title: ADN301

source_name: Total DNA from sample ADN301 labeled with Cyanine-5 (red).


title: 453P

status: Public on Jan 07 2014

type: genomic

city: BARCELONA

first: Lluis

last: Armengol

state: Catalonia

address: Doctor Aiguader, 88

country: Spain

institute: qGenomics

description: biological sample used as control/testing purposes in the study.

hyb_protocol: Hybridisation was performed as described in Wang. NJ. et al, Am. J. Hum. Genet, 75(2), 267-81, 2004.

scan_protocol: Agilent Microarray Scanner (G2565CA - Agilent Inc., Palo Alto, CA). Images were extracted with Genepix Pro 6.0 (Axon, Inc) using the irregular spot finding features with default flagging settings.

data_processing: In order to extract information from the GenePix generated files, we used an in-house developed pipeline called Bacanal (Lozano et al, unpublished). For lowess normalization of spot signals it relies on a bioconductor package called LIMMA. Values provided correspond to the log2 Cy5/Cy3 (test/reference) ratios.

molecule: genomic DNA

organism: Homo sapiens

source_name: Total DNA from sample 453P labeled with Cyanine-5 (red).

label_protocol: Between 300 and 400ng of total genomic DNA were labeled using Cy5-modified dCTP by random priming method, according to a slightly modified Bioprime Kit protocol (Invitrogen). Absorbance measures at 532 and 650nm. determined the amounts of dye incorporated to the DNA.

extract_protocol: QIAamp DNA Mini Kit

tag: tissue

value: Amniotic Fluid

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).

label_protocol: Between 300 and 400ng of total genomic DNA were labeled using Cy3-modified dCTP by random priming method, according to a slightly modified Bioprime Kit protocol (Invitrogen). Absorbance measures at 532 and 650nm. after removing unincorporated dye determined the amount of dye incorporation.

extract_protocol: Chemagen magnetic beads. Chemagic DNA Blood Kit special (cat. num 703, Chemagen)

value: fresh peripheral blood


title: 458P

source_name: Total DNA from sample 458P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN299

source_name: Total DNA from sample ADN299 labeled with Cyanine-5 (red).


title: ADN294

source_name: Total DNA from sample ADN294 labeled with Cyanine-5 (red).


title: ADN300

source_name: Total DNA from sample ADN300 labeled with Cyanine-5 (red).


title: 460P

source_name: Total DNA from sample 460P labeled with Cyanine-5 (red).


title: ADN251.2

source_name: Total DNA from sample ADN251.2 labeled with Cyanine-5 (red).


title: ADN246.2

source_name: Total DNA from sample ADN246.2 labeled with Cyanine-5 (red).


title: ADN256

source_name: Total DNA from sample ADN256 labeled with Cyanine-5 (red).


title: ADN260

source_name: Total DNA from sample ADN260 labeled with Cyanine-5 (red).


title: ADN245.2

source_name: Total DNA from sample ADN245.2 labeled with Cyanine-5 (red).


title: ADN255

source_name: Total DNA from sample ADN255 labeled with Cyanine-5 (red).


title: ADN259

source_name: Total DNA from sample ADN259 labeled with Cyanine-5 (red).


title: ADN257

source_name: Total DNA from sample ADN257 labeled with Cyanine-5 (red).


title: 183.02P

source_name: Total DNA from sample 183.02P labeled with Cyanine-5 (red).


title: ADN250

source_name: Total DNA from sample ADN250 labeled with Cyanine-5 (red).


title: 176.02P

source_name: Total DNA from sample 176.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 172.02P

source_name: Total DNA from sample 172.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN253

source_name: Total DNA from sample ADN253 labeled with Cyanine-5 (red).


title: 173.02P

source_name: Total DNA from sample 173.02P labeled with Cyanine-5 (red).


title: 240P

source_name: Total DNA from sample 240P labeled with Cyanine-5 (red).


title: 165.02P

source_name: Total DNA from sample 165.02P labeled with Cyanine-5 (red).


title: 166.02P

source_name: Total DNA from sample 166.02P labeled with Cyanine-5 (red).


title: 280P

source_name: Total DNA from sample 280P labeled with Cyanine-5 (red).


title: 281P

source_name: Total DNA from sample 281P labeled with Cyanine-5 (red).


title: 170.02P

source_name: Total DNA from sample 170.02P labeled with Cyanine-5 (red).


title: ADN252

source_name: Total DNA from sample ADN252 labeled with Cyanine-5 (red).


title: ADN254

source_name: Total DNA from sample ADN254 labeled with Cyanine-5 (red).


title: 282P

source_name: Total DNA from sample 282P labeled with Cyanine-5 (red).


title: 279P

source_name: Total DNA from sample 279P labeled with Cyanine-5 (red).


title: 277P

source_name: Total DNA from sample 277P labeled with Cyanine-5 (red).


title: DNA54

source_name: Total DNA from sample DNA54 labeled with Cyanine-5 (red).


title: DNA55

source_name: Total DNA from sample DNA55 labeled with Cyanine-5 (red).


title: DNA52

source_name: Total DNA from sample DNA52 labeled with Cyanine-5 (red).


title: 278P

source_name: Total DNA from sample 278P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: 533P

source_name: Total DNA from sample 533P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: DNA53

source_name: Total DNA from sample DNA53 labeled with Cyanine-5 (red).


title: DNA57

source_name: Total DNA from sample DNA57 labeled with Cyanine-5 (red).


title: DNA56

source_name: Total DNA from sample DNA56 labeled with Cyanine-5 (red).


title: DNA49

source_name: Total DNA from sample DNA49 labeled with Cyanine-5 (red).


title: 534P

source_name: Total DNA from sample 534P labeled with Cyanine-5 (red).


title: DNA50

source_name: Total DNA from sample DNA50 labeled with Cyanine-5 (red).


title: 537P

source_name: Total DNA from sample 537P labeled with Cyanine-5 (red).


title: DNA48

source_name: Total DNA from sample DNA48 labeled with Cyanine-5 (red).


title: 529P

source_name: Total DNA from sample 529P labeled with Cyanine-5 (red).


title: 528P

source_name: Total DNA from sample 528P labeled with Cyanine-5 (red).


title: 530P

source_name: Total DNA from sample 530P labeled with Cyanine-5 (red).


title: CO-33

source_name: Total DNA from sample CO-33 labeled with Cyanine-5 (red).


title: 526P

source_name: Total DNA from sample 526P labeled with Cyanine-5 (red).


title: 513.02P

source_name: Total DNA from sample 513.02P labeled with Cyanine-5 (red).


title: 527P

source_name: Total DNA from sample 527P labeled with Cyanine-5 (red).


title: ADN458

source_name: Total DNA from sample ADN458 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN426.2

source_name: Total DNA from sample ADN426.2 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 531P

source_name: Total DNA from sample 531P labeled with Cyanine-5 (red).


title: 505.02P

source_name: Total DNA from sample 505.02P labeled with Cyanine-5 (red).


title: 512.02P

source_name: Total DNA from sample 512.02P labeled with Cyanine-5 (red).


title: ADN439.2

source_name: Total DNA from sample ADN439.2 labeled with Cyanine-5 (red).


title: ADN459

source_name: Total DNA from sample ADN459 labeled with Cyanine-5 (red).


title: ADN438.2

source_name: Total DNA from sample ADN438.2 labeled with Cyanine-5 (red).


title: 557P

source_name: Total DNA from sample 557P labeled with Cyanine-5 (red).


title: 550P

source_name: Total DNA from sample 550P labeled with Cyanine-5 (red).


title: 554P

source_name: Total DNA from sample 554P labeled with Cyanine-5 (red).


title: 551P

source_name: Total DNA from sample 551P labeled with Cyanine-5 (red).


title: 553P

source_name: Total DNA from sample 553P labeled with Cyanine-5 (red).


title: 509.02P

source_name: Total DNA from sample 509.02P labeled with Cyanine-5 (red).


title: CO-22

source_name: Total DNA from sample CO-22 labeled with Cyanine-5 (red).


title: 365.02P

source_name: Total DNA from sample 365.02P labeled with Cyanine-5 (red).


title: 366.02P

source_name: Total DNA from sample 366.02P labeled with Cyanine-5 (red).


title: 555P

source_name: Total DNA from sample 555P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: 362.02P

source_name: Total DNA from sample 362.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 356.02P

source_name: Total DNA from sample 356.02P labeled with Cyanine-5 (red).


title: 358.02P

source_name: Total DNA from sample 358.02P labeled with Cyanine-5 (red).


title: CO-23

source_name: Total DNA from sample CO-23 labeled with Cyanine-5 (red).


title: 354.02P

source_name: Total DNA from sample 354.02P labeled with Cyanine-5 (red).


title: 357.02P

source_name: Total DNA from sample 357.02P labeled with Cyanine-5 (red).


title: 360.02P

source_name: Total DNA from sample 360.02P labeled with Cyanine-5 (red).


title: 364.02P

source_name: Total DNA from sample 364.02P labeled with Cyanine-5 (red).


title: 349.02P

source_name: Total DNA from sample 349.02P labeled with Cyanine-5 (red).


title: 556P

source_name: Total DNA from sample 556P labeled with Cyanine-5 (red).


title: 351.02P

source_name: Total DNA from sample 351.02P labeled with Cyanine-5 (red).


title: 350.02P

source_name: Total DNA from sample 350.02P labeled with Cyanine-5 (red).


title: 348.02P

source_name: Total DNA from sample 348.02P labeled with Cyanine-5 (red).


title: 359.02P

source_name: Total DNA from sample 359.02P labeled with Cyanine-5 (red).


title: 353.02P

source_name: Total DNA from sample 353.02P labeled with Cyanine-5 (red).


title: ADN384

source_name: Total DNA from sample ADN384 labeled with Cyanine-5 (red).


title: 355.02P

source_name: Total DNA from sample 355.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN383

source_name: Total DNA from sample ADN383 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN386

source_name: Total DNA from sample ADN386 labeled with Cyanine-5 (red).


title: 215.02P

source_name: Total DNA from sample 215.02P labeled with Cyanine-5 (red).


title: ADN385

source_name: Total DNA from sample ADN385 labeled with Cyanine-5 (red).


title: ADN382

source_name: Total DNA from sample ADN382 labeled with Cyanine-5 (red).


title: 214.02P

source_name: Total DNA from sample 214.02P labeled with Cyanine-5 (red).


title: 216.02P

source_name: Total DNA from sample 216.02P labeled with Cyanine-5 (red).


title: 347.02P

source_name: Total DNA from sample 347.02P labeled with Cyanine-5 (red).


title: 292P

source_name: Total DNA from sample 292P labeled with Cyanine-5 (red).


title: 293P

source_name: Total DNA from sample 293P labeled with Cyanine-5 (red).


title: 287P

source_name: Total DNA from sample 287P labeled with Cyanine-5 (red).


title: 286P

source_name: Total DNA from sample 286P labeled with Cyanine-5 (red).


title: 209.02P

source_name: Total DNA from sample 209.02P labeled with Cyanine-5 (red).


title: CO-13

source_name: Total DNA from sample CO-13 labeled with Cyanine-5 (red).


title: 210.02P

source_name: Total DNA from sample 210.02P labeled with Cyanine-5 (red).


title: 212.02P

source_name: Total DNA from sample 212.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN211

source_name: Total DNA from sample ADN211 labeled with Cyanine-5 (red).


