title: whole blood, symptomatic replicate 14, training set, batch 2

value: symptomatic


title: whole blood, symptomatic replicate 12, training set, batch 2

status: Public on May 27 2010

type: RNA

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip HuGene 1.0 ST v1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with fluidics protocol FS450_0001.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner using GCOS version 1.4 software with default settings.

data_processing: Raw CEL-files were imported into Expression Console 1.0 (Affymetrix). PLIER was used for array normalization and signal calculation independently for each hybridization batch. Normalized signal values were imported into Genespring GX 7.3 (Agilent Technologies) and gene wise Z-score normalization across all samples of each hybridization batch was applied.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Samples were enzymatically amplified, fragmented and biotinylated using GeneChip® Whole Transcript (WT) Sense Target Labeling Kit (Affymetrix).

extract_protocol: Whole blood was collected in BD PAXgene Blood RNA Tubes (BD Diagnostics) according the recommendations of the manufacturer. RNA was extracted with PAXGene Blood RNA Kit (Qiagen) according to the manfacturer.

tag: dyt1 mutation status

value: delta GAG

tag: dystonia

tag: hybridization batch

tag: dataset

value: training set


title: whole blood, symptomatic replicate 15, training set, batch 2


title: whole blood, symptomatic replicate 11, training set, batch 2


title: NT2_undiff_R5

city: Ottawa

first: Brandon

last: Smith

state: Ontario

address: 1200 Montreal Road

department: Institute for Biological Sciences

country: Canada

institute: National Research Council Canada

description: no additional information

hyb_protocol: Labelled RNA samples were hybridized to microarrays in a 35 µl final volume composed of 400 mM Na2HPO4 (pH 7.0), 5% SDS, 0.8% BSA, and 12% formamide. Hybridisation mixtures were denatured at 95°C for 4 minutes and immediately pipetted onto glass slides covered with 22×25 mm LifterSlips (Erie Scientific Company, Portsmouth, NH). Hybridizations were performed in custom-made sealed chambers submerged in a 37°C water bath overnight (18 hours).  Slide washes were 3 min long: once in 2X SSC/0.025% SDS, three times in 0.8X SSC, and twice in cold 0.4X SSC. Immediately following the last wash, slides were dried by centrifugation.

scan_protocol: Slides were scanned with a ScanArray 5000XL (Packard BioScience, Meriden, CT) confocal scanner at 10 µm resolution.

data_processing: Microarray scans were analysed with QuantArray software version 3.0 (Packard BioScience, Meriden, CT) using an adaptive quantitation method. Spots of poor quality on the arrays were flagged for removal from the data processing. Cy3 mean pixel intensities were background subtracted, log transformed, and replicate spots on the arrays were averaged. Microarray data were normalised between arrays using a standard median centering procedure. miRNAs were considered expressed if their normalised log2 hybridisation signal was ≥ 2. Differentially-expressed miRNAs were identified using a SAM (significance analysis of microarrays) threshold of 5% and a fold-change of 2.

source_name: Ntera2/D1 cells, untreated

label_protocol: RNA labelling and hybridization to the microarrays was carried out using a method adapted from Thomson et al. 2004 (Thomson JM, Parker J, Perou CM, Hammond SM. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat Methods 1: 47-53). Briefly, 10 or 25 µg total RNA was PEG-precipitated (as above), resuspended in 6 µl water, and mixed into a labelling reaction (final volume 10 µl) consisting of 500 ng 5’-phophate-cytidyl-uridyl-Cy3-3’ (Dharmacon, Chicago, IL), 10% DMSO, 0.1 mM ATP, 50 mM HEPES (pH 7.8), 3.5 mM DTT, 20 mM MgCl2, 0.1 µg BSA, and 20 U T4 RNA ligase (NEB, Ipswitch, MA). Reactions were incubated on ice in the dark for 2 hours before precipitation with 0.27 M sodium acetate, 20 µg glycogen, and 2.7 volumes ethanol in a 200 µl final volume. Following 10 min incubation on ice and 10 min centrifugation, the pellet was washed in 70% ethanol, centrifuged 5 min, briefly dried, and resuspended in 6 µl water.

growth_protocol: Human embryonal teratocarcinoma Ntera2/D1 (NT2) cells (Stratagene, La Jolla, CA) were cultured in high glucose Dulbecco’s modified Eagle’s medium (HG/DMEM, Invitrogen, Burlington, Ontario, Canada) supplemented with 10% fetal bovine serum (FBS, Wisent, Saint-Jean, Quebec, Canada).

extract_protocol: Total RNA was isolated from the cells using TRI-Reagent (Molecular Research Center, Cincinnati, OH) according to the manufacturer’s instructions. High molecular-weight RNAs were removed by precipitation with 12.5% PEG-8000 and 1.25 M NaCl.

treatment_protocol: The cells were seeded at a density of 2 × 106 cells per T75 flask and treated with 10µM all-trans retinoic acid (RA, Sigma, Oakville, Ontario, Canada) in fresh medium every two days during a 28-day differentiation timecourse. Cells were harvested by tripsinization and centrifugation 0, 2, 4, 6, 8, 12, 14, 21, and 28 days following addition of RA. Time-course experiments were repeated several times to ensure multiple biological replicates for microarray analysis.

tag: cell type

tag: agent

value: untreated

tag: time

value: control


title: whole blood, symptomatic replicate 13, training set, batch 2


title: whole blood, symptomatic replicate 10, training set, batch 2


title: NT2_undiff_R1

description: no additional information


title: whole blood, symptomatic replicate 9, training set, batch 2


title: whole blood, symptomatic replicate 8, training set, batch 2


title: whole blood, symptomatic replicate 7, training set, batch 2


title: NT2_undiff_R2

description: no additional information


title: liver_WT_control_rep2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: liver from control (Gp130f/f ) mice, no prior treatment, replicate 2

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.

organism: Mus musculus

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

growth_protocol: Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID  15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.

extract_protocol: Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.

tag: tissue

value: liver

tag: genotype/variation

value: control mice [Gp130f/f]

tag: treatment

value: no previous treatment

tag: gender

value: male

tag: age

value: 8-12 weeks


title: liver_WT_control_rep1

description: liver from control (Gp130f/f ) mice, no prior treatment, replicate 1


title: whole blood, Carrier replicate 15, training set, batch 2

value: Carrier


title: whole blood, Carrier replicate 14, training set, batch 2


title: NT2_14D_R2

description: no additional information

source_name: Ntera2/D1 cells, 14 Day Retinoic Acid treated

value: Retinoic Acid

value: 14 Days


title: liver_WT_control_rep3

description: liver from control (Gp130f/f ) mice, no prior treatment, replicate 3


title: whole blood, symptomatic replicate 6, training set, batch 2


title: whole blood, symptomatic replicate 4, training set, batch 1


title: whole blood, Carrier replicate 11, training set, batch 1


title: whole blood, symptomatic replicate 5, training set, batch 2


title: liver_gp130delta(hepa)_control_rep2

description: liver from liver-specific Gp130 knockout  [Gp130delta(hepa)] mice, no prior treatment, replicate 2

value: liver-specific Gp130 knockout mice [Gp130delta(hepa)]


