: IPF patient P101

tag: diffusing capacity of the lung for carbon monoxide (dlco) percent predicted


title: op346_CNT (exon level)

first: Michelle

middle: GK

last: Tan

address: 20 College Road

department: Clinical Translational Research

institute: Singapore General Hospital

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Human Exon 1.0 ST arrays at 45°C for 16 hours, then washed and stained in a Fluidics Station 450.

scan_protocol: GeneChips were scanned by a GCS3000 Scanner (Affymetrix).

data_processing:
CEL files were generated using Affymetrix GCOS software and exported to the Partek Genomics Suite V6.3. After GC content and Robust Multi-Chip analysis (RMA) background corrections, data across different batches were subject to quantile normalization.

Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
Genome build: hg18

source_name: neocortex of control patient

label_protocol: Samples were fragmented and end-labeled using the WT Sense Target Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated using Trizol reagents. Samples were first processed for rRNA depletion with the RiobMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen). cDNA synthesis and amplification were then performed using the GeneChip Whole Transcript (WT) cDNA Synthesis and Amplification Kit (Affymetrix).

tag: Sex

tag: pmi

tag: disease status

value: control

value: neocortex


title: IPF patient P104

tag: age


title: 1_SAH 1

description: Sacrifice

source_name: SAH operated

value: 6 hrs of subarachnoid haemorrhage (SAH)


title: CP-CML_11

description: Sample 11

tag: sokal score

value: High

tag: molecular response

tag: cell type


title: IPF patient P102

tag: tissue peripheral blood mononuclear cells

tag: ethnicity

tag: diagnosis


title: Healthy control C62


title: 5_SAH 5

description: Sacrifice

tag: sample group


title: op107_AD (exon level)

source_name: neocortex of AD patient

value: female

value: Alzheimer's disease (AD)


title: op1112_CNT (exon level)


title: 4_SAH 4

description: Sacrifice

tag: gender


title: 6_SHAM 6

description: Sacrifice


title: CP-CML_10

description: Sample 10


title: CP-CML_13

description: Sample 13

value: Low


title: CP-CML_9

description: Sample 9


title: Healthy control C61

value: Male

tag: forced vital capacity (fvc) percent predicted


title: op450_AD (exon level)

tag: tissue


title: Healthy control C60


title: Healthy control C59


title: CP-CML_12

description: Sample 12

tag: disease state


title: CP-CML_8

description: Sample 8

tag: imatinib dose (mg/day)


title: CP-CML_7

description: Sample 7


title: Healthy control C58

tag: diffusing capacity of the lung for carbon monoxide (dlco) percent predicted


title: op1132_CNT (exon level)

tag: Sex


title: Ssn6_Nmyc_AHY498_Array123 Normalized Log2 Ratio

city: San Francisco

first: Aaron

last: Hernday

state: Ca

institute: UC San Francisco

hyb_protocol: Hybridization followed the Agilent protocol

scan_protocol: Arrays were scanned with an Axon 4000B scanner

data_processing: Data was extracted and lowess normalized using Agilent ChIP analytics v1.3 software.

organism: Candida albicans

label_protocol: Aminoallyl dUTP was incorporated during linear amplification of the genomic DNA using exo- Klenow fragment

extract_protocol: Crosslinked cells were lysed by mechanical disruption. Genomic DNA was sheared by sonication then immunoprecipitated with monoclonal or polyclonal antibodies.

