title: Postnatal day 4 lateral subventricular zone transiently amplifying progenitors replicate 3

description: Gene expression of isolated P4 lateral subventricular zone progenitors

source_name: (Ascl1-EGFP+) Progenitor cells isolated from earlier stages of postnatal forebrain development of the subventricular zone at P4


title: Postnatal day 8 dorsal subventricular zone tissue replicate 2

status: Public on Apr 07 2015

type: RNA

city: Zurich

first: Kaz

last: Azim

address: Brain Research Institute

country: Switzerland

institute: Univ of Zurich

description: Gene expression of P8 dorsal subventricular zone tissue

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to Mouse Genome 430-2.0 Array (Affymetrix) as per manufacturer guidelines. Affymetrix chips were incubated at 45°C for 16 hours with biotin-labelled cRNA probes. Following this, these were washed and stained using a streptavidin-phycoerythrin conjugate antibody with an amplification step as described in Affymetrix protocol.

scan_protocol: Chips were scanned on a GC3000 scanner (Affymetrix).

data_processing: Microarray data were preprocessed (background subtraction, normalization, and summarization) via robust multi-chip analysis using the Partek® Genomic Suite software package version 6.6.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Early-mid stages of postnatal forebrain development of the subventricular zone at P8

label_protocol: 400 ng cRNA was reverse transcribed for obtaining biotinylated cRNAs  generated from double-strand cDNAs using an in vitro transcription labelling kit (Affymetrix).

extract_protocol: For the case of the whole SVZ microdomains, microdissected samples were snap frozen in PrepProtect (Miltenyi Biotech), stored in -80 and pooled. Thawed sampled were spun at 2000 g to remove storage stabilizer. For the case FACsed NSCs or early progenitor, following microdissection, tissues were pooled in HBSS (Gibco/Invitrogen) and dissociated using a trypsin-based kit following manufacturer's guidelines (Miltenyl Biotec). NSCs were further immunostained for Prominin1 (Prom1; 1:100, ebiosciences) for 15 mins. Facsed cells were sorted directly into lysis buffer. Tissues/cells were homogenized in RNA lysis buffer containing β-mercaptoethanol, then subsequentlypassed through Qiashredder columns (Qiagen) to obtain lysates. RNAeasy Minikit (Qiagen) containing DNAase treatment as per manufacturer's instructions. RNA quality was assed via a Bioanalyzer. 200 ngs of total RNA was amplified using the Ambion MEGAscript T7 kit and following manufacturers guidelines.

tag: cell type

tag: strain

tag: Stage


title: Postnatal day 4 dorsal subventricular zone transiently amplifying progenitors replicate 2

description: Gene expression of isolated P4 dorsal subventricular zone progenitors


title: Postnatal day 4 dorsal subventricular zone purified neural stem cells replicate 3

description: Gene expression of isolated P4 dorsal subventricular zone neural stem cells

source_name: (Hes5-EGFP+/Prom1+) Stem cells isolated from earlier stages of postnatal forebrain development of the subventricular zone at P4


title: Postnatal day 8 lateral subventricular zone  tissue replicate 1

description: Gene expression of P8 lateral subventricular zone tissue


title: Postnatal day 4 dorsal subventricular zone transiently amplifying progenitors replicate 1


title: normal breast tissue N007

type: genomic

city: Chapel Hill

first: Kathleen

middle: Conway

last: Dorsey

state: NC

address: CB 7435, 2101 McGavran-Greenberg Hall

department: Epidemiology

country: USA

institute: University of North Carolina at Chapel Hill

description: FFPE

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Cancer Panel I array using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: non-study

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from FFPE tumor using a proteinase K digestion protocol

tag: gender

value: female


title: normal breast tissue N009

description: FFPE


title: normal breast tissue N008

description: FFPE


title: Postnatal day 4 dorsal subventricular zone transiently amplifying progenitors replicate 3


title: Postnatal day 4 dorsal subventricular zone purified neural stem cells replicate 1


title: Postnatal day 4 lateral subventricular zone  tissue replicate 2

description: Gene expression of P4 lateral subventricular zone tissue

source_name: Earlier stages of postnatal forebrain development of the subventricular zone at P4


title: Postnatal day 4 lateral subventricular zone  tissue replicate 1


title: Postnatal day 8 dorsal subventricular zone tissue replicate 1


title: Postnatal day 4 dorsal subventricular zone tissue replicate 1

description: Gene expression of P4 dorsal subventricular zone tissue


title: Postnatal day 4 lateral subventricular zone purified neural stem cells replicate 1

description: Gene expression of isolated P4 lateral subventricular zone neural stem cells


title: Postnatal day 8 lateral subventricular zone  tissue replicate 2


title: ABP1 knockdown short treatment, replicate 2

city: Valencia

first: David

last: Alabadi

state: Valencia

address: Av de los Naranjos s/n, Campus UPV, Edificio 8E

department: Biologia del Desarrollo

country: Spain

institute: Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)

description:
Amplified RNA.
4-day-old etiolated seedlings.
SS12K9 short-term treated samples labelled with Cy5 compared to Alc-GUS samples labelled with Cy3 (replica 2).

hyb_protocol: DNA onto slides was rehydrated by placing the slide upside-down over a water bath at 60°C for 3 s, and snap dry onto a heat block at 65°C. Rehydratation was repeated 3 times. DNA was immobilized by UV light by exposing the slides DNA-side-up to 65 mJ in a UV cross-linker (Stratagene). Slides were then washed twice in 0.1% SDS and 4 times in water, 2 min each wash at RT, and finally dipped in 96% ethanol for 1 min and dried by centrifugation at 2000 rpm 1 min at RT. Slides were prehybridized for 30 min at 42°C with 100 µL of prehybridization solution (6x SSC (Sigma), 1% BSA (Sigma) and 0.5% SDS (Sigma)), under a 60x22 mm coverslip LifterSlip (Erie Scientific) in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were rinsed 5 times in H2O in a slide rack at RT and dried by centrifugation at 2000 rpm 1 min at RT. Slides were hybridized immediately. Both coupled aa-aRNA (Cy3 and Cy5) were mixed and fragmented in the presence of 20 µg of tRNA (Ambion) and 20 µg of poly(A) (Roche) using the RNA fragmentation Reagent (Ambion) as described by the manufacturer, in a final volume of 10 µL. Fragmented aa-aRNA was used directly in the hybridization mix, which contains 50 µL deionized formamide (Sigma), 30 µL 20x SSC, 5 µL 100x Denhardt´s solution (Sigma), and 5 µL 10% SDS in a final volume of 100 µL. Hybridization mixture was denatured at 95 °C for 5 min, spun briefly, and applied by capillarity between a pre-treated slide (see above) and a 60x42 mm coverslip LifterSlip. Slides were incubated o/n at 37°C in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were washed sequentially once in 1x SSC 0.1% SDS 5 min at 30°C; once in 0.2x SSC 0.1% SDS 5 min at 30°C; twice in 0.1x SSC 2 min each at 30°C; and finally 0.01x SSC 10 sec at RT. Slides were dried by centrifugation at 2000 rpm 1 min at RT.

scan_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 10-mm resolution and 100% laser power.

data_processing: Spot intensities were quantified using GenePix Pro 6.0 microarray-analysis software (Axon Molecular Devices, Sunnyvale CA). Spots with a net intensity in both channels lower than the median signal background plus twice standard deviations were removed as low signal spots. Data were normalized by median global intensity using the GenePix Pro 6.0 software.

organism: Arabidopsis thaliana

source_name: SS12K9 line ethanol-treated for 8 h

label_protocol: RNA was amplified using the MessageAmp II aRNA Amplification kit (Ambion), basically as described by the manufacturer. 5-(3-aminoallyl)-UTP (aa-UTP) (Ambion) was incorporated into the amplified RNA (aRNA) at ratio 1:1 with UTP. After purification 7.5 µg of aminoallyl-aRNA (aa-aRNA) were used in a coupling reaction with either fluorescent Cy3 or Cy5 as reactive N-hydroxyl succinimidal dyes (NHS-dyes) (Amersham Pharmacia Biotech, Piscataway, NJ). For this, each aliquot of Cy3 or Cy5 were dissolved in 20 µL of DMSO and used in four coupling reactions. aa-aRNA was dissolved in 15 µL of freshly-made 0.1 M NaCO3 pH 9.0, and mixed with 5 µl of either Cy-3 or Cy-5 dye. Coupling was allowed for 1 h at RT in the dark. Reaction was stopped with 35 µL of 100 mM sodium acetate pH 5.2 and incubated 5 min in the dark. Fluorescent aa-aRNA was purified using a MegaClear purification column (Ambion) as described by the manufacturer. Coupled aa-aRNA (250-300 pmol Cy dye in 5-7 µg aa-aRNA) was dried in a speedvac and dissolved in 2.5 µL of filtered water.

growth_protocol: Four-day-old dark grown seedlings of WT and SS12K ABP1 conditional line were harvested under green light at day 4 (96h) after culture in the dark.

extract_protocol: RNA was extracted using a Qiagen RNeasy kit and digested with RNase-free DNase on the column following the manufacturer's instructions (Qiagen S.A., Courtaboeuf, France) and RNA quantification and quality control were achieved using 2100 Bioanalyzer RNA chip (Agilent).

treatment_protocol: Seedlings were induced by ethanol vapor either since their transfer in darkness (96 h) or 8h before harvesting. Three independent biological replicates were used for each condition.

tag: line

tag: tissue

value: seedlings

tag: age

value: 4 days

tag: treatment

value: ethanol for 8 h

source_name: Alc-GUS line ethanol-treated for 8 h

value: Alc-GUS


title: Postnatal day 4 lateral subventricular zone purified neural stem cells replicate 2


title: Postnatal day 4 dorsal subventricular zone purified neural stem cells replicate 2


title: Postnatal day 4 lateral subventricular zone transiently amplifying progenitors replicate 2


title: normal breast tissue N006

description: FFPE


title: Postnatal day 11 dorsal subventricular zone tissue replicate 1

description: Gene expression of P11 dorsal subventricular zone tissue

source_name: Later stages of postnatal forebrain development of the subventricular zone at P11


title: ABP1 knockdown short treatment, replicate 3

description:
Amplified RNA.
4-day-old etiolated seedlings.
SS12K9 short-term treated samples labelled with Cy3 compared to Alc-GUS samples labelled with Cy5 (replica 3).