title: liver_gp130delta(hepa)_control_rep3

description: liver from liver-specific Gp130 knockout  [Gp130delta(hepa)] mice, no prior treatment, replicate 3


title: whole blood, Carrier replicate 13, training set, batch 2


title: whole blood, Carrier replicate 10, training set, batch 1


title: liver_WT_CLP_rep1

description: liver from control (Gp130f/f ) mice, 12 hrs after cecal ligation and puncture, replicate 1


title: liver_WT_CLP_rep3

description: liver from control (Gp130f/f ) mice, 12 hrs after cecal ligation and puncture, replicate 3


title: whole blood, Carrier replicate 9, training set, batch 1


title: whole blood, Carrier replicate 12, training set, batch 2


title: liver_WT_CLP_rep2

description: liver from control (Gp130f/f ) mice, 12 hrs after cecal ligation and puncture, replicate 2


title: liver_gp130delta(hepa)_control_rep1

description: liver from liver-specific Gp130 knockout  [Gp130delta(hepa)] mice, no prior treatment, replicate 1


title: liver_gp130delta(hepa)_CLP_rep2

description: liver from liver-specific Gp130 knockout  [Gp130delta(hepa)] mice, 12 hrs after cecal ligation and puncture, replicate 2


title: liver_gp130delta(hepa)_CLP_rep3

description: liver from liver-specific Gp130 knockout  [Gp130delta(hepa)] mice, 12 hrs after cecal ligation and puncture, replicate 3


title: liver_gp130delta(hepa)_CLP_rep1

description: liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, 12 hrs after cecal ligation and puncture, replicate 1


title: whole blood, symptomatic replicate 3, training set, batch 1


title: whole blood, Carrier replicate 8, training set, batch 1


title: drought (4 cycles of drought over 36 days) vs. drought (4 cycles of drought over 36 days) V3D H3D

city: Portland

first: Heather

last: Machado

state: OR

address: 1719 SW 10th Avenue, SB2 Room 246

department: Biology

country: USA

institute: Portland State University

hyb_protocol: Paired samples were combined, cleaned using a PCR Purification Kit (Qiagen), and dried down to 12.5 μl in a speed vacuum (ThermoSavant SC210A SpeedVac® Plus).  To reduce non-specific hybridization, 1.5 μl of tRNA was added to each sample pair, which were then placed in 95 ºC water for three minutes.  Fourteen microliters of 2X hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) was added to each sample pair prior to application to the microarray slide. The slides were obtained cross-linked from the University of Illinois, were blocked with a series of washes (two with 0.2% SDS, one with 95 ºC Nanopure water, and four with room temperature Nanopure water), and then prepared for hybridization with a one-hour incubation in Prehybridzation Buffer (5X SSC, 0.1% SDS, 1% BSA) at 42 °C.  Each sample was applied to the top half of one of the microarray slides under 22 mm X 25 mm LifterSlips (Erie Scientific) covering 10,000 features, and allowed to hybridize at 42 °C for 16–20 hours.

scan_protocol: Slides were then scanned with a GenePix 4000B scanner (Axon Instruments) and fluorescence data was collected (GenePix Pro 5.1).

data_processing: Features not significantly greater than background (background + 2 standard deviations) were identified in GenePix Pro 5.1 and discarded.  GenePix files were converted into MEV files readable by TIGR MIDAS by Express Converter V.1.8 [58].  LOWESS normalization was used to equalize signal intensities within each block of each slide.  Genes that did not pass quality controls for 13 or more of the 18 slides were omitted from further analysis.

organism: Piriqueta cistoides subsp. caroliniana

source_name: drought treatment (4 cycles of drought over 36 days)

label_protocol: 4 μg total RNA per target sample and was amplified using MessageAmpIItm aRNA Amplification Kit (Ambion Cat.#AM1751). Three-point-five micrograms of aRNA per sample was reverse transcribed, using both random hexamer and oligoDT primers. The single-stranded cDNA product was amino-allyl labelled with Amersham Cy3 and Cy5 mono-reactive fluorescent dyes (GE Healthcare).

growth_protocol: Greenhouse raised, with cuttings grown in sand.  The temperature in the greenhouse was maintained near 35/27 ºC (day/night) with a 12 hour day length through the entirety of the experiment.

extract_protocol: Leaves were removed and immediately frozen in liquid nitrogen. Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen) according to manufacturer instructions, with the addition of an initial preparation step in which leaf tissue was ground into a fine powder under liquid nitrogen and incubated for ten minutes at 56 °C in buffer RLT.

treatment_protocol: Control treatment (well-watered). Drought treatment (4 cycles of drought over 36 days).

tag: morphotype

value: hybrid

value: leaf

value: viridis


title: whole blood, symptomatic replicate 2, training set, batch 1

value: symptomatic


title: control (well-watered) vs. control (well-watered) V2W C3W

source_name: control treatment (well-watered)

value: caroliniana


title: whole blood, Carrier replicate 7, test set, batch 3

value: delta GAG

value: test set


title: control (well-watered) vs. control (well-watered) V3W H1W


title: drought (4 cycles of drought over 36 days) vs. drought (4 cycles of drought over 36 days) V2D C3D


title: drought (4 cycles of drought over 36 days) vs. control (well-watered) V1W V2D


title: control (well-watered) vs. control (well-watered) H3W C1W


title: whole blood, Carrier replicate 7, training set, batch 1

value: training set


title: control (well-watered) vs. drought (4 cycles of drought over 36 days) V1D V2W


title: whole blood, Control replicate 3, training set, batch 1

value: WT

value: Control


title: whole blood, Carrier replicate 5, training set, batch 1


title: drought (4 cycles of drought over 36 days) vs. drought (4 cycles of drought over 36 days) H3D C1D


title: Macrophage2 Kdo2 6h Expression rep2 (Cy5)

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
Macrophage Expression in response to Kdo2 at 6 hours.
raw data file: Slide6.US22502657_251486814075_S01_GE2-v5_91_0806_1_1.txt

hyb_protocol: 4x 44 k Agilent arrays were hybridized with 825 ng of each cDNA using the manufacturer's hybridization kit according to the instructions.

scan_protocol: Scanned on an Agilent Technologies Scanner using the extended dynamic range scan mode with a 5 µm pitch. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing:
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Data was further normalized between arrays using a multi-loess technique described in Corbeil et al (Journal of Molecular Endocrinology (2004) 33:1–9).
Dual-channel hybridization was analyzed as single-channel (ratios were not used).  Each channel is therefore represented as a single Sample and the same raw data file is linked to two Sample records.

label_protocol: Total RNA (250 ng) of two biological replicates was amplified and labeled using the Agilent Quick-Amp labeling kit according to the manufacturer's instructions.

growth_protocol: CD43-negative splenic B cells were isolated by magnetic depletion of CD43- and CD11b-expressing cells using MACS (Miltenyi, Bergisch Gladbach, Germany) according to the manufacturer's instructions. Peritoneal macrophages were harvested by peritoneal lavage with 10 ml ice-cold PBS 3 days after peritoneal injection of 3 ml thioglycollate broth. Peritoneal cells were washed once with PBS, and seeded in 10% fetal calf serum (FCS)/DMEM containing 100 U/ml penicillin/streptomycin in tissue culture-treated petri dishes overnight. Non-adherent cells were washed off with room temperature PBS.