title: ADN210

source_name: Total DNA from sample ADN210 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN208

source_name: Total DNA from sample ADN208 labeled with Cyanine-5 (red).


title: ADN212

source_name: Total DNA from sample ADN212 labeled with Cyanine-5 (red).


title: ADN209

source_name: Total DNA from sample ADN209 labeled with Cyanine-5 (red).


title: ADN207

source_name: Total DNA from sample ADN207 labeled with Cyanine-5 (red).


title: ADN203

source_name: Total DNA from sample ADN203 labeled with Cyanine-5 (red).


title: 289P

source_name: Total DNA from sample 289P labeled with Cyanine-5 (red).


title: ADN205

source_name: Total DNA from sample ADN205 labeled with Cyanine-5 (red).


title: ADN131.2

source_name: Total DNA from sample ADN131.2 labeled with Cyanine-5 (red).


title: ADN279

source_name: Total DNA from sample ADN279 labeled with Cyanine-5 (red).


title: ADN282

source_name: Total DNA from sample ADN282 labeled with Cyanine-5 (red).


title: ADN275

source_name: Total DNA from sample ADN275 labeled with Cyanine-5 (red).


title: ADN121c

source_name: Total DNA from sample ADN121c labeled with Cyanine-5 (red).


title: ADN130

source_name: Total DNA from sample ADN130 labeled with Cyanine-5 (red).


title: ADN120

source_name: Total DNA from sample ADN120 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN129

source_name: Total DNA from sample ADN129 labeled with Cyanine-5 (red).


title: ADN128

source_name: Total DNA from sample ADN128 labeled with Cyanine-5 (red).


title: ADN124

source_name: Total DNA from sample ADN124 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN202

source_name: Total DNA from sample ADN202 labeled with Cyanine-5 (red).


title: ADN123c

source_name: Total DNA from sample ADN123c labeled with Cyanine-5 (red).


title: ADN274c

source_name: Total DNA from sample ADN274c labeled with Cyanine-5 (red).


title: ADN116

source_name: Total DNA from sample ADN116 labeled with Cyanine-5 (red).


title: ADN206

source_name: Total DNA from sample ADN206 labeled with Cyanine-5 (red).


title: ADN118

source_name: Total DNA from sample ADN118 labeled with Cyanine-5 (red).


title: ADN236.2

source_name: Total DNA from sample ADN236.2 labeled with Cyanine-5 (red).


title: ADN119

source_name: Total DNA from sample ADN119 labeled with Cyanine-5 (red).


title: ADN114

source_name: Total DNA from sample ADN114 labeled with Cyanine-5 (red).


title: ADN113

source_name: Total DNA from sample ADN113 labeled with Cyanine-5 (red).


title: ADN117

source_name: Total DNA from sample ADN117 labeled with Cyanine-5 (red).


title: ADN80

source_name: Total DNA from sample ADN80 labeled with Cyanine-5 (red).


title: ADN112

source_name: Total DNA from sample ADN112 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN5.2

source_name: Total DNA from sample ADN5.2 labeled with Cyanine-5 (red).


title: ADN110

source_name: Total DNA from sample ADN110 labeled with Cyanine-5 (red).


title: ADN4.2

source_name: Total DNA from sample ADN4.2 labeled with Cyanine-5 (red).


title: ADN78

source_name: Total DNA from sample ADN78 labeled with Cyanine-5 (red).


title: ADN79

source_name: Total DNA from sample ADN79 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN262.2

source_name: Total DNA from sample ADN262.2 labeled with Cyanine-5 (red).


title: ADN317

source_name: Total DNA from sample ADN317 labeled with Cyanine-5 (red).


title: ADN314

source_name: Total DNA from sample ADN314 labeled with Cyanine-5 (red).


title: ADN307

source_name: Total DNA from sample ADN307 labeled with Cyanine-5 (red).


title: ADN310

source_name: Total DNA from sample ADN310 labeled with Cyanine-5 (red).


title: ADN304

source_name: Total DNA from sample ADN304 labeled with Cyanine-5 (red).


title: 199P

source_name: Total DNA from sample 199P labeled with Cyanine-5 (red).


title: ADN308

source_name: Total DNA from sample ADN308 labeled with Cyanine-5 (red).


title: ADN309

source_name: Total DNA from sample ADN309 labeled with Cyanine-5 (red).


title: 192P

source_name: Total DNA from sample 192P labeled with Cyanine-5 (red).


title: ADN107

source_name: Total DNA from sample ADN107 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: 197P

source_name: Total DNA from sample 197P labeled with Cyanine-5 (red).


title: 194P

source_name: Total DNA from sample 194P labeled with Cyanine-5 (red).


title: ADN313

source_name: Total DNA from sample ADN313 labeled with Cyanine-5 (red).


title: 196P

source_name: Total DNA from sample 196P labeled with Cyanine-5 (red).


title: 198P

source_name: Total DNA from sample 198P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 193P

source_name: Total DNA from sample 193P labeled with Cyanine-5 (red).


title: 204.02P

source_name: Total DNA from sample 204.02P labeled with Cyanine-5 (red).


title: ADN312

source_name: Total DNA from sample ADN312 labeled with Cyanine-5 (red).


title: 195P

source_name: Total DNA from sample 195P labeled with Cyanine-5 (red).


title: 189P

source_name: Total DNA from sample 189P labeled with Cyanine-5 (red).


title: 190P

source_name: Total DNA from sample 190P labeled with Cyanine-5 (red).


title: ADN315

source_name: Total DNA from sample ADN315 labeled with Cyanine-5 (red).


title: 188P

source_name: Total DNA from sample 188P labeled with Cyanine-5 (red).


title: 177P

source_name: Total DNA from sample 177P labeled with Cyanine-5 (red).


title: 186P

source_name: Total DNA from sample 186P labeled with Cyanine-5 (red).


title: 178P

source_name: Total DNA from sample 178P labeled with Cyanine-5 (red).


title: 184P

source_name: Total DNA from sample 184P labeled with Cyanine-5 (red).


title: 185P

source_name: Total DNA from sample 185P labeled with Cyanine-5 (red).


title: 175P

source_name: Total DNA from sample 175P labeled with Cyanine-5 (red).


title: 179P

source_name: Total DNA from sample 179P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: 171P

source_name: Total DNA from sample 171P labeled with Cyanine-5 (red).


title: ADN494

source_name: Total DNA from sample ADN494 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 180P

source_name: Total DNA from sample 180P labeled with Cyanine-5 (red).


title: 0911-256

source_name: Total DNA from sample 0911-256 labeled with Cyanine-5 (red).


title: 174P

source_name: Total DNA from sample 174P labeled with Cyanine-5 (red).


title: 181P

source_name: Total DNA from sample 181P labeled with Cyanine-5 (red).


title: 169P

source_name: Total DNA from sample 169P labeled with Cyanine-5 (red).


title: 492

source_name: Total DNA from sample 492 labeled with Cyanine-5 (red).


title: 187P

source_name: Total DNA from sample 187P labeled with Cyanine-5 (red).


title: 200P

source_name: Total DNA from sample 200P labeled with Cyanine-5 (red).


title: 182P

source_name: Total DNA from sample 182P labeled with Cyanine-5 (red).


title: ADN495

source_name: Total DNA from sample ADN495 labeled with Cyanine-5 (red).


title: ADN465.2

source_name: Total DNA from sample ADN465.2 labeled with Cyanine-5 (red).


title: ADN498

source_name: Total DNA from sample ADN498 labeled with Cyanine-5 (red).


title: 602P

source_name: Total DNA from sample 602P labeled with Cyanine-5 (red).


title: 470.2

source_name: Total DNA from sample 470.2 labeled with Cyanine-5 (red).


title: ADN497

source_name: Total DNA from sample ADN497 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: 601P

source_name: Total DNA from sample 601P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 167P

source_name: Total DNA from sample 167P labeled with Cyanine-5 (red).


title: 604P

source_name: Total DNA from sample 604P labeled with Cyanine-5 (red).


title: ADN491

source_name: Total DNA from sample ADN491 labeled with Cyanine-5 (red).


title: 597P

source_name: Total DNA from sample 597P labeled with Cyanine-5 (red).


title: ADN437

source_name: Total DNA from sample ADN437 labeled with Cyanine-5 (red).


title: 506P

source_name: Total DNA from sample 506P labeled with Cyanine-5 (red).


title: ADN412.2

source_name: Total DNA from sample ADN412.2 labeled with Cyanine-5 (red).


title: 507P

source_name: Total DNA from sample 507P labeled with Cyanine-5 (red).


title: ADN436

source_name: Total DNA from sample ADN436 labeled with Cyanine-5 (red).


title: CO-30

source_name: Total DNA from sample CO-30 labeled with Cyanine-5 (red).


title: 503P

source_name: Total DNA from sample 503P labeled with Cyanine-5 (red).


title: 504P

source_name: Total DNA from sample 504P labeled with Cyanine-5 (red).


title: ADN435

source_name: Total DNA from sample ADN435 labeled with Cyanine-5 (red).


title: 596P

source_name: Total DNA from sample 596P labeled with Cyanine-5 (red).


title: CO37P

source_name: Total DNA from sample CO37P labeled with Cyanine-5 (red).


title: ADN413c

source_name: Total DNA from sample ADN413c labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: 598P

source_name: Total DNA from sample 598P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 599P

source_name: Total DNA from sample 599P labeled with Cyanine-5 (red).


title: ADN496

source_name: Total DNA from sample ADN496 labeled with Cyanine-5 (red).


title: CO-29

source_name: Total DNA from sample CO-29 labeled with Cyanine-5 (red).


title: 501P

source_name: Total DNA from sample 501P labeled with Cyanine-5 (red).


title: CO-31

source_name: Total DNA from sample CO-31 labeled with Cyanine-5 (red).


title: 496P

source_name: Total DNA from sample 496P labeled with Cyanine-5 (red).


title: CO38P

source_name: Total DNA from sample CO38P labeled with Cyanine-5 (red).


title: 497P

source_name: Total DNA from sample 497P labeled with Cyanine-5 (red).


title: ADN411.2

source_name: Total DNA from sample ADN411.2 labeled with Cyanine-5 (red).


title: 594P

source_name: Total DNA from sample 594P labeled with Cyanine-5 (red).


title: 500P

source_name: Total DNA from sample 500P labeled with Cyanine-5 (red).


title: ADN440

source_name: Total DNA from sample ADN440 labeled with Cyanine-5 (red).


title: ADN09-1510_B

source_name: Total DNA from sample ADN09-1510_B labeled with Cyanine-5 (red).


title: ADN410.2

source_name: Total DNA from sample ADN410.2 labeled with Cyanine-5 (red).


title: 499P

source_name: Total DNA from sample 499P labeled with Cyanine-5 (red).


title: ADN490

source_name: Total DNA from sample ADN490 labeled with Cyanine-5 (red).


title: ADN489

source_name: Total DNA from sample ADN489 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN481

source_name: Total DNA from sample ADN481 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN487

source_name: Total DNA from sample ADN487 labeled with Cyanine-5 (red).


title: 587P

source_name: Total DNA from sample 587P labeled with Cyanine-5 (red).


title: ADN482

source_name: Total DNA from sample ADN482 labeled with Cyanine-5 (red).


title: 294.02P

source_name: Total DNA from sample 294.02P labeled with Cyanine-5 (red).