title: normal breast tissue N004

description: FFPE


title: normal breast tissue N005

description: FFPE


title: Postnatal day 4 lateral subventricular zone transiently amplifying progenitors replicate 1


title: Postnatal day 4 dorsal subventricular zone tissue replicate 2


title: invasive breast tumor C155

description: FFPE

source_name: CBCS

tag: hr+ (1=pos, 0=neg)

tag: intrinsic subtype

tag: vital status (1=dead, 0=censored at 12/31/06)

tag: age at diagnosis (yrs)


title: invasive breast tumor C596

description: FFPE


title: invasive breast tumor C725

description: FFPE


title: invasive breast tumor C554

description: FFPE


title: normal breast tissue N003

description: FFPE


title: normal breast tissue N002

description: FFPE


title: normal breast tissue N001

description: FFPE


title: invasive breast tumor C280

description: FFPE


title: invasive breast tumor C278

description: FFPE


title: invasive breast tumor C196

description: FFPE


title: invasive breast tumor C134

description: FFPE


title: invasive breast tumor C493

description: FFPE


title: invasive breast tumor C543

description: FFPE


title: invasive breast tumor C423

description: FFPE


title: invasive breast tumor C768

description: FFPE


title: invasive breast tumor C150

description: FFPE


title: invasive breast tumor C135

description: FFPE


title: invasive breast tumor C161

description: FFPE


title: invasive breast tumor C765

description: FFPE


title: invasive breast tumor C615

description: FFPE


title: ABP1 knockdown short treatment, replicate 1

description:
Amplified RNA.
4-day-old etiolated seedlings.
SS12K9 short-term treated samples labelled with Cy5 compared to Alc-GUS samples labelled with Cy3 (replica 1).