treatment_protocol: formaldehyde crosslinking

tag: chip antibody

value: No antibody


title: Untagged-myc_Opaque_Array136_Normalized Log2 Ratio

value: myc

tag: phenotype

value: opaque


title: CP-CML_5

description: Sample 5

value: Chronic phase

value: Leucocyte


title: op133_AD (exon level)

tag: age

value: male

tag: pmi

tag: disease status


title: op340_AD (exon level)


title: Ssn6-664_AHY343_Array227_Normalized Log2 Ratio


title: Healthy control C56

value: Caucasian American

value: Healthy control


title: Healthy control C55


title: Healthy control C54


title: Ssn6-664_AHY347a2_Array179_Normalized Log2 Ratio


title: Ssn6-664_AHY136a1_Array177_Normalized Log2 Ratio


title: CP-CML_4

description: Sample 4

tag: sokal score

tag: molecular response

value: peripheral blood

tag: cell type


title: Ssn6-664_AHY135a1_Array175_Normalized Log2 Ratio

value: white


title: op9_CNT (exon level)

value: control

value: neocortex


title: CP-CML_3

description: Sample 3


title: Healthy control C53

tag: tissue peripheral blood mononuclear cells

tag: ethnicity

value: African American

tag: diagnosis


title: op1146_CNT (exon level)


title: op91_AD (exon level)


title: CP-CML_2

description: Sample 2

tag: gender

value: Int


title: Healthy control C52

tag: forced vital capacity (fvc) percent predicted


title: op223_CNT (exon level)

tag: tissue


title: Healthy control C57


title: Tcacao_endophyteinoculated_leaf_rep3_GBU9

city: Panama

first: Luis

last: Mejia

address: Roosvelt Ave. Tupper Building – 401

department: Smithsonian Tropical Research Institute

country: Panama

institute: Smithsonian Institution

hyb_protocol: Hybridizations were performed by the Pennsylvania State University Core Genomics Faciliy, according to published facility protocols (http://www.huck.psu.edu/facilities/genomics-up/protocols/nimblegen-protocols).

scan_protocol: Arrays were scanned with an Axon GenePix 4000B scanner.

data_processing: Data was background corrected and normalized using the RMA algorithm available in the Limma package of the Bioconductor software for bioinformatics Gentleman et al. Genome Biology 5(10):R80), Smyth 2005, in Bioinformatics and Computational Biology Solutions using R and Bioconductor 397-420,

organism: Theobroma cacao

source_name: Theobroma cacao leaf inoculated with fungal endophyte Colletotrichum tropicale strain 5103

label_protocol: One µg of total RNA was amplified using mRNA amplification kit (Amino Allyl MessageAmp II™, Ambion, Austin, TX) prior to labeling and hybridization. aRNA was dye coupled with Cy3 or Cy5 (GE Health Care #RPN5661) and subsequently purified according to manufacturer’s instructions.

growth_protocol: Theobroma cacao seedlings used in this experiment were grown in Percival growth chambers (model I35LL, 115 volts, 1/4 Hp, series: 8503122.16, Percival Scientific, Inc., Perry IA) with 12/12 h light/dark photoperiod and temperatures of 30ºC and 26ºC respectively.

extract_protocol: Total RNA was extracted as in Verica et al. Plant Cell Rep. 23(6):404)

treatment_protocol: Seedlings were inoculated one time by spraying conidia (asexual spores) suspended in water (2X10^6 spore/ml) of endhopytic fungus Colletitrichum tropicale as in Mejia et al. 46(1):4) to treated seedlings. Leaves from inoculated and un-inoculated seedlings were harvested 3 days post inoculation (dpi) and placed in RNA stabilizing solution RNAlater until RNA was extracted.

tag: genotype

value: leaf

tag: treatment


title: CP-CML_1

description: Sample 1

tag: disease state

tag: imatinib dose (mg/day)


title: Healthy control C45

tag: diffusing capacity of the lung for carbon monoxide (dlco) percent predicted


title: Ssn6-1004_AHY347a2_Array180_Normalized Log2 Ratio

tag: chip antibody


title: Ssn6-664_AHY135_Array226_Normalized Log2 Ratio

tag: phenotype


title: HZAU_WH_M_huakuii_Free-living_MH7653R1

city: Wuhan

first: Youguo

last: Li

state: Hebei

address: No.1,Shizishan Street · Hongshan District

department: College of Life Science and Technology

institute: Huazhong Agricultural University

description: This sample is of free-living M. huakuii 7653R. It is the first of three controls biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, (Roche NimbleGen, Inc.).