title: 582P

source_name: Total DNA from sample 582P labeled with Cyanine-5 (red).


title: 577P

source_name: Total DNA from sample 577P labeled with Cyanine-5 (red).


title: ADN483

source_name: Total DNA from sample ADN483 labeled with Cyanine-5 (red).


title: 293.02P

source_name: Total DNA from sample 293.02P labeled with Cyanine-5 (red).


title: 588P

source_name: Total DNA from sample 588P labeled with Cyanine-5 (red).


title: ADN486

source_name: Total DNA from sample ADN486 labeled with Cyanine-5 (red).


title: ADN488

source_name: Total DNA from sample ADN488 labeled with Cyanine-5 (red).


title: 286.02P

source_name: Total DNA from sample 286.02P labeled with Cyanine-5 (red).


title: 580P

source_name: Total DNA from sample 580P labeled with Cyanine-5 (red).


title: 275.02P

source_name: Total DNA from sample 275.02P labeled with Cyanine-5 (red).


title: 585P

source_name: Total DNA from sample 585P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 583P

source_name: Total DNA from sample 583P labeled with Cyanine-5 (red).


title: 579P

source_name: Total DNA from sample 579P labeled with Cyanine-5 (red).


title: 578P

source_name: Total DNA from sample 578P labeled with Cyanine-5 (red).


title: 337P

source_name: Total DNA from sample 337P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN485

source_name: Total DNA from sample ADN485 labeled with Cyanine-5 (red).


title: 584P

source_name: Total DNA from sample 584P labeled with Cyanine-5 (red).


title: ADN268.2

source_name: Total DNA from sample ADN268.2 labeled with Cyanine-5 (red).


title: 586P

source_name: Total DNA from sample 586P labeled with Cyanine-5 (red).


title: ADN263.2

source_name: Total DNA from sample ADN263.2 labeled with Cyanine-5 (red).


title: ADN267.2

source_name: Total DNA from sample ADN267.2 labeled with Cyanine-5 (red).


title: ADN156

source_name: Total DNA from sample ADN156 labeled with Cyanine-5 (red).


title: ADN155

source_name: Total DNA from sample ADN155 labeled with Cyanine-5 (red).


title: ADN153

source_name: Total DNA from sample ADN153 labeled with Cyanine-5 (red).


title: ADN98.2

source_name: Total DNA from sample ADN98.2 labeled with Cyanine-5 (red).


title: ADN145

source_name: Total DNA from sample ADN145 labeled with Cyanine-5 (red).


title: ADN102.2

source_name: Total DNA from sample ADN102.2 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN104.2

source_name: Total DNA from sample ADN104.2 labeled with Cyanine-5 (red).


title: ADN148

source_name: Total DNA from sample ADN148 labeled with Cyanine-5 (red).


title: ADN96.2

source_name: Total DNA from sample ADN96.2 labeled with Cyanine-5 (red).


title: ADN150

source_name: Total DNA from sample ADN150 labeled with Cyanine-5 (red).


title: ADN146

source_name: Total DNA from sample ADN146 labeled with Cyanine-5 (red).


title: ADN103.2

source_name: Total DNA from sample ADN103.2 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN88.2

source_name: Total DNA from sample ADN88.2 labeled with Cyanine-5 (red).


title: ADN363

source_name: Total DNA from sample ADN363 labeled with Cyanine-5 (red).


title: ADN147

source_name: Total DNA from sample ADN147 labeled with Cyanine-5 (red).


title: ADN358

source_name: Total DNA from sample ADN358 labeled with Cyanine-5 (red).


title: ADN360

source_name: Total DNA from sample ADN360 labeled with Cyanine-5 (red).


title: ADN356

source_name: Total DNA from sample ADN356 labeled with Cyanine-5 (red).


title: ADN100.2

source_name: Total DNA from sample ADN100.2 labeled with Cyanine-5 (red).


title: ADN362

source_name: Total DNA from sample ADN362 labeled with Cyanine-5 (red).


title: ADN90.2

source_name: Total DNA from sample ADN90.2 labeled with Cyanine-5 (red).


title: ADN154

source_name: Total DNA from sample ADN154 labeled with Cyanine-5 (red).


title: ADN355

source_name: Total DNA from sample ADN355 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN352

source_name: Total DNA from sample ADN352 labeled with Cyanine-5 (red).


title: ADN354

source_name: Total DNA from sample ADN354 labeled with Cyanine-5 (red).


title: ADN320.2

source_name: Total DNA from sample ADN320.2 labeled with Cyanine-5 (red).


title: ADN351

source_name: Total DNA from sample ADN351 labeled with Cyanine-5 (red).


title: ADN316.2

source_name: Total DNA from sample ADN316.2 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN305.2

source_name: Total DNA from sample ADN305.2 labeled with Cyanine-5 (red).


title: 370P

source_name: Total DNA from sample 370P labeled with Cyanine-5 (red).


title: ADN306.2

source_name: Total DNA from sample ADN306.2 labeled with Cyanine-5 (red).


title: 373P

source_name: Total DNA from sample 373P labeled with Cyanine-5 (red).


title: ADN344c

source_name: Total DNA from sample ADN344c labeled with Cyanine-5 (red).


title: ADN361

source_name: Total DNA from sample ADN361 labeled with Cyanine-5 (red).


title: ADN346

source_name: Total DNA from sample ADN346 labeled with Cyanine-5 (red).


title: ADN350

source_name: Total DNA from sample ADN350 labeled with Cyanine-5 (red).


title: ADN336

source_name: Total DNA from sample ADN336 labeled with Cyanine-5 (red).


title: ADN331

source_name: Total DNA from sample ADN331 labeled with Cyanine-5 (red).


title: ADN343c

source_name: Total DNA from sample ADN343c labeled with Cyanine-5 (red).


title: ADN330

source_name: Total DNA from sample ADN330 labeled with Cyanine-5 (red).


title: ADN75

source_name: Total DNA from sample ADN75 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN72

source_name: Total DNA from sample ADN72 labeled with Cyanine-5 (red).


title: ADN76

source_name: Total DNA from sample ADN76 labeled with Cyanine-5 (red).


title: DNA1807

source_name: Total DNA from sample DNA1807 labeled with Cyanine-5 (red).


title: ADN73

source_name: Total DNA from sample ADN73 labeled with Cyanine-5 (red).


title: ADN345

source_name: Total DNA from sample ADN345 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: Sb6

source_name: Total DNA from sample Sb6 labeled with Cyanine-5 (red).


title: ADN65

source_name: Total DNA from sample ADN65 labeled with Cyanine-5 (red).


title: ADN71

source_name: Total DNA from sample ADN71 labeled with Cyanine-5 (red).


title: ADN74

source_name: Total DNA from sample ADN74 labeled with Cyanine-5 (red).


title: ADN62

source_name: Total DNA from sample ADN62 labeled with Cyanine-5 (red).


title: ADN61

source_name: Total DNA from sample ADN61 labeled with Cyanine-5 (red).


title: ADN104

source_name: Total DNA from sample ADN104 labeled with Cyanine-5 (red).


title: ADN63.1

source_name: Total DNA from sample ADN63.1 labeled with Cyanine-5 (red).


title: ADN68

source_name: Total DNA from sample ADN68 labeled with Cyanine-5 (red).


title: ADN70

source_name: Total DNA from sample ADN70 labeled with Cyanine-5 (red).


title: ADN64

source_name: Total DNA from sample ADN64 labeled with Cyanine-5 (red).


title: ADN69

source_name: Total DNA from sample ADN69 labeled with Cyanine-5 (red).


title: ADN68.2

source_name: Total DNA from sample ADN68.2 labeled with Cyanine-5 (red).


title: ADN111

source_name: Total DNA from sample ADN111 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN221

source_name: Total DNA from sample ADN221 labeled with Cyanine-5 (red).


title: ADN228

source_name: Total DNA from sample ADN228 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN67.2

source_name: Total DNA from sample ADN67.2 labeled with Cyanine-5 (red).


title: ADN311.2

source_name: Total DNA from sample ADN311.2 labeled with Cyanine-5 (red).


title: ADN60

source_name: Total DNA from sample ADN60 labeled with Cyanine-5 (red).


title: ADN222

source_name: Total DNA from sample ADN222 labeled with Cyanine-5 (red).


title: ADN226

source_name: Total DNA from sample ADN226 labeled with Cyanine-5 (red).


title: ADN109

source_name: Total DNA from sample ADN109 labeled with Cyanine-5 (red).


title: ADN115

source_name: Total DNA from sample ADN115 labeled with Cyanine-5 (red).


title: ADN220

source_name: Total DNA from sample ADN220 labeled with Cyanine-5 (red).


title: ADN219

source_name: Total DNA from sample ADN219 labeled with Cyanine-5 (red).


title: ADN224

source_name: Total DNA from sample ADN224 labeled with Cyanine-5 (red).


title: ADN214

source_name: Total DNA from sample ADN214 labeled with Cyanine-5 (red).


title: ADN218

source_name: Total DNA from sample ADN218 labeled with Cyanine-5 (red).


title: 397P

source_name: Total DNA from sample 397P labeled with Cyanine-5 (red).


title: 396P

source_name: Total DNA from sample 396P labeled with Cyanine-5 (red).


title: 395P

source_name: Total DNA from sample 395P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 394P

source_name: Total DNA from sample 394P labeled with Cyanine-5 (red).


title: 399P

source_name: Total DNA from sample 399P labeled with Cyanine-5 (red).


title: 288.02P

source_name: Total DNA from sample 288.02P labeled with Cyanine-5 (red).


title: 390P

source_name: Total DNA from sample 390P labeled with Cyanine-5 (red).


title: 391P

source_name: Total DNA from sample 391P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: 389P

source_name: Total DNA from sample 389P labeled with Cyanine-5 (red).


title: ADN379

source_name: Total DNA from sample ADN379 labeled with Cyanine-5 (red).


title: 1187879

source_name: Total DNA from sample 1187879 labeled with Cyanine-5 (red).


title: ADN378

source_name: Total DNA from sample ADN378 labeled with Cyanine-5 (red).


title: 393P

source_name: Total DNA from sample 393P labeled with Cyanine-5 (red).


title: 400P

source_name: Total DNA from sample 400P labeled with Cyanine-5 (red).


title: 306.02P

source_name: Total DNA from sample 306.02P labeled with Cyanine-5 (red).


title: ADN376

source_name: Total DNA from sample ADN376 labeled with Cyanine-5 (red).


title: 307.02P

source_name: Total DNA from sample 307.02P labeled with Cyanine-5 (red).


title: ADN373

source_name: Total DNA from sample ADN373 labeled with Cyanine-5 (red).


title: 308.02P

source_name: Total DNA from sample 308.02P labeled with Cyanine-5 (red).


title: ADN331B

source_name: Total DNA from sample ADN331B labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN377

source_name: Total DNA from sample ADN377 labeled with Cyanine-5 (red).


title: ADN375

source_name: Total DNA from sample ADN375 labeled with Cyanine-5 (red).


title: 304.02P

source_name: Total DNA from sample 304.02P labeled with Cyanine-5 (red).


title: 283.03P

source_name: Total DNA from sample 283.03P labeled with Cyanine-5 (red).


title: 310.02P

source_name: Total DNA from sample 310.02P labeled with Cyanine-5 (red).


title: 302.02P

source_name: Total DNA from sample 302.02P labeled with Cyanine-5 (red).