title: invasive breast tumor C432

description: FFPE


title: invasive breast tumor C288

description: FFPE


title: invasive breast tumor C582

description: FFPE


title: invasive breast tumor C173

description: FFPE


title: invasive breast tumor C258

description: FFPE


title: invasive breast tumor C576

description: FFPE


title: invasive breast tumor C478

description: FFPE


title: invasive breast tumor C098

description: FFPE


title: invasive breast tumor C209

description: FFPE


title: invasive breast tumor C568

description: FFPE


title: invasive breast tumor C531

description: FFPE


title: invasive breast tumor C043

description: FFPE


title: invasive breast tumor C003

description: FFPE


title: invasive breast tumor C143

description: FFPE


title: invasive breast tumor C420

description: FFPE


title: invasive breast tumor C509

description: FFPE


title: invasive breast tumor C289

description: FFPE


title: invasive breast tumor C242

description: FFPE


title: invasive breast tumor C163

description: FFPE


title: invasive breast tumor C170

description: FFPE


title: invasive breast tumor C490

description: FFPE


title: invasive breast tumor C399

description: FFPE


title: invasive breast tumor C515

description: FFPE


title: invasive breast tumor C544

description: FFPE


title: invasive breast tumor C407

description: FFPE


title: invasive breast tumor C549

description: FFPE


title: invasive breast tumor C055

description: FFPE


title: invasive breast tumor C310

description: FFPE


title: invasive breast tumor C311

description: FFPE


title: invasive breast tumor C421

description: FFPE


title: invasive breast tumor C315

description: FFPE


title: invasive breast tumor C205

description: FFPE


title: invasive breast tumor C418

description: FFPE


title: invasive breast tumor C545

description: FFPE


title: invasive breast tumor C306

description: FFPE


title: invasive breast tumor C009

description: FFPE


title: invasive breast tumor C775

description: FFPE


title: invasive breast tumor C539

description: FFPE


title: invasive breast tumor C424

description: FFPE


title: invasive breast tumor C789

description: FFPE


title: invasive breast tumor C039

description: FFPE


title: invasive breast tumor C670

description: FFPE


title: invasive breast tumor C731

description: FFPE


title: invasive breast tumor C417

description: FFPE


title: invasive breast tumor C411

description: FFPE


title: invasive breast tumor C585

description: FFPE


title: invasive breast tumor C814

description: FFPE


title: invasive breast tumor C342

description: FFPE


title: invasive breast tumor C500

description: FFPE


title: invasive breast tumor C449

description: FFPE


title: invasive breast tumor C279

description: FFPE


title: invasive breast tumor C722

description: FFPE


title: invasive breast tumor C303

description: FFPE


title: invasive breast tumor C588

description: FFPE


title: invasive breast tumor C665

description: FFPE


title: invasive breast tumor C065

description: FFPE


title: invasive breast tumor C059

description: FFPE


title: invasive breast tumor C696

description: FFPE


title: invasive breast tumor C669

description: FFPE


title: invasive breast tumor C384

description: FFPE


title: invasive breast tumor C133

description: FFPE


title: invasive breast tumor C224

description: FFPE


title: invasive breast tumor C176

description: FFPE


title: invasive breast tumor C505

description: FFPE


title: invasive breast tumor C298

description: FFPE


title: invasive breast tumor C247

description: FFPE


title: invasive breast tumor C559

description: FFPE


title: invasive breast tumor C575

description: FFPE


title: invasive breast tumor C617

description: FFPE


title: invasive breast tumor C159

description: FFPE


title: invasive breast tumor C222

description: FFPE


title: invasive breast tumor C817

description: FFPE


title: invasive breast tumor C773

description: FFPE


title: invasive breast tumor C212

description: FFPE


title: invasive breast tumor C409

description: FFPE


title: invasive breast tumor C428

description: FFPE


title: invasive breast tumor C439

description: FFPE


title: invasive breast tumor C370

description: FFPE


title: invasive breast tumor C366

description: FFPE


title: invasive breast tumor C566

description: FFPE


title: invasive breast tumor C309

description: FFPE


title: invasive breast tumor C704

description: FFPE


title: invasive breast tumor C667

description: FFPE


title: invasive breast tumor C260

description: FFPE


title: invasive breast tumor C551

description: FFPE


title: invasive breast tumor C807

description: FFPE


title: invasive breast tumor C191

description: FFPE


title: invasive breast tumor C629

description: FFPE


title: invasive breast tumor C263

description: FFPE


title: invasive breast tumor C710

description: FFPE


title: invasive breast tumor C297

description: FFPE


title: invasive breast tumor C234

description: FFPE


title: invasive breast tumor C154

description: FFPE


title: invasive breast tumor C188

description: FFPE


title: invasive breast tumor C606

description: FFPE


title: invasive breast tumor C136

description: FFPE


title: invasive breast tumor C202

description: FFPE


title: invasive breast tumor C520

description: FFPE


title: invasive breast tumor C504

description: FFPE


title: invasive breast tumor C447

description: FFPE


title: invasive breast tumor C253

description: FFPE


title: invasive breast tumor C022

description: FFPE


title: invasive breast tumor C208

description: FFPE


title: invasive breast tumor C633

description: FFPE


title: invasive breast tumor C092

description: FFPE


title: invasive breast tumor C050

description: FFPE


title: invasive breast tumor C076

description: FFPE


title: invasive breast tumor C684

description: FFPE


title: invasive breast tumor C581

description: FFPE


title: invasive breast tumor C630

description: FFPE


title: invasive breast tumor C623

description: FFPE


title: invasive breast tumor C046

description: FFPE


title: invasive breast tumor C327

description: FFPE


title: invasive breast tumor C524

description: FFPE


title: invasive breast tumor C783

description: FFPE


title: invasive breast tumor C122

description: FFPE


title: invasive breast tumor C707

description: FFPE


title: invasive breast tumor C402

description: FFPE


title: invasive breast tumor C818

description: FFPE


title: invasive breast tumor C312

description: FFPE


title: invasive breast tumor C517

description: FFPE


title: invasive breast tumor C087

description: FFPE


title: invasive breast tumor C511

description: FFPE


title: invasive breast tumor C574

description: FFPE


title: invasive breast tumor C681

description: FFPE


title: invasive breast tumor C442

description: FFPE


title: invasive breast tumor C433

description: FFPE


title: invasive breast tumor C179

description: FFPE


title: invasive breast tumor C393

description: FFPE


title: invasive breast tumor C379

description: FFPE


title: invasive breast tumor C232

description: FFPE


title: invasive breast tumor C586

description: FFPE


title: invasive breast tumor C678

description: FFPE


title: invasive breast tumor C101

description: FFPE


title: invasive breast tumor C203

description: FFPE


title: invasive breast tumor C437

description: FFPE


title: invasive breast tumor C277

description: FFPE


title: invasive breast tumor C201

description: FFPE


title: invasive breast tumor C376

description: FFPE


title: invasive breast tumor C625

description: FFPE


title: invasive breast tumor C412

description: FFPE


title: invasive breast tumor C648

description: FFPE


title: invasive breast tumor C711

description: FFPE


title: invasive breast tumor C294

description: FFPE


title: invasive breast tumor C206

description: FFPE


title: invasive breast tumor C640

description: FFPE


title: invasive breast tumor C523

description: FFPE


title: invasive breast tumor C434

description: FFPE


title: invasive breast tumor C374

description: FFPE


title: invasive breast tumor C772

description: FFPE


title: invasive breast tumor C017

description: FFPE


title: invasive breast tumor C137

description: FFPE


title: invasive breast tumor C151

description: FFPE


title: invasive breast tumor C467

description: FFPE


title: invasive breast tumor C115

description: FFPE


title: invasive breast tumor C609

description: FFPE


title: invasive breast tumor C507

description: FFPE


title: invasive breast tumor C753

description: FFPE


title: invasive breast tumor C698

description: FFPE


title: invasive breast tumor C645

description: FFPE


title: invasive breast tumor C251

description: FFPE


title: invasive breast tumor C075

description: FFPE


title: invasive breast tumor C380

description: FFPE


title: invasive breast tumor C403

description: FFPE


title: invasive breast tumor C218

description: FFPE


title: invasive breast tumor C473

description: FFPE


title: invasive breast tumor C274

description: FFPE


title: invasive breast tumor C410

description: FFPE


title: invasive breast tumor C716

description: FFPE


title: invasive breast tumor C010

description: FFPE


title: invasive breast tumor C636

description: FFPE


title: invasive breast tumor C806

description: FFPE


title: invasive breast tumor C616

description: FFPE


title: invasive breast tumor C720

description: FFPE


title: invasive breast tumor C414

description: FFPE


title: invasive breast tumor C708

description: FFPE


title: invasive breast tumor C354

description: FFPE


title: invasive breast tumor C215

description: FFPE


title: invasive breast tumor C812

description: FFPE


title: invasive breast tumor C683

description: FFPE


title: invasive breast tumor C265

description: FFPE


title: invasive breast tumor C042

description: FFPE


title: invasive breast tumor C141

description: FFPE


title: invasive breast tumor C550

description: FFPE


title: invasive breast tumor C469

description: FFPE


title: invasive breast tumor C656

description: FFPE


title: invasive breast tumor C565

description: FFPE


title: invasive breast tumor C628

description: FFPE


title: invasive breast tumor C578

description: FFPE


title: invasive breast tumor C107

description: FFPE


title: invasive breast tumor C051

description: FFPE


title: invasive breast tumor C041

description: FFPE


title: invasive breast tumor C394

description: FFPE


title: invasive breast tumor C127

description: FFPE


title: invasive breast tumor C169

description: FFPE


title: invasive breast tumor C264

description: FFPE


title: invasive breast tumor C255

description: FFPE


title: invasive breast tumor C372

description: FFPE


title: invasive breast tumor C254

description: FFPE


title: invasive breast tumor C787

description: FFPE


title: invasive breast tumor C307

description: FFPE


title: invasive breast tumor C197

description: FFPE


title: invasive breast tumor C660

description: FFPE


title: invasive breast tumor C181

description: FFPE


title: invasive breast tumor C112

description: FFPE


title: invasive breast tumor C129

description: FFPE


title: invasive breast tumor C008

description: FFPE


title: invasive breast tumor C438

description: FFPE


title: invasive breast tumor C465

description: FFPE


title: invasive breast tumor C506

description: FFPE


title: invasive breast tumor C529

description: FFPE


title: invasive breast tumor C589

description: FFPE


title: invasive breast tumor C679

description: FFPE


title: invasive breast tumor C650

description: FFPE


title: invasive breast tumor C634

description: FFPE


title: invasive breast tumor C256

description: FFPE


title: invasive breast tumor C210

description: FFPE


title: invasive breast tumor C352

description: FFPE


title: invasive breast tumor C221

description: FFPE


title: invasive breast tumor C326

description: FFPE


title: invasive breast tumor C416

description: FFPE


title: invasive breast tumor C752

description: FFPE


title: invasive breast tumor C651

description: FFPE


title: invasive breast tumor C652

description: FFPE


title: invasive breast tumor C266

description: FFPE


title: invasive breast tumor C758

description: FFPE


title: invasive breast tumor C104

description: FFPE


title: invasive breast tumor C175

description: FFPE


title: invasive breast tumor C117

description: FFPE


title: invasive breast tumor C063

description: FFPE


title: invasive breast tumor C083

description: FFPE


title: invasive breast tumor C737

description: FFPE


title: invasive breast tumor C719

description: FFPE


title: invasive breast tumor C702

description: FFPE


title: invasive breast tumor C644

description: FFPE


title: invasive breast tumor C430

description: FFPE


title: invasive breast tumor C602

description: FFPE


title: invasive breast tumor C608

description: FFPE


title: invasive breast tumor C571

description: FFPE


title: invasive breast tumor C555

description: FFPE


title: invasive breast tumor C579

description: FFPE


title: invasive breast tumor C563

description: FFPE


title: invasive breast tumor C510

description: FFPE


title: invasive breast tumor C386

description: FFPE


title: invasive breast tumor C425

description: FFPE


title: invasive breast tumor C466

description: FFPE


title: invasive breast tumor C351

description: FFPE


title: invasive breast tumor C358

description: FFPE


title: invasive breast tumor C811

description: FFPE


title: invasive breast tumor C267

description: FFPE


title: invasive breast tumor C023

description: FFPE


title: invasive breast tumor C171

description: FFPE


title: invasive breast tumor C108

description: FFPE


title: invasive breast tumor C100

description: FFPE


title: invasive breast tumor C746

description: FFPE


title: invasive breast tumor C244

description: FFPE


title: invasive breast tumor C231

description: FFPE


title: invasive breast tumor C805

description: FFPE


title: invasive breast tumor C740

description: FFPE


title: invasive breast tumor C114

description: FFPE


title: invasive breast tumor C729

description: FFPE


title: invasive breast tumor C572

description: FFPE


title: invasive breast tumor C688

description: FFPE


title: invasive breast tumor C635

description: FFPE


title: invasive breast tumor C613

description: FFPE


title: invasive breast tumor C627

description: FFPE


title: invasive breast tumor C604

description: FFPE


title: invasive breast tumor C632

description: FFPE


title: invasive breast tumor C077

description: FFPE


title: invasive breast tumor C458

description: FFPE


title: invasive breast tumor C489

description: FFPE


title: invasive breast tumor C534

description: FFPE


title: invasive breast tumor C530

description: FFPE


title: invasive breast tumor C448

description: FFPE


title: invasive breast tumor C365

description: FFPE


title: invasive breast tumor C713

description: FFPE


title: invasive breast tumor C018

description: FFPE


title: invasive breast tumor C113

description: FFPE


title: invasive breast tumor C165

description: FFPE


title: invasive breast tumor C094

description: FFPE


title: invasive breast tumor C031

description: FFPE


title: invasive breast tumor C121

description: FFPE


title: invasive breast tumor C526

description: FFPE


title: invasive breast tumor C198

description: FFPE


title: invasive breast tumor C487

description: FFPE


title: invasive breast tumor C495

description: FFPE


title: invasive breast tumor C471

description: FFPE


title: invasive breast tumor C250

description: FFPE


title: invasive breast tumor C781

description: FFPE


title: invasive breast tumor C214

description: FFPE


title: invasive breast tumor C272

description: FFPE


title: invasive breast tumor C348

description: FFPE


title: invasive breast tumor C317

description: FFPE


title: invasive breast tumor C532

description: FFPE


title: invasive breast tumor C001

description: FFPE


title: invasive breast tumor C419

description: FFPE


title: invasive breast tumor C391

description: FFPE


title: invasive breast tumor C378

description: FFPE


title: invasive breast tumor C367

description: FFPE


title: invasive breast tumor C355

description: FFPE


title: invasive breast tumor C369

description: FFPE


title: invasive breast tumor C350

description: FFPE


title: invasive breast tumor C441

description: FFPE


title: invasive breast tumor C427

description: FFPE


title: invasive breast tumor C760

description: FFPE


title: invasive breast tumor C193

description: FFPE


title: invasive breast tumor C235

description: FFPE


title: invasive breast tumor C329

description: FFPE


title: invasive breast tumor C217

description: FFPE


title: invasive breast tumor C381

description: FFPE


title: invasive breast tumor C245

description: FFPE


title: invasive breast tumor C364

description: FFPE


title: invasive breast tumor C292

description: FFPE


title: invasive breast tumor C125

description: FFPE


title: invasive breast tumor C162

description: FFPE


title: invasive breast tumor C800

description: FFPE


title: invasive breast tumor C709

description: FFPE


title: invasive breast tumor C605

description: FFPE


title: invasive breast tumor C700

description: FFPE


title: invasive breast tumor C693

description: FFPE


title: invasive breast tumor C677

description: FFPE


title: invasive breast tumor C556

description: FFPE