extract_protocol: Total RNA was extracted from 5 Mio cells on Rneasy columns (Qiagen) with on-column DNase digestion following the manufacturer's instructions. RNA quality was assessed on an Agilent 2100 BioAnalyzer .

tag: strain


title: Macrophage2 Kdo2 6h Expression rep2 (Cy3)

value: Kdo2 for 6 hours


title: whole blood, Carrier replicate 4, training set, batch 1


title: whole blood, Carrier replicate 6, training set, batch 1


title: drought (4 cycles of drought over 36 days) vs. drought (4 cycles of drought over 36 days) H2D V3D BAD


title: Macrophage2 ctrl Expression rep2 (Cy5)

description:
Biological replicates of Macrophage Expression (untreated).
raw data file: Slide5.US22502657_251486814074_S01_GE2-v5_91_0806_1_4.txt


title: drought (4 cycles of drought over 36 days) vs. control (well-watered) H1W H2D


title: Macrophage2 ctrl Expression rep2 (Cy3)


title: control (well-watered) vs. control (well-watered) H2W V3W


title: whole blood, Carrier replicate 3, training set, batch 1


title: control (well-watered) vs. drought (4 cycles of drought over 36 days) H1D H2W


title: whole blood, Carrier replicate 2, training set, batch 1


title: whole blood, symptomatic replicate 1, training set, batch 1


title: Macrophage2 Kdo2 6h Expression rep1 (Cy5)

description:
Macrophage Expression in response to Kdo2 at 6 hours.
raw data file: Slide4.US22502657_251486814074_S01_GE2-v5_91_0806_1_2.txt


title: whole blood, Carrier replicate 1, training set, batch 1


title: Macrophage2 ctrl Expression rep1 (Cy3)

description:
Biological replicates of Macrophage Expression (untreated).
raw data file: Slide3.US22502657_251486814074_S01_GE2-v5_91_0806_1_1.txt


title: Macrophage2 ctrl Expression rep1 (Cy5)


title: control (well-watered) vs. control (well-watered) C3W H3W


title: drought (4 cycles of drought over 36 days) vs. drought (4 cycles of drought over 36 days) C3D V1D


title: control (well-watered) vs. control (well-watered) C2W V1W


title: drought (4 cycles of drought over 36 days) vs. drought (4 cycles of drought over 36 days) C2D H1D


title: NL158_Chip1

status: Public on May 26 2010

city: Yokohama

first: Hiroyuki

last: Oshima

address: 10-1 Daikoku-cho, Tsurumi-ku

country: Japan

institute: Mitsubishi Rayon Co.,LTD

description: healthy control

hyb_protocol: 5 μg of biotinylated aRNA, which was fragmented using Fragmentation Reagents (AppliedBiosystems), was suspended in a hybridization buffer containing 0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl, and 0.05% Tween 20. The hybridization mixture was heated to 94°C for 2 min, then cooled to 37°C and injected into a hybridization chamber (Mitsubishi Rayon). Hybridization was carried out at 65°C for 16 hr. Microarrays were washed by soaking 48times in 0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl, 0.05% and Tween 20 at 65°C for 4 min, then 16times in 0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl at 65°C for 4 min. Microarrays were stained with 2 μg/ml Streptavidin-Cy5 (GE Healthcare) in a solution (0.12 M Tris-HCl (pH 7.5), and 0.12 M NaCl, and 0.05% Tween 20) at room temperature for 30 min, then washed 4 times by soaking in a wash solution (0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl) at room temperature each for 5 min.

scan_protocol: Microarray was scanned at multiple exposure times ranging from 0 to 40s by DNA microarray reader (Yokogawa Electric Corporation). The intensity values with the best exposure condition for each spot were selected. Fluorescent intensity of images was quantified automatically with the software supplied with the microarray reader.

data_processing: All data were subtracted by background signal intensity of each array and normalized between arrays by constants calculated from signal raitio of 9 internal control probes(ACTB, ATP5F1, GAPDH, GTF2B, PLA2G5, RPS5, TUBA1B, GUSB, RPLP0).

source_name: liver

label_protocol: aRNA were amplified and biotinylated by MessageAmpTM II-Biotin Enhanced kit (AppliedBiosystems) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted by using mirVana(TM) miRNA Isolation kit (AppliedBiosystems)

tag: disease type

value: none, healthy control


title: Macrophage2 Kdo2 6h Expression rep1 (Cy3)


title: drought (4 cycles of drought over 36 days) vs. control (well-watered) C1W C2D best


title: RNA Mix Control 9_Chip1

source_name: RNA MIX Control

value: none, RNA mix control


title: NLnccT_Chip1

description: healthy control


title: NL269_Chip1

description: healthy control


title: NL75_Chip1

description: healthy control


title: NLncc40_Chip1

description: healthy control


title: whole blood, Control replicate 1, training set, batch 1


title: RNA Mix Control 9_Chip2


title: 6h Wound vs unpollinated ovules (replica 2)

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

institute: CHU Québec

description:
6h Wound (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

hyb_protocol: The microarray slides were pre-hybridized for1 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. The slides were washed twice for 10 min at 42°C with 1× SSC, 0.1% SDS, twice for 10 min at 37°C with 0.1× SSC, 0.1% SDS, and finally, with quick consecutive washes in three 0.1× SSC baths. Slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Solanum chacoense

source_name: Ovules at 6h style wounding  from G4 genotype ; greenhouse growth with an average photoperiod of 14-16h per day)

label_protocol: 30 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of cyanine 3-dCTP (1 mM) or cyanine 5-dCTP (1 mM; Perkin Elmer-Cetus/NEN, Boston, MA, catalog # NEL999) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 30 min at 37°C. The labeled cDNAs were purified using CyScribe GFX Purification Kit (GE Healthcare Bio-Sciences Inc., Baie d'Urfé, QC, Canada) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using the TRIzol ® Reagent according to the manufacturer’s protocol (Invitrogen, Burlington, ON, Canada).

treatment_protocol: The self-incompatible wild potato species Solanum chacoense (2n=2x=24) was greenhouse grown with an average photoperiod of 14-16h per day. Plant material was collected from female progenitor, S. chacoense genotype G4 (S12 and S14 self-incompatibility alleles) (Van Sint Jan et al., 1996). For pollination-related events, different genotypes were used as pollen donor. For fully compatible pollinations, S. chacoense genotype V22 (S11 and S13 SI alleles) was used to pollinate S. chacoense genotype G4 (S12 and S14 SI alleles). For fully incompatible pollinations, S. chacoense G4 was selfed. For semi-compatible pollinations, S. chacoense PI230582 (S13 and S14 SI alleles) was used. For interspecific pollinations, pollen from the self-incompatible Solanum microdontum (PI500041 from NRSP-6 Potato Genebank) was used. Control pollinations to detect and eliminate touch-induced genes were accomplished by gently touching the stigmas with sterile 100 mm zirconia/silica beads (Biospec Products Inc., Bartlesville, OK, USA). For wounding experiments, the upper region of the style was slightly crushed with small forceps as described previously (Lantin et al., 1999). For methyl jasmonate treatment, MeJA was diluted in methanol (MeOH) to obtain a 0.1 M solution and 100 µl of the diluted compound (equivalent to 10 µl /l of air space) was added to a piece of Whatman paper suspended over the plant in a closed chamber. As controls, untreated plants in closed chambers and plants treated with 100 µl of MeOH were used (Lantin et al., 1999).