organism: Mesorhizobium huakuii 7653R

source_name: M. huakuii 7653R free-living cells

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
M. huakuii 7653R was grown to mid-log phase (O.D.600nm 1-2)at 28°C in TY medium(Beringer, J.E.J Gen Microbiol, 1974. 84(1): p. 188-98)
A. sinicus seeds were sterilized, germinated, planted, and inoculated with M. huakuii 7653R strains(Chen, D.S.et al.Plant Cell Rep, 2007. 26(8): p. 1421-30.)At 32 days postinoculation, the nodules of plants were harvested.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA) and purified by column NucleoSpin® RNA clean-up kit（Macherey-Nagel,Germany）RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.
To isolate bacteroids RNA, total nodules RNA passed though MICROBEnrich™ kit (Ambion) according to the manufacturer's instruction.

tag: developmental stage

value: plate cultures


title: Ssn6-1004_AHY136a1_Array178_Normalized Log2 Ratio


title: op80_AD (exon level)

tag: age

tag: Sex

value: female

tag: pmi

tag: disease status

value: Alzheimer's disease (AD)


title: Healthy control C38

tag: tissue peripheral blood mononuclear cells

value: Male

tag: ethnicity


title: Healthy control C41

tag: gender

tag: diagnosis


title: Tcacao_endophyteinoculated_leaf_rep1_GBU7

source_name: Theobroma cacao leaf inoculated with fungal endophyte Colletotrichum tropicale strain 5101

tag: tissue


title: Tcacao_endophyteinoculated_leaf_rep2_GBU8

source_name: Theobroma cacao leaf inoculated with fungal endophyte Colletotrichum tropicale strain 5102

tag: genotype


title: Healthy control C44

tag: forced vital capacity (fvc) percent predicted


title: op388_AD (exon level)


title: HZAU_WH_M_huakuii_Free-living_MH7653R3

description: This sample is of free-living M. huakuii 7653R. It is the third of three controls biological replicates used in this experiment, each from separate cultures.


title: op1151_CNT (exon level)


title: HZAU_WH_M_huakuii_Bacteroid_BT7653R1

description: This sample is of M. huakuii 7653R during bacteroid at 32 days postinoculation. It is the first of three experimental groups biological replicates used in this experiment, each from separate plants.

value: bacteroids


title: Healthy control C37


title: HZAU_WH_M_huakuii_Bacteroid_BT7653R3

description: This sample is of M. huakuii 7653R during bacteroid at 32 days postinoculation. It is the third of three experimental groups biological replicates used in this experiment, each from separate plants.


title: Tcacao_Control_leaf_rep4_GBU6R

source_name: Theobroma cacao leaf Control un-inoculated

tag: treatment


title: 27_p5_C

city: Santa Barbara

first: Roxanne

middle: H

last: Croze

address: UCSB: NRI Bldg. 571 Room 5166

department: Molecular, Cellular and Developmental Biology

institute: UCSB

description:
DCL_8
raw data file: 27_p5.txt

hyb_protocol: Probe fragmentation and hybridization was carried out using the Agilent Gene Expression Hybridization Kit (Part #: 5188-5242) according to the methods of the manufacturer (Quick Amp Labeling Protocol, Version 5.7). Two samples (one labeled with Cy3 and the other with Cy5 were hybidized to each array for 17 hr at 65°C. Arrays were washed for 1 min using Agilent Gene Expression Wash Buffer 1 (Part #: 5188-5325) + 0.005% Triton X-102 at room temperature and for 1 min at 37°C with Agilent Gene Expression Wash Buffer 2 (Part #: 5188-5326) + 0.005% Triton X-102. The washed arrays were then rinsed with acetonitrile for 10 sec and coated with Agilent Stabilization and Drying solution for 30 sec.