title: invasive breast tumor C664

description: FFPE


title: invasive breast tumor C603

description: FFPE


title: invasive breast tumor C362

description: FFPE


title: invasive breast tumor C318

description: FFPE


title: invasive breast tumor C375

description: FFPE


title: invasive breast tumor C200

description: FFPE


title: invasive breast tumor C248

description: FFPE


title: invasive breast tumor C187

description: FFPE


title: invasive breast tumor C119

description: FFPE


title: invasive breast tumor C270

description: FFPE


title: invasive breast tumor C690

description: FFPE


title: invasive breast tumor C717

description: FFPE


title: invasive breast tumor C797

description: FFPE


title: invasive breast tumor C600

description: FFPE


title: invasive breast tumor C610

description: FFPE


title: invasive breast tumor C649

description: FFPE


title: invasive breast tumor C472

description: FFPE


title: invasive breast tumor C502

description: FFPE


title: invasive breast tumor C484

description: FFPE


title: invasive breast tumor C542

description: FFPE


title: invasive breast tumor C607

description: FFPE


title: invasive breast tumor C451

description: FFPE


title: invasive breast tumor C445

description: FFPE


title: invasive breast tumor C237

description: FFPE


title: invasive breast tumor C271

description: FFPE


title: invasive breast tumor C207

description: FFPE


title: invasive breast tumor C395

description: FFPE


title: invasive breast tumor C776

description: FFPE


title: invasive breast tumor C491

description: FFPE


title: invasive breast tumor C706

description: FFPE


title: invasive breast tumor C537

description: FFPE


title: invasive breast tumor C597

description: FFPE


title: invasive breast tumor C682

description: FFPE


title: invasive breast tumor C443

description: FFPE


title: invasive breast tumor C048

description: FFPE


title: invasive breast tumor C453

description: FFPE


title: invasive breast tumor C105

description: FFPE


title: invasive breast tumor C413

description: FFPE


title: invasive breast tumor C426

description: FFPE


title: invasive breast tumor C695

description: FFPE


title: invasive breast tumor C211

description: FFPE


title: invasive breast tumor C184

description: FFPE


title: invasive breast tumor C199

description: FFPE


title: invasive breast tumor C160

description: FFPE


title: invasive breast tumor C126

description: FFPE


title: invasive breast tumor C392

description: FFPE


title: invasive breast tumor C771

description: FFPE


title: invasive breast tumor C002

description: FFPE


title: invasive breast tumor C779

description: FFPE


title: invasive breast tumor C110

description: FFPE


title: invasive breast tumor C361

description: FFPE


title: invasive breast tumor C680

description: FFPE


title: invasive breast tumor C573

description: FFPE


title: invasive breast tumor C359

description: FFPE


title: invasive breast tumor C314

description: FFPE


title: invasive breast tumor C406

description: FFPE


title: invasive breast tumor C514

description: FFPE


title: invasive breast tumor C291

description: FFPE


title: invasive breast tumor C796

description: FFPE


title: invasive breast tumor C724

description: FFPE


title: invasive breast tumor C732

description: FFPE


title: invasive breast tumor C029

description: FFPE


title: invasive breast tumor C782

description: FFPE


title: invasive breast tumor C474

description: FFPE


title: invasive breast tumor C533

description: FFPE


title: invasive breast tumor C770

description: FFPE


title: invasive breast tumor C675

description: FFPE


title: invasive breast tumor C642

description: FFPE


title: invasive breast tumor C755

description: FFPE


title: invasive breast tumor C637

description: FFPE


title: invasive breast tumor C598

description: FFPE


title: invasive breast tumor C663

description: FFPE


title: invasive breast tumor C174

description: FFPE


title: invasive breast tumor C456

description: FFPE


title: invasive breast tumor C276

description: FFPE


title: invasive breast tumor C404

description: FFPE


title: invasive breast tumor C120

description: FFPE


title: invasive breast tumor C734

description: FFPE


title: invasive breast tumor C792

description: FFPE


title: invasive breast tumor C612

description: FFPE


title: invasive breast tumor C631

description: FFPE


title: invasive breast tumor C257

description: FFPE


title: invasive breast tumor C654

description: FFPE


title: invasive breast tumor C661

description: FFPE


title: invasive breast tumor C528

description: FFPE


title: invasive breast tumor C096

description: FFPE


title: invasive breast tumor C477

description: FFPE


title: invasive breast tumor C799

description: FFPE


title: invasive breast tumor C259

description: FFPE


title: invasive breast tumor C577

description: FFPE


title: invasive breast tumor C714

description: FFPE


title: invasive breast tumor C777

description: FFPE


title: invasive breast tumor C095

description: FFPE


title: invasive breast tumor C082

description: FFPE


title: invasive breast tumor C591

description: FFPE


title: invasive breast tumor C759

description: FFPE


title: invasive breast tumor C308

description: FFPE


title: invasive breast tumor C249

description: FFPE


title: invasive breast tumor C697

description: FFPE


title: invasive breast tumor C694

description: FFPE


title: invasive breast tumor C767

description: FFPE


title: invasive breast tumor C590

description: FFPE


title: invasive breast tumor C189

description: FFPE


title: invasive breast tumor C111

description: FFPE


title: invasive breast tumor C527

description: FFPE


title: invasive breast tumor C536

description: FFPE


title: invasive breast tumor C521

description: FFPE


title: invasive breast tumor C798

description: FFPE


title: invasive breast tumor C252

description: FFPE


title: invasive breast tumor C190

description: FFPE


title: invasive breast tumor C241

description: FFPE


title: invasive breast tumor C459

description: FFPE


title: invasive breast tumor C148

description: FFPE


title: invasive breast tumor C349

description: FFPE


title: invasive breast tumor C541

description: FFPE


title: invasive breast tumor C692

description: FFPE


title: invasive breast tumor C109

description: FFPE


title: invasive breast tumor C118

description: FFPE


title: invasive breast tumor C519

description: FFPE


title: invasive breast tumor C816

description: FFPE


title: invasive breast tumor C508

description: FFPE


title: invasive breast tumor C535

description: FFPE


title: invasive breast tumor C653

description: FFPE


title: invasive breast tumor C243

description: FFPE


title: invasive breast tumor C676

description: FFPE


title: invasive breast tumor C460

description: FFPE


title: invasive breast tumor C455

description: FFPE


title: invasive breast tumor C286

description: FFPE


title: invasive breast tumor C762

description: FFPE


title: invasive breast tumor C285

description: FFPE


title: invasive breast tumor C130

description: FFPE


title: invasive breast tumor C705

description: FFPE


title: invasive breast tumor C168

description: FFPE


title: invasive breast tumor C685

description: FFPE


title: invasive breast tumor C499

description: FFPE


title: invasive breast tumor C192

description: FFPE


title: invasive breast tumor C673

description: FFPE


title: invasive breast tumor C687

description: FFPE


title: invasive breast tumor C373

description: FFPE


title: invasive breast tumor C089

description: FFPE


title: invasive breast tumor C007

description: FFPE


title: invasive breast tumor C547

description: FFPE


title: invasive breast tumor C401

description: FFPE


title: invasive breast tumor C646

description: FFPE


title: invasive breast tumor C268

description: FFPE


title: ABP1 knockdown long treatment, replicate 3

description:
Amplified RNA.
4-day-old etiolated seedlings.
SS12K9 long-term treated samples labelled with Cy5 compared to Alc-GUS samples labelled with Cy3 (replica 3).

source_name: SS12K9 line ethanol-treated for 96 h

value: ethanol for 96 h

source_name: Alc-GUS line ethanol-treated for 96 h


title: invasive breast tumor C476

description: FFPE


title: invasive breast tumor C368

description: FFPE


title: P.gingivalis W83_inoculated_rep3

city: Shenyang

first: Jian

last: Zhao

state: Liaoning Province

address: Nanjing North St. 117

department: Department of Periodontology

country: China

institute: School of Stomatology, China Medical University

description: This sample is of Porphyromonas gingivalis W83 inoculated in oral cavity for 8 weeks. It is the third of three inoculated Porphyromonas gingivalis W83 biological replicates used in this experiment, each from separate infected rat .

hyb_protocol: Hybridization was performed at the CapitalBio Corporation (http://www.capitalbio.com/en/index.asp, Beijing, China), a service provider authorized by Roche NimbleGen (Wisconsin, USA), according to the NimbleGen’s Expression user’s guide.

scan_protocol: Scanning was performed at the CapitalBio Corporation (http://www.capitalbio.com/en/index.asp, Beijing, China), a service provider authorized by Roche NimbleGen (Wisconsin, USA), according to the NimbleGen’s Expression user’s guide.

data_processing: Data analysis was performed at the CapitalBio Corporation (http://www.capitalbio.com/en/index.asp, Beijing, China), a service provider authorized by Roche NimbleGen (Wisconsin, USA). The expression data of probes were normalized using quantile normalization and expression data of genes were generated using the Robust Multichip Average (RMA) algorithm.

organism: Porphyromonas gingivalis W83

source_name: P.gingivalis W83 inoculated in oral cavity

label_protocol: Labeling was performed at the CapitalBio Corporation (http://www.capitalbio.com/en/index.asp, Beijing, China), a service provider authorized by Roche NimbleGen (Wisconsin, USA), according to the NimbleGen’s Expression user’s guide.

growth_protocol: Porphyromonas gingivalis strain W83 was grown anaerobically (10% CO2, 10% H2, 80% N2 ) in enriched brain–heart infusion (BHI) broth containing 5% fiber-free sheep blood, 1% vitamin K and hemin, 37℃.

extract_protocol: Total RNA was extracted using Trizol reagent and was further purified using NucleoSpin® RNA clean-up（MACHEREY-NAGEL，Germany） according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.

treatment_protocol: After P.gingivalis W83 inoculation in rat oral cavity for 8 weeks, plaques were acquired from periodontal pockets and dispersed by oscillator. 100μl ten-fold serial dilutions were inoculated on BHI culture medium anaerobically at 37oC for 5-7 days. The single clone was purified in BHI medium for subcultures in order to detect the differences in the gene of P.gingivalis W83.

tag: source

value: inoculated in oral cavity


title: invasive breast tumor C072

description: FFPE


title: ABP1 knockdown long treatment, replicate 2

description:
Amplified RNA.
4-day-old etiolated seedlings.
SS12K9 long-term treated samples labelled with Cy5 compared to Alc-GUS samples labelled with Cy3 (replica 2).


title: invasive breast tumor C723

description: FFPE


title: P.gingivalis W83_inoculated_rep2

description: This sample is of Porphyromonas gingivalis W83 inoculated in oral cavity for 8 weeks. It is the second of three inoculated Porphyromonas gingivalis W83 biological replicates used in this experiment, each from separate infected rat .


title: invasive breast tumor C553

description: FFPE


title: invasive breast tumor C357

description: FFPE


title: invasive breast tumor C647

description: FFPE


title: invasive breast tumor C512

description: FFPE


title: P.gingivalis W83_wild strain_rep2

description: This sample is of wild strain Porphyromonas gingivalis W83. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: P.gingivalis W83 wild strain

value: wild strain


title: P.gingivalis W83_inoculated_rep1

description: This sample is of Porphyromonas gingivalis W83 inoculated in oral cavity for 8 weeks. It is the first of three inoculated Porphyromonas gingivalis W83 biological replicates used in this experiment, each from separate infected rat .


title: P.gingivalis W83_wild strain_rep3

description: This sample is of wild strain Porphyromonas gingivalis W83. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: invasive breast tumor C305

description: FFPE


title: P.gingivalis W83_wild strain_rep1

description: This sample is of wild strain Porphyromonas gingivalis W83. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: invasive breast tumor C282

description: FFPE


title: invasive breast tumor C262

description: FFPE


title: invasive breast tumor C226

description: FFPE


title: invasive breast tumor C195

description: FFPE


title: invasive breast tumor C808

description: FFPE


title: invasive breast tumor C655

description: FFPE


title: Huh7 shRNA MEF2D

city: ChongQing

first: leina

last: ma

address: Gaotanyan Main Street, No. 35

department: Southwest Hospital

institute: Third Military Medical University

hyb_protocol: Each Slide was hybridized with 1.65μg 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=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm,Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Huh7 infected with lentivirus silencing MEF2D

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

extract_protocol: RNA extraction and purification Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: cell line

value: shRNA MEF2D


title: ABP1 knockdown long treatment, replicate 1

description:
Amplified RNA.
4-day-old etiolated seedlings.
SS12K9 long-term treated samples labelled with Cy3 compared to Alc-GUS samples labelled with Cy5 (replica 1).


title: S. cerevisiae BY4741_dodecane vs undecane_48hrs_rep1

city: Singapore

first: Hua

last: Ling

address: 62 Nanyang Drive

department: Department of Chemical and Biomolecular Engineering, SCBE

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Standard Agilent procedures

scan_protocol: Scanned on Agilent Scanner G2505B US45103124, and images were quantified using Agilent Feature Extraction Software v. 10.7

data_processing: Agilent Feature Extraction Software v. 10.7  was used for background subtraction and LOWESS normalization.

organism: Saccharomyces cerevisiae

source_name: n-dodecane, 48hrs

label_protocol: Approximately 200ng of total RNA was processed to produce Cy5 or Cy3-labeled cRNA targets by using Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) according to the manufacture's protocol

growth_protocol: In YPD yeast cells were grown for overnight at 225rpm and 30 Celsius degree.

extract_protocol: Total RNA was isolated using RNeasy Mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol

treatment_protocol: Multiple conditons: yeast cells from overnight cell culture were diluted to OD600=0.2 in medium (1.6g/L yeast nitrogen base, 2% D-glucose,0.1g/L uracine, 0.2g/L, leucine) added with 2% n-alkanes (n-nonane, n-decane, n-undecane, n-dodecane, respectively), and  were incubated at 225rpm and 28 Celsius degree in 50mL falcon tubes, for 24hrs or 48hrs. Cells added with sterile H2O instead of n-alkanes were used as control.

source_name: n-undecane, 48hrs


title: invasive breast tumor C584

description: FFPE


title: Huh7 siRNA Control

source_name: Huh7 transfected by control siRNA

value: siRNA Control


title: S. cerevisiae BY4741_decane_48hrs vs 24hrs_rep2

source_name: n-decane, 48hrs

source_name: n-decane, 24hrs


title: Huh7 siRNA MEF2D

source_name: Huh7 transfected by siRNA of MEF2D

value: siRNA MEF2D


title: S. cerevisiae BY4741_dodecane vs undecane_48hrs_rep2

description: dye-swap


title: Huh7 shRNA Control

source_name: Huh7 infected with control lentivirus

value: shRNA Control


title: S. cerevisiae BY4741_decane_48hrs vs 24hrs_rep1


title: S. cerevisiae BY4741_dodecane vs control_24hrs_rep2

source_name: n-dodecane, 24hrs

source_name: non-treatment (control), 24hrs


title: invasive breast tumor C240

description: FFPE


title: invasive breast tumor C157

description: FFPE


title: S. cerevisiae BY4741_dodecane vs control_24hrs_rep1


title: invasive breast tumor C552

description: FFPE


title: S. cerevisiae BY4741_nonane vs control_48hrs_rep1

source_name: n-nonane, 48hrs

source_name: non-treatment (control), 48hrs


title: invasive breast tumor C643

description: FFPE

source_name: CBCS


title: S. cerevisiae BY4741_nonane vs control_48hrs_rep2


title: invasive breast tumor C810

description: FFPE


title: invasive breast tumor C261

description: FFPE


title: invasive breast tumor C213

description: FFPE


title: invasive breast tumor C204

description: FFPE


title: c3h14c3h15 double mutants, biological rep3

city: Qingdao

first: Chai

last: Guohua

state: Shandong

address: No.189 Songling Road, Laoshan District

department: Qingdao Institute of BioEnergy and Bioprocess Technology

institute: Chinese Academy of Sciences

description: Gene expression data from c3h14c3h15 plants

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 °C  on Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized using Robust Multi-array Average(RMA) .

label: biotin

source_name: plants in glasshouse

label_protocol: Biotinylated cRNA were prepared from 200 ng total RNA using Affymetrix 3’ IVT Express kit according to the standard Affymetrix protocol

growth_protocol: Arabidopsis plants were grown side by side in the glasshouse with 22 °C and 16 h/8 h light/dark cycle.