tag: sample type

value: ovule

source_name: Unpollinated ovules

value: Unpollinated ovules


title: NLnccT_Chip2

description: healthy control


title: whole blood, Control replicate 2, training set, batch 1


title: 6h Wound vs unpollinated ovules (replica 3)

description:
6h Wound (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: Ovules at 6h style wounding  from G4 genotype ; greenhouse growth with an average photoperiod of 14-16h per day)


title: control (well-watered) vs. drought (4 cycles of drought over 36 days) C1D C2W


title: 6h Wound vs unpollinated ovules (replica 1)

description:
6h Wound (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: NLncc40_Chip2

description: healthy control


title: NL75_Chip2

description: healthy control


title: 6h Wound vs unpollinated ovules (replica 4)

description:
6h Wound (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: unpollinatedovules

value: unpollinatedovules


title: NL269_Chip2

description: healthy control


title: NL158_Chip2

description: healthy control


title: 6h SeC vs unpollinated ovules (replica 3)

description:
6h SeC (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 6h pollinated ovules from G4 genotype; semi compatible genotype (S13 and S14 self-incompatibility alleles)  was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: 6h SeC vs unpollinated ovules (replica 2)

description:
6h SeC (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 6h pollinated ovules from G4 genotype; semi compatible genotype (S13 and S14 self-incompatibility alleles)  was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: 6h SeC vs unpollinated ovules (replica 4)

description:
6h SeC (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: 6h Touch vs unpollinated ovules (replica 4)

description:
6h Touch (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: Ovule from G4 genotype at 6h after touching the stigmas with sterile 100 mm zirconia/silica beads; greenhouse growth with an average photoperiod of 14-16h per day)


title: 6h SeC vs unpollinated ovules (replica 1)

description:
6h SeC (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: 6h SI vs unpollinated ovules (replica 4)

description:
6h SI (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 6h pollinated ovules from G4 genotype; genotype G4 (S12 and S14 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: 6h Touch vs unpollinated ovules (replica 1)

description:
6h Touch (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: Ovule from G4 genotype at 6h after touching the stigmas with sterile 100 mm zirconia/silica beads; greenhouse growth with an average photoperiod of 14-16h per day)


title: 6h Touch vs unpollinated ovules (replica 3)

description:
6h Touch (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: 6h Touch vs unpollinated ovules (replica 2)

description:
6h Touch (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: 6h SI vs unpollinated ovules (replica 2)

description:
6h SI (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 6h pollinated ovules from G4 genotype; genotype G4 (S12 and S14 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: 6h SI vs unpollinated ovules (replica 1)

description:
6h SI (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: 6h SC vs unpollinated ovules (replica 4)

description:
6h SC (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 6h pollinated ovules from G4 genotype;genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: 6h SI vs unpollinated ovules (replica 3)

description:
6h SI (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: K-RTA, doxycycline 24 h, rep1

city: Miaoli Conunty

first: Su-Fang

last: Lin

address: No 35, Keyan Road, Zhunan Town

department: NICR

country: Taiwan

institute: National Health Research Institutes, Taiwan

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymatrix HG-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a confocal laser scanner(Affymatrix)

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 total intensity of each array was scaled to 125 in order to normalize for inter-array variations.

source_name: 293-K-RTA inducible line, doxycycline 24 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Cells were grown to log-phase in DMEM supplemented with 10% tetracycline-free fetal bovine serum before induction.

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

treatment_protocol: Cells were treated with doxycycline (1 microgram / ml) for 24 h. Cell densitiy was maintained at 200,000 / ml before induction.

tag: cell line

value: embryonic kidney cell

tag: immortalization method

value: transformed with sheared Ad5 DNA


title: K-RTA, doxycycline 24 h, rep3


title: 6h SC vs unpollinated ovules (replica 1)

description:
6h SC (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 6h pollinated ovules from G4 genotype;genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: Control, doxycycline 24 h, repl

source_name: 293-luciferase inducible line, doxycycline 24 h


title: 6h IS vs unpollinated ovules (replica 3)

description:
6h IS (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 6h pollinated ovules from G4 genotype; S.microdontum was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: Healthy Subject NORM8

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

country: Italy

institute: Schena Foundation

description: After hybridization, the microarray chips were washed using the Affymetrix fluidics station in a buffer containing biotinylated antistreptavidin antibody and stained with streptavidin-PE.

hyb_protocol: After a step of purification, 15 ug of newly synthesized cRNA were fragmented by metal-induced hydrolisis and hybridized for 16 hours at 45°C to the GeneChip Human Genome U133A oligonucleotide microarray (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The intensity of the fluorescence was measured with an Affymetrix scanner.

data_processing: Scaled gene expression values were calculated using the default setting of Affymetrix Microarray Suite (MAS) software version 5.0.

label: Biotin

source_name: Whole blood: healthy subject

label_protocol: cDNA was obtained using the GeneChip One-Cycle cDNA Synthesis kit with globin peptide nucleic acid (PNAs) inclusion (Affymetrix, Santa Clara, California). After that an in vitro transcription was performed to generate biotinylated cRNA to be hybridized on microarrays using the Gene Chip IVT Labelling kit (Affymetrix). The T7 fagus promoter triggered the process of transcription.

extract_protocol: Peripheral blood was collected with PaxGene tubes (Qiagen, Valencia, CA, USA), which stabilize and protect RNA. Total RNA was extracted immediately using PaxGene blood RNA isolation kit (PreAnalytiX).

value: male


title: 6h IS vs unpollinated ovules (replica 1)

description:
6h IS (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 6h pollinated ovules from G4 genotype; S.microdontum was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: Healthy Subject NORM7


title: 6h IS vs unpollinated ovules (replica 4)

description:
6h IS (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: 6h IS vs unpollinated ovules (replica 2)

description:
6h IS (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: 6h SC vs unpollinated ovules (replica 2)

description:
6h SC (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: K-RTA, doxycycline 24 h, rep2


title: 6h SC vs unpollinated ovules (replica 3)

description:
6h SC (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Control, untreated, rep1

source_name: 293-luciferase inducible line, untreated


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10496

city: Seattle

first: Dan

last: Tenenbaum

state: WA

institute: Institute for Systems Biology

description: Cells incubated under entrainment conditions

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: AnalyzerDG software for spotfinding. Intensities were normalized between the Alexa 546 and Alexa 647 channels by scaling all intensities in one channel such that the 75th percentile in each channel was made equal. See http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details.

label: Alexa 647

organism: Halobacterium salinarum

source_name: Halobacterium salinarum, paraquat, recovery

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium salinarum reference sample.