scan_protocol: Scanner: Bio-Rad VersArray™ ChipReader 3mm System.  Median Raw Spot intensities (Threshold = 5 to 6535) were determined using  VersArray™ Analyzer 4.5. LOWESS Net Intensity Spot Intensity was calculated using Global Median Background Subtraction (global background from negative control cells, zero order polynomial approximation) and the uncorrected net intensity values were normalized using local regression cross-channel normalization of net intensity values (span = 10%, sub-sampling = 5, single pass). Raw data files contain the raw intensity values, the background values and the LOWESS normalixed net intensity values.

data_processing: The Lowess normalized raw data were further background corrected by subtraction of the minimum value of the Agilent negative controls (3xSLv1) to obtain the net intensity. Any values less than one standard deviation of the negative control probes were set to a value equal to the standard deviation of the negative controls for that sample. For the 200 unique probes with 10 replicates each, the average of the replicates were determined.

source_name: hESC-RPE Enrichment_control

label_protocol: All probe labeling was carried out using the Agilent Low Input Quick Amp Labeling Kit (Part #: 5190-2306, Version 5.7) according to the methods of the manufacturer using 250 ng of total RNA with the exception that spike-in controls were not used.

growth_protocol: hESC-RPE were generated from a spontaneous differentiation protocol using H9 hESC. After enrichment of hESC-RPE, cells either treated with H2O as a control, or Y-27632 and were passaged every five days. Control and Y-27632 treated samples were collected from passage 5 hESC-RPE two days after plating.

extract_protocol: Total RNA was extracted using QIAzol and the Qiagen miRNeasy Mini Kit following manufacturer's instructions

treatment_protocol: 10µM Y-27632 or an equal volume of H2O was added to cells throughout passaging. Media was changed every other day, with new additions of treatments.

tag: cell type

value: Human embryonic stem cell derived retinal pigmented epithelial cells (hESC-RPE)

tag: enrichment id

value: hESC-RPE Enrichment #27

tag: seeding density

tag: passage number

tag: culture time

value: day 2

tag: plate coating

value: Matrigel

tag: medium

tag: cultureware

value: 6 well plate

tag: treated with

value: equal volume of water as a control


title: HZAU_WH_M_huakuii_Bacteroid_BT7653R2

description: This sample is of M. huakuii 7653R during bacteroid at 32 days postinoculation. It is the second of three experimental groups biological replicates used in this experiment, each from separate plants.

tag: developmental stage


title: Healthy control C36

tag: tissue peripheral blood mononuclear cells

tag: age

tag: ethnicity

value: Caucasian American

value: Healthy control

tag: diffusing capacity of the lung for carbon monoxide (dlco) percent predicted


title: Tcacao_Control_leaf_rep2_GBU5

tag: genotype

tag: tissue

value: control


title: 26_p5_C_

description:
DCL_6
raw data file: 26_p5.txt

value: hESC-RPE Enrichment #26


title: Healthy control C35

tag: gender

value: Female

tag: diagnosis

tag: forced vital capacity (fvc) percent predicted


title: Tcacao_Control_leaf_rep1_GBU4

value: leaf

tag: treatment


title: 27_p5_Y27

description:
DCL_7
raw data file: 27_p5.txt

source_name: hESC-RPE Enrichment_Y27

tag: cell type

tag: enrichment id

tag: seeding density

tag: passage number


title: op417_AD (exon level)