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

treatment_protocol: Total RNA was extracted from the base 4 cm part of inflorescence stems whose heights were between 12 and 17 cm of three independent wild type, C3H14/15 overexpressing lines and c3h14c3h15 double mutants.

value: basal stem of 12-17 cm-height plants

tag: ecotype

tag: genotype/variation

value: c3h14c3h15 double mutant


title: C3H15 overexpressing plants, biological rep3

description: Gene expression data from C3H15 overexpressors

value: C3H15 overexpressors


title: C3H15 overexpressing plants, biological rep2


title: c3h14c3h15 double mutants, biological rep1


title: c3h14c3h15 double mutants, biological rep2


title: invasive breast tumor C047

description: FFPE


title: invasive breast tumor C815

description: FFPE


title: invasive breast tumor C172

description: FFPE


title: invasive breast tumor C557

description: FFPE


title: C3H15 overexpressing plants, biological rep1


title: C3H14 overexpressing plants, biological rep3

description: Gene expression data from C3H14 overexpressors

value: C3H14 overexpressors


title: invasive breast tumor C091

description: FFPE


title: invasive breast tumor C156

description: FFPE


title: WT(Col-0), biological rep3

description: Gene expression data from wild-type (Col-0) plants

value: WT


title: GBM-E3-miR340: miR340 overexpressed glioma-initiating cells (GICs)

city: Toon

first: Daisuke

last: Yamashita

address: Shitsukawa

department: Neurosurgery

country: Japan

institute: Ehime University Graduate School of Medicine

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: The cell lines were cultured as tumor spheres in serum-free Dulbecco's modified Eagle's medium (DMEM) /Ham's F-12 (Wako) containing human basic fibroblast growth factor (bFGF; 10 nM), human epidermal growth factor (EGF; 10 nM), heparin (5 μM), N2 supplement (Wako), 10 μg/ml insulin (Wako), GlutaMAX supplement, 100 units/ml penicillin G and 100 μg/ml streptomycin.  cultured as tumor spheres in serum-free Dulbecco's modified Eagle's medium (DMEM) /Ham's F-12 (Wako) containing human basic fibroblast growth factor (bFGF; 10 nM), human epidermal growth factor (EGF; 10 nM), heparin (5 μM), N2 supplement (Wako), 10 μg/ml insulin (Wako), GlutaMAX supplement, 100 units/ml penicillin G and 100 μg/ml streptomycin.

extract_protocol: Total RNA was extracted from cells using the TRIzol Plus RNA Purification System (Invitrogen).

treatment_protocol: The precursor form of miR-340 or control miRNA was overexpressed in glioma cells using miRNA lentiviral particles (pEZX-MR03, Genecopoeia), according to the supplier’s instructions. Briefly, glioma cells were incubated with recombinant virus at 37°C for 12 hr and cultured in the presence of puromycin (2 µg/ml, Sigma) for 3 days. Infection efficiency was monitored by GFP expression, and miR-340 expression was verified by RT-PCR after selection.


title: WT(Col-0), biological rep1


title: U251-miR340: miR340 overexpressed glioma cell lines

source_name: miR340 overexpressed glioma cell lines

value: miR340 overexpressed glioma cell lines


title: C3H14 overexpressing plants, biological rep2


title: GBM-E2-miR340: miR340 overexpressed glioma-initiating cells (GICs)


title: invasive breast tumor C269

description: FFPE

value: female


title: AO: glioma-initiating cells (GICs)

source_name: glioma-initiating cells (GICs) from anaplastic oligodendroglioma

value: AO


title: invasive breast tumor C488

description: FFPE


title: WT(Col-0), biological rep2


title: GBM-E5-miR340: miR340 overexpressed glioma-initiating cells (GICs)


title: U215: glioma cell lines

source_name: glioma cell lines

value: glioma cell lines


title: C3H14 overexpressing plants, biological rep1


title: DA: glioma-initiating cells (GICs)

source_name: glioma-initiating cells (GICs) diffuse astrocytoma

value: DA


title: ARPE-19_FAC_2d_rep3

city: Philadelphia

first: Joshua

middle: L.

last: Dunaief

state: PA

address: 422 Curie Blvd, 305 Stellar Chance labs

department: Ophthalmology

institute: University of Pennsylvania

description: Gene expression data from FAC-treated ARPE-19 cells in serum-free media for 2d.

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99oC for 5 min and hybridized for 16h at 45oC to the array.  The microarrays were then washed at low (6X SSPE) and high (100 mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin.

scan_protocol: Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.  A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: The data in .cel files were imported to Partek Genomics Suite v6.6 where RMA normalization was applied.

source_name: ARPE-19 cells, FAC-treated, 2d

label_protocol: First, 250 ng of total RNA were converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence.  Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: ARPE-19 cells were grown to confluency and maintained at low serum (1%) to differentiate for 4 weeks prior to experiments, which were done in serum-free media.

extract_protocol: Total RNA was extracted per manufacturer's instructions on the Qiagen miRNeasy Mini Kit.

treatment_protocol: ARPE-19 cells were left untreated (vehicle) or treated with 250 μM FAC for 2d prior to analysis.

value: FAC


title: Scramble siRNA rep1

city: Nanchang

first: Jian-feng

last: Zheng

state: Jiangxi

address: No.1 Min De Road

institute: Nanchang University

description: Gene expression data from SMMC-7721 cell transfected with EIF3B siRNA to SMMC-7721 cell transfected with Scramble siRNA

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

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.

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

growth_protocol: SMMC-7721 cell transfected with EIF3B siRNA or Scramble siRNA

treatment_protocol: siRNA

value: SMMC-7721 cell

value: Scramble siRNA


title: Scramble siRNA rep2

source_name: SMMC-7721 cell transfected with Scramble siRNA


title: GBM-E6: glioma-initiating cells (GICs)

source_name: glioma-initiating cells (GICs) from glioblastomas


title: Scramble siRNA rep3


title: ARPE-19_FAC_2d_rep2


title: U87: glioma cell lines


title: ARPE-19_FAC_2d_rep1


title: GBM-E3: glioma-initiating cells (GICs)

value: glioma-initiating cells (GICs) from glioblastomas


title: ARPE-19_untreated_2d_rep2

description: Gene expression data from untreated ARPE-19 cells in serum-free media for 2d.

source_name: ARPE-19 cells, untreated, 2d

value: NT


title: GBM-E2: glioma-initiating cells (GICs)


title: EIF3B siRNA rep1

source_name: SMMC-7721 cell transfected with EIF3B siRNA

value: EIF3B siRNA


title: Neutrophils, Healthy control, biological replicate 13

city: Buffalo

first: kaiyu

last: Jiang

state: NY

address: 875 Ellicott Street

department: Pediatrics

institute: University at Buffalo

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Affymetrix Human U133 Plus 2.0 GeneChips following manufacturer's directions. GeneChips were washed and stained in an Affymetrix 450 Fluidics Station

scan_protocol: GeneChips were scanned using an Affymetrix 3000 7G scanner

data_processing: CHP files were generated by Affymetrix expression console software using the 3' exp array -RMA program

source_name: neutrophil RNA

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA)

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were separated from granulocytes and red blood cells by density-gradient centrifugation. Red cells were removed from granulocytes by hypotonic lysis. PBMC and granulocytes were then immediately placed in TRIzol® reagent (Invitrogen, Carlsbad, CA) and stored at -80C.

value: neutrophil

tag: disease state

value: Healthy control


title: EIF3B siRNA rep3


title: ARPE-19_untreated_2d_rep3


title: Neutrophils, Healthy control, biological replicate 7

tag: cell type


title: Neutrophils, Healthy control, biological replicate 9


title: Neutrophils, Healthy control, biological replicate 10


title: ARPE-19_untreated_2d_rep1


title: Neutrophils, Healthy control, biological replicate 8


title: Neutrophils, Healthy control, biological replicate 2


title: Neutrophils, Healthy control, biological replicate 3


title: Neutrophils, Healthy control, biological replicate 6


title: Neutrophils, Healthy control, biological replicate 12


title: Neutrophils, Healthy control, biological replicate 11


title: Neutrophils, Healthy control, biological replicate 4


title: Neutrophils, Healthy control, biological replicate 5


title: EIF3B siRNA rep2

source_name: SMMC-7721 cell transfected with EIF2B siRNA


title: OPCL61: glioma-initiating cells (GICs) from oligodendrocyte precursor cells

hyb_protocol: Agilent miRNA expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies Scanner G2505C at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 031184_D_F_20111226).

label_protocol: 100 ng of total RNA was used by Agilent’s miRNA Complete Labeling and Hybridization Kit

growth_protocol: The cell lines were cultured as described in EMBO J. 2000;19:1998-2007. Kondo T, Raff M.


title: Neutrophils, Healthy control, biological replicate 1


title: NSCL61: glioma-initiating cells (GICs) from neural stem cells


title: Neutrophils, Patient, Pauciarticular,Biological replicate 7

value: Pauciarticular JIA


title: Neutrophils, Patient, Pauciarticular,Biological replicate 8


title: Neutrophils, Patient, Pauciarticular,Biological replicate 5


title: Neutrophils, Patient, Pauciarticular,Biological replicate 6


title: Neutrophils, Patient, Pauciarticular,Biological replicate 4


title: NSC: neural stem cells

source_name: neural stem cells

value: NSC

value: neural stem cells


title: Neutrophils, Patient, Pauciarticular,Biological replicate 1


title: Neutrophils, Patient, Polyrticular,Biological replicate 14

value: Polyrticular JIA


title: Neutrophils, Patient, Pauciarticular,Biological replicate 3


title: Neutrophils, Patient, Polyrticular,Biological replicate 13


title: Neutrophils, Patient, Pauciarticular,Biological replicate 2


title: OPC: oligodendrocyte precursor cells

source_name: oligodendrocyte precursor cells

value: OPC

value: oligodendrocyte precursor cells


title: Neutrophils, Patient, Polyrticular,Biological replicate 12


title: genomic DNA from SJOS010930_D1

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

description: osteosarcoma sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina HiScan Array Scanner using the default scanner setting

data_processing: GenomeStudio Methylation Module 1.9.0

label: Cy5 and Cy3

source_name: tissue

label_protocol: Infinium HD Assay Methylation Protocol

extract_protocol: genomic DNA was extracted and purified from fresh frozen osteosarcoma primary tumor samples using Qiagen DNeasy Kit according to standard instructions.