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

tag: od

tag: medium

value: CM

value: paraquat

tag: time course

value: recovery

label: Alexa 546

source_name: Halobacterium standard reference sample


title: Healthy Subject NORM6

value: female


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10494

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10491

value: 60 min.


title: 6h Methanol vs unpollinated ovules (replica 4)

description:
6h Methanol (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 6h Methanol treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)

value: ovule


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10492


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10490

value: 50 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10495


title: IGANORM 15

source_name: Whole Blood: IgAN patient with normal renal function

tag: creatinine clearance

value: >90 ml/min/1.73 m2 body surface area (evaluated by Cockcroft-Gault formula)

tag: serum creatinine

tag: clinical follow up

value: at least 7 years


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10493

tag: time

tag: agent


title: IGANORM 16

source_name: Whole blood:IgAN patient with normal renal function


title: 6h Methanol vs unpollinated ovules (replica 1)

description:
6h Methanol (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 6h Methanol treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)

tag: tissue

value: Unpollinated ovules


title: IGANORM 13

tag: gender


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10486

value: 30 min.


title: 6h Meja vs 6h Methanol (replica 4)

description:
6h Meja (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 6h Meja treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)

source_name: Methanol treated ovules


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10488

value: 40 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10483

value: 20 min.


title: 6h Methanol vs unpollinated ovules (replica 2)

description:
6h Methanol (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: Unpollinated ovules


title: IGANORM 14


title: 6h Methanol vs unpollinated ovules (replica 3)

description:
6h Methanol (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10484


title: 6h Meja vs 6h Methanol (replica 2)

description:
6h Meja (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 6h Meja treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10485


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10489


title: IGANORM 7


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10487


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10468

value: 0 min.


title: 6h Meja vs 6h Methanol (replica 3)

description:
6h Meja (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: 6h Meja vs 6h Methanol (replica 1)

description:
6h Meja (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: IGANORM 10

value: male


title: IGANORM 9

scan_protocol: The intensity of the fluorescence was measured with an Affymetrix scanner at 570 nm.

data_processing: Scaled gene expression values were calculated using the default setting of Affymetrix Microarray Suite (MAS) software version 5.0


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10469

value: CM


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10482

value: 10 min.

value: paraquat


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10481

value: recovery


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10257


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10256


title: IGANORM 5


title: 48h Wound vs unpollinated ovules (replica 4)

description:
48h Wound (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: Ovules at 48h style wounding  from G4 genotype ; greenhouse growth with an average photoperiod of 14-16h per day)


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10253

value: 60 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10252


title: HF-23896-(1), Affymetrix SNP6.0 array

type: genomic

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: Affymetrix Genome-Wide SNP Nsp/Sty Assay Kit 5.0/6.0

scan_protocol: Affymetrix user manual (GeneChip scanner 3000)

data_processing: Raw intensity data from the Affymetrix SNP 6.0 array was obtained for the tumor sample  and matched normal. These data were normalized using a method first described for  Illumina genotyping arrays. Specifically, we followed an adaptation of the Illumina  method adapted for Affymetrix arrays normalization protocol implemented in the  PennCNV package  (http://www.openbioinformatics.org/penncnv/penncnv_tutorial_affy_gw6.html) to obtain  normalized B-allele Frequency (BAF) and LogR Ratio (LRR) values for each probeset.  BAF represents the raw proportion of signal coming from allele B (Theta) normalized  using Theta values from a pool of normal samples with pre-determined AA, AB, or BB  genotypes at that probe position. LRR represents the log of the ration of the total signal  from A and B alleles for a sample divided by expected total signal from a pool of normal  samples given the same value of Theta. In brief, the raw intensity values (CEL files) were processed to obtain normalized allele-specific values for each probe using the Affymetrix Power Tools version 1.10  (http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx#1_1) tools apt-probeset-genotype and apt-probeset-summarize. A reference probe-intensity distribution obtained from the HapMap project samples was used for the  quantile normalization step. BAF and LRR values were calculated with the script  “normalize_affy_geno_cluster.pl” from the PennCVN-Affy package. This script  additionally implements a correction for GC-content bias in the LRR values. Data from  the HapMap project were used for the reference clusters of AA, AB, and BB genotype  signal intensity values. LRR values for somatic CNVs were calculated as the difference of the Tumor and Normal LRR values.

molecule: genomic DNA

extract_protocol: Qiagen AllPrep extraction kit was used according to the manufacturer's instructions

tag: organ

value: Lung Cancer


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10255


title: IGANORM 4


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10251

value: 50 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10250


title: 48h wound vs unpollinated ovules(replica 3)

description:
48h wound (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: Ovules at 48h style wounding  from G4 genotype ; greenhouse growth with an average photoperiod of 14-16h per day)

value: ovule


title: HF-23897-(1), Affymetrix SNP6.0 array

label_protocol: Affymetrix Genome-Wide SNP Nsp/Sty Assay Kit 5.0/6.0

value: Adjacent Normal


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10254


title: IGANORM 1

description: After hybridization, the microarray chips were washed using the Affymetrix fluidics station in a buffer containing biotinylated antistreptavidin antibody and stained with streptavidin-PE.

value: >90 ml/min/1.73 m2 body surface area (evaluated by Cockcroft-Gault formula)

value: at least 7 years


title: Healthy Subject NORM5

source_name: Whole Blood: healthy subject

extract_protocol: Peripheral blood was collected with PaxGene tubes (Qiagen, Valencia, CA, USA), which stabilize and protect RNA. Total RNA was extracted immediately using PaxGene blood RNA isolation kit (PreAnalytiX)


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10249

value: 40 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10244

value: 20 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10248


title: 48h Touch vs unpollinated ovules (replica 4)

description:
48h Touch (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: Ovule from G4 genotype at 48h after touching the stigmas with sterile 100 mm zirconia/silica beads; greenhouse growth with an average photoperiod of 14-16h per day)

value: Unpollinated ovules


title: 48h Touch vs unpollinated ovules (replica 3)

description:
48h Touch (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: Ovule from G4 genotype at 48h after touching the stigmas with sterile 100 mm zirconia/silica beads; greenhouse growth with an average photoperiod of 14-16h per day)


title: Healthy Subject NORM4

value: female


title: 48h wound vs unpollinated ovules (replica 1)

description:
48h wound (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10246

value: 30 min.

value: CM


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10243

value: 10 min.

value: paraquat


title: IGANORM 3

value: male


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10247

value: recovery


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10245


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10228

value: 0 min.


title: Healthy Subject NORM3

extract_protocol: Peripheral blood was collected with PaxGene tubes (Qiagen, Valencia,CA, USA), which stabilize and protect RNA. Total RNA was extracted immediately using PaxGene blood RNA isolation kit (PreAnalytiX)


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10220


title: 48h wound vs unpollinated ovules (replica 2)

description:
48h wound (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: Ovules at 48h style wounding  from G4 genotype ; greenhouse growth with an average photoperiod of 14-16h per day)


title: 48h SI vs unpollinated ovules (replica 4)

description:
48h SI (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 48h pollinated ovules from G4 genotype; genotype G4 (S12 and S14 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: ovule