title: ADN374

source_name: Total DNA from sample ADN374 labeled with Cyanine-5 (red).


title: ADN369

source_name: Total DNA from sample ADN369 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: 298.02P

source_name: Total DNA from sample 298.02P labeled with Cyanine-5 (red).


title: 295.02P

source_name: Total DNA from sample 295.02P labeled with Cyanine-5 (red).


title: ADN367

source_name: Total DNA from sample ADN367 labeled with Cyanine-5 (red).


title: ADN366

source_name: Total DNA from sample ADN366 labeled with Cyanine-5 (red).


title: ADN365

source_name: Total DNA from sample ADN365 labeled with Cyanine-5 (red).


title: 369P

source_name: Total DNA from sample 369P labeled with Cyanine-5 (red).


title: ADN364

source_name: Total DNA from sample ADN364 labeled with Cyanine-5 (red).


title: 268P

source_name: Total DNA from sample 268P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 270P

source_name: Total DNA from sample 270P labeled with Cyanine-5 (red).


title: 265P

source_name: Total DNA from sample 265P labeled with Cyanine-5 (red).


title: 266P

source_name: Total DNA from sample 266P labeled with Cyanine-5 (red).


title: 258P

source_name: Total DNA from sample 258P labeled with Cyanine-5 (red).


title: ADN200

source_name: Total DNA from sample ADN200 labeled with Cyanine-5 (red).


title: 260P

source_name: Total DNA from sample 260P labeled with Cyanine-5 (red).


title: ADN174

source_name: Total DNA from sample ADN174 labeled with Cyanine-5 (red).


title: ADN194

source_name: Total DNA from sample ADN194 labeled with Cyanine-5 (red).


title: ADN173

source_name: Total DNA from sample ADN173 labeled with Cyanine-5 (red).


title: ADN168

source_name: Total DNA from sample ADN168 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN162

source_name: Total DNA from sample ADN162 labeled with Cyanine-5 (red).


title: ADN199

source_name: Total DNA from sample ADN199 labeled with Cyanine-5 (red).


title: ADN164

source_name: Total DNA from sample ADN164 labeled with Cyanine-5 (red).


title: ADN161

source_name: Total DNA from sample ADN161 labeled with Cyanine-5 (red).


title: ADN165

source_name: Total DNA from sample ADN165 labeled with Cyanine-5 (red).


title: ADN193

source_name: Total DNA from sample ADN193 labeled with Cyanine-5 (red).


title: ADN163

source_name: Total DNA from sample ADN163 labeled with Cyanine-5 (red).


title: ADN160

source_name: Total DNA from sample ADN160 labeled with Cyanine-5 (red).


title: ADN192

source_name: Total DNA from sample ADN192 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN159

source_name: Total DNA from sample ADN159 labeled with Cyanine-5 (red).


title: ADN198

source_name: Total DNA from sample ADN198 labeled with Cyanine-5 (red).


title: ADN195

source_name: Total DNA from sample ADN195 labeled with Cyanine-5 (red).


title: ADN158

source_name: Total DNA from sample ADN158 labeled with Cyanine-5 (red).


title: ADN151

source_name: Total DNA from sample ADN151 labeled with Cyanine-5 (red).


title: ADN477

source_name: Total DNA from sample ADN477 labeled with Cyanine-5 (red).


title: ADN453.2

source_name: Total DNA from sample ADN453.2 labeled with Cyanine-5 (red).


title: ADN471

source_name: Total DNA from sample ADN471 labeled with Cyanine-5 (red).


title: ADN473

source_name: Total DNA from sample ADN473 labeled with Cyanine-5 (red).


title: ADN476

source_name: Total DNA from sample ADN476 labeled with Cyanine-5 (red).


title: ADN469

source_name: Total DNA from sample ADN469 labeled with Cyanine-5 (red).


title: ADN468

source_name: Total DNA from sample ADN468 labeled with Cyanine-5 (red).


title: ADN467

source_name: Total DNA from sample ADN467 labeled with Cyanine-5 (red).


title: 575P

source_name: Total DNA from sample 575P labeled with Cyanine-5 (red).


title: 571P

source_name: Total DNA from sample 571P labeled with Cyanine-5 (red).


title: 569P

source_name: Total DNA from sample 569P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN466

source_name: Total DNA from sample ADN466 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 576P

source_name: Total DNA from sample 576P labeled with Cyanine-5 (red).


title: CO-34

source_name: Total DNA from sample CO-34 labeled with Cyanine-5 (red).


title: 568P

source_name: Total DNA from sample 568P labeled with Cyanine-5 (red).


title: 567P

source_name: Total DNA from sample 567P labeled with Cyanine-5 (red).


title: ADN167

source_name: Total DNA from sample ADN167 labeled with Cyanine-5 (red).


title: 566P

source_name: Total DNA from sample 566P labeled with Cyanine-5 (red).


title: 565P

source_name: Total DNA from sample 565P labeled with Cyanine-5 (red).


title: SNT 2 (transcript-level)

type: RNA

city: Malaga

first: James

middle: R

last: Perkins

address: Pl. Hosp. Civil

department: Hospital Civil

institute: Hospital Carlos Haya

hyb_protocol: Standard protcol performed by UCL genomics, following Affymetrix instructions

data_processing: CEL files were processed in R using the oligo Bioconductor package. Background correction, normalisation and summarisation were performed using robust multi-array average (RMA), quantile normalisation and median polish respectively. Summarisation was performed at the exon level (where each probeset corresponds to an exon, with some exons being probed by more than one probeset) or the transcript cluster/gene level, where all probesets from different exons belonging to the same gene were summarised to produce a single transcript cluster measurement.

label: biotin

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Dorsal root ganglia, L5

extract_protocol: RNA extracted using the miRNEasy kit (QIAGEN) according to manufacturer’s instructions. RNA concentration was measured using the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA).

treatment_protocol: Spinal nerve transection (SNT) of the L5 spinal nerve was performed. Dorsal root ganglia (DRG) were harvested 7 days after surgery fresh dissection

value: Dorsal root ganglia, L5

tag: strain

value: Wistar

tag: treatment

value: SNT or naïve:SNT


title: 564P

source_name: Total DNA from sample 564P labeled with Cyanine-5 (red).


title: SNT 3 (transcript-level)

scan_protocol: Standard protcol performed by UCL genomics, following Affymetrix instructions


title: SNT 1 (transcript-level)

label_protocol: Standard protcol performed by UCL genomics, following Affymetrix instructions


title: DGM-00906_gt

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

country: USA

institute: Weill Cornell Medical College

hyb_protocol: Following labelling, 50 nanograms of DNA were hybridized for 16 hr at 50C on Affymetrix GeneChip Genome-Wide Human SNP Array 5.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite software, version 6.2 using default analysis settings and global scaling as normalization method. CHP files were created from CEL files after running BRLMM_p.

source_name: small airway epithelium from healthy nonsmokers or healthy smokers

label_protocol: DNA labeling was done according to the standard Affymetrix protocol from 50 nanograms total DNA (Affymetrix Genome-Wide Human SNP Nsp/Sty Assay 5.0, 702419 Rev.1, Affymetrix).

extract_protocol: DNA was extracted from blood samples using the Autogen FX robotic system in according to the manufacturer's instructions

tag: department of genetic medicine id

tag: smoking status

value: NS


title: 563P

source_name: Total DNA from sample 563P labeled with Cyanine-5 (red).


title: Naïve 2 (transcript-level)

value: SNT or naïve:Naïve


title: Naïve 3 (transcript-level)


title: 562P

source_name: Total DNA from sample 562P labeled with Cyanine-5 (red).


title: 561P

source_name: Total DNA from sample 561P labeled with Cyanine-5 (red).


title: Naïve 1 (transcript-level)


title: DGM-00208_gt

source_name: small airways

value: smoker

tag: disease status

value: disease


title: 560P

source_name: Total DNA from sample 560P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: DGM-00167_gt

source_name: small airway epithelium from healthy nonsmokers or smokers with COPD

value: S

tag: copd status

value: yes


title: DGM-00286_gt


title: DGM-00236_gt


title: 522.02P

source_name: Total DNA from sample 522.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 521.02P

source_name: Total DNA from sample 521.02P labeled with Cyanine-5 (red).


title: 559P

source_name: Total DNA from sample 559P labeled with Cyanine-5 (red).


title: 519.02P

source_name: Total DNA from sample 519.02P labeled with Cyanine-5 (red).


title: DGM-00153_gt


title: DGM-00738_gt

data_processing:
The data were analyzed with Partek Genomics Suite software, version 6.2 using default analysis settings and global scaling as normalization method.
CHP files were created from CEL files after running BRLMM_p

source_name: Blood from healthy nonsmokers or healthy smokers

label_protocol: DNA labeling was done according to the standard Affymetrix protocol from 50 nanograms total DNA (Affymetrix® Genome-Wide Human SNP Nsp/Sty Assay 5.0, 702419 Rev.1, Affymetrix).

tag: ethnicity

value: Afr


title: DGM-02164_gt


title: DGM-00196_gt

value: Eur


title: 516.02P

source_name: Total DNA from sample 516.02P labeled with Cyanine-5 (red).


title: 518.02P

source_name: Total DNA from sample 518.02P labeled with Cyanine-5 (red).


title: ADN359.2

source_name: Total DNA from sample ADN359.2 labeled with Cyanine-5 (red).


title: 520.02P

source_name: Total DNA from sample 520.02P labeled with Cyanine-5 (red).


title: DGM-00993_gt


title: DGM-00050_gt


title: ADN394

source_name: Total DNA from sample ADN394 labeled with Cyanine-5 (red).


title: ADN393

source_name: Total DNA from sample ADN393 labeled with Cyanine-5 (red).


title: ADN392

source_name: Total DNA from sample ADN392 labeled with Cyanine-5 (red).


title: ADN389

source_name: Total DNA from sample ADN389 labeled with Cyanine-5 (red).


title: G300-2

source_name: Total DNA from sample G300-2 labeled with Cyanine-5 (red).


title: 495.02P

source_name: Total DNA from sample 495.02P labeled with Cyanine-5 (red).


title: DGM-00217_gt

source_name: small airways


title: DGM-00470_gt


title: ADN292.2

source_name: Total DNA from sample ADN292.2 labeled with Cyanine-5 (red).


title: ADN286.2

source_name: Total DNA from sample ADN286.2 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN288c

source_name: Total DNA from sample ADN288c labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: DGM-00233_gt

source_name: Blood from healthy nonsmokers or healthy smokers


title: DGM-00742_gt


title: DGM-00297_gt


title: ADN283c

source_name: Total DNA from sample ADN283c labeled with Cyanine-5 (red).


title: Iso17q

source_name: Total DNA from sample Iso17q labeled with Cyanine-5 (red).

value: DNA from Control Sample


title: ADN387

source_name: Total DNA from sample ADN387 labeled with Cyanine-5 (red).


title: ADN280.2

source_name: Total DNA from sample ADN280.2 labeled with Cyanine-5 (red).


title: ADN281.2

source_name: Total DNA from sample ADN281.2 labeled with Cyanine-5 (red).


title: DGM-00808_gt


title: ADN284c

source_name: Total DNA from sample ADN284c labeled with Cyanine-5 (red).


title: DGM-00522_gt


title: DGM-00083_gt


title: DGM-00405_gt


title: ADN326

source_name: Total DNA from sample ADN326 labeled with Cyanine-5 (red).