value: female

tag: sample type

value: tissue

value: osteosarcoma


title: Neutrophils, Patient, Polyrticular,Biological replicate 11


title: genomic DNA from SJOS010929_D1

description: osteosarcoma sample

value: male


title: Neutrophils, Patient, Polyrticular,Biological replicate 7


title: genomic DNA from SJOS010931_D1

description: osteosarcoma sample


title: Neutrophils, Patient, Polyrticular,Biological replicate 8


title: genomic DNA from SJOS013_D

description: osteosarcoma sample


title: Neutrophils, Patient, Polyrticular,Biological replicate 9


title: genomic DNA from SJOS011_D

description: osteosarcoma sample


title: Neutrophils, Patient, Polyrticular,Biological replicate 6


title: invasive breast tumor C668

description: FFPE

tag: Stage


title: genomic DNA from SJOS001121_D1

description: osteosarcoma sample

tag: gender


title: genomic DNA from SJOS001126_D1

description: osteosarcoma sample


title: Neutrophils, Patient, Polyrticular,Biological replicate 5


title: genomic DNA from SJOS001118_D1

description: osteosarcoma sample


title: genomic DNA from SJOS001112_D1

description: osteosarcoma sample


title: Neutrophils, Patient, Polyrticular,Biological replicate 10


title: Neutrophils, Patient, Polyrticular,Biological replicate 4


title: genomic DNA from SJOS001125_D1

description: osteosarcoma sample


title: U87: glioma cell lines

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 031181_D_F_20110707) .

value: glioma cell lines


title: Neutrophils, Patient, Polyrticular,Biological replicate 1


title: genomic DNA from SJOS001120_D1

description: osteosarcoma sample


title: genomic DNA from SJOS001117_D1

description: osteosarcoma sample


title: genomic DNA from SJOS001109_D1

description: osteosarcoma sample


title: genomic DNA from SJOS001124_D1

description: osteosarcoma sample


title: genomic DNA from SJOS001123_D1

description: osteosarcoma sample


title: genomic DNA from SJOS001119_D1

description: osteosarcoma sample


title: genomic DNA from SJOS001106_D1

description: osteosarcoma sample


title: GBM-E6: glioma-initiating cells (GICs)


title: AO: glioma-initiating cells (GICs)

value: AO

value: glioma-initiating cells (GICs) from anaplastic oligodendroglioma


title: Neutrophils, Patient, Polyrticular,Biological replicate 2


title: genomic DNA from SJOS001105_D1

description: osteosarcoma sample


title: GBM-E2: glioma-initiating cells (GICs)

value: glioma-initiating cells (GICs) from glioblastomas


title: genomic DNA from hOB cell ine, rep3

description: osteosarcoma cell line

source_name: cell line

value: cell line


title: Ovarian cancer cell TGF-beta treated 120+48 hours (rep1)

city: Indianapolis

first: Horacio

last: Cardenas

state: IN

address: 980 West Walnut Street

institute: Indiana University

description: Ovarian cancer cells stimulated with TGF-beta for 120 hours then 48 hours off.

hyb_protocol: DNA was amplified, fragmented, and hybridized to Illumina Infinium HumanMethylation450 BeadChip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Arrays were imaged with HiScan Reader using recommended Illumina scanner settings.

data_processing:
GenomeStudio v2011.2 with Methylation module v1.8.5
Unmethylated and methylated signal intensities

label_protocol: Standard Infinium HD Methylation Assay Protocol

growth_protocol: Cells were maintained in medium DMGM.

extract_protocol: Genomic DNA was extracted and purified from cells using Qiagen QiaAMP kit according to standard instructions.

treatment_protocol: Cells were treated with TGF-beta at the dose of 5 ng/ml.

value: ovarian cancer

value: TGF-beta 120+48H


title: genomic DNA from hOB cell ine, rep2

description: osteosarcoma cell line


title: MCF10CA1a

status: Public on Apr 06 2015

city: Herston

first: Georgia

last: Trench

state: QLD

address: 300 Herston Rd

department: Cancer Genetics

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Genomic DNA extracted from breast tumors was genotyped using Human Omni 2.5M SNP arrays (2.5-8 v1.1) (Illumina).

hyb_protocol: 20 hours at 48°C, according to manufacturers instructions

scan_protocol: arrays were scanned using iScan

data_processing: Data was extracted using Genome Studio (Illumina).

label: Cy3 Cy5

source_name: breast tissue

label_protocol: 200 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix, according to the manufacturer's instructions

growth_protocol: The cells were maintained in DMEM/F12 supplemented with 5% horse serum, 500ng/ml hydrocortisone, 100ng/ml cholera toxin, 10 μg/ml  insulin and 20ng/ml epidermal growth factor.

extract_protocol: Genomic DNA from the cell lines was extracted using the DNeasy Blood & Tissues Kit  from Qiagen according to manufacturer’s instructions.  DNA concentration was determined by measuring absorbance at 260nm on a Nanodrop2000

value: Breast cell line

value: fibrocystic disease


title: NSC: neural stem cells

value: NSC

value: neural stem cells


title: U215: glioma cell lines


title: Ovarian cancer cell TGF-beta treated 120+48 hours (rep3)


title: Ovarian cancer cell TGF-beta treated 120+48 hours (rep2)


title: DA: glioma-initiating cells (GICs)

value: DA

value: glioma-initiating cells (GICs) diffuse astrocytoma


title: genomic DNA from SJOS001105_D2

description: osteosarcoma sample

value: female


title: Ovarian cancer cell TGF-beta treated 48 hours (rep2)

description: Ovarian cancer cells stimulated with TGF-beta for 48 hours.

value: TGF-beta 48H


title: genomic DNA from SJOS001103_D1

description: osteosarcoma sample

value: tissue

value: osteosarcoma


title: Bedaquiline (Cy3) vs. DMSO (Cy5) 45min

city: Dunedin

first: Jennifer

middle: R

last: Robson

address: 720 Cumberland Street

department: Microbiology and Immunology

country: New Zealand

institute: University of Otago

description: Time course 45 mins exposure

hyb_protocol: Hybrization performed according to SOP M008 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

scan_protocol: Scanned Genepix 4000A scanner . Images were quantified using Spotfinder (TIGR).

data_processing: Total normalization and LOWESS normalization with MIDAS software (TIGR)

organism: Mycolicibacterium smegmatis MC2 155

source_name: Batch flask HdB 0.2% glycerol, tween 0.05% bedaquiline challenge

label_protocol: 10 µg of total RNA were reverse transcribed and labelled in a two step protocol according to SOP M007 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

growth_protocol: M. smegmatis was grown in Hartmans de bont supplemented with 0.2% glycerol and 0.05% Tween80 challenged with either bedaquiline or DMSO (control) in flasks at 37°C with agitation (200 rpm).

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

value: bedaquiline challenge

source_name: Batch flaskl HdB 0.2% glycerol, tween80 0.05% DMSO challenge

value: DMSO challenge


title: Ovarian cancer cell TGF-beta treated 48 hours (rep1)


title: Bedaquiline (Cy5) vs. DMSO (Cy3) 60min

description: Time course 60 mins exposure

source_name: Batch flask HdB 0.25% glycerol, tween 0.05% DMSO challenge

source_name: Batch flaskl HdB 0.2% glycerol, tween80 0.05% bedaquiline challenge


title: Neutrophils, Patient, Polyrticular,Biological replicate 3

value: neutrophil

value: Polyrticular JIA


title: E15 negative control

city: Yufu-shi

first: Kaei

last: Nasu

state: Oita

address: Idaigaoka 1-1, Hasama-machi

department: Obstetrics and Gynecology

institute: Oita University, Faculty of Medicine

description:
Gene expression after 48 hr
E15 normal endometrial stromal cells transfected with negative control precursor miRNA

hyb_protocol: 1.5 ug of fragmented Cy3-labelled cRNA was hybridized to human mRNA microarray (G4845A, Human Gene Expression 4x44K v2, Agilent Technologies) following the manufacturer’s instructions.

scan_protocol: The microarray slides were scanned with a laser confocal scanner (G2565BA Microarray Scanner System, Agilent Technologies).

data_processing: Microarray images were analyzed using Feature Extraction v.9.5.3.1 (Agilent Technologies) with the manufacturer’s recommended settings.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng of total RNA with Cy3 and amplified with the Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA)

extract_protocol: Forty-eight hours after transfection, total RNA from cultured NESCs transfected with precursor hsa-miR-210 (n=4) and NESCs (n=4) transfected with negative control precursor miRNA was extracted with an RNeasy Mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Normal endometrial stromal cells were transfected with precursor hsa-miR-210 (Pre-miRTM miRNA precursor- hsa-miR-210, Ambion, Austin, TX, USA) or negative control precursor miRNA (Pre-miRTM miRNA precursor-negative control #1 Ambion) at a final concentration of 10 nM, using LipofectamineTM RNAiMAX (Invitrogen, Carlsbad, CA, USA).

value: Human proliferative-phase endometrium

value: endometrial stromal cells

value: primary cultured normal endometrial stromal cells

value: Forty-eight hours after transfection


title: Ovarian cancer cell TGF-beta treated 120 hours (rep1)

description: Ovarian cancer cells stimulated with TGF-beta for 120 hours.

value: ovarian cancer

value: TGF-beta 120H


title: Ovarian cancer cell TGF-beta treated 120 hours (rep3)


title: Ovarian cancer cell TGF-beta treated 120 hours (rep2)


title: E15 mir210 precursor

description:
Gene expression after 48 hr
E15 normal endometrial stromal cells transfected with precursor hsa-miR-210


title: genomic DNA from hOB cell ine, rep1

description: osteosarcoma cell line

value: cell line


title: genomic DNA from SJOS001107_D1

description: osteosarcoma sample

value: male


title: E14 mir210 precursor

description:
Gene expression after 48 hr
E14 normal endometrial stromal cells transfected with precursor hsa-miR-210


title: E6 mir210 precursor

description:
Gene expression after 48 hr
E6 normal endometrial stromal cells transfected with precursor hsa-miR-210


title: Ovarian cancer cell control (rep3)

description: Ovarian cancer cells without TGF-beta stimulation used as control.

value: control


title: NF90-NF45 dbTg 1

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

institute: Kochi University

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

hyb_protocol: Following fragmentaion, single-stranded cDNA were hybridized for 20 hours at 48 ℃ with MoGene2.1ST Array Strip (Affymetrix)  and GeneChip Expression 3'-Amplification Reagents Hybridization Control kit (Affymetrix).

scan_protocol: The array was scanned using Imaging Station (Affymetrix) according to the manufacture's instructions..

data_processing: Arrays were summarized and normalized with Expression Console using RMA-sketch.

source_name: NF90-NF45 dbTg mouse, quadriceps

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Amplification Kit Module 1(Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA isolated from the quadriceps of WT and NF90-NF45 dbTg mouse using miRNeasy Mini Kit (Qiagen).

value: NF90-NF45 dbTg

value: Quadriceps

value: 16 weeks


title: NF90-NF45 dbTg 2

value: female


title: E6 negative control

description:
Gene expression after 48 hr
E6 normal endometrial stromal cells transfected with negative control precursor miRNA


title: WT 2

source_name: WT mouse, quadriceps

value: wild type


title: Ovarian cancer cell TGF-beta treated 48 hours (rep3)

value: TGF-beta 48H


title: Castel_Gala_field_winter_rep2 [10_rep2_CGjuly2010_F_BZ14]

city: Petrolina

first: Diogo

middle: Denardi

last: Porto

state: Pernambuco

address: BR428 road, Km 152

department: Embrapa Semiárido

country: Brazil

institute: EMBRAPA

description:
10_rep2_CGjuly2010_F_BZ14
Frozen in the field

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2.1 software (Roche).

data_processing: Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.

organism: Malus domestica

source_name: 'Castel Gala', harvested during winter

label_protocol: 200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.

growth_protocol: 'Royal Gala' and 'Castel Gala' buds were harvested from a commercial orchard in 2009 and 2010

extract_protocol: LiCl precipitation, improved from the pine tree isolation method  (Chang et al., 1993) by Zeng and Yang (2002)

treatment_protocol: Harvested buds were exposed to low temperatures under controlled conditions.

tag: genetic background

value: Castel Gala

value: Wild-type

tag: tissues developmental stage

value: Harvested while dormant (A stage sensu Fleckinger)

value: Bud


title: Castel_Gala_field_winter_rep2 [10_rep2_CGjuly2010_F_BZ12]

description:
10_rep2_CGjuly2010_F_BZ12
Frozen in the field

tag: tissue


title: Castel_Gala_short_chilling_autumn_rep2 [8_rep2_CGapril2010_240CH_BZ15]

description:
8_rep2_CGapril2010_240CH_BZ15
Frozen after chilling exposure under controlled conditions

source_name: 'Castel Gala', harvested during autumn, chilled until 240 CH

tag: treatment

value: cold exposure until 240 chilling hours


title: Castel_Gala_short_chilling_autumn_rep2 [8_rep2_CGapril2010_240CH_BZ16]

description:
8_rep2_CGapril2010_240CH_BZ16
Frozen after chilling exposure under controlled conditions


title: Royal_Gala_long_chilling_winter_rep1 [7_rep1_RGjune2009_800CH]

description:
7_rep1_RGjune2009_800CH
Frozen after chilling exposure under controlled conditions

source_name: 'Royal Gala', harvested during winter, chilled until 800 CH

value: Royal Gala

value: cold exposure until 800 chilling hours


title: Bedaquiline (Cy3) vs. DMSO (Cy5) 120min

description: Time course 120 mins exposure

value: bedaquiline challenge

value: DMSO challenge


title: Bedaquiline (Cy3) vs. DMSO (Cy5) 30min

description: Time course 30 mins exposure

source_name: Batch flask HdB 0.2% glycerol tween 0.05% bedaquiline challenge


title: Ovarian cancer cell control (rep2)

value: ovarian cancer


title: Bedaquiline (Cy5) vs. DMSO (Cy3) 15min

description: Time course 15 mins exposure

source_name: Batch flask HdB 0.2% glycerol, Tween80 0.05%, DMSO challenge

source_name: Batch flask HdB 0.2% glycerol, tween80 0.05% bedaquiline challenge


title: Royal_Gala_long_chilling_winter_rep2 [7_rep2_RGapril2010_800CH]

description:
7_rep2_RGapril2010_800CH
Frozen after chilling exposure under controlled conditions


title: Royal_Gala_short_chilling_winter_rep2 [6_rep2_RGapril2010_600CH_BZ13]

description:
6_rep2_RGapril2010_600CH_BZ13
Frozen after chilling exposure under controlled conditions

source_name: 'Royal Gala', harvested during winter, chilled until 600 CH

value: cold exposure until 600 chilling hours


title: Royal_Gala_short_chilling_winter_rep1 [6_rep1_RGjune2009_600CH_BZ5]

description:
6_rep1_RGjune2009_600CH_BZ5
Frozen after chilling exposure under controlled conditions


title: Royal_Gala_short_chilling_winter_rep1 [6_rep1_RGjune2009_600CH_BZ3]

description:
6_rep1_RGjune2009_600CH_BZ3
Frozen after chilling exposure under controlled conditions


title: MCF10A

description: Genomic DNA extracted from breast tumors was genotyped using Human Omni 2.5M SNP arrays (2.5-8 v1.1) (Illumina).

value: Breast cell line

value: fibrocystic disease


title: Royal_Gala_short_chilling_winter_rep2 [6_rep2_RGapril2010_600CH_BZ11]

description:
6_rep2_RGapril2010_600CH_BZ11
Frozen after chilling exposure under controlled conditions


title: Castel_Gala_field_autumn_rep1 [5_rep1_CGmay2009_F_BZ6]

description:
5_rep1_CGmay2009_F_BZ6
Frozen in the field

source_name: 'Castel Gala', harvested during autumn


title: E16 mir210 precursor

description:
Gene expression after 48 hr
E16 normal endometrial stromal cells transfected with precursor hsa-miR-210

value: Human proliferative-phase endometrium

value: endometrial stromal cells

value: primary cultured normal endometrial stromal cells

tag: age

value: Forty-eight hours after transfection


title: Ovarian cancer cell control (rep1)

value: control


title: E14 negative control

description:
Gene expression after 48 hr
E14 normal endometrial stromal cells transfected with negative control precursor miRNA


title: Castel_Gala_field_winter_rep1 [10_rep1_CGjune2009_F_BZ6]

description:
10_rep1_CGjune2009_F_BZ6
Frozen in the field

value: Castel Gala

value: Wild-type


title: Royal_Gala_field_winter_rep1 [3_rep1_RGjune2009_F_BZ4]

description:
3_rep1_RGjune2009_F_BZ4
Frozen in the field

source_name: 'Royal Gala', harvested during winter

value: Harvested while dormant (A stage sensu Fleckinger)

value: Bud


title: Castel_Gala_long_chilling_autumn_rep1 [9_rep1_CGmay2009_400CH]

description:
9_rep1_CGmay2009_400CH
Frozen after chilling exposure under controlled conditions

source_name: 'Castel Gala', harvested during autumn, chilled until 400 CH

value: cold exposure until 400 chilling hours


title: Castel_Gala_short_chilling_autumn_rep1 [8_rep1_CGmay2009_240CH_BZ7]

description:
8_rep1_CGmay2009_240CH_BZ7
Frozen after chilling exposure under controlled conditions

value: cold exposure until 240 chilling hours


title: Castel_Gala_long_chilling_autumn_rep2 [9_rep2_CGapril2010_400CH]

description:
9_rep2_CGapril2010_400CH
Frozen after chilling exposure under controlled conditions


title: Castel_Gala_field_winter_rep1 [10_rep1_CGjune2009_F_BZ4]

description:
10_rep1_CGjune2009_F_BZ4
Frozen in the field


title: E16 negative control

description:
Gene expression after 48 hr
E16 normal endometrial stromal cells transfected with negative control precursor miRNA


title: Royal_Gala_field_autumn_rep2 [1_rep2_RGapril2010_F_BZ9]

description:
1_rep2_RGapril2010_F_BZ9
Frozen in the field

source_name: 'Royal Gala', harvested during autumn

value: Royal Gala


title: Castel_Gala_short_chilling_autumn_rep1 [8_rep1_CGmay2009_240CH_BZ8]

description:
8_rep1_CGmay2009_240CH_BZ8
Frozen after chilling exposure under controlled conditions


title: HuCCT1_WTAP_p5

city: Daejon

first: Seon-Young

last: Kim

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: HuCCT1 cells overexpressing WTAP

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Quantile-quantile normalization using Illumina' Beadstudio (ver. 3.3). Data in table below are average expression in normal scale

label_protocol: Standard Illumina protocol

growth_protocol: Cells were cultured in RPMI1640 supplemented with 10% FBS, 25 mM HEPES and 100 ug/ml of penicillin/streptomycin

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: cholangiocarcinoma cell line

value: overexpressiong WTAP


title: Castel_Gala_field_autumn_rep2 [5_rep2_CGapril2010_F_BZ15]

description:
5_rep2_CGapril2010_F_BZ15
Frozen in the field


title: Castel_Gala_field_autumn_rep2 [5_rep2_CGapril2010_F_BZ14]

description:
5_rep2_CGapril2010_F_BZ14
Frozen in the field


title: GBM-E3: glioma-initiating cells (GICs)

source_name: glioma-initiating cells (GICs) from glioblastomas


title: ΔcdaA_rep01

city: Chengdu

first: Yu-Qing

last: Li

address: No.14, Section 3, Renmin Road South

institute: State Key Laboratory of Oral Diseases, Sichuan University

description: S. mutans ΔcdaA

hyb_protocol: Hybridization was performed following the standard operating protocol (Agilent). Please see the website http://www.agilent.com/.

scan_protocol: Scanning was performed following the standard operating protocol (Agilent). Please see the website http://www.agilent.com/.

data_processing: The Raw data (txt files) were processed and quantile-normalized by GeneSpring GX software.

organism: Streptococcus mutans

source_name: Streptococcus mutans ΔcdaA, replicate 1

label_protocol: Labeling was performed following the standard operating protocol (Agilent). Please see the website http://www.agilent.com/.

growth_protocol: For microarray analysis, S. mutans UA159 and S. mutans ΔcdaA cells were routinely grown at 37°C anaerobically (90% N2, 5% CO2, 5% H2) in brain heart infusion broth (BHI; Difco, Sparks, MD, USA) to an optical density at 600 nm (OD600) of 0.5.

extract_protocol: Cell cultures were collected and treated with RNAprotect reagent (Qiagen, Valencia, CA, USA). RNA was extracted and purified using RNeasy Mini kits (Qiagen) and digested with RNase-free DNase I (Qiagen). The concentration of purified RNA samples were analyzed by Nanodrop ND 1000 spectrophotometer (Thermo Fisher Scientific, Pittsburgh, PA, USA)

tag: strain

value: cdaA mutant


title: Royal_Gala_field_winter_rep2 [3_rep2_RGjuly2010_F_BZ12]

description:
3_rep2_RGjuly2010_F_BZ12
Frozen in the field


title: Royal_Gala_field_winter_rep2 [3_rep2_RGjuly2010_F_BZ10]

description:
3_rep2_RGjuly2010_F_BZ10
Frozen in the field


title: Castel_Gala_field_autumn_rep1 [5_rep1_CGmay2009_F_BZ7]

description:
5_rep1_CGmay2009_F_BZ7
Frozen in the field


title: UA159_rep01

description: S. mutans UA159

source_name: Streptococcus mutans UA159, replicate 1

treatment_protocol: S. mutans UA159 and S. mutans ΔcdaA cells were routinely grown at 37°C anaerobically (90% N2, 5% CO2, 5% H2) in brain heart infusion broth (BHI; Difco, Sparks, MD, USA) to an optical density at 600 nm (OD600) of 0.5.

value: wildtype control


title: Royal_Gala_field_winter_rep2 [3_rep2_RGjuly2010_F_BZ11]

description:
3_rep2_RGjuly2010_F_BZ11
Frozen in the field


title: Royal_Gala_field_winter_rep1 [3_rep1_RGjune2009_F_BZ2]

description:
3_rep1_RGjune2009_F_BZ2
Frozen in the field


title: HuCCT1_MOCK_p6

description: HuCCT1 cells overexpressing the empty vector

value: overexpressing the empty vector


title: Royal_Gala_field_winter_rep1 [3_rep1_RGjune2009_F_BZ3]

description:
3_rep1_RGjune2009_F_BZ3
Frozen in the field


title: Royal_Gala_field_autumn_rep1 [1_rep1_RGmay2009_F_BZ1]

description:
1_rep1_RGmay2009_F_BZ1
Frozen in the field


title: Royal_Gala_chilling_autumn_rep2 [2_rep2_RGapril2010_240CH]

description:
2_rep2_RGapril2010_240CH
Frozen after chilling exposure under controlled conditions

source_name: 'Royal Gala', harvested during autumn, chilled until 240 CH


title: WT 1

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

value: wild type

value: Quadriceps

value: male

value: 17-18 weeks


title: Royal_Gala_field_autumn_rep2 [1_rep2_RGapril2010_F_BZ10]

description:
1_rep2_RGapril2010_F_BZ10
Frozen in the field


title: ΔcdaA_rep04

description: S. mutans ΔcdaA

source_name: Streptococcus mutans ΔcdaA, replicate 4


title: UA159_rep02

description: S. mutans UA159

source_name: Streptococcus mutans UA159, replicate 2


title: UA159_rep04

description: S. mutans UA159

source_name: Streptococcus mutans UA159, replicate 4


title: HuCCT1_WTAP_p6

description: HuCCT1 cells overexpressing WTAP


title: ΔcdaA_rep02

description: S. mutans ΔcdaA

source_name: Streptococcus mutans ΔcdaA, replicate 2


title: UA159_rep03

description: S. mutans UA159

source_name: Streptococcus mutans UA159, replicate 3


title: ATH1 - E1728::GFP (E1728G) - replicate 2

city: Stanford

first: Dominique

middle: C

last: Bergmann

state: CA

address: 371 Serra Mall

department: Biology Department

institute: Stanford University

description: Microarray-based expression profiles of FACS-sorted mature guard cells

hyb_protocol: Labeled cDNA was hybridized, washed and stained on an ATH1-121501 Arabidopsis full genome microarray using a Hybridization Control Kit (Affymetrix), a GeneChip Hybridization, Wash, and Stain Kit (Affymetrix), and a GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using a GeneChip Scanner (Affymetrix).

data_processing: The data were analyzed with the R Bioconductor package affy using following parameters: RMA background correction, quantile normalization across all arrays, no perfect match (PM) probe correction, and the median polish method for summarization.

source_name: Mature guard cells

label_protocol: RNA was reverse-transcribed and amplified using the Ovation Pico WTA System (NuGen) and cDNA was labeled with the Encore Biotin Module (NuGen).

growth_protocol: Seedlings were grown for 14 days on 1/2 strength Murashige and Skoog (MS) medium supplemented with 1% (w/v) sucrose under long day (16-hours light, 8-hours dark) conditions at 25C.

extract_protocol: GFP/YFP-positive protoplasts were identified with a FACS Aria II cell sorter and directly sorted into RNA extraction buffer. Total RNA of sorted protoplasts was extracted with the RNeasy Micro Kit (QIAGEN) including on column DNase treatment according to the manufacturer’s instructions.  RNA quality was checked on a Bioanalyzer (Agilent).

treatment_protocol: Arial tissue of seedlings was harvested and incubated in protoplasting solution for 2 hours.

tag: marker line

value: Enhancer trap line E1728::GFP in Col

value: FACS-sorted protoplasts from aerial tissue of 14-day old seedlings


title: Royal_Gala_field_autumn_rep1 [1_rep1_RGmay2009_F_BZ2]

description:
1_rep1_RGmay2009_F_BZ2
Frozen in the field

value: Wild-type


title: HuCCT1_MOCK_p4


title: HuCCT1_MOCK_p5


title: ATH1 - E1728::GFP (E1728G) - replicate 1


title: HCV blood, 370

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

country: Netherlands

institute: Erasmus MC

description: Blood gene expression data from chronic HCV infection

hyb_protocol: cRNA were hybridized to the Affymetrix Human Genome U133 plus 2.0 GeneChip

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner 3000

data_processing: The data was normalized by GC-RMA algorithm

source_name: HCV Blood_4_years_after_HCV_therapy

extract_protocol: Total RNA was isolated from whole blood using the Tempus Spin RNA isolation kit

value: blood

value: Male

tag: ethnicity

value: Asian


title: ΔcdaA_rep03

description: S. mutans ΔcdaA

source_name: Streptococcus mutans ΔcdaA, replicate 3


title: ATH1 - FAMAp::GFP-FAMA (FGF) - replicate 2

description: Microarray-based expression profiles of FACS-sorted mature guard mother cells and young guard cells

source_name: Mature guard mother cells and young guard cells

value: FAMAp::GFP-FAMA in Col


title: ATH1 - E1728::GFP (E1728G) - replicate 3


title: HCV blood, 371

value: Caucasian


title: HuCCT1_WTAP_p4

description: HuCCT1 cells overexpressing WTAP

value: cholangiocarcinoma cell line


title: Royal_Gala_chilling_autumn_rep1 [2_rep1_RGmay2009_240CH]

description:
2_rep1_RGmay2009_240CH
Frozen after chilling exposure under controlled conditions

value: Royal Gala

value: Harvested while dormant (A stage sensu Fleckinger)

value: Bud

value: cold exposure until 240 chilling hours


title: ATH1 - MUTEp::nucGFP (MG) - replicate 1

description: Microarray-based expression profiles of FACS-sorted late meristemoids and young guard mother cells

source_name: Late meristemoids and young guard mother cells

value: MUTEp::nucGFP in Col


title: HCV blood, 369

value: Female


title: ATH1 - SPCHp::SPCH-YFP (SSY) - replicate 3

description: Microarray-based expression profiles of FACS-sorted meristemios mother cells and young meristemoids

source_name: Meristemios mother cells and young meristemoids

value: SPCHp::SPCH-YFP in Col


title: Virus_2

city: Beijing

first: Wei

last: Wang

address: HaiDian District, Mingyuanxilu No.2

institute: College of Veterinary Medicine

description: Gene expression data at a given time

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000.

data_processing: data were normalized and summarized using the Affymetrix Microarray Suite 5.0 (MAS5)

source_name: infection of virus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and endothelial cell growth supplement at 37°C in a 5% CO2 incubator.

treatment_protocol: Monolayers of cells were washed with PBS, inoculated with virus and then incubated for 1 hour. After washing, Dulbecco's modified Eagle's medium supplemented with 0.2 % bovine serum albumin and trypsin was added to each well.

value: Human Umbilical Vein Endothelial Cells


title: ATH1 - FAMAp::GFP-FAMA (FGF) - replicate 3


title: Inactivate_2

description: Gene expression data at a given time

source_name: inoculation of inactivated virus


title: ATH1 - MUTEp::nucGFP (MG) - replicate 3


title: ATH1 - SPCHp::SPCH-YFP (SSY) - replicate 2


title: ATH1 - ML1p::YFP-RCI2A (ML1Y) - replicate 2

description: Microarray-based expression profiles of FACS-sorted epidermis cells

source_name: Epidermis cells

value: ML1p::YFP-RCI2A in Col


title: ATH1 - MUTEp::nucGFP (MG) - replicate 2

value: FACS-sorted protoplasts from aerial tissue of 14-day old seedlings


title: HCV blood, 368


title: ATH1 - ML1p::YFP-RCI2A (ML1Y) - replicate 3


title: Virus_1

description: Gene expression data at a given time


title: ATH1 - FAMAp::GFP-FAMA (FGF) - replicate 1


title: Inactivate_1

description: Gene expression data at a given time


title: ATH1 - SPCHp::SPCH-YFP (SSY) - replicate 1


title: DM2 sample 09

status: Public on Apr 05 2015

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

description: male,47 years

hyb_protocol: Following fragmentation, 30 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: Summarized signal intensities were generated by Partek Genomics Suite (Partek Inc.). The output signals were normalized using the Partek Robust Multi-Chip Average analysis adjusted for the GC content of probe sequence (GCRMA). The genes that were differentially expressed among the two classes were identified using the Analysis of Variance (ANOVA) as implemented in the Partek Gene Expression tool. An estimate of the associated False Discovery Rate (FDR) was computed per gene using the method of Benjamini and Hochberg.

source_name: biceps brachii,DM2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA Ambion WT Expression Kit (Life Technologies Co.)

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy mini kit following standard RNA cleanup protocol

value: biceps brachii biopsy taken from Myotoni Dystrophy type 2 subjects

value: myotonic dystrophy type 2

value: male

value: 47 years


title: ATH1 - ML1p::YFP-RCI2A (ML1Y) - replicate 1


title: DM2 sample 10

description: male,61 years

value: 61 years


title: Control_2

description: Gene expression data at a given time

source_name: inoculation of equivalent amounts of virus-free media


title: HCV blood, 367

value: blood

value: Caucasian


title: DM2 sample 06

description: female, 59 years

value: female

value: 59 years


title: Control sample 10

description: female, 58 years

source_name: biceps brachii, CONTROL

value: biceps brachii biopsy taken from control subjects

value: control

value: 58 years


title: DM2 sample 08

description: male,70 years

value: 70 years


title: DM2 sample 05

description: male,62 years

value: 62 years


title: DM2 sample 03

description: male,61 years


title: DM2 sample 04

description: male,64 years

value: 64 years


title: DM2 sample 01

description: male, 56 years

value: 56 years


title: Control sample 06

description: male, 74 years

value: 74 years


title: DM2 sample 02

description: male,60 years

value: biceps brachii biopsy taken from Myotoni Dystrophy type 2 subjects

value: 60 years


title: Control sample 03

description: male, 47 years

value: male


title: Control sample 01

description: male, 35 years

value: 35 years


title: DM2 sample 07

description: female,59 years

value: myotonic dystrophy type 2


title: Control sample 07

description: female, 54 years

value: 54 years


title: Control sample 04

description: male, 37 years

value: 37 years


title: Control sample 05

description: male, 44 years

value: 44 years


title: Control sample 02

description: male, 47 years

value: 47 years


title: Control sample 08

description: female, 52 years

value: biceps brachii biopsy taken from control subjects

value: female

value: 52 years


title: Control sample 09

description: male, 62 years

value: control


title: Control_1

description: Gene expression data at a given time

value: Human Umbilical Vein Endothelial Cells