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10242

description: Cells incubated under entrainment conditions


title: 48h SI vs unpollinated ovules (replica 3)

description:
48h SI (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 48h pollinated ovules from G4 genotype; genotype G4 (S12 and S14 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11527

source_name: Halobacterium salinarum, paraquat, constant stress

value: constant stress


title: 48h Touch vs unpollinated ovules (replica 2)

description:
48h Touch (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: 48h Touch vs unpollinated ovules (replica 1)

description:
48h Touch (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11525


title: 48h SI vs unpollinated ovules (replica 1)

description:
48h SI (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11523


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11524


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11526


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11522


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11517


title: 48h SeC vs unpollinated ovules (replica 3)

description:
48h SeC (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 48h pollinated ovules from G4 genotype; semi compatible genotype (S13 and S14 self-incompatibility alleles)  was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: Healthy Subject NORM2


title: Healthy Subject NORM1


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11515


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11519


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11514


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11516


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11513


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11518


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11512


title: 48h SeC vs unpollinated ovules (replica 4)

description:
48h SeC (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 48h pollinated ovules from G4 genotype; semi compatible genotype (S13 and S14 self-incompatibility alleles)  was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: 48h SeC vs unpollinated ovules (replica 2)

description:
48h SeC (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11511


title: 48h SeC vs unpollinated ovules (replica 1)

description:
48h SeC (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11509


title: IGANORM 6

value: >90 ml/min/1.73 m2 body surface area (evaluated by Cockcroft-Gault formula)

value: at least 7 years


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11508


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11510


title: tc252.hypoxia.adherent.2

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

hyb_protocol: Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-A microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the gcRMA algorithm.

source_name: Ewing's sarcoma cell line cell line grown under adherent culture condition and under hypoxia, replica 2

label_protocol: 1.5µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).

growth_protocol: adherent monolayers, maintained in RPMI 1640 (Invitrogen, Germany) supplemented with 10% fetal calf serum (PAA, Pasching, Austria) and 0,01% Penicillin/Streptomycin (PAA, Pasching, Austria). Cells were allowed to recover for 18 h before hypoxia/normoxia treatment.

extract_protocol: RNA was extrated using the Qiagen RNA extrction kit according to the manufacturer's instructions.

treatment_protocol: Hypoxic treatment of cells was achieved by incubating cells in a PROOX model 110 chamber (Biospherix, Redfield, NY) flushed with a gas mixture of 5% CO2/95% N2. Oxygen concentration within the chamber was maintained at 1% using a ProOx 110 oxygen regulator (Biospherix, USA).  treatment was applied for 24h.

tag: disease status

value: Ewing's sarcoma

tag: genome/variation

value: EWS-FLI1 fusion type 1

tag: p53 status

value: wild type

tag: culture conditions

value: adherent, hypoxia


title: sknmc.hypoxia.adherent.2

description: Ewing's sarcoma cell line cell line grown under adherent culture condition and under hypoxia

tag: cell line

value: SK-N-MC

value: mutant


title: 48h SC vs unpollinated ovules (replica 2)

description:
48h SC (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 48h pollinated ovules from G4 genotype;genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

tag: sample type

value: Unpollinated ovules


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11506

tag: strain

value: CM

value: paraquat


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11507

tag: medium


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11504

tag: time course


title: tc252.normoxia.adherent.2

source_name: Ewing's sarcoma cell line cell line grown under adherent culture condition and under normoxia, replica 2

treatment_protocol: For incubations under normoxia (21% O2), cells were placed in a Thermo-CO2 incubator and grown in a humidified atmosphere containing 5% CO2 (Thermo Electron Corp., Asheville, NC). treatment was applied for 24h.

value: adherent, normoxia


title: 48h SC vs unpollinated ovules (replica 1)

description:
48h SC (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 48h pollinated ovules from G4 genotype;genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11503


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11505


title: sknmc.normoxia.adherent.2

description: Ewing's sarcoma cell line cell line grown under adherent culture condition and under normoxia


title: 48h SC vs unpollinated ovules (replica 4)

description:
48h SC (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: ovule


title: 48h SC vs unpollinated ovules (replica 3)

description:
48h SC (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: 48h IS vs unpollinated ovules (replica 4)

description:
48h IS (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 48h pollinated ovules from G4 genotype; S.microdontum was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11502

source_name: Halobacterium standard reference sample


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11501


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11500


title: sknmc.hypoxia.adherent.1

source_name: Ewing's sarcoma cell line cell line grown under adherent culture condition and under hypoxia, replica 1


title: tc252.hypoxia.adherent.1


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11499


title: tc252.normoxia.adherent.1

source_name: Ewing's sarcoma cell line cell line grown under adherent culture condition and under normoxia, replica 1


title: 48h IS vs unpollinated ovules (replica 2)

description:
48h IS (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 48h pollinated ovules from G4 genotype; S.microdontum was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: 48h IS vs unpollinated ovules (replica 1)

description:
48h IS (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10457

description: Cells incubated under entrainment conditions

tag: od

value: constant stress


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10455


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10452

value: 60 min.


title: 48h Methanol vs unpollinated ovules (replica 4)

description:
48h Methanol (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 48h Methanol treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)


title: 48h IS vs unpollinated ovules (replica 3)

description:
48h IS (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11498


title: N637_microdeletion_characterization

city: Paris

first: Eric

last: Pasmant

address: Faculté de Pharmacie de Paris, 4 avenue de l’Observatoire

country: France

institute: Paris Descartes University

description: Reference sample: Pool of six normal control DNAs from six healthy donors

hyb_protocol: Labeled products were purified with Microcon YM-30 filters (Millipore, Billerica, MA). Patient and normal control DNAs (reference) were mixed and hybridized with Human Cot I DNA (Invitrogen) at 65°C for 24 hours. The sandwiched slides were hybridized for 24 hours at 65°C with 15 rotations per minute and washed according to the Agilent protocol.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner (G2565BA).

data_processing:
Log2 ratios (contained in sample data table below) were determined with Agilent Feature Extraction software (v 9.1.3.1). Results were visualized and analyzed with Agilent’s CGH Analytics v3.5 software, and copy number aberrations were detected with the Aberration Detection Method 2 (ADM-2) algorithm using a threshold value of 6.0. This threshold value of the altered copy number was determined from the normal variation in the control hybridization.