tag: Sex

value: male

tag: pmi

tag: disease status

value: neocortex


title: Healthy control C33

tag: tissue peripheral blood mononuclear cells


title: Tcacao_Control_leaf_rep3_GBU6G


title: Healthy control C24

tag: age


title: Healthy control C21

tag: ethnicity


title: Healthy control C30

tag: diffusing capacity of the lung for carbon monoxide (dlco) percent predicted


title: 26_p5_Y27

description:
DCL_5
raw data file: 26_p5.txt

tag: culture time

tag: plate coating

tag: medium

tag: cultureware

tag: treated with


title: 21_p5_Y27

description:
DCL_3
raw data file: 21_p5.txt

value: hESC-RPE Enrichment #21


title: 21_p5_C

description:
DCL_4
raw data file: 21_p5.txt


title: Healthy control C23

tag: gender

tag: diagnosis

tag: forced vital capacity (fvc) percent predicted


title: HZAU_WH_M_huakuii_Free-living_MH7653R2

description: This sample is of free-living M. huakuii 7653R. It is the second of three controls biological replicates used in this experiment, each from separate cultures.

tag: developmental stage

value: plate cultures


title: estrogen receptor negative BC sample 41

city: Torrevieja

first: Ramon

middle: G

last: Manzano

state: Alicante

address: Partida la Loma s/n

department: Unidad de Consejo Genetico, Plataforma de Oncologia

country: Spain

institute: Hospital Quiron Torrevieja

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: TEDECAR24

hyb_protocol: Hybridization was done with the Agilent Hybridisation kit, according to the manufacturer´s instructions in a hybridization oven for 17 hours at 65º C.

scan_protocol: Agilent whole human genome 4x44K microarrays were scanned with a G2505B scanner from Agilent Technologies and data were extracted with the Agilent Feature Extraction software (version 9.5) according to standard Agilent protocols

data_processing: Cy3 data from feature extraction files (both 2 color arrays and 1 color arrays) were background corrected (normexp), quantile normalized and log2 transformed using the limma package (Bioconductor project) in the R statistical environment (version 2.10.1).

source_name: Primary breast tumor biopsy after surgery

label_protocol: Labelling was performed with Agilent QuickAmp labelling kit according to the manufacturer´s instructions

extract_protocol: Total RNA was extracted with Rneasy columns (QIAGEN)

tag: erbb2 status (by ihc)

tag: tumor grade

tag: tumor diameter

source_name: Stratagene Human Universal RNA

tag: reference composition

value: 10 human tumor cell lines


title: 20_p5_Y27

description:
DCL_1
raw data file: 20_p5.txt

tag: cell type

value: Human embryonic stem cell derived retinal pigmented epithelial cells (hESC-RPE)

tag: enrichment id

value: hESC-RPE Enrichment #20

tag: seeding density

tag: passage number


title: Metastasis

city: Fukuoka

first: Takahiro

last: Fujinaga

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Faculty of Dental Science

country: Japan

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8×60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: metastatic lesion

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: age

tag: tissue

value: cervical lymph node


title: PBMC_SNG001_visit3_rep27

city: Southampton

first: Phillip

last: Monk

address: Tremona Road

department: Southampton General Hospital

institute: Synairgen Research Ltd

hyb_protocol: The 8 pack format mastermixes were followed (Two color microarray-based gene expression analysis: Low input quick amp labeling (v 6.5, May 2010))

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C US84300231 using protocol GE2_107_Sep09.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: Peripheral blood mononuclear cells, SNG001

label_protocol: Followed the protocol described in Two color microarray-based gene expression analysis: Low input quick amp labeling (v 6.5, May 2010) using 200ng of total RNA

extract_protocol: Total RNA extracted using Qiagen PAXgene RNA extraction kit following manufacturer's instructions

tag: agent

tag: timepoint

value: Day 4

value: Peripheral blood mononuclear cells

source_name: Stratagene Universal Human Reference RNA

tag: reference


title: PBMC_SNG001_visit4_rep27

value: Day 7

value: Stratagene Universal Human Reference RNA


title: estrogen receptor negative BC sample 40

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: TEDECAR21

tag: gender

value: Positive


title: Healthy control C20

tag: tissue peripheral blood mononuclear cells

value: Male

tag: ethnicity

value: Caucasian American

tag: diagnosis

value: Healthy control

tag: diffusing capacity of the lung for carbon monoxide (dlco) percent predicted


title: 20_p5_C

description:
DCL_2
raw data file: 20_p5.txt

tag: culture time

value: day 2

tag: plate coating

value: Matrigel

tag: medium

tag: cultureware

value: 6 well plate

tag: treated with

value: equal volume of water as a control


title: Healthy control C18

value: Female

value: African American

tag: forced vital capacity (fvc) percent predicted


title: Primary Tumor

source_name: primary lesion

value: male

value: oral squamous cell


title: Healthy control C19

source_name: Healthy control


title: estrogen receptor negative BC sample 39

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedecaR19d

tag: erbb2 status (by ihc)

tag: tumor grade

tag: tumor diameter

tag: reference composition

value: 10 human tumor cell lines


title: PBMC_SNG001_visit2_rep27

tag: agent

tag: timepoint

value: Day 1

tag: cell type


title: estrogen receptor negative BC sample 38

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedecaR17d

tag: gender

value: Negative

tag: age


title: PBMC_SNG001_visit3_rep26

value: Day 4

value: Peripheral blood mononuclear cells

tag: reference


title: CP-CML_6

first: Marc

last: Delord

institute: Centre hospitalier de Versailles

description: Sample 6

hyb_protocol: Array were prepared for hybridization in the capillary flow-through chamber. Samples were applied to BeadChips and incubated overnight. After hybridization, allelic specificity was conferred by enzymatic base extension. Products were subsequently fluorescently stained.

scan_protocol: Illumina  iScan System

data_processing: GenomeStudio Genotyping (GT) Module

source_name: chronic phase chronic myeloid leukemia (CP-CML)

label_protocol: Cy3 and Cy5; according to standard protocol

extract_protocol: DNA sample were isothermally amplified. Amplified product were then fragmented by a controlled enzymatic process.

tag: disease state

value: Chronic phase

value: female

tag: imatinib dose (mg/day)

tag: sokal score

value: Int

tag: molecular response

tag: tissue

value: peripheral blood

value: Leucocyte


title: PBMC_SNG001_visit2_rep26

value: Stratagene Universal Human Reference RNA


title: PBMC_SNG001_visit4_rep24

value: Day 7


title: estrogen receptor negative BC sample 37

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedecaR16

value: Positive


title: PBMC_SNG001_visit4_rep26


title: Healthy control C16

tag: tissue peripheral blood mononuclear cells

value: Female

tag: ethnicity

tag: diagnosis

value: Healthy control

tag: diffusing capacity of the lung for carbon monoxide (dlco) percent predicted


title: estrogen receptor negative BC sample 35

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: TEDECAR14

tag: erbb2 status (by ihc)

tag: tumor grade

tag: tumor diameter


title: estrogen receptor negative BC sample 34

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: TEDECAR13

tag: reference composition


title: Healthy control C17

value: Caucasian American

tag: forced vital capacity (fvc) percent predicted


title: estrogen receptor negative BC sample 36

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: TEDECAR15

tag: gender


title: Healthy control C14

tag: age

value: Male


title: estrogen receptor negative BC sample 33

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedecaR9d

value: 10 human tumor cell lines


title: Healthy control C15

value: African American


title: PBMC_SNG001_visit2_rep24

tag: agent

tag: timepoint

value: Day 1

tag: cell type

tag: reference


title: Healthy control C13


title: estrogen receptor negative BC sample 32

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: TEDECAR7


title: Healthy control C11

description: Gene expression data from PBMC total RNA from healthy control.


title: PBMC_SNG001_visit4_rep23


title: PBMC_SNG001_visit3_rep24

value: Day 4


title: estrogen receptor negative BC sample 31

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: TEDECAR6d


title: estrogen receptor negative BC sample 30

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedecaR5


title: IPF patient P31

description: Gene expression data from PBMC total RNA from IPF patient.

source_name: IPF patient

value: Idiopathic pulmonary fibrosis (IPF)


title: PBMC_SNG001_visit2_rep22

value: Peripheral blood mononuclear cells


title: PBMC_SNG001_visit3_rep22


title: PBMC_SNG001_visit2_rep23


title: PBMC_SNG001_visit4_rep21


title: IPF patient P27


title: IPF patient P29


title: PBMC_SNG001_visit3_rep21


title: Healthy control C12


title: IPF patient P28


title: PBMC_SNG001_visit2_rep21


title: IPF patient P22


title: estrogen receptor negative BC sample 28

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedecaR2


title: PBMC_SNG001_visit4_rep20


title: IPF patient P26


title: IPF patient P21


title: estrogen receptor negative BC sample 25

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedecaNS2d


title: estrogen receptor negative BC sample 26

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedecaNS5

value: Negative


title: PBMC_SNG001_visit3_rep20


title: PBMC_SNG001_visit2_rep20


title: estrogen receptor negative BC sample 29

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedecaR3


title: op1044_CNT (exon level)

source_name: neocortex of control patient

tag: Sex

value: male

tag: pmi

tag: disease status

value: control

value: neocortex


title: IPF patient P20

tag: tissue peripheral blood mononuclear cells

tag: ethnicity


title: estrogen receptor negative BC sample 27

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedecaNS7


title: PBMC_SNG001_visit4_rep19

value: Stratagene Universal Human Reference RNA


title: IPF patient P19

tag: diagnosis

tag: diffusing capacity of the lung for carbon monoxide (dlco) percent predicted


title: PBMC_SNG001_visit2_rep19


title: PBMC_SNG001_visit4_rep18

value: Day 7


title: IPF patient P24


title: estrogen receptor negative BC sample 22

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedeca38

tag: erbb2 status (by ihc)

tag: tumor grade


title: estrogen receptor negative BC sample 24

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedeca43

tag: tumor diameter

tag: reference composition


title: estrogen receptor negative BC sample 21

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedeca37

tag: gender


title: estrogen receptor negative BC sample 23

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedeca42

tag: age


title: estrogen receptor negative BC sample 19

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedeca31B


title: PBMC_SNG001_visit3_rep19

tag: agent


title: IPF patient P15

tag: forced vital capacity (fvc) percent predicted


title: IPF patient P11

value: Asian American


title: IPF patient P13

value: Female


title: PBMC_SNG001_visit3_rep18

tag: timepoint

tag: cell type


title: IPF patient P16


title: PBMC_SNG001_visit2_rep18

tag: reference


title: PBMC_SNG001_visit3_rep17


title: IPF patient P10


title: estrogen receptor negative BC sample 15

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedeca18B


title: estrogen receptor negative BC sample 17

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedeca25B


title: estrogen receptor negative BC sample 14

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: TEDECAsamI


title: estrogen receptor negative BC sample 18

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedeca30B


title: PBMC_SNG001_visit4_rep17


title: PBMC_SNG001_visit4_rep16


title: estrogen receptor negative BC sample 16

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedeca24B


title: IPF patient P9


title: IPF patient P8


title: IPF patient P7


title: IPF patient P5


title: estrogen receptor negative BC sample 11

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: TEDECAsamC


title: IPF patient P14

description: Gene expression data from PBMC total RNA from IPF patient.


title: PBMC_SNG001_visit4_rep13


title: PBMC_SNG001_visit2_rep16


title: estrogen receptor negative BC sample 12

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: TEDECAsamD


title: estrogen receptor negative BC sample 13

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: TEDECAsamG


title: estrogen receptor negative BC sample 20

description:
2 color array
Data table reports Cy3 tumor data only.
Sample name: tedeca34


title: PBMC_SNG001_visit2_rep13


title: IPF patient P6


title: IPF patient P4


title: PBMC_SNG001_visit2_rep17


title: IPF patient P3


title: PBMC_SNG001_visit3_rep16


title: estrogen receptor negative BC sample 6

description:
1 color array
Fresh total RNA from surgical specimen
Sample name: sj2

hyb_protocol: Hybridization was done with the Agilent Hybridization kit, according to the manufacturer´s instructions in a hybridization oven for 17 hours at 65Âº C.


title: estrogen receptor negative BC sample 7

description:
1 color array
Fresh total RNA from surgical specimen
Sample name: sampleB


title: Healthy control C10

description: Gene expression data from PBMC total RNA from healthy control.

value: Healthy control


title: PBMC_SNG001_visit2_rep11


title: Healthy control C9

value: Caucasian American


title: estrogen receptor negative BC sample 8

description:
1 color array
Fresh total RNA from surgical specimen
Sample name: sampleE


title: PBMC_SNG001_visit4_rep10


title: IPF patient P1

value: Male


title: estrogen receptor negative BC sample 5

description:
1 color array
Fresh total RNA from surgical specimen
Sample name: sample29B


title: PBMC_SNG001_visit4_rep11


title: PBMC_SNG001_visit2_rep12


title: PBMC_SNG001_visit3_rep12


title: PBMC_SNG001_visit3_rep10


title: estrogen receptor negative BC sample 4

description:
1 color array
Fresh total RNA from surgical specimen
Sample name: sample27B


title: Healthy control C8


title: Healthy control C6

value: Hispanic American


title: Healthy control C7


title: Healthy control C5

value: African American


title: estrogen receptor negative BC sample 1

description:
1 color array
Fresh total RNA from surgical specimen
Sample name: samplesj1no


title: Healthy control C4


title: PBMC_SNG001_visit2_rep10

value: Day 1


title: PBMC_SNG001_visit4_rep9


title: estrogen receptor negative BC sample 9

description:
1 color array
Fresh total RNA from surgical specimen
Sample name: sampleH


title: Healthy control C3


title: PBMC_SNG001_visit3_rep9

value: Day 4


title: estrogen receptor negative BC sample 3

description:
1 color array
Fresh total RNA from surgical specimen
Sample name: sample26B


title: estrogen receptor negative BC sample 2

description:
1 color array
Fresh total RNA from surgical specimen
Sample name: samplesj4no


title: PBMC_SNG001_visit2_rep9


title: Healthy control C2


title: PBMC_SNG001_visit4_rep8


title: Healthy control C1


title: PBMC_SNG001_visit3_rep8


title: H3277

city: Niigata

first: Masayuki

last: Nashimoto

state: Niigata

address: Higashijima 265-1, Akihaku

institute: Niigata University of Pharmacy and Applied Life Sciences

description: Gene expression after 18-hour incubation in the presence of 1 μM of the heptamer-type sgRNA H3277.

hyb_protocol: 1.65 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Scaled signal intensity that adjusts the average intensity value to 2500.

source_name: HL60, H3277 (ACACACA)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 μg total RNA using the Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HL60 cells were cultured in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in 5% CO2 humidified incubator.

extract_protocol: After 18 hours, total RNA was extracted with ISOGEN (Nippon Gene, Tokyo, Japan) from the cells.

treatment_protocol: HL60 cells were plated at 8 × 104 cells/500 μl/well on a 24-well dish in RPMI-1640 media containing 1 μM of various naked heptamer-type sgRNAs.

tag: treatment

tag: cell line

tag: origin

value: Acute promyelocytic leukemia


title: PBMC_SNG001_visit2_rep8

value: Peripheral blood mononuclear cells


title: H13260

description: Gene expression after 18-hour incubation in the presence of 1 μM of the heptamer-type sgRNA H13260.

source_name: HL60, H13260 (CACCAGC)


title: mock

description: Gene expression after 18-hour incubation in the absence of heptamer-type sgRNA.

source_name: HL60, mock

value: mock


title: PBMC_SNG001_visit2_rep7