title: ADN372.2

source_name: Total DNA from sample ADN372.2 labeled with Cyanine-5 (red).


title: ADN323

source_name: Total DNA from sample ADN323 labeled with Cyanine-5 (red).


title: ADN325

source_name: Total DNA from sample ADN325 labeled with Cyanine-5 (red).


title: ADN318

source_name: Total DNA from sample ADN318 labeled with Cyanine-5 (red).


title: ADN319

source_name: Total DNA from sample ADN319 labeled with Cyanine-5 (red).


title: ADN324

source_name: Total DNA from sample ADN324 labeled with Cyanine-5 (red).


title: ADN285.2

source_name: Total DNA from sample ADN285.2 labeled with Cyanine-5 (red).


title: ADN278.2

source_name: Total DNA from sample ADN278.2 labeled with Cyanine-5 (red).


title: ADN321

source_name: Total DNA from sample ADN321 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN277.2

source_name: Total DNA from sample ADN277.2 labeled with Cyanine-5 (red).


title: DGM-00595_gt

source_name: Blood from healthy nonsmokers or healthy smokers


title: ADN371.2

source_name: Total DNA from sample ADN371.2 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: DGM-00581_gt


title: ADN370.2

source_name: Total DNA from sample ADN370.2 labeled with Cyanine-5 (red).


title: ADN276.2

source_name: Total DNA from sample ADN276.2 labeled with Cyanine-5 (red).


title: ADN404

source_name: Total DNA from sample ADN404 labeled with Cyanine-5 (red).


title: ADN368.2

source_name: Total DNA from sample ADN368.2 labeled with Cyanine-5 (red).


title: ADN403

source_name: Total DNA from sample ADN403 labeled with Cyanine-5 (red).


title: ADN327

source_name: Total DNA from sample ADN327 labeled with Cyanine-5 (red).


title: ADN402

source_name: Total DNA from sample ADN402 labeled with Cyanine-5 (red).


title: ADN399c

source_name: Total DNA from sample ADN399c labeled with Cyanine-5 (red).


title: ADN328

source_name: Total DNA from sample ADN328 labeled with Cyanine-5 (red).


title: ADN397

source_name: Total DNA from sample ADN397 labeled with Cyanine-5 (red).


title: ADN395

source_name: Total DNA from sample ADN395 labeled with Cyanine-5 (red).


title: ADN398

source_name: Total DNA from sample ADN398 labeled with Cyanine-5 (red).


title: 379.02P

source_name: Total DNA from sample 379.02P labeled with Cyanine-5 (red).


title: ADN401

source_name: Total DNA from sample ADN401 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN396

source_name: Total DNA from sample ADN396 labeled with Cyanine-5 (red).


title: 363.02P

source_name: Total DNA from sample 363.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: 367.02P

source_name: Total DNA from sample 367.02P labeled with Cyanine-5 (red).


title: 374.02P

source_name: Total DNA from sample 374.02P labeled with Cyanine-5 (red).


title: 371.02P

source_name: Total DNA from sample 371.02P labeled with Cyanine-5 (red).


title: ADN322

source_name: Total DNA from sample ADN322 labeled with Cyanine-5 (red).


title: 372.02P

source_name: Total DNA from sample 372.02P labeled with Cyanine-5 (red).


title: 368.02P

source_name: Total DNA from sample 368.02P labeled with Cyanine-5 (red).


title: DGM-00867_gt

source_name: Blood from healthy nonsmokers or healthy smokers


title: ADN178

source_name: Total DNA from sample ADN178 labeled with Cyanine-5 (red).


title: 378.02P

source_name: Total DNA from sample 378.02P labeled with Cyanine-5 (red).


title: 369.02P

source_name: Total DNA from sample 369.02P labeled with Cyanine-5 (red).


title: ADN181c

source_name: Total DNA from sample ADN181c labeled with Cyanine-5 (red).


title: ADN179

source_name: Total DNA from sample ADN179 labeled with Cyanine-5 (red).


title: 361.02P

source_name: Total DNA from sample 361.02P labeled with Cyanine-5 (red).


title: ADN187

source_name: Total DNA from sample ADN187 labeled with Cyanine-5 (red).


title: ADN184

source_name: Total DNA from sample ADN184 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN182c

source_name: Total DNA from sample ADN182c labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN180

source_name: Total DNA from sample ADN180 labeled with Cyanine-5 (red).


title: ADN172

source_name: Total DNA from sample ADN172 labeled with Cyanine-5 (red).


title: 1211701

source_name: Total DNA from sample 1211701 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 2702871 labeled with Cyanine-3 (green).


title: ADN431

source_name: Total DNA from sample ADN431 labeled with Cyanine-5 (red).


title: ADN391.2

source_name: Total DNA from sample ADN391.2 labeled with Cyanine-5 (red).


title: ADN428

source_name: Total DNA from sample ADN428 labeled with Cyanine-5 (red).


title: ADN400.2

source_name: Total DNA from sample ADN400.2 labeled with Cyanine-5 (red).


title: ADN425

source_name: Total DNA from sample ADN425 labeled with Cyanine-5 (red).


title: ADN427

source_name: Total DNA from sample ADN427 labeled with Cyanine-5 (red).


title: ADN430

source_name: Total DNA from sample ADN430 labeled with Cyanine-5 (red).


title: 428.02P

source_name: Total DNA from sample 428.02P labeled with Cyanine-5 (red).


title: 425.02P

source_name: Total DNA from sample 425.02P labeled with Cyanine-5 (red).


title: 437.02P

source_name: Total DNA from sample 437.02P labeled with Cyanine-5 (red).


title: 436.02P

source_name: Total DNA from sample 436.02P labeled with Cyanine-5 (red).


title: 443.02P

source_name: Total DNA from sample 443.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 433.02P

source_name: Total DNA from sample 433.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: 431.02P

source_name: Total DNA from sample 431.02P labeled with Cyanine-5 (red).


title: 434.02P

source_name: Total DNA from sample 434.02P labeled with Cyanine-5 (red).


title: 424.02P

source_name: Total DNA from sample 424.02P labeled with Cyanine-5 (red).


title: ADN390.2

source_name: Total DNA from sample ADN390.2 labeled with Cyanine-5 (red).


title: CO-24

source_name: Total DNA from sample CO-24 labeled with Cyanine-5 (red).


title: 450.02P

source_name: Total DNA from sample 450.02P labeled with Cyanine-5 (red).


title: ADN432

source_name: Total DNA from sample ADN432 labeled with Cyanine-5 (red).


title: 910027

source_name: Total DNA from sample 910027 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 910026 labeled with Cyanine-3 (green).


title: 445.02P

source_name: Total DNA from sample 445.02P labeled with Cyanine-5 (red).


title: 442.02P

source_name: Total DNA from sample 442.02P labeled with Cyanine-5 (red).


title: ADN434

source_name: Total DNA from sample ADN434 labeled with Cyanine-5 (red).


title: ADN433

source_name: Total DNA from sample ADN433 labeled with Cyanine-5 (red).


title: 435.02P

source_name: Total DNA from sample 435.02P labeled with Cyanine-5 (red).


title: ADN09-1510

source_name: Total DNA from sample ADN09-1510 labeled with Cyanine-5 (red).


title: 299.02P

source_name: Total DNA from sample 299.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 488P

source_name: Total DNA from sample 488P labeled with Cyanine-5 (red).


title: 370.02P

source_name: Total DNA from sample 370.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: 486P

source_name: Total DNA from sample 486P labeled with Cyanine-5 (red).


title: CO-25

source_name: Total DNA from sample CO-25 labeled with Cyanine-5 (red).


title: 481P

source_name: Total DNA from sample 481P labeled with Cyanine-5 (red).


title: 482P

source_name: Total DNA from sample 482P labeled with Cyanine-5 (red).


title: 483P

source_name: Total DNA from sample 483P labeled with Cyanine-5 (red).


title: 484P

source_name: Total DNA from sample 484P labeled with Cyanine-5 (red).


title: 485P

source_name: Total DNA from sample 485P labeled with Cyanine-5 (red).


title: 473P

source_name: Total DNA from sample 473P labeled with Cyanine-5 (red).


title: 475P

source_name: Total DNA from sample 475P labeled with Cyanine-5 (red).


title: 476P

source_name: Total DNA from sample 476P labeled with Cyanine-5 (red).


title: 480P

source_name: Total DNA from sample 480P labeled with Cyanine-5 (red).


title: 487P

source_name: Total DNA from sample 487P labeled with Cyanine-5 (red).


title: 477P

source_name: Total DNA from sample 477P labeled with Cyanine-5 (red).


title: CO-28

source_name: Total DNA from sample CO-28 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 474P

source_name: Total DNA from sample 474P labeled with Cyanine-5 (red).


title: 447.02P

source_name: Total DNA from sample 447.02P labeled with Cyanine-5 (red).


title: 478P

source_name: Total DNA from sample 478P labeled with Cyanine-5 (red).


title: CO-26

source_name: Total DNA from sample CO-26 labeled with Cyanine-5 (red).


title: 335P

source_name: Total DNA from sample 335P labeled with Cyanine-5 (red).


title: 343P

source_name: Total DNA from sample 343P labeled with Cyanine-5 (red).


title: 303.02P

source_name: Total DNA from sample 303.02P labeled with Cyanine-5 (red).


title: CO-27

source_name: Total DNA from sample CO-27 labeled with Cyanine-5 (red).


title: 524P

source_name: Total DNA from sample 524P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: 297.02P

source_name: Total DNA from sample 297.02P labeled with Cyanine-5 (red).


title: 514P

source_name: Total DNA from sample 514P labeled with Cyanine-5 (red).


title: 515P

source_name: Total DNA from sample 515P labeled with Cyanine-5 (red).


title: 479P

source_name: Total DNA from sample 479P labeled with Cyanine-5 (red).


title: 517P

source_name: Total DNA from sample 517P labeled with Cyanine-5 (red).


title: 352P

source_name: Total DNA from sample 352P labeled with Cyanine-5 (red).


title: 510P

source_name: Total DNA from sample 510P labeled with Cyanine-5 (red).


title: 511P

source_name: Total DNA from sample 511P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN457

source_name: Total DNA from sample ADN457 labeled with Cyanine-5 (red).


title: ADN423

source_name: Total DNA from sample ADN423 labeled with Cyanine-5 (red).


title: ADN429.2

source_name: Total DNA from sample ADN429.2 labeled with Cyanine-5 (red).


title: ADN455

source_name: Total DNA from sample ADN455 labeled with Cyanine-5 (red).


title: ADN420

source_name: Total DNA from sample ADN420 labeled with Cyanine-5 (red).


title: ADN454

source_name: Total DNA from sample ADN454 labeled with Cyanine-5 (red).


title: ADN452

source_name: Total DNA from sample ADN452 labeled with Cyanine-5 (red).


title: ADN418

source_name: Total DNA from sample ADN418 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN388.2

source_name: Total DNA from sample ADN388.2 labeled with Cyanine-5 (red).


title: CO-10P

source_name: Total DNA from sample CO-10P labeled with Cyanine-5 (red).


title: CO-11P

source_name: Total DNA from sample CO-11P labeled with Cyanine-5 (red).


title: ADN416

source_name: Total DNA from sample ADN416 labeled with Cyanine-5 (red).


title: ADN456

source_name: Total DNA from sample ADN456 labeled with Cyanine-5 (red).


title: ADN419

source_name: Total DNA from sample ADN419 labeled with Cyanine-5 (red).


title: CO-08P

source_name: Total DNA from sample CO-08P labeled with Cyanine-5 (red).


title: ADN415

source_name: Total DNA from sample ADN415 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN408

source_name: Total DNA from sample ADN408 labeled with Cyanine-5 (red).


title: ADN381.2

source_name: Total DNA from sample ADN381.2 labeled with Cyanine-5 (red).


title: ADN409

source_name: Total DNA from sample ADN409 labeled with Cyanine-5 (red).


title: 429P

source_name: Total DNA from sample 429P labeled with Cyanine-5 (red).


title: ADN407

source_name: Total DNA from sample ADN407 labeled with Cyanine-5 (red).


title: ADN175.2

source_name: Total DNA from sample ADN175.2 labeled with Cyanine-5 (red).


title: XDR1221_INH

city: Shanghai

first: Yu

last: Guohua

state: Shanghai

address: Handan road

country: China

institute: Fudan university

description: Gene expression exposed to INH for 6 hrs in a concentration of 10 x MIC

hyb_protocol: Microarray hybridization was carried out in Agilent’s SureHyb Hybridization Chambers for 17hr at 65℃ while rotating

scan_protocol: Scanned with the Agilent DNA microarray scanner (part number G2505B) using settings recommended by Agilent Technologies.  Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Raw data was extracted using the Agilent Feature Extraction Software, then processed using R package limma. Briefly, background correction was performed by the method normexp, and corrected data was then normalized using quantile method.

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: 10 x MIC INH, 6hrs

label_protocol: The samples were labeled using the Agilent Quick Amp labeling kit.

growth_protocol: Strains were grown in Middlebrook 7H9 broth supplemented with ADC, 0.05% Tween 80 and 0.2% glycerol to an OD600 of 0.5-0.6

extract_protocol: Total RNA extracted using Trizol bead beater method following manufacturer's instructions

treatment_protocol: respectively treated with control (water), 10×MIC INH, 1×MIC RIF and CAP for 6hr

value: Extensively drug-resistant strain XDR1221

tag: drug

value: isoniazid (INH)


title: XDR1221_RIF

description: Gene expression exposed to RIF for 6 hrs in a concentration of 1 x MIC

source_name: 1 x MIC RIF, 6hrs

value: rifampicin (RIF)


title: ADN171.2

source_name: Total DNA from sample ADN171.2 labeled with Cyanine-5 (red).

value: Amniotic Fluid


title: ADN177.2

source_name: Total DNA from sample ADN177.2 labeled with Cyanine-5 (red).

value: fresh peripheral blood


title: XDR1221_Ctrl

description: Gene expression exposed to water for 6 hrs

source_name: Water, 6hrs

value: water (control)


title: ADN176.2

source_name: Total DNA from sample ADN176.2 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: XDR1219_RIF

value: Extensively drug-resistant strain XDR1219


title: XDR1221_CAP

description: Gene expression exposed to CAP for 6 hrs in a concentration of 1 x MIC

source_name: 1 x MIC CAP, 6hrs

value: capreomycin (CAP)


title: ADN235

source_name: Total DNA from sample ADN235 labeled with Cyanine-5 (red).


title: H37Rv_RIF


title: XDR1219_INH


title: ADN232

source_name: Total DNA from sample ADN232 labeled with Cyanine-5 (red).


title: XDR1219_CAP


title: ADN234

source_name: Total DNA from sample ADN234 labeled with Cyanine-5 (red).


title: H37Rv_Ctrl


title: H37Rv_INH


title: ADN230

source_name: Total DNA from sample ADN230 labeled with Cyanine-5 (red).


title: XDR1219_Ctrl


title: ADN169c

source_name: Total DNA from sample ADN169c labeled with Cyanine-5 (red).


title: ADN166c

source_name: Total DNA from sample ADN166c labeled with Cyanine-5 (red).


title: ADN233

source_name: Total DNA from sample ADN233 labeled with Cyanine-5 (red).


title: F-50D

source_name: Total DNA from sample F-50D labeled with Cyanine-5 (red).


title: ADN229

source_name: Total DNA from sample ADN229 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: F-47D

source_name: Total DNA from sample F-47D labeled with Cyanine-5 (red).


title: 13-NT-317

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Abrreviation: non-p-MyoFb

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Rat Gene 2.0 ST Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: The RMA expression values were computed with the xps package (version 1.20.2) of Bioconductor.

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.

growth_protocol: second passaged Fb were seeded at a density of 2600 cells/cm2 and cultured in DMEM medium with 10% fetal bovine serum and 1% of penicillin/streptomycin. To test fibroblast differentiation pathways we used SD-208 (3 µmol/L; Sigma-Aldrich, Belgium), a specific TGF-β receptor I kinase inhibitor during 4 days and recombinant human TGF-β1 (400 pmol/L; PeproTech, USA) during 6 days in culture. Spontaneous differentiation in standard culture medium was performed during 4 days in culture. All the experiments comparing cell differentiation were a paired study design, i.e. the different treatments were applied to cultures from the same heart. Experiments were repeated in 4 animals.

extract_protocol: Total RNA was isolated from p-MyoFb, SD-208 treated and TGF-β1 treated cell cultures using TRIzol reagent (Invitrogen, Belgium) and purified on RNeasy Mini Kit columns (Qiagen). 0.5 µg of total RNA was used for cDNA synthesis with the SuperScript VILO cDNA synthesis kit (Invitrogen, Belgium). The cDNA was diluted 50-fold. qRT-PCR was performed on a 7500 Fast Real-Time PCR machine using the SYBRGreen master mix (Applied Biosystems, Belgium).  The relative gene expression was calculated by comparing cycle times for target PCR using the following equation: relative gene expression = 2−(ΔCtsample—ΔCtcontrol.

treatment_protocol: Treatment with TGF-β1

value: Wistar rats

tag: gender

value: male

tag: weight

value: left ventricular cardiac tissue

tag: cells

value: cardiac fibroblasts


title: ADN231

source_name: Total DNA from sample ADN231 labeled with Cyanine-5 (red).


title: H37Rv_CAP


title: F-40D

source_name: Total DNA from sample F-40D labeled with Cyanine-5 (red).


title: 10-RC-317

description: Abrreviation: p-MyoFb

source_name: Cardiac proliferating myofibroblasts

treatment_protocol: Spontaneous differentiation in standard DMEM culture medium + 10 % fetal bovine serum


title: 11-RS-317

description: Abrreviation: Fb

source_name: Cardiac fibroblasts

treatment_protocol: Inhibition of TGF-β1-receptor 1 kinase with SD-208


title: 8-RS-314

description: Abrreviation: Fb


title: 538.02P

source_name: Total DNA from sample 538.02P labeled with Cyanine-5 (red).


title: 535.02P

source_name: Total DNA from sample 535.02P labeled with Cyanine-5 (red).


title: 533.02P

source_name: Total DNA from sample 533.02P labeled with Cyanine-5 (red).


title: 7-RC-314

description: Abrreviation: p-MyoFb


title: CHO-K1_0mM-MIDEXP-R2

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

hyb_protocol: Slides were hybridized over night at 56°C in a Tecan HS 400 hybridization station, followed by automated washing and drying with nitrogen (Tecan, Austria).

scan_protocol: Immediately after drying, arrays were scanned using the Roche Nimblegen MS200 scanner (Roche, Germany) at 10 µM resolution and auto-gain settings.

data_processing: Feature extraction from high-resolution tiff-images was performed using GenePix software (Molecular Devices, Sunnyvale, CA). Background correction, normalization and statistical analysis were performed as previously described (Hackl et al., 2010), using the LIMMA package under R/Bioconductor (Smyth, 2004). Normexp background correction and Global Loess normalization were performed and log2-fold changes of miRNAs for each sample were calculated against the common reference sample and served as relative expression value for each miRNA. Pearson correlation was performed to test for positive or negative correlation of miRNA expression with specific growth rate.

organism: Cricetulus griseus

source_name: Chinese hamster ovary cell line, 48 hours post seeding

label_protocol: End-labeling of 800 ng of total RNA was performed using the Exiqon Power Labeling Kit (Exiqon, Denmark) together with synthetic spike-in controls according to the instructions by the manufacturer.

growth_protocol: Suspension and serum-free adapted CHO-DUKXB-11 cells were grown in DMEM:Ham´s F12 (1:1) supplemented with 4 mM L-Glutamine and protein-free additives without growth-factors (CHO-DUKXB-11). All other cell lines were cultivated in CD CHO media (Life Technologies) supplemented with 8 mM L-Glutamine (CHO-K1-8mM and CHO-S) or without (CHO K1 0mM) and 1:500 anti-clumping agent (Life Technologies). Recombinant CHO-DUKXB-11 cells expressing an erythropoietin-Fc fusion protein were grown in suspension in CD CHO media with 0.019 µM methotrexate and without L-glutamine supplementation (Taschwer et al., 2011). No defined growth factors such as Insulin or IGF were used as additives in this study.  All cell lines were cultivated in suspension in Erlenmeyer shake flasks in 50 ml volume at 140 rpm in a shaking incubator (Kuhner, Switzerland) in a humidified atmosphere (90%) conditioned with 7% CO2. Total RNA was extracted 48 hours post seeding in a new Erlenmeyer flask.

extract_protocol: Isolation of total RNA was performed using phenol-chloroform extraction from Trizol lysed CHO cell pellets. In brief, CHO suspension cells were lysed in 1ml TRI reagent (Sigma-Aldrich) and stored at -80°C or processed immediately. Adherent CHO cell lines were detached from the surface by trypsinization, PBS-washed and lysed in 1 ml TRI reagent. RNA extraction using chloroform and purification were performed as described previously (Hackl et al., 2011). RNA pellets were resuspended in nuclease-free water (Life Technologies) and concentrations and purity were analyzed through absorption at 230, 260, and 280 nm using a NanoDrop spectrophotometer (Thermo Scientific).

treatment_protocol: No treatments were performed

tag: cell line

value: CHO-K1 host

tag: growth phase

value: midexp

tag: growth rate

source_name: Chinese hamster ovary cell pool

value: DUKXB-11, CHO-K1, CHO-S

value: not applicable


title: CHO-S-MIDEXP-R2

value: CHO-S host


title: CHO-S-MIDEXP-R1


title: CHO-K1_8mM-MIDEXP-R2


title: 525.02P

source_name: Total DNA from sample 525.02P labeled with Cyanine-5 (red).


title: CHO-K1_8mM-MIDEXP-R1


title: ADN461.2

source_name: Total DNA from sample ADN461.2 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN460.2

source_name: Total DNA from sample ADN460.2 labeled with Cyanine-5 (red).


title: 5-RS-401

description: Abrreviation: Fb


title: ADN480

source_name: Total DNA from sample ADN480 labeled with Cyanine-5 (red).


title: 9-RT-314

description: Abrreviation: non-p-MyoFb


title: CHO-EpoFc-MIDEXP-R2

value: DUKXB-11 recombinant


title: CHO-EpoFc-MIDEXP-R1


title: 508.02P

source_name: Total DNA from sample 508.02P labeled with Cyanine-5 (red).


title: 523.02P

source_name: Total DNA from sample 523.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 3-RT-284

description: Abrreviation: non-p-MyoFb


title: 4-RC-401

description: Abrreviation: p-MyoFb


title: CHO-DUKXB11-MIDEXP-R2

value: DUKXB-11 host


title: CHO-DUKXB11-MIDEXP-R1


title: ADN506

source_name: Total DNA from sample ADN506 labeled with Cyanine-5 (red).


title: ADN516.2

source_name: Total DNA from sample ADN516.2 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 22F labeled with Cyanine-3 (green).


title: MOSTRA-D1

source_name: Total DNA from sample MOSTRA-D1 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample REF-D labeled with Cyanine-3 (green).


title: MOSTRA-C1

source_name: Total DNA from sample MOSTRA-C1 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample REF-C labeled with Cyanine-3 (green).


title: ADN505

source_name: Total DNA from sample ADN505 labeled with Cyanine-5 (red).


title: 6-RT-401

description: Abrreviation: non-p-MyoFb


title: 2-RS-284

description: Abrreviation: Fb

source_name: Cardiac fibroblasts


title: 1-RC-284

description: Abrreviation: p-MyoFb

source_name: Cardiac proliferating myofibroblasts


title: 0912-132

source_name: Total DNA from sample 0912-132 labeled with Cyanine-5 (red).


title: MOSTRA-A1

source_name: Total DNA from sample MOSTRA-A1 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample REF-A labeled with Cyanine-3 (green).


title: MOSTRA-B1

source_name: Total DNA from sample MOSTRA-B1 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample REF-B labeled with Cyanine-3 (green).


title: ADN478

source_name: Total DNA from sample ADN478 labeled with Cyanine-5 (red).


title: 10F05P

source_name: Total DNA from sample 10F05P labeled with Cyanine-5 (red).


title: 1003-185_2

source_name: Total DNA from sample 1003-185_2 labeled with Cyanine-5 (red).


title: 1003-159_2

source_name: Total DNA from sample 1003-159_2 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: HESCs, coup-TFII siRNA, patient #2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: HESCs, coup-TFII siRNA, patient #2

hyb_protocol: According to Affymetix protocol.

scan_protocol: According to Affymetix protocol.

data_processing: Microarray CEL files were analyzed using dChip (www.dchip.org, PM-MM model, Quantile normalization). The combat software (http://statistics.byu.edu/johnson/ComBat/Abstract.html) was used to normalize patient-specific differences.

label_protocol: According to Affymetix protocol.

growth_protocol: Primary human endometrial stromal cells (HESCs) were seeded in 6-well plates and allowed to reach approximately 70% confluency.

extract_protocol: Total RNA was extracted using the Qiagen RNAeasy total RNA isolation kit (Qiagen, Valencia, CA). The RNA from three replicates (wells) was pooled for each treatment per cell line. The integrity of all RNA samples were tested with the Bioanalyzer 2100 (Agilent Technologies, Wilmington, DE). The concentration of RNA was quantified on the Nanodrop Spectrophotometer (Nanodrop Technologies, Wilmington, DE). The samples with 260/280 greater than 1.8 were used for microarray hybridization.

treatment_protocol: Transfection of non-targeting control or COUP-TFII on-target siRNA was done using Lipofectamine 2000 (Life technologies, Carlsbad, CA) according to manufacturer’s protocol. Forty-eight hours after transfection, HESC decidualization was induced by treatment with decidual media (Opti-MEM media containing 2% charcoal-stripped FBS, 1% antibiotic-antimycotic, 1 µM Medroxyprogesterone acetate (MPA), 10 nM E2, and 50 µM dibutyryl Cyclic adenosine monophosphate (cAMP)). Media containing decidual hormones was changed every 48 h.

tag: cell type

tag: transfection

value: coup-TFII siRNA


title: ADN479

source_name: Total DNA from sample ADN479 labeled with Cyanine-5 (red).

tag: tissue

value: Amniotic Fluid

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: HESCs, coup-TFII siRNA, patient #3

description: HESCs, coup-TFII siRNA, patient #3

source_name: Primary human endometrial stromal cells (HESCs)


title: NLP6-SUPRD_line7_0hr_rep3

city: Bunkoy-ku

first: Shuichi

last: Yanagisawa

state: Tokyo

address: Yayoi 1-1-1

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

description: Gene expression before treatment in seedlings of NLP6-SUPRD line 7

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Arabidopsis Gene Expression 4x44k Microarrays (G1529F015241) 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 Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (eXtended Dynamic range scan, Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 021169_D_F_20080807) to obtain background subtracted and spatially detrended Processed Signal intensities.
The 75th percentile signal intensity for each array was calculated using Microsoft Excel software

organism: Arabidopsis thaliana

source_name: NLP6-SUPRD line 7 seedling, 0hr, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1000 ng RNA using the Low-input Quick Amp Labeling Kit, One-Color (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked using a Spectrophotometer.

growth_protocol: Seeds of the parental line (4xNRE-min-GUS line 1) and NLP6-SUPRD lines 7 and 14 were sown into liquid medium containing 2.5 mM ammonium succinate as sole nitrogen source (half-strength Murashige-Skoog medium from which KNO3 and NH4NO3 were omitted, Gamborg's vitamin, 0.5 g/L 2-morpholinoethanesulfonic acid, monohydrate, pH adjusted to 6.5 with KOH, 2.5 mM ammonium succinate). After stratification for 3 days, plates containing the liquid medium and the seeds were transferred to a growth chamber set to a continuous light condition at 23°C.

extract_protocol: Total RNA was isolated using Isogen reagent and then treated with DNase I. RNA was purified using the RNeasy mini kit (QIAGEN). The quality of RNA was checked by measuring absorbance at 230, 260 and 280 nm using a spectrophotometer.

treatment_protocol: After incubation for 3.5 days at 23°C, medium was changed to a fresh medium containing 10 mM KNO3, and after 1 hour of incubation, whole seedlings were collected.

value: whole seedling

tag: age

tag: genotype/variation

value: 35SΩ-NLP6-NLS-SUPRD transgenic line 7

tag: agent

value: untreated


title: HESCs, control siRNA, patient #2

description: HESCs, control siRNA, patient #2

value: Primary human endometrial stromal cells (HESCs)

value: control siRNA


title: NLP6-SUPRD_line7_1hr_10mMKNO3_rep1

description: Gene expression after 1hr in 10 mM KNO3 treatment in seedlings of NLP6-SUPRD line 7

source_name: NLP6-SUPRD line 7 seedling, 1hr,10 mM KNO3, replicate 1


title: HESCs, control siRNA, patient #3

description: HESCs, control siRNA, patient #3


title: HESCs, coup-TFII siRNA, patient #1

description: HESCs, coup-TFII siRNA, patient #1


title: ADN524

source_name: Total DNA from sample ADN524 labeled with Cyanine-5 (red).

value: fresh peripheral blood


title: ADN522

source_name: Total DNA from sample ADN522 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 22F labeled with Cyanine-3 (green).


title: NLP6-SUPRD_line7_1hr_10mMKNO3_rep2

source_name: NLP6-SUPRD line 7 seedling, 1hr,10 mM KNO3, replicate 2


title: NLP6-SUPRD_line7_1hr_10mMKNO3_rep3

source_name: NLP6-SUPRD line 7 seedling, 1hr,10 mM KNO3, replicate 3


title: ADN521

source_name: Total DNA from sample ADN521 labeled with Cyanine-5 (red).


title: HESCs, control siRNA, patient #1

description: HESCs, control siRNA, patient #1


title: NLP6-SUPRD_line14_1hr_10mMKNO3_rep3

description: Gene expression after 1hr in 10 mM KNO3 treatment in seedlings of NLP6-SUPRD line 14

source_name: NLP6-SUPRD line 14 seedling, 1hr,10 mM KNO3, replicate 1

value: 35SΩ-NLP6-NLS-SUPRD transgenic line 14


title: NLP6-SUPRD_line7_0hr_rep1

source_name: NLP6-SUPRD line 7 seedling, 0hr, replicate 1


title: F29P

source_name: Total DNA from sample F29P labeled with Cyanine-5 (red).


title: NLP6-SUPRD_line7_0hr_rep2

source_name: NLP6-SUPRD line 7 seedling, 0hr, replicate 2


title: HV3_6

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

institute: CIMA

description: venous endothelial cells

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133Plus2 chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.

data_processing: Data were normalized with Bioconductor software using RMA algorithm.

source_name: cultured hepatic vein endothelial cells

label_protocol: The cDNA was prepared from 2 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affymetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy MiniKit (Qiagen, Hilden, Germany).

value: cultured hepatic vein endothelial cells

tag: cell culture bank

value: Cells were isolated in Clinica Universidad de Navarra after obtaining informed consent

tag: isolation method

value: Corresponding vessel was perfused with Collagenase Type I. Harvested cells were cultured for 24 hours, washed to discard non-attached cells, grown until 100% confluence and split 1:3 every 3-4 days


title: ADN520

source_name: Total DNA from sample ADN520 labeled with Cyanine-5 (red).


title: HV2_5

description: venous endothelial cells


title: ADN519

source_name: Total DNA from sample ADN519 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: HUVEC_F9_5

description: venous endothelial cells

source_name: freshly isolated umbilical vein endothelial cells

value: human umbilical vein endothelial cells were magnetically purified using CD34 antibody and check for EC purity by CD31, CD34 and CD45 FACS analysis. Samples were directly processed for RNA extraction without any kind of culture


title: HV1_4

description: venous endothelial cells


title: NLP6-SUPRD_line14_1hr_10mMKNO3_rep1


title: WT_1hr_10mMKNO3_rep3

description: Gene expression after 1hr in 10 mM KNO3 treatment in seedlings of the parental line

source_name: WT seedling, 1hr,10 mM KNO3, replicate 3

value: WT parental line


title: NLP6-SUPRD_line14_1hr_10mMKNO3_rep2


title: ADN518

source_name: Total DNA from sample ADN518 labeled with Cyanine-5 (red).


title: ADN517

source_name: Total DNA from sample ADN517 labeled with Cyanine-5 (red).


title: ADN513

source_name: Total DNA from sample ADN513 labeled with Cyanine-5 (red).


title: HUVEC_F7_14

description: venous endothelial cells

value: freshly isolated umbilical vein endothelial cells


title: HUVEC_F6_7

description: venous endothelial cells


title: NLP6-SUPRD_line14_0hr_rep2

description: Gene expression before treatment in seedlings of NLP6-SUPRD line 14

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 021169_D_F_20080807) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: NLP6-SUPRD line 14 seedling, 0hr, replicate 2


title: 620P

source_name: Total DNA from sample 620P labeled with Cyanine-5 (red).


title: ADN514

source_name: Total DNA from sample ADN514 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 22F labeled with Cyanine-3 (green).


title: WT_1hr_10mMKNO3_rep1

source_name: WT seedling, 1hr,10 mM KNO3, replicate 1


title: 27b_ADM

first: Lijian

last: Hui

address: Yueyang Road 320

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy for Sciences

description:
Cells transfected with miR-27b mimics followed by 48 hours doxorubicin treatment
Gene expression 48h after doxorubicin treatment

hyb_protocol: Each Slide was hybridized with 1.65 ug Cy3-labeled cRNA using Gene Expression Hybridization Kit(Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer's instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer's instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5um, PMT 100%, 10%, 16 bit.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Hela

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labelling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer's instructions. Labeled cRNA were purified by Rneasy mini Kit(Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Cells were cultured in DMEM medium

extract_protocol: Total RNA was isolated from cells by Trizol (Invitrogen) and further purified by RNeasy mini Kit and RNase-Free DNase Set following manufacturer's introductions,

treatment_protocol: Cells were transfected with nontarget miRNA control or miR-27b mimics, 48h later cells were treated with doxorubicin for 48h

value: Hela

value: Female

value: miR-27b mimics


title: HUVEC_C4_6

description: venous endothelial cells

source_name: cultured umbilical vein endothelial cells


title: HUVEC_F5_6

description: venous endothelial cells


title: HUVEC_C5_15

description: venous endothelial cells

value: cultured umbilical vein endothelial cells


title: NLP6-SUPRD_line14_0hr_rep3

source_name: NLP6-SUPRD line 14 seedling, 0hr, replicate 3

value: whole seedling


title: CHO-K1_0mM-MIDEXP-R1

source_name: Chinese hamster ovary cell line, 48 hours post seeding

value: CHO-K1 host

value: midexp

source_name: Chinese hamster ovary cell pool

value: DUKXB-11, CHO-K1, CHO-S

value: not applicable


title: NLP6-SUPRD_line14_0hr_rep1

source_name: NLP6-SUPRD line 14 seedling, 0hr, replicate 1

value: untreated


title: Breast tissue_Pt_121

city: New Taipei City

first: Chi-Cheng

last: Huang

address: No.2, Lane 59, Jiancheng Rd. Xizhi Dist.

department: Department of Medical Education and Research

country: Taiwan

institute: Cathay General Hospital SiJhih

description: Array comparative genomic hybridization between normal and cancer breast tissues without chemotherapy.

hyb_protocol: DNA were hybridized according to Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, V6.0.

scan_protocol: Scanned on an GenePix 4000B.

data_processing: GenePix Pro 6.0.1.12 was used for background subtraction and Linear Normalization Using Rank Consistent Probes.

source_name: Normal breast tissue

label_protocol: Cy3 or Cy5 labeled DNA were prepared by Agilent Genomic DNA Enzymatic Labeling Kit.

extract_protocol: DNA was extracted from cancerous and matching normal breast tissues from the same subject (n=23) by using a QIAamp DNA mini kit (Qiagen, Valencia, CA).

value: Breast

value: Over-expression

tag: er

value: Negative

source_name: Breast cancer tumor tissue


title: HUVEC_C2_15

description: venous endothelial cells

value: Cells were isolated in Clinica Universidad de Navarra after obtaining informed consent

value: Corresponding vessel was perfused with Collagenase Type I. Harvested cells were cultured for 24 hours, washed to discard non-attached cells, grown until 100% confluence and split 1:3 every 3-4 days


title: Non_ADM

description:
Cells transfected with nontarget control followed by 48 hours doxorubicin treatment
Gene expression 48h after doxorubicin treatment

value: nontarget miRNA control


title: 1001-202

source_name: Total DNA from sample 1001-202 labeled with Cyanine-5 (red).

value: Amniotic Fluid

value: fresh peripheral blood


title: WT_1hr_10mMKNO3_rep2

source_name: WT seedling, 1hr,10 mM KNO3, replicate 2

value: WT parental line


title: 594P_B

source_name: Total DNA from sample 594P_B labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: Breast tissue_Pt_108


title: WT_0hr_rep3

description: Gene expression before treatment in seedlings of the parental line

source_name: WT seedling, 0hr, replicate 3


title: WT_0hr_rep2

source_name: WT seedling, 0hr, replicate 2


title: WT_0hr_rep1

source_name: WT seedling, 0hr, replicate 1


title: 622_02P

source_name: Total DNA from sample 622_02P labeled with Cyanine-5 (red).


title: Breast tissue_Pt_78

value: Normal


title: HUAEC_F8_3

description: arterial endothelial cells

source_name: freshly isolated umbilical artery endothelial cells

value: human umbilical artery endothelial cells were magnetically purified using CD34 antibody and check for EC purity by CD31, CD34 and CD45 FACS analysis. Samples were directly processed for RNA extraction without any kind of culture


title: HUVEC_C3_16

description: venous endothelial cells

value: cultured umbilical vein endothelial cells


title: 594_02P

source_name: Total DNA from sample 594_02P labeled with Cyanine-5 (red).


title: HUAEC_F13_2

description: arterial endothelial cells

value: freshly isolated umbilical artery endothelial cells


title: HUVEC_C1_8

description: venous endothelial cells

source_name: cultured umbilical vein endothelial cells


title: Breast tissue_Pt_119

value: Positive


title: 593_02P

source_name: Total DNA from sample 593_02P labeled with Cyanine-5 (red).


title: Breast tissue_Pt_76


title: HUAEC_F10_12

description: arterial endothelial cells


title: HUAEC_F12_10

description: arterial endothelial cells


title: AIM-KO (HFD 20W), biological rep2

city: Osaka

first: Toshihiro

last: Kai

state: Osaka

address: 3-1-98 Kasugade-naka, Konohana-ku

department: Genomics Research

institute: Dainippon Sumitomo Pharma Co., Ltd.

description:
AIM-KO_20w_2
Gene expression data from liver of AIM-deficient mouse fed high fat diet for 20 weeks

hyb_protocol: Standard Affymetrix procedures using Affymetrix GeneChip Hybridization Oven 640 and Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Mus musculus

source_name: Liver of AIM-deficient mouse fed high fat diet for 20 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

extract_protocol: Liver samples were homogenized with Trizol, and total RNA was extracted according to the manufacturer's instructions.

treatment_protocol: AIM+/+ and AIM-/- mice were fed an HFD for 0, 12 or 20 weeks.

tag: strain background

value: AIM-KO; AIM-/-

tag: diet

value: high-fat diet (HFD) for 20 weeks

value: liver


title: WT (HFD 20W), biological rep3

description:
WT_20w_3
Gene expression data from liver of wild type mouse fed high fat diet for 20 weeks

source_name: Liver of wild type mouse fed high fat diet for 20 weeks

value: wild type; AIM+/+


title: Breast tissue_Pt_75

value: Breast

value: Over-expression


title: Breast tissue_Pt_72

value: Negative


title: 595_02P

source_name: Total DNA from sample 595_02P labeled with Cyanine-5 (red).


title: WT (HFD 20W), biological rep1

description:
WT_20w_1
Gene expression data from liver of wild type mouse fed high fat diet for 20 weeks


title: AIM-KO (HFD 20W), biological rep1

description:
AIM-KO_20w_1
Gene expression data from liver of AIM-deficient mouse fed high fat diet for 20 weeks


title: 592_02P

description: biological sample used as control/testing purposes in the study.

source_name: Total DNA from sample 592_02P labeled with Cyanine-5 (red).


title: AIM-KO (HFD 12W), biological rep3

description:
AIM-KO_12w_3
Gene expression data from liver of AIM-deficient mouse fed high fat diet for 12 weeks

source_name: Liver of AIM-deficient mouse fed high fat diet for 12 weeks

value: high-fat diet (HFD) for 12 weeks


title: 591_02P

source_name: Total DNA from sample 591_02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 22F labeled with Cyanine-3 (green).


title: 590_02P

source_name: Total DNA from sample 590_02P labeled with Cyanine-5 (red).


title: Breast tissue_Pt_69

source_name: Breast cancer tumor tissue

source_name: Normal breast tissue


title: WT (HFD 20W), biological rep2

description:
WT_20w_2
Gene expression data from liver of wild type mouse fed high fat diet for 20 weeks


title: AIM-KO (HFD 20W), biological rep3

description:
AIM-KO_20w_3
Gene expression data from liver of AIM-deficient mouse fed high fat diet for 20 weeks


title: Breast tissue_Pt_65


title: HUAEC_C6_3

description: arterial endothelial cells

source_name: cultured umbilical artery endothelial cells

value: Cells were isolated in Clinica Universidad de Navarra after obtaining informed consent

value: Corresponding vessel was perfused with Collagenase Type I. Harvested cells were cultured for 24 hours, washed to discard non-attached cells, grown until 100% confluence and split 1:3 every 3-4 days


title: AIM-KO (HFD 12W), biological rep2

description:
AIM-KO_12w_2
Gene expression data from liver of AIM-deficient mouse fed high fat diet for 12 weeks


title: 538_02P

source_name: Total DNA from sample 538_02P labeled with Cyanine-5 (red).

value: Amniotic Fluid

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).

value: fresh peripheral blood


title: WT (HFD 12W), biological rep3

description:
WT_12w_3
Gene expression data from liver of wild type mouse fed high fat diet for 12 weeks

source_name: Liver of wild type mouse fed high fat diet for 12 weeks


title: Breast tissue_Pt_66


title: X964572.1

source_name: Total DNA from sample X964572.1 labeled with Cyanine-5 (red).


title: HUAEC_C1_3

description: arterial endothelial cells

value: cultured umbilical artery endothelial cells


title: Breast tissue_Pt_70

value: Normal


title: WT (HFD 12W), biological rep1

description:
WT_12w_1
Gene expression data from liver of wild type mouse fed high fat diet for 12 weeks


title: AIM-KO (HFD 12W), biological rep1

description:
AIM-KO_12w_1
Gene expression data from liver of AIM-deficient mouse fed high fat diet for 12 weeks


title: Breast tissue_Pt_59


title: Breast tissue_Pt_62


title: HUAEC_C5_12

description: arterial endothelial cells


title: WT (HFD 12W), biological rep2

description:
WT_12w_2
Gene expression data from liver of wild type mouse fed high fat diet for 12 weeks


title: AIM-KO (normal chow), biological rep3

description:
AIM-KO_0w_3
Gene expression data from liver of AIM-deficient mouse fed normal chow diet

source_name: Liver of AIM-deficient mouse fed normal chow diet

value: normal chow


title: AIM-KO (normal chow), biological rep2

description:
AIM-KO_0w_2
Gene expression data from liver of AIM-deficient mouse fed normal chow diet


title: 581_02P

source_name: Total DNA from sample 581_02P labeled with Cyanine-5 (red).


title: HUAEC_C3_11

description: arterial endothelial cells


title: 605P

source_name: Total DNA from sample 605P labeled with Cyanine-5 (red).


title: HUAEC_C2_4

description: arterial endothelial cells


title: HPVE3_12

description: venous endothelial cells

source_name: cultured pulmonary vein endothelial cells

value: ATCC CatNº CRL-2607

value: non-applicable


title: 606P

source_name: Total DNA from sample 606P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: ADN464.2

source_name: Total DNA from sample ADN464.2 labeled with Cyanine-5 (red).


title: AIM-KO (normal chow), biological rep1

description:
AIM-KO_0w_1
Gene expression data from liver of AIM-deficient mouse fed normal chow diet

value: AIM-KO; AIM-/-


title: HPAE5_1

description: arterial endothelial cells

source_name: cultured pulmonary artery endothelial cells

value: ATCC CatNº CRL-2598


title: HPAE4_9

description: arterial endothelial cells

value: cultured pulmonary artery endothelial cells


title: Breast tissue_Pt_42

description: Array comparative genomic hybridization between normal and cancer breast tissues without chemotherapy.


title: Breast tissue_Pt_48


title: HPVE2_4

description: venous endothelial cells

value: cultured pulmonary vein endothelial cells


title: HPAE1_1

description: arterial endothelial cells


title: ADN503

source_name: Total DNA from sample ADN503 labeled with Cyanine-5 (red).