A visual estimation of ADM-2 microdeletions length was obtained with the last proximal and distal non deleted probe locations using a *DNA analytics* (Agilent software) algorithm. The result of this analysis can be found in the 'microdeletion sub type' sample characteristic listed above.

source_name: whole blood leukocytes

label_protocol: 300 ng of genomic DNA from each sample was double digested with AluI and RsaI (Promega, Madison, WI) for 2 hours at 37°C. The digested DNAs were labeled by random priming with the Agilent Genomic DNA Labeling Kit Plus (Agilent technologies) for 2 hours at 37°C, according to the manufacturer’s instructions. Patients’ DNA and pooled normal control DNAs (reference) were labeled with Cy5-dUTP and Cy3-dUTP, respectively.

extract_protocol:
High-molecular-weight DNAs from patients and healthy donors were prepared by standard proteinase K digestion followed by phenol-chloroform extraction from whole blood leukocytes.
The quantity and quality of the DNA samples were assessed with Nanodrop technology (Coleman Technologies, Orlando, FL) and verified by electrophoresis through agarose gels and staining with ethidium bromide.

tag: cell type

value: whole blood leukocytes

value: neurofibromatosis type 1 (NF1)

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

value: de novo

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling

value: Present

tag: subcutaneous neurofibromas

value: Absent

tag: cutaneous neurofibromas

tag: plexiform neurofibromas:

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis

source_name: POOL

value: healthy controls


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10363

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10438

value: 0 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10437


title: 48h Methanol vs unpollinated ovules (replica 2)

description:
48h Methanol (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

value: 48h Methanol treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)

tag: tissue

source_name: Methanol treated ovules


title: N2285_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years):

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling:

tag: subcutaneous neurofibromas:

tag: cutaneous neurofibromas:

tag: lisch nodules:

tag: glioma:

tag: learning disabilities:

tag: facial dysmorphism:

tag: scoliosis:


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10454

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: 48h Methanol vs unpollinated ovules (replica 1)

description:
48h Methanol (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

tag: tissue

value: Unpollinated ovules


title: NF01094_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10451

tag: od

tag: time

value: 30 min.

tag: strain

tag: medium

value: CM

tag: agent

tag: time course


title: sknmc.normoxia.adherent.1

tag: disease status

value: Ewing's sarcoma

tag: cell line

value: SK-N-MC

tag: genome/variation

value: EWS-FLI1 fusion type 1

tag: p53 status

value: mutant

tag: culture conditions

value: adherent, normoxia


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10219

value: paraquat

value: constant stress


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10453

value: 60 min.


title: N849_microdeletion_characterization

tag: cell type

value: whole blood leukocytes

value: neurofibromatosis type 1 (NF1)

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

value: de novo

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas:

tag: lisch nodules:

tag: tissue


title: MAR_microdeletion_characterization

tag: cell type

tag: disease status

tag: weight (kg)

tag: height (cm)

tag: large café-au-lait macules (number)

value: Absent

tag: plexiform neurofibromas

tag: lisch nodules

tag: glioma

value: Present

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis

value: healthy controls


title: 48h Methanol vs unpollinated ovules (replica 3)

description:
48h Methanol (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

value: 48h Methanol treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)

value: ovule

value: Unpollinated ovules


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10216

tag: od

tag: time

tag: strain

tag: medium

value: CM

tag: agent

tag: time course


title: HUM_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

value: Inherited

tag: parental origin

value: Paternal

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas:

tag: lisch nodules:

tag: glioma:

tag: facial dysmorphism:

tag: scoliosis:

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10218

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10439

value: 30 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10217


title: 48h MeJavs 48h Methanol (replica 3)

description:
48h MeJa (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 48h Meja treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)

tag: sample type

source_name: Unpollinated ovules


title: 48h MeJa vs 48h Methanol (replica 2)

description:
48h MeJa (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 48h Meja treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)


title: 48h SI vs unpollinated ovules (replica 2)

description:
48h SI (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 48h pollinated ovules from G4 genotype; genotype G4 (S12 and S14 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: 48h MeJa vs 48h Methanol (replica 4)

description:
48h MeJa (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: 48h MeJa vs 48h Methanol (replica 1)

description:
48h MeJa (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10207

value: paraquat

value: constant stress


title: LEC_microdeletion_characterization

tag: cell type

value: whole blood leukocytes

tag: disease status

tag: microdeletion sub-type

tag: age (years):

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling:

tag: subcutaneous neurofibromas:

tag: plexiform neurofibromas:

tag: learning disabilities:


title: N2456_microdeletion_characterization

value: neurofibromatosis type 1 (NF1)

tag: age (years)

tag: nf1 inheritance

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10205

tag: od

tag: time

value: 0 min.

tag: strain

tag: medium

tag: agent

tag: time course


title: N2289_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years):

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling:

tag: subcutaneous neurofibromas:

tag: cutaneous neurofibromas:

tag: plexiform neurofibromas:

tag: lisch nodules:

tag: glioma:

tag: learning disabilities:

tag: facial dysmorphism:

tag: scoliosis:


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10169

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10209

value: 60 min.


title: 24h Wound vs unpollinated ovules (replica 4)

description:
24h Wound (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: Ovules at 24h style wounding  from G4 genotype ; greenhouse growth with an average photoperiod of 14-16h per day)

tag: sample type

tag: tissue


title: GUI_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number):

tag: skin-fold freckling

value: Present

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules

tag: glioma

value: Absent

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10168

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10210


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10155


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10208


title: N2288_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

value: de novo

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: plexiform neurofibromas:

tag: tissue

value: healthy controls


title: 24h Wound vs unpollinated ovules (replica 2)

description:
24h Wound (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

value: Ovules at 24h style wounding  from G4 genotype ; greenhouse growth with an average photoperiod of 14-16h per day)

value: ovule

value: Unpollinated ovules


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10154

tag: od

tag: time

tag: strain

tag: medium

value: CM


title: N2217_microdeletion_characterization

tag: cell type

tag: disease status

tag: café-au-lait macules (number):

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: 24h Wound vs unpollinated ovules (replica 1)

description:
24h Wound (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: tissue


title: N2179_microdeletion_characterization

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: plexiform neurofibromas:


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10153

tag: od

tag: time

value: 80 min.

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10150

value: 40 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10152


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10206


title: 24h Wound vs unpollinated ovules (replica 3)

description:
24h Wound (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10151


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10149

value: 20 min.


title: N2178_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years):

tag: nf1 inheritance:

tag: café-au-lait macules (number):

tag: skin-fold freckling:

tag: subcutaneous neurofibromas:

tag: cutaneous neurofibromas:

tag: lisch nodules:

tag: glioma:

tag: learning disabilities:

tag: facial dysmorphism:

tag: scoliosis:


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10146

tag: od

tag: time

value: 10 min.

tag: strain

tag: medium

tag: agent

value: paraquat

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10148

value: constant stress


title: 24h Touch vs unpollinated ovules (replica 3)

description:
24h Touch (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: Ovule from G4 genotype at 24h after touching the stigmas with sterile 100 mm zirconia/silica beads; greenhouse growth with an average photoperiod of 14-16h per day)

tag: sample type

tag: tissue


title: N2166_microdeletion_characterization

tag: cell type

value: whole blood leukocytes

tag: disease status

value: neurofibromatosis type 1 (NF1)

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas:

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10147

description: Cells incubated under entrainment conditions

source_name: Halobacterium salinarum, paraquat, constant stress

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: 24h SI vs unpollinated ovules (replica 4)

description:
24h SI (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 24h pollinated ovules from G4 genotype; genotype G4 (S12 and S14 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

tag: sample type

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10139

value: 5 min.


title: 24h Touch vs unpollinated ovules (replica 1)

description:
24h Touch (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: Ovule from G4 genotype at 24h after touching the stigmas with sterile 100 mm zirconia/silica beads; greenhouse growth with an average photoperiod of 14-16h per day)


title: 24h Touch vs unpollinated ovules (replica 2)

description:
24h Touch (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10136

value: 0 min.


title: N1918_microdeletion_characterization

description: Reference sample: Pool of six normal control DNAs from six healthy donors

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

value: de novo

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling

value: Present

value: Absent


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10137

tag: od

tag: time

tag: strain

tag: medium

tag: agent


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10135

value: -1 min.

tag: time course


title: N2165_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years):

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas:

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis

tag: tissue

value: healthy controls


title: 24h SI vs unpollinated ovules (replica 3)

description:
24h SI (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

value: 24h pollinated ovules from G4 genotype; genotype G4 (S12 and S14 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: ovule

value: Unpollinated ovules


title: N2164_microdeletion_characterization

tag: age (years)

tag: nf1 inheritance

value: Inherited

tag: parental origin

value: Maternal

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling


title: 24h SI vs unpollinated ovules (replica 1)

description:
24h SI (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10573

source_name: Halobacterium salinarum, hydrogen peroxide, recovery

tag: od

tag: time

value: 50 min.

tag: strain

tag: medium

value: CM

tag: agent

tag: time course

value: recovery


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10583


title: N1248_microdeletion_characterization

tag: cell type

value: whole blood leukocytes

tag: disease status

value: neurofibromatosis type 1 (NF1)

tag: microdeletion sub-type

tag: parental origin:

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas:

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10134

tag: od

tag: time

tag: strain

value: paraquat

value: constant stress


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10574

value: 60 min.

tag: medium

tag: agent

tag: time course


title: 24h SeC vs unpollinated ovules (replica 4)

description:
24h SeC (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 24h pollinated ovules from G4 genotype; semi compatible genotype (S13 and S14 self-incompatibility alleles)  was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

tag: sample type


title: 24h SI vs unpollinated ovules (replica 2)

description:
24h SI (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: N1666_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

value: de novo

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling

value: Present


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10584

tag: od

tag: time

tag: strain

tag: medium


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10585

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10138

value: 5 min.


title: SOL_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: parental origin

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

value: Absent

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules:

tag: glioma:

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis

tag: tissue

value: healthy controls


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10575

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: 24h Touch vs unpollinated ovules (replica 4)

description:
24h Touch (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

value: Ovule from G4 genotype at 24h after touching the stigmas with sterile 100 mm zirconia/silica beads; greenhouse growth with an average photoperiod of 14-16h per day)

value: ovule


title: N1683_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

value: Inherited

tag: parental origin

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling

tag: plexiform neurofibromas:

tag: lisch nodules

tag: glioma


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10572

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10581

value: 30 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10571

value: 40 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10569

value: CM


title: 24h SeC vs unpollinated ovules (replica 3)

description:
24h SeC (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

value: 24h pollinated ovules from G4 genotype; semi compatible genotype (S13 and S14 self-incompatibility alleles)  was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

tag: tissue

value: Unpollinated ovules


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10582

value: recovery


title: 24h SeC vs unpollinated ovules(replica 2)

description:
24h SeC (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: SHC_microdeletion_characterization

tag: cell type

value: whole blood leukocytes

tag: disease status

value: neurofibromatosis type 1 (NF1)

tag: microdeletion sub-type

tag: age (years):

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: skin-fold freckling:

tag: subcutaneous neurofibromas:

tag: cutaneous neurofibromas:

tag: lisch nodules:

tag: glioma:

tag: learning disabilities:

tag: facial dysmorphism:

tag: scoliosis:


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10579

tag: od

tag: time

value: 20 min.

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10580


title: 24h SeC vs unpollinated ovules (replica 1)

description:
24h SeC (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10578


title: PRO_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years):

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: plexiform neurofibromas:


title: 24h SC vs unpollinated ovules (replica 4)

description:
24h SC (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 24h pollinated ovules from G4 genotype;genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: 24h SC vs unpollinated ovules (replica 3)

description:
24h SC (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 24h pollinated ovules from G4 genotype;genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: N986_microdeletion_characterization

tag: age (years)

tag: nf1 inheritance

value: de novo

tag: skin-fold freckling

value: Present

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: N2603_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: parental origin:

tag: weight (kg):

value: Absent

tag: tissue


title: PAN_microdeletion_characterization

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: plexiform neurofibromas

value: healthy controls


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10576

tag: od

tag: time

value: 10 min.

tag: strain

tag: medium

tag: agent

tag: time course


title: N1283_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas:

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: JAF_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: plexiform neurofibromas

tag: glioma:

tag: learning disabilities:

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10558

tag: od

tag: time

value: 0 min.

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10577


title: 24h SC vs unpollinated ovules (replica 2)

description:
24h SC (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

value: ovule


title: LEM_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years):

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling:

tag: subcutaneous neurofibromas:

tag: cutaneous neurofibromas:

tag: plexiform neurofibromas:

tag: lisch nodules:

tag: facial dysmorphism:

tag: scoliosis:


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10358

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10348


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10346

value: 60 min.


title: 24h IS vs unpollinated ovules (replica 4)

description:
24h IS (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 24h pollinated ovules from G4 genotype; S.microdontum was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

tag: sample type

tag: tissue


title: 24h SC vs unpollinated ovules (replica 1)

description:
24h SC (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10357

description: Cells incubated under entrainment conditions

source_name: Halobacterium standard reference sample


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10557


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10347


title: 24h IS vs unpollinated ovules (replica 3)

description:
24h IS (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 24h pollinated ovules from G4 genotype; S.microdontum was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10345

value: 50 min.

value: CM


title: GAI_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years):

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: glioma:

tag: learning disabilities:


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10349

tag: od

tag: time

tag: strain

tag: medium

tag: agent


title: 24h IS vs unpollinated ovules (replica 2)

description:
24h IS (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

tag: tissue

value: Unpollinated ovules


title: 24h IS vs unpollinated ovules (replica 1)

description:
24h IS (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10344

tag: time course

value: recovery


title: COG_microdeletion_characterization

description: Reference sample: Pool of six normal control DNAs from six healthy donors

tag: cell type

value: whole blood leukocytes

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: café-au-lait macules (number):

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules:

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10342

tag: od

tag: time

value: 40 min.

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10341

value: 30 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10343


title: DEV_microdeletion_characterization

tag: cell type

tag: disease status

value: neurofibromatosis type 1 (NF1)

tag: microdeletion sub-type

tag: age (years):

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: skin-fold freckling:

tag: subcutaneous neurofibromas:

tag: cutaneous neurofibromas:

tag: plexiform neurofibromas:

tag: glioma:

tag: learning disabilities:

tag: facial dysmorphism:

tag: scoliosis:

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10340

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: PAW_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

value: de novo

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: café-au-lait macules (number):

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10339

tag: od

tag: time

value: 20 min.

tag: strain

tag: medium

tag: agent

tag: time course


title: 24h Methanol vs unpollinated ovules (replica 4)

description:
24h Methanol (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 24h Methanol treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)

tag: sample type

tag: tissue


title: 24h Methanol vs unpollinated ovules (replica 2)

description:
24h Methanol (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

value: 24h Methanol treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)


title: 24h Methanol vs unpollinated ovules (replica 3)

description:
24h Methanol (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: LAF_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling

value: Absent

value: Present

tag: scoliosis:

value: healthy controls


title: BOR_microdeletion_characterization

value: Inherited

tag: parental origin

value: Maternal

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number):

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules:

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis