title: A13 UT

description: HUVEC Isolate A13 UT Biological replicate 15

source_name: HUVEC, untreated, cultured in fully supplemented media

extract_protocol: Cell cultures were washed with 1 x PBS and lysed using TRIzol® reagent. Total RNA was extracted using phenol chloroform, with the precipitated RNA washed in 70% ethanol and resuspended in RNase free water. RNA concentration and quality was assess by spectrophotometer and Agilent BioAnalyser.

treatment_protocol: Passage 4 cultured HUVEC isolates were untreated in fully supplemented media to maintain basal growth conditions.


title: 20 IM

status: Public on Jul 20 2011

type: RNA

city: Cambridge

first: Muna

last: Affara

address: Tennis Court Road

department: Pathology

country: United Kingdom

institute: University of Cambridge

description: HUVEC, Inflammatory mediator treated, Biological replicate 1

hyb_protocol: 10 µg biotin incorporated cRNA was fragmented and then denatured. The denatured cRNA was slowly loaded into the bioarray flex chamber without the introduction of air bubbles. All samples were loaded within 30 minutes of cRNA denaturation. The sealed bioarrays were left to hybridise in a 37°C shaker-incubator for 18 hours. The slides were washed and placed in a solution of Cy5-streptavidin for 30 minutes, before stringent washes were used to remove any unbound dye.

scan_protocol: All microarray slides were scanned using an Axon 4100B scanner at the following settings; 635mn wavelength, 600V PMT voltage, 100% laser power, 10µm pixel size

data_processing: The scanned Tagged Image File Format (TIFF) files were pre-processed using CodeLink Expression Analysis v4.0 software. Subsequent normalisation was carried out using Loess normalisation in R.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: HUVEC, Inflammatory mediator treated

label_protocol: Total RNA was converted to cDNA. This was then used in an invitro transcription (IVT) reaction with biotin to generate biotin incorporated cRNA.

growth_protocol: HUVEC isolates from different individuals were cultured in fully supplemented media until passage 4 (P4).

extract_protocol: Cell cultures were washed with 1 x PBS and lysed using TRIzol® reagent. Total RNA was extracted using phenol chloroform, with the precipitated RNA washed in 70% ethanol and resuspended in Rnase free water. RNA concentration and quality was assess by spectrophotometer and Agilent BioAnalyser.

treatment_protocol: Passage 4 cultured HUVEC isolates were treated with an inflammatory cocktail of 10ng/ml TNF-α, Il-1β, Il-8 for 24 hours prior to RNA extraction.

tag: tissue

value: Primary endothelial cells

tag: culture

value: Passage 4 cultured HUVECs


title: time-24h, dosage-0ng, rep-1

city: New York

first: Ajish

middle: D

last: George

state: NY

address: 1425 Madison Ave

department: Dept of Genetics & Genomics

country: USA

institute: Mt Sinai School of Medicine

description: Gene expression data from cells treated with 0ng for 24h

hyb_protocol: Samples were hybridized to WT Human Gene 1.0 ST arrays using Affymetrix hybridization kit materials, according to the manufacturrer's instructions.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Raw CEL file data from Affymetrix GeneChip Operating Software (GCOS) were background corrected, normalized, and summarized using both gcrma and plier functions in parallel using the Affymetrix power tools package (http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx). The power tools package was also used to estimate a p value for expression of gene in each array according to the Detection Above Background (DABG) method. The data was imported into an R Bioconductor session. Genes that were not expressed at DABG p < 10^ 8 in all replicates of a set were discarded. Linear models of differential expression were fit to each of the transformed data sets using the R Bioconductor limma package, and contrasts were estimated between each group of p53 regulated samples and its corresponding set of controls. The genes were tested for significant differential expression between each pair of groups at a level of p <=0.05 after multiple testing correction according to Benjamini Hochberg procedure (Benjamini & Hochberg, 1995).

label: biotin

source_name: time-24h, dosage-0ng, rep-1

label_protocol: WT expression kit (Ambion), WT Terminal Labeling Kit (Affymetrix), according to the manufatcturer's instructions

growth_protocol: The immortalized B5/589 human mammary epithelial cells (Stampfer and Bartley, 1985) were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (Invitrogen), 1% penicillin/streptomycin (GIBCO) and 5 ng/ml hEGF (Peprotech). Cells were cultured at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was isolated with an RNAeasy kit (QIAGEN).

treatment_protocol: For all experiments, cells were plated at 800,000 cells/10cm plate 12 24h before treatment, induced with doxycycline at the same time and collected after indicated time periods. Media with or without doxycycline were replaced every 24h.  Doxycycline was purchased from Clontech (631311). Doxorubicin was purchased from Sigma (D1515). TrypLE Express Stable Trypsin Replacement Enzyme (Invitrogen, 12604) was used for the dissociation of attached cells.

tag: cell line

tag: time

tag: treatment

value: 0ng Dox

tag: transgene

value: inducible p53


title: 13 UT

description: HUVEC Isolate 13 UT Biological replicate 13


title: time-12h, dosage-5ng, rep-3

description: Gene expression data from cells treated with 5ng for 12h

source_name: time-12h, dosage-5ng, rep-3

value: immortalized B5/589 human mammary epithelial cells

value: 5ng Dox


title: normal glucose LG3

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

description:
HAEC cells grown in medium containing normal glucose level (4mM)
4676008067_E

hyb_protocol: according to Illumina standard protocol for iSCAN

data_processing: Illumina Genome Studio, remove backgroung and Cubic Spline normalisation

source_name: Endothelial cell response to glucose levels/ control

growth_protocol: Primary HAECs (human aortic endothelial cells), purchased from Lonza (Walkersville, MD, USA), were cultured in EBM-2 medium (Lonza) containing EGM-2 growth factors and supplements (Lonza) and 10% fetal bovine serum (Gibco).

extract_protocol: TriReagent + Qiagen Rneasy mini as described in Tothill et al, Cancer Research 2008

treatment_protocol: Glucose response was analyzed in cells treated 48 hours with medium containing 30 mM high glucose (HG) or 5.5 mM low glucose (LG).

tag: cell type

value: primary human aortic endothelial cells

value: normal glucose


title: time-12h, dosage-5ng, rep-2

source_name: time-12h, dosage-5ng, rep-2


title: 18 UT

description: HUVEC Isolate18 UT Biological replicate 14


title: dox_2 with array type SUNFLOWER from Affymetrix

type: other

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: We focus our research on the release of embryonic dormancy in sunflower seeds and more precisely on the molecular mechanisms controlling seed dormancy release during dry after-ripening. Our data show an increase of ROS during dormancy release associated with an increase of stored mRNA oxidation during after-ripening as shown with determination of the RNA oxidation marker : 8-hydroxyguanosine (8OHG) To assess to role of mRNA oxidation in this process, we isolated 8OHG-containing mRNA to identify oxidized transcript using microarray analysis.

hyb_protocol: labelled extract quantity: 5.5ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

molecule: other

organism: Helianthus annuus

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: embryonic axis - Localization: Montélimar, Drôme, France Month of the period of cultivation Apr. 2009 May 2009 June. 2009 July. 2009 Aug. 2009 Sept. 2009 Total Sunshine duration (hours)  278 188 207 243 207 230  1353 Précipitations (mm) 16 168 104 120 118 57 583 Average temperatures (°C) 15.9 17.0 20.0 20.9 20.1 16.5 18.4

treatment_protocol: no treatment

tag: dev.stage (boyes et al. plant cell 2001)

value: seed

tag: seed type

value: dormant seed


title: high glucose HG2

description:
HAEC cells grown in medium containing high glucose level (30mM)
4676008067_D

scan_protocol: according to Illumina standard protocol for iSCAN

source_name: Endothelial cell response to glucose levels/ test sample

value: high glucose


title: NDox_2 with array type SUNFLOWER from Affymetrix

treatment_protocol: Name:Damp Storage - environmental treatment - hygrometry,relative humidity:quantity 70 percent time 2 month . Storage protocol Dormant seeds have been stored at 25°C in desiccators over different saturated salt solution in order to control relative humidity. 70% RH : solution of sodium chloride.

value: non dormant seed


title: high glucose HG5

description:
HAEC cells grown in medium containing high glucose level (30mM)
4662010040_F

label_protocol: according to Illumina standard protocol for iSCAN


title: dox_1 with array type SUNFLOWER from Affymetrix


title: normal glucose LG2

description:
HAEC cells grown in medium containing normal glucose level (4mM)
4676008067_C


title: high glucose HG1

description:
HAEC cells grown in medium containing high glucose level (30mM)
4676008067_B


title: Leaf_rep1

city: Gainesville

first: Andre

last: Chanderbali

state: FL

address: Museum Road

institute: Univrsity of Florida

hyb_protocol: Arrays were hybridized in accordance with the Agilent Microarrray processing protocol

scan_protocol: Arrays were scanned with and Agilent DNA microarray scanner using Agilent’s Feature Extraction Software 9.1.3 (Agilent Technologies)

data_processing: Arrays were background-corrected and loess normalized within arrays and A-quantile normalized between arrays , using the Bioconductor package Limma. Significantly differentially expressed genes among the eight tissue samples were identifed using a one-way empirical Bayes ANOVA using single channel analysis while considering correlation between channels at each spot.

organism: Nuphar advena

source_name: Leaves

label_protocol: RNA transcripts were labeled using the Low-input RNA Labeling Kit (Agilent Technologies)

growth_protocol: wild populations of water lily in Pennsylvania, USA

extract_protocol: Total RNA was extracted from all tissue samples using the RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: harvested tissues were flash frozen in liquid nitrogen

value: Vegetative


title: 11 UT

description: HUVEC Isolate 11 UT Biological replicate 12


title: normal glucose LG1

description:
HAEC cells grown in medium containing normal glucose level (4mM)
4676008067_A


title: NDox_1 with array type SUNFLOWER from Affymetrix


title: time-24h, dosage-0ng, rep-3

source_name: time-24h, dosage-0ng, rep-3


title: d_1 with array type SUNFLOWER from Affymetrix

value: dormant


title: d_2 with array type SUNFLOWER from Affymetrix


title: 5 UT

description: HUVEC Isolate 5 UT Biological replicate 11


title: F.pla_benzene, rep 2

city: Amherst

first: Dawn

middle: E

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

institute: University of Massachusetts Amherst

description: F. placidus grown with 1 mM benzene. Second biological replicate of three.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Ferroglobus placidus DSM 10642

source_name: 1 mM benzene as electron donor and 56 mM ferric citrate as electron acceptor

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

growth_protocol: Ferroglobus placidus DSM 10642 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Tor et al., Env. Micro. 2001, 3(4) p281) with 1 mM benzene as electron donor and Fe(III) citrate as electron acceptor. Cultures were incubated at 85C in the dark.

extract_protocol:
Cultures (100 ml in 156 ml serum bottles) were divided into 50 ml conical tubes (Falcon), and cells were pelleted with centrifugation at 3,000 xg for 15 min. Pellets were then immediately frozen in liquid nitrogen and stored at –80°C.

Total RNA was extracted according to the HG protocol described in Holmes et al., ISME Journal, 2011.

tag: strain

tag: electron donor

value: benzene

tag: electron donor type

value: aromatic hydrocarbon


title: time-12h, dosage-5ng, rep-1

source_name: time-12h, dosage-5ng, rep-1


title: 1 UT

description: HUVEC Isolate 1 UT Biological replicate 10


title: F.pla_benzene, rep 3

description: F. placidus grown with 1 mM benzene. Third biological replicate of three.


title: time-12h, dosage-3ng, rep-3

description: Gene expression data from cells treated with 3ng for 12h

source_name: time-12h, dosage-3ng, rep-3

value: 3ng Dox


title: S_1 with array type SUNFLOWER from Affymetrix

treatment_protocol: Name:Dry Storage - environmental treatment - hygrometry,relative humidity:quantity 2 percent time 2 month . Storage protocol Dormant seeds have been stored at 25°C in desiccators over different saturated salt solution in order to control relative humidity. 2% RH : solution of zinc chloride.

value: control


title: 12 UT

description: HUVEC Isolate 12 UT Biological replicate 8

value: Primary endothelial cells

value: Passage 4 cultured HUVECs


title: time-12h, dosage-3ng, rep-4

source_name: time-12h, dosage-3ng, rep-4

value: inducible p53


title: 23 UT

description: HUVEC Isolate 23 UT Biological replicate 9


title: 20 UT

description: HUVEC Isolate 20 UT Biological replicate 7


title: time-12h, dosage-3ng, rep-1

source_name: time-12h, dosage-3ng, rep-1

value: immortalized B5/589 human mammary epithelial cells


title: time-12h, dosage-5ng, rep-4

description: Gene expression data from cells treated with 5ng for 12h

source_name: time-12h, dosage-5ng, rep-4

value: 5ng Dox


title: time-12h, dosage-3ng, rep-2

source_name: time-12h, dosage-3ng, rep-2


title: passive smoker 201, placenta

city: Prague 2

first: Hana

last: Bruchova

address: U nemocnice 1

department: Molecular Genetics

country: Czech Republic

institute: Institute of Hematology and Transfusion

description: middle part of the placenta villi parenchyma sections

hyb_protocol: 750 ng of biotinylated cRNA was hybridized to the array for 17 hours according to the manufacturer manual. Final staining was performed with streptavidin conjugated to Cy-3 fluorescent dye.

scan_protocol: Arrays were scaned using BeadArray Reader (Illumina) and bead level data were extracted by BeadStudio Software (Illumina).

data_processing: Bead summary data were imported into R statistical environment (www.r-project.org) and normalized by quantile method in Lumi package. Only probes, which reached detection P-value < 0.01 in all samples, were used for further analyses. Differentially expressed genes were analysed in the Limma package. A linear model was fitted for each gene given a series of arrays using lmFit function. Using Benjamini and Hochberg method P-values were corrected for multiple testing.

source_name: term placenta

label_protocol: Biotinylated cRNA was prepared from 200 ng of total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion). In vitro transcription (IVT) was performed at 37°C for 14 hours.

extract_protocol: Umbilical cord bloods were sampled and processed using LeukoLOC Total RNA Isolation System (Ambion, Austin, TX, USA) according to the manufacturer manual. The system employs filter-based leukocyte-depletion technology to isolate leukocytes from whole blood and RNAlater™ (Ambion) to stabilize the cells on the filter. By removal of red blood cells, the RNA purified from captured leukocytes is inherently depleted of globin mRNA, which improves sample quality for expression profiling and other applications. The middle parts of placenta sections were frozen in RNA Later solution (Ambion) and stored at –20°C until RNA isolation. Placental total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer instructions. Integrity of the total RNAs was assayed by Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and only samples with RNA integrity number (RIN) above 7.0 were used for gene expression profiling.

tag: smoking status

value: passive smoker

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

value: vaginal

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex

value: F

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: S_2 with array type SUNFLOWER from Affymetrix

description: We focus our research on the release of embryonic dormancy in sunflower seeds and more precisely on the molecular mechanisms controlling seed dormancy release during dry after-ripening. Our data show an increase of ROS during dormancy release associated with an increase of stored mRNA oxidation during after-ripening as shown with determination of the RNA oxidation marker : 8-hydroxyguanosine (8OHG) To assess to role of mRNA oxidation in this process, we isolated 8OHG-containing mRNA to identify oxidized transcript using microarray analysis.

tag: dev.stage (boyes et al. plant cell 2001)

value: seed

tag: seed type


title: ND_1 with array type SUNFLOWER from Affymetrix

growth_protocol: embryonic axis - Localization: Montélimar, Drôme, France Month of the period of cultivation Apr. 2009 May 2009 June. 2009 July. 2009 Aug. 2009 Sept. 2009 Total Sunshine duration (hours) 278 188 207 243 207 230 1353 Précipitations (mm) 16 168 104 120 118 57 583 Average temperatures (°C) 15.9 17.0 20.0 20.9 20.1 16.5 18.4

value: non dormant


title: crl1_3

city: Montpellier

first: Yoan

last: Coudert

address: UM2 Place Eugène Bataillon

institute: Montpellier 2 University

hyb_protocol: Twelve μg of biotin-labelled antisens RNAs were fragmented and hybridized to GeneChip Rice Genome Arrays (Affymetrix) for 16h at 45°C and 60rpm in a Hybridisation Oven 645. Arrays were washed, labelled with phycoerythrin on the Fluidic Station 450.

scan_protocol: Arrays were read with the Scanner 3000 7G.

data_processing: Array pictures were analysed with MAS5 algorithm of the Expression Console software (Affymetrix). Default parameters were applied, global scaling method was used to normalise data (TGT value set at 100).

organism: Oryza sativa

source_name: crl1 stem base - experiment 3

label_protocol: 200ng of total RNA were used for a single amplification. Antisense RNA strand were then biotynilated according the Affymetrix (Affymetrix, CA, USA) IVT Express protocol.

growth_protocol: Wild-type and crl1 mutant rice (Oryza sativa cultivar Taichung 65) were inoculated under sterile conditions in square Petri dishes (Corning, NY, USA) containing half strength Murashige and Skoog (MS) medium (Duchefa Biochemie B.V., The Nederlands) and 0,8% agar type II (Sigma, MO, USA) and were incubated in a vertical position at 26°C and under a 12h light/12h dark photoperiod. Stem bases used for transcriptome analysis were collected from 7 day-old plantlets.

extract_protocol: Plant Rneasy + DNAse treatment (QIAGEN) according manufacturer's instructions

tag: genotype

value: mutant :crown rootless1


title: Astrocytes expressing CTE-SUMO1 #3

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

hyb_protocol: Labeled cRNA was hybridized on Affymetrix GeneChip Mouse Genome 430A 2.0 Arrays, containing 22,690 probesets corresponding to approximately 14,000 well-characterized mouse genes. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).

scan_protocol: Hybridized arrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment (http://www.r-project.org/) version 2.8.0 with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Data were then filtered based on Affymetrix detection call and probeset intensity, so that only probesets that had a present call and intensity value >100 in at least one of the arrays were retained. Statistical analysis was performed with limma. P-values were adjusted for multiple testing using Benjamini and Hochberg’s method to control the false discovery rate. Genes with adjusted P values below 0.05 were considered differentially expressed.

organism: Mus musculus

source_name: Spinal cord astrocytes cultured at post-natal day 2 transduced with AdV virus encoding Myc-CTE-SUMO1

label_protocol: A 2μg-amount of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).

growth_protocol: Primary astrocyte cultures were prepared from spinal cord of newborn mice (P2-P4) as previously described (Gibb SL, Boston-Howes W, Lavina SZ, Gustincich S, Brown RH, Jr., Pasinelli P, Trotti D. 2007. A caspase-3 cleaved fragment of the glial glutamate transporter EAAT2 is sumoylated and targeted to promyelocytic leukemia nuclear bodies in mutant SOD1 linked ALS. J Biol Chem:M704314200.). Cell monolayers were >95% astrocyte-pure as determined by GFAP immunoreactivity.

extract_protocol: Total RNA was isolated from spinal cord astrocytes transfected with CTE or CTE-SUMO1 constructs at day 6 post-trasnduction using TRIzol (Invitrogen) according to manufacturer's instructions, and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).

treatment_protocol: Viral infections were performed on astrocyte monolayer for 72 h. Adenoviral vector was added in fresh OPTI-MEM medium with primacin, and the medium was changed again 18 h later. Multiplicity of infection (m.o.i.) ranged from 1 to 2.

tag: cell type

value: Spinal cord astrocytes


title: A6 UT

description: HUVEC Isolate A6 UT Biological replicate 3

source_name: HUVEC, untreated, cultured in fully supplemented media

tag: tissue

tag: culture


title: A10 UT

description: HUVEC Isolate A10 UT Biological replicate 5


title: A4 UT

description: HUVEC Isolate A4 UT Biological replicate 2


title: ND_2 with array type SUNFLOWER from Affymetrix


title: A8 UT

description: HUVEC Isolate A8 UT Biological replicate 4


title: Astrocytes expressing CTE-SUMO1 #1


title: Astrocytes expressing CTE-SUMO1 #4


title: A12 UT

description: HUVEC Isolate A12 UT Biological replicate 6


title: crl1_2

source_name: crl1 stem base - experiment 2


title: WT_2

source_name: WT stem base - experiment 2

value: wild type :Taichung 65


title: Astrocytes expressing CTE #4

source_name: Spinal cord astrocytes cultured at post-natal day 2 transduced with AdV virus encoding Myc-CTE


title: crl1_1

source_name: crl1 stem base - experiment 1


title: Astrocytes expressing CTE-SUMO1 #2


title: Astrocytes expressing CTE #3


title: WT_1

source_name: WT stem base - experiment 1


title: Astrocytes expressing CTE #2


title: 22 UT

description: HUVEC Isolate 22UT Biological replicate 1


title: WT_3

source_name: WT stem base - experiment 3


title: squamous 4292

status: Public on Jul 19 2011

city: Kyoto

first: T

last: Fujiwara

address: 46-29 Yoshida Shimoadachi-cho Sakyo-ku

country: Japan

institute: Kyoto University

hyb_protocol: Labelled cDNA was hybridized overnight at 42°C in a buffer containing 50% formamide, 5xSSC, 0.1% SDS, 0.25μg/μl human cot1 DNA and 0.125μg/μl poly dT and washed to a final stringency of 1x SSC at 42°C.

scan_protocol: After washing, slides were immediately scanned using an Axon GenePix 4000B scanner and quantified using Axon GenePix Pro software (Axon, Union city, CA).

data_processing: All samples were subjected to LOcally WEighted Scatter plot Smoother (LOWESS); smoothing rate 20%. Control signals were cut off by 10.  (GeneSpring 7.2, Agilent Technologies)

source_name: squamous 4292

label_protocol: cDNA derived from 2μg of cRNA was aminoallyl labeled with Cy5 (sample) or Cy3 (reference),

extract_protocol: cDNA derived from 2 g cRNA, essentially as Proc Natl Acad Sci USA 1990; 87: 1663–67.  described in

value: lung adenocarcinoma

tag: tumor type

value: NE Subtype

source_name: lung reference

value: mixture of total RNA 80% from 10 lung cancer cell lines & >20% normal lung


title: squamous 594

source_name: squamous 594


title: F.pla_benzene, rep 1

description: F. placidus grown with 1 mM benzene. First biological replicate of three.

source_name: 1 mM benzene as electron donor and 56 mM ferric citrate as electron acceptor

tag: strain

tag: electron donor

value: benzene

tag: electron donor type

value: aromatic hydrocarbon


title: Astrocytes expressing CTE #1


title: squamous 3161

source_name: squamous 3161

value: SQ Subtype


title: squamous 2639

source_name: squamous 2639


title: squamous 2278

source_name: squamous 2278

value: AL Subtype


title: squamous 3038

source_name: squamous 3038


title: squamous 1116

source_name: squamous 1116


title: squamous 2207

source_name: squamous 2207


title: squamous 2240

source_name: squamous 2240


title: adenocarcinoma 952

source_name: adenocarcinoma 952


title: squamous 1584

source_name: squamous 1584


title: adenocarcinoma 948

source_name: adenocarcinoma 948


title: adenocarcinoma 864

source_name: adenocarcinoma 864


title: adenocarcinoma 747

source_name: adenocarcinoma 747


title: adenocarcinoma 707

source_name: adenocarcinoma 707


title: adenocarcinoma 762

source_name: adenocarcinoma 762


title: adenocarcinoma 5858

source_name: adenocarcinoma 5858

source_name: lung reference


title: adenocarcinoma 795

source_name: adenocarcinoma 795


title: adenocarcinoma 833

source_name: adenocarcinoma 833


title: adenocarcinoma 704

source_name: adenocarcinoma 704


title: adenocarcinoma 794

source_name: adenocarcinoma 794


title: adenocarcinoma 668

source_name: adenocarcinoma 668


title: adenocarcinoma 583

source_name: adenocarcinoma 583


title: adenocarcinoma 553

source_name: adenocarcinoma 553


title: adenocarcinoma 4833

source_name: adenocarcinoma 4833


title: adenocarcinoma 4552

source_name: adenocarcinoma 4552


title: adenocarcinoma 556

source_name: adenocarcinoma 556


title: adenocarcinoma 4458

source_name: adenocarcinoma 4458


title: adenocarcinoma 5785

source_name: adenocarcinoma 5785


title: adenocarcinoma 4562

source_name: adenocarcinoma 4562


title: adenocarcinoma 4975

source_name: adenocarcinoma 4975


title: adenocarcinoma 4607

source_name: adenocarcinoma 4607


title: adenocarcinoma 4584

source_name: adenocarcinoma 4584


title: adenocarcinoma 4558

source_name: adenocarcinoma 4558

source_name: lung reference


title: adenocarcinoma 4435

source_name: adenocarcinoma 4435


title: adenocarcinoma 4408

source_name: adenocarcinoma 4408


title: adenocarcinoma 4317

source_name: adenocarcinoma 4317


title: adenocarcinoma 4391

source_name: adenocarcinoma 4391


title: adenocarcinoma 4505

source_name: adenocarcinoma 4505


title: adenocarcinoma 4384

source_name: adenocarcinoma 4384


title: adenocarcinoma 4536

source_name: adenocarcinoma 4536


title: adenocarcinoma 4276

source_name: adenocarcinoma 4276


title: adenocarcinoma 4449

source_name: adenocarcinoma 4449


title: adenocarcinoma 4442

source_name: adenocarcinoma 4442


title: adenocarcinoma 4286

source_name: adenocarcinoma 4286


title: adenocarcinoma 4241

source_name: adenocarcinoma 4241


title: adenocarcinoma 4244

source_name: adenocarcinoma 4244


title: adenocarcinoma 4226

source_name: adenocarcinoma 4226


title: adenocarcinoma 3966

source_name: adenocarcinoma 3966


title: adenocarcinoma 4189

source_name: adenocarcinoma 4189


title: adenocarcinoma 3914

source_name: adenocarcinoma 3914

source_name: lung reference


title: adenocarcinoma 3956

source_name: adenocarcinoma 3956


title: adenocarcinoma 3455

source_name: adenocarcinoma 3455


title: adenocarcinoma 3409

source_name: adenocarcinoma 3409


title: adenocarcinoma 3414

source_name: adenocarcinoma 3414


title: adenocarcinoma 4231

source_name: adenocarcinoma 4231


title: adenocarcinoma 4154

source_name: adenocarcinoma 4154


title: adenocarcinoma 4164

source_name: adenocarcinoma 4164


title: adenocarcinoma 3405

source_name: adenocarcinoma 3405


title: adenocarcinoma 3323

source_name: adenocarcinoma 3323


title: adenocarcinoma 3276

source_name: adenocarcinoma 3276


title: adenocarcinoma 3564

source_name: adenocarcinoma 3564


title: adenocarcinoma 3707

source_name: adenocarcinoma 3707


title: adenocarcinoma 3429

source_name: adenocarcinoma 3429


title: adenocarcinoma 3767

source_name: adenocarcinoma 3767


title: adenocarcinoma 3244

source_name: adenocarcinoma 3244


title: adenocarcinoma 3888

source_name: adenocarcinoma 3888


title: adenocarcinoma 3221

source_name: adenocarcinoma 3221

source_name: lung reference


title: adenocarcinoma 3237

source_name: adenocarcinoma 3237


title: Maffucci chondrosarcoma

type: genomic

city: Leiden

first: Twinkal

middle: Chandubhai

last: Pansuriya

state: Zuid-Holland

address: Albinusdreef 2

country: Netherlands

institute: LUMC

hyb_protocol: According to Affymetrix SNP 6.0 standard protocol

data_processing: Genotyping was performed using the CRLMM algorithm in the Oligo package (Lin, 2008), copy number analysis using the aroma affymetrix package (Bengtsson, 2009), and we constructed LAIR plots to visualize regions of LOH and allelic imbalance (Corver, 2008) in R software (version 2.8). We have used CNCHP log ratio file as an input in Nexus (BioDiscovery, USA) software (version 4.1) and performed HMM based SNP-FASST segmentation for copy number analysis.

molecule: genomic DNA

source_name: Maffucci chondrosarcoma

extract_protocol: DNA from fresh frozen tissue was isolated using the wizard genomic DNA purification kit (Promega, Madison, WI), according to the manufacturer instructions.

tag: disease

value: Maffucci

tag: tumor

value: chondrosarcoma


title: Maffucci Enchondroma (L1684)

scan_protocol: According to Affymetrix SNP 6.0 standard protocol

source_name: Maffucci Enchondroma (L1684)

value: enchondroma


title: adenocarcinoma 3184

source_name: adenocarcinoma 3184


title: adenocarcinoma 3042

source_name: adenocarcinoma 3042


title: adenocarcinoma 3067

source_name: adenocarcinoma 3067


title: adenocarcinoma 3091

source_name: adenocarcinoma 3091


title: adenocarcinoma 3121

source_name: adenocarcinoma 3121


title: Maffucci enchondroma

source_name: Maffucci enchondroma (L2097a)

label_protocol: According to Affymetrix SNP 6.0 standard protocol


title: Maffucci Enchondroma (L2097c)

source_name: Maffucci Enchondroma (L2097c)

value: enchondroma (L2097c)


title: adenocarcinoma 2993

source_name: adenocarcinoma 2993


title: adenocarcinoma 2914

source_name: adenocarcinoma 2914


title: adenocarcinoma 2888

source_name: adenocarcinoma 2888


title: adenocarcinoma 2964

source_name: adenocarcinoma 2964


title: adenocarcinoma 2915

source_name: adenocarcinoma 2915


title: Maffucci Enchondroma

source_name: Maffucci Enchondroma

value: enchondroma (L2101)


title: adenocarcinoma 2839

source_name: adenocarcinoma 2839

source_name: lung reference


title: adenocarcinoma 2725

source_name: adenocarcinoma 2725


title: adenocarcinoma 2780

source_name: adenocarcinoma 2780


title: adenocarcinoma 2784

source_name: adenocarcinoma 2784


title: adenocarcinoma 2773

source_name: adenocarcinoma 2773


title: adenocarcinoma 2668

source_name: adenocarcinoma 2668


title: adenocarcinoma 2751

source_name: adenocarcinoma 2751


title: adenocarcinoma 2713

source_name: adenocarcinoma 2713


title: Maffucci Chondrosarcoma II

source_name: Maffucci Chondrosarcoma II (L2102)

value: chondrosarcoma II


title: adenocarcinoma 2706

source_name: adenocarcinoma 2706


title: adenocarcinoma 2803

source_name: adenocarcinoma 2803


title: adenocarcinoma 3074

source_name: adenocarcinoma 3074


title: adenocarcinoma 2766

source_name: adenocarcinoma 2766


title: adenocarcinoma 2697

source_name: adenocarcinoma 2697


title: L2195N

scan_protocol: GeneChip GSC3000 7G Whole-Genome Association System. According to Affymetrix SNP 6.0 standard protocol.

data_processing: Genotyping was performed using the CRLMM algorithm in the Oligo package (Lin, 2008), copy number analysis using the aroma affymetrix package (Bengtsson, 2009), and we constructed LAIR plots to visualize regions of LOH and allelic imbalance (Corver, 2008) in R software (version 2.8). We have used CNCHP log ratio file as an input in Nexus (BioDiscovery, USA) software (version 4.1) and performed HMM based SNP-FASST segmentation for copy number analysis. Copy number inferred after correction with the 5 closest normals.

source_name: Maffucci patient normal (fresh frozen)

extract_protocol: DNA from fresh frozen tissue was isolated using the Wizard genomic DNA purification kit (Promega, Madison, WI), according to the manufacturer instructions.

value: fresh frozen normal

tag: sample type

value: control


title: adenocarcinoma 2650

source_name: adenocarcinoma 2650


title: adenocarcinoma 2654

source_name: adenocarcinoma 2654


title: adenocarcinoma 2532

source_name: adenocarcinoma 2532

source_name: lung reference


title: adenocarcinoma 2480

source_name: adenocarcinoma 2480


title: adenocarcinoma 2524

source_name: adenocarcinoma 2524


title: adenocarcinoma 2463

source_name: adenocarcinoma 2463


title: adenocarcinoma 2248

source_name: adenocarcinoma 2248


title: adenocarcinoma 2435

source_name: adenocarcinoma 2435


title: adenocarcinoma 2247

source_name: adenocarcinoma 2247


title: adenocarcinoma 2031

source_name: adenocarcinoma 2031


title: adenocarcinoma 2335

source_name: adenocarcinoma 2335


title: adenocarcinoma 2326

source_name: adenocarcinoma 2326


title: adenocarcinoma 2199

source_name: adenocarcinoma 2199


title: adenocarcinoma 2447

source_name: adenocarcinoma 2447


title: adenocarcinoma 2093

source_name: adenocarcinoma 2093


title: adenocarcinoma 2075

source_name: adenocarcinoma 2075


title: adenocarcinoma 2525

source_name: adenocarcinoma 2525


title: adenocarcinoma 2245

source_name: adenocarcinoma 2245


title: adenocarcinoma 2001

source_name: adenocarcinoma 2001


title: adenocarcinoma 2393

source_name: adenocarcinoma 2393

source_name: lung reference


title: adenocarcinoma 2178

source_name: adenocarcinoma 2178


title: adenocarcinoma 2071

source_name: adenocarcinoma 2071


title: adenocarcinoma 2022

source_name: adenocarcinoma 2022


title: adenocarcinoma 2374

source_name: adenocarcinoma 2374


title: adenocarcinoma 1959

source_name: adenocarcinoma 1959


title: adenocarcinoma 1907

source_name: adenocarcinoma 1907


title: adenocarcinoma 2006

source_name: adenocarcinoma 2006


title: adenocarcinoma 2101

source_name: adenocarcinoma 2101


title: adenocarcinoma 1939

source_name: adenocarcinoma 1939


title: adenocarcinoma 1836

source_name: adenocarcinoma 1836


title: adenocarcinoma 1795

source_name: adenocarcinoma 1795


title: adenocarcinoma 2088

source_name: adenocarcinoma 2088


title: adenocarcinoma 1811

source_name: adenocarcinoma 1811


title: adenocarcinoma 1750

source_name: adenocarcinoma 1750


title: adenocarcinoma 1765

source_name: adenocarcinoma 1765


title: adenocarcinoma 2440

source_name: adenocarcinoma 2440


title: adenocarcinoma 1729

source_name: adenocarcinoma 1729

source_name: lung reference


title: adenocarcinoma 1735

source_name: adenocarcinoma 1735


title: adenocarcinoma 1691

source_name: adenocarcinoma 1691


title: adenocarcinoma 1545

source_name: adenocarcinoma 1545


title: adenocarcinoma 1643

source_name: adenocarcinoma 1643


title: adenocarcinoma 1515

source_name: adenocarcinoma 1515


title: adenocarcinoma 1638

source_name: adenocarcinoma 1638


title: adenocarcinoma 1625

source_name: adenocarcinoma 1625


title: adenocarcinoma 1671

source_name: adenocarcinoma 1671


title: adenocarcinoma 1635

source_name: adenocarcinoma 1635


title: adenocarcinoma 1468

source_name: adenocarcinoma 1468


title: adenocarcinoma 1547

source_name: adenocarcinoma 1547


title: adenocarcinoma 1474

source_name: adenocarcinoma 1474


title: adenocarcinoma 1458

source_name: adenocarcinoma 1458


title: adenocarcinoma 1539

source_name: adenocarcinoma 1539


title: adenocarcinoma 1420

source_name: adenocarcinoma 1420


title: adenocarcinoma 1422

source_name: adenocarcinoma 1422


title: adenocarcinoma 1449

source_name: adenocarcinoma 1449

source_name: lung reference


title: adenocarcinoma 1330

source_name: adenocarcinoma 1330


title: adenocarcinoma 1360

source_name: adenocarcinoma 1360


title: adenocarcinoma 1462

source_name: adenocarcinoma 1462


title: adenocarcinoma 1434

source_name: adenocarcinoma 1434


title: adenocarcinoma 1336

source_name: adenocarcinoma 1336


title: adenocarcinoma 1454

source_name: adenocarcinoma 1454


title: adenocarcinoma 1417

source_name: adenocarcinoma 1417


title: adenocarcinoma 1341

source_name: adenocarcinoma 1341


title: adenocarcinoma 1354

source_name: adenocarcinoma 1354


title: adenocarcinoma 1187

source_name: adenocarcinoma 1187


title: adenocarcinoma 1405

source_name: adenocarcinoma 1405


title: adenocarcinoma 1307

source_name: adenocarcinoma 1307


title: adenocarcinoma 1142

source_name: adenocarcinoma 1142


title: adenocarcinoma 1078

source_name: adenocarcinoma 1078


title: adenocarcinoma 1047

source_name: adenocarcinoma 1047


title: adenocarcinoma 1029

source_name: adenocarcinoma 1029


title: C1 100mg/kg_24hr_B96199_F_Stomach

city: Thousand Oaks

first: Scott

last: Taylor

state: CA

address: One Amgen Center Drive

institute: Amgen Inc.

hyb_protocol: 10 ug of biotinylated cRNA spiked with hybridization controls (bioB, bioC, bioD and cre) was hybridized to an Affymetrix RAE 230 array.

scan_protocol: GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: Each tissue and time point was analyzed independently. Expression data was pre-processed using Rosetta Resolver (Rosetta Inpharmatics LLC, Seattle, WA).  A probe set was considered present if the p-value associated with its intensity being different from the background intensity was ≤ 0.05. Probe sets with intensities that were not significantly different from the corresponding backround intensities were set to the background levels. Probe sets that were present on at least 5 microarrays out of 10 at each given time point were included for further analysis.  The data was normalized using quantile normalization (Guatier et al., 2004) prior to further analysis.

organism: Rattus norvegicus

source_name: C1-treated, non-glandular stomach, 24hr

label_protocol: 1 ug of total RNA was reverse transcribed to double-stranded cDNA using the Bioarray Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences, Farmingdale, NY), and biotinylated cRNA was generated using the BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY).

extract_protocol: Total RNA was isolated from ~30 ug pieces of tissue according to the RNeasy extraction procedure (Qiagen, Valencia, CA).

treatment_protocol: Rats (25/group) were assigned to groups receiving vehicle or 100 mg/kg of compound C1 by oral gavage (10 mL/kg). Five sets of 5 females/dose group received either a single dose on Day 1 with necropsy 4 to 5 hours post-dose; a single dose on Day 1 with necropsy on Day 2 (approximately 24 hours post-Day 1 dosing); 2 daily doses with necropsy on Day 3; 4 daily doses with necropsy on Day 5; or 7 daily doses with necropsy on Day 8.

value: Sprague Dawley

tag: gender

value: female

value: non-glandular stomach

tag: treatment

tag: treatment duration


title: C1 100mg/kg_5hr_B96192_F_Stomach

source_name: C1-treated, non-glandular stomach, 5hr


title: Vehicle_5hr_B96169_F_Stomach

source_name: Vehicle-treated, non-glandular stomach, 5hr

value: vehicle


title: Vehicle_5hr_B96168_F_Stomach


title: C1 100mg/kg_5hr_B96191_F_Stomach


title: C1 100mg/kg_5hr_B96195_F_Stomach


title: adenocarcinoma 1327

source_name: adenocarcinoma 1327

value: lung adenocarcinoma

source_name: lung reference

value: mixture of total RNA 80% from 10 lung cancer cell lines & >20% normal lung


title: Vehicle_5hr_B96170_F_Stomach


title: Vehicle_5hr_B96167_F_Stomach


title: C1 100mg/kg_5hr_B96193_F_Stomach


title: adenocarcinoma 1001

source_name: adenocarcinoma 1001


title: Vehicle_24hr_B96175_F_Stomach

source_name: Vehicle-treated, non-glandular stomach, 24hr


title: C1 100mg/kg_5hr_B96194_F_Stomach


title: C1 100mg/kg_24hr_B96200_F_Stomach


title: C1 100mg/kg_24hr_B96196_F_Stomach


title: Vehicle_5hr_B96166_F_Stomach


title: C1 100mg/kg_24hr_B96197_F_Stomach


title: Vehicle_24hr_B96171_F_Stomach


title: Vehicle_24hr_B96172_F_Stomach


title: C1 100mg/kg_24hr_B96198_F_Stomach


title: C1 100mg/kg_168hr_B96214_F_Bladder

source_name: C1-treated, urinary bladder, 168hr

value: urinary bladder


title: Vehicle_24hr_B96173_F_Stomach


title: C1 100mg/kg_168hr_B96213_F_Bladder


title: C1 100mg/kg_168hr_B96215_F_Bladder


title: C1 100mg/kg_168hr_B96212_F_Bladder


title: Vehicle_24hr_B96174_F_Stomach


title: C1 100mg/kg_168hr_B96211_F_Bladder


title: C1 100mg/kg_96hr_B96209_F_Bladder

source_name: C1-treated, urinary bladder, 96hr


title: C1 100mg/kg_96hr_B96210_F_Bladder


title: C1 100mg/kg_96hr_B96208_F_Bladder


title: C1 100mg/kg_48hr_B96205_F_Bladder

source_name: C1-treated, urinary bladder, 48hr


title: C1 100mg/kg_96hr_B96206_F_Bladder


title: C1 100mg/kg_96hr_B96207_F_Bladder


title: C1 100mg/kg_48hr_B96204_F_Bladder


title: C1 100mg/kg_48hr_B96201_F_Bladder


title: AML 2008-229 CD34+

city: Groningen

first: JJ

last: Schuringa

address: Hanzeplein 1

department: Experimental Hematology

institute: UMCG

description:
2008-229 CD34+
4811636082_K

hyb_protocol: Standard Illumina  protocol

scan_protocol: Illumina i-Scan reader

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: AML

label_protocol: Standard Illumina  protocol

growth_protocol: Mononuclear cells from AML patients (n=46) were thawed, sorted into CD34+ and CD34- subfractions and genome-wide expression analysis was performed using Illumina BeadChip Arrays (HT12 v3). AML CD34+ and CD34- gene expression was compared to a large group of normal CD34+ bone marrow cells (n=31).

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cell were directly sorted after thawing

value: CD34+ mononuclear

tag: disease state

value: AML


title: AML 2004 168 CD34+

description:
2004 168 CD34+
4811636064_I


title: AML 2008 023 CD34+

description:
2008 023 CD34+
4811636064_L


title: AML 2006 014 CD34-

description:
2006 014 CD34-
4811636114_I

value: CD34- mononuclear


title: AML 2003 163 CD34+

description:
2003 163 CD34+
4811636111_I


title: AML 2007 003 CD34+

description:
2007 003 CD34+
4811636114_B


title: normal 2009 150 CD34+

description:
2009 150 CD34+
4811636114_H

source_name: normal

value: normal


title: AML 2007 272 CD34+

description:
2007 272 CD34+
4811636114_F


title: AML 2006 239 CD34+

description:
2006 239 CD34+
4811636064_D


title: AML 2008 101 CD34-

description:
2008 101 CD34-
4811636064_C


title: normal HC2 CD34+

description:
HC2 CD34+
4811636082_D


title: AML 2006 100 CD34-

description:
2006 100 CD34-
4811636114_D


title: AML 2004 168 CD34-

description:
2004 168 CD34-
4811636114_K


title: AML 2005 258 CD34-

description:
2005 258 CD34-
4811636114_E


title: C1 100mg/kg_48hr_B96203_F_Bladder


title: C1 100mg/kg_24hr_B96200_F_Bladder

source_name: C1-treated, urinary bladder, 24hr


title: normal 2009 297 CD34+

description:
2009 297 CD34+
4811636082_B


title: AML 2005 145 CD34+

description:
2005 145 CD34+
4811636111_J


title: normal 2008 247 CD34+

description:
2008 247 CD34+
4811636064_H


title: AML 2008-012 CD34+

description:
2008-012 CD34+
4811636082_E


title: AML 2007 013 CD34-

description:
2007 013 CD34-
4811636064_G


title: C1 100mg/kg_24hr_B96199_F_Bladder


title: AML 2003 119 CD34+

description:
2003 119 CD34+
4811636064_A


title: C1 100mg/kg_24hr_B96198_F_Bladder


title: C1 100mg/kg_24hr_B96196_F_Bladder


title: AML 2005 062 CD34+

description:
2005 062 CD34+
4811636060_H


title: AML 2001 054 CD34+

description:
2001 054 CD34+
4811636060_K


title: AML 2003 179 CD34+

description:
2003 179 CD34+
4811636060_J


title: AML 2007 003 CD34-

description:
2007 003 CD34-
4811636060_L


title: AML 2007 046 CD34-

description:
2007 046 CD34-
4811636045_D


title: normal 2008 057 CD34+

description:
2008 057 CD34+
4811636042_J


title: C1 100mg/kg_5hr_B96195_F_Bladder

source_name: C1-treated, urinary bladder, 5hr


title: AML 2001 113 CD34-

description:
2001 113 CD34-
4811636060_G


title: AML 2005 024 CD34-

description:
2005 024 CD34-
4811636060_C


title: AML 2004 060 CD34-

description:
2004 060 CD34-
4811636045_L


title: AML 2006 014 CD34+

description:
2006 014 CD34+
4811636045_H


title: AML 2002 144 CD34-

description:
2002 144 CD34-
4811636045_I


title: C1 100mg/kg_24hr_B96197_F_Bladder


title: normal 2008 253 CD34+

description:
2008 253 CD34+
4811636042_K


title: AML 2006 080 CD34+

description:
2006 080 CD34+
4811636045_A


title: AML 2005 289 CD34+

description:
2005 289 CD34+
4811636045_C


title: AML 2005 049 CD34+

description:
2005 049 CD34+
4811636045_K


title: normal HC8 CD34+

description:
HC8 CD34+
4811636042_L


title: Vehicle_168hr_B96190_F_Bladder

source_name: Vehicle-treated, urinary bladder, 168hr


title: AML 2003 160 CD34-

description:
2003 160 CD34-
4811636045_J


title: L2195

hyb_protocol: As per manufacturer's instructions

scan_protocol: As per manufacturer's instructions

data_processing: For the expression array, unprocessed data were collected from bead studio and processed using VST and quantile normalization with the R bead array package. The processed data was analyzed using Limma (linear models for microarray data) analysis which uses moderated t-test to detect differentially expressed genes between two groups by taking into account natural variance within these groups and correcting for multiple testing using false discovery rate indicating the number of differentially expressed genes between two groups.

source_name: Maffucci chondrosarcoma grade II

label_protocol: As per manufacturer's instructions.

extract_protocol: Tumor samples were selected that contained more than 80% of tumor cells, as estimated on haematoxylin and eosin-stained frozen sections. RNA was isolated using TRIzol reagent (Invitrogen), followed by RNA clean-up using the QIAGEN Rneasy mini kit (Qiagen GmbH, Hilden, Germany) according to manufacturers instructions. RNA concentration was measured spectrophotometrically and the fragment sizes were determined using RNA 6000 Nano Labchip kit.

value: Male

tag: age

value: Maffucci

value: Chondrosarcoma grade II

tag: tumor location

value: knee


title: L1684

source_name: Maffucci Enchondroma

value: Female

value: Enchondroma

value: phalanx


title: C1 100mg/kg_5hr_B96192_F_Bladder

value: Sprague Dawley

value: female


title: C1 100mg/kg_5hr_B96194_F_Bladder


title: normal HC9 CD34+

description:
HC9 CD34+
4811636042_G


title: Vehicle_168hr_B96189_F_Bladder

value: vehicle


title: C1 100mg/kg_5hr_B96191_F_Bladder


title: normal 2009 037 CD34+

description:
2009 037 CD34+
4811636060_F


title: C1 100mg/kg_5hr_B96193_F_Bladder


title: Vehicle_168hr_B96188_F_Bladder


title: normal HC7 CD34+

description:
HC7 CD34+
4811636042_E


title: normal 2008 252 CD34+

description:
2008 252 CD34+
4811636042_B


title: AML 2008-229 CD34-

description:
2008-229 CD34-
4811636042_D


title: GAS_DIS_GC_YG76TV3_GIST-like_C3

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48804 probes on the Human-6 beadChip ver. 3 were used. Clinical data provided as a supplementary file on Series record: GSE13861_GE_MDACC_DepSysB_ClinicalInformation.xls.gz

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 3 of the Illumina Human-6 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformation. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: Primary gastric cancer

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina?? TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer's protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: gastric adenocarcinoma


title: Vehicle_96hr_B96184_F_Bladder

source_name: Vehicle-treated, urinary bladder, 96hr


title: normal 2009 007 CD34+

description:
2009 007 CD34+
4811636042_C

tag: cell type


title: normal 2009 005 CD34+

description:
2009 005 CD34+
4811636035_K


title: Vehicle_168hr_B96186_F_Bladder

tag: tissue


title: normal 2009 118 CD34+

description:
2009 118 CD34+
4811636035_J


title: normal HC1 CD34+

description:
HC1 CD34+
4811636035_H


title: normal 2009 281 CD34+

description:
2009 281 CD34+
4811636035_G


title: normal 2008 251 CD34+

description:
2008 251 CD34+
4811636035_L


title: AML 2008-186 CD34+

description:
2008-186 CD34+
4811636035_I


title: Vehicle_168hr_B96187_F_Bladder


title: L2102

value: Femur


title: GAS_DIS_GC_YG75T_C1


title: Vehicle_96hr_B96183_F_Bladder


title: Vehicle_96hr_B96185_F_Bladder


title: Vehicle_96hr_B96182_F_Bladder


title: GAS_DIS_GC_YG71T_C1


title: GAS_DIS_GC_YG74T_C2


title: AML 2003 022 CD34-

description:
2003 022 CD34-
4811636033_K


title: Vehicle_96hr_B96181_F_Bladder


title: AML 2008-012 CD34-

description:
2008-012 CD34-
4811636035_C


title: GAS_DIS_GC_YG73TV3_C1


title: GIST_YG72T_C3_GIST_V3_C3

tag: GIST


title: AML 2007 013 CD34+

description:
2007 013 CD34+
4811636033_F


title: AML 2005 145 CD34-

description:
2005 145 CD34-
4811636033_E


title: AML 2005 251 CD34+

description:
2005 251 CD34+
4811636033_C


title: GAS_DIS_GC_YG69T_C1


title: AML 2007 272 CD34-

description:
2007 272 CD34-
4811636019_L


title: Vehicle_48hr_B96178_F_Bladder

source_name: Vehicle-treated, urinary bladder, 48hr


title: GAS_DIS_GC_YG66T_C2


title: AML 2005 219 CD34-

description:
2005 219 CD34-
4811636019_K


title: Vehicle_24hr_B96175_F_Bladder

source_name: Vehicle-treated, urinary bladder, 24hr


title: GAS_DIS_GC_YG70T_C2


title: Vehicle_48hr_B96177_F_Bladder


title: Vehicle_48hr_B96180_F_Bladder


title: Vehicle_48hr_B96179_F_Bladder


title: GAS_DIS_GC_YG68T_C1


title: Vehicle_48hr_B96176_F_Bladder


title: GAS_DIS_GC_YG65T_C1


title: AML 2005 051 CD34+

description:
2005 051 CD34+
4811636033_B


title: GAS_DIS_GC_YG67T_C2


title: Vehicle_24hr_B96174_F_Bladder


title: GAS_DIS_GC_YG64TV3_C2


title: AML 2002 120 CD34+

description:
2002 120 CD34+
4811636019_C


title: AML 2004 032 CD34+

description:
2004 032 CD34+
4811636019_J


title: AML 1999 078 CD34+

description:
1999 078 CD34+
4811636018_F


title: AML 2006 080 CD34-

description:
2006 080 CD34-
4811636019_E


title: AML 2007 319 CD34+

description:
2007 319 CD34+
4811636018_K


title: AML 2002 120 CD34-

description:
2002 120 CD34-
4811636018_H


title: AML 2005 219 CD34+

description:
2005 219 CD34+
4811636019_B


title: normal BM HC6 CD34+

description:
BM HC6 CD34+
4811636018_C


title: AML 2001 113 CD34+

description:
2001 113 CD34+
4811636018_E


title: GAS_DIS_GC_YG63T_C1


title: normal 2008 254 CD34+

description:
2008 254 CD34+
4811636018_B


title: GAS_DIS_GC_YG62T_C2


title: Vehicle_24hr_B96172_F_Bladder


title: normal 2008 256 CD34+

description:
2008 256 CD34+
4811636017_L


title: AML 2005 274 CD34-

description:
2005 274 CD34-
4811636017_G


title: Vehicle_24hr_B96173_F_Bladder


title: Vehicle_24hr_B96171_F_Bladder


title: AML 2005 274 CD34+

description:
2005 274 CD34+
4811636018_A


title: GAS_DIS_GC_YG61T_C1


title: normal BM HC3 CD34+

description:
BM HC3 CD34+
4811636019_A


title: AML 2004 060 CD34+

description:
2004 060 CD34+
4811636017_D


title: normal BM HC4 CD34+

description:
BM HC4 CD34+
4811636017_I


title: GAS_DIS_GC_YG60T_C1


title: GIST_YG59T_C3_GIST


title: AML 2003 117 CD34+

description:
2003 117 CD34+
4811636017_J


title: AML 2003 179 CD34-

description:
2003 179 CD34-
4811636017_C


title: AML 2007 320 CD34-

description:
2007 320 CD34-
4811636017_B


title: AML 2003 028 CD34-

description:
2003 028 CD34-
4811636019_H


title: Vehicle_5hr_B96170_F_Bladder

source_name: Vehicle-treated, urinary bladder, 5hr


title: GIST_YG57T_C3_GIST


title: Vehicle_5hr_B96169_F_Bladder


title: Vehicle_5hr_B96168_F_Bladder


title: GAS_DIS_GC_YG58T_GIST-like_C3


title: AML 2006 239 CD34-

description:
2006 239 CD34-
4811636016_K


title: Vehicle_5hr_B96167_F_Bladder


title: AML 2007 319 CD34-

description:
2007 319 CD34-
4811636016_F


title: normal 2008 248 CD34+

description:
2008 248 CD34+
4811636016_H


title: normal 2008 022 CD34+

description:
2008 022 CD34+
4811636016_E


title: AML 2005 024 CD34+

description:
2005 024 CD34+
4811636016_G


title: GAS_DIS_GC_YG56T_C1


title: GAS_DIS_GC_YG54T_C2


title: AML 2007 046 CD34+

description:
2007 046 CD34+
4809000056_L


title: MDA_PR_Paclitaxel_4

city: San Diego

first: Wen

last: Luo

address: 6331 Nancy Ridge Drive

institute: Denovo Biopharma

description: Gene expression data from paclitaxel resistant MDA-MB-231 Cells and paclitaxel sensitive cells with bexarotene treatment

hyb_protocol: The labeled target was subsequently hybridized to a human Affymetrix U133A microarray in an Affymetrix Hybridization Oven 640

scan_protocol: After washing and staining on Affymetrix Fluidics Station 450, the arrays were scanned with the Affymetrix GeneArray 2500 Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

source_name: MDA cells resistant to paclitaxel were treated with 30 nM Paclitaxel

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA

growth_protocol: The human breast cancer cell line MDA-MB-231 was obtained from American Type Culture Collection (Manassas, VA), and MDA-MB-231cells were routinely cultured in RPMI 1640 supplemented with 10% fetal bovine serum and 2 mM glutamine in 5% CO2.

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

treatment_protocol: MDA-MB-231cells were exposed to regimens on a 10-day cycle:  a 3-day treatment with 30 nM paclitaxel and followed by a 7-day exposure to control medium.  Paclitaxel resistant MDA-MB-231 cells (MDA-PR) were established within 8 cycles of such treatment (80 days).  When these MDA-PR cells were then treated with the combination of  30 nM paclitaxel ( 3 days on and 7 days off) and 1 µM Targretin (10 days on) in a new 10-day cycle for 3 months, MDA-PR cells became re-sensitized to paclitaxel again.

tag: Paclitaxel-resistant


title: AML 2003 152 CD34-

description:
2003 152 CD34-
4811636016_D


title: AML 2007 320 CD34+

description:
2007 320 CD34+
4809000056_K


title: GAS_DIS_GC_YG53T_C2


title: MDA_PR_4

source_name: MDA cells resistant to paclitaxel


title: Vehicle_5hr_B96166_F_Bladder

tag: strain


title: AML 2003 088 CD34+

description:
2003 088 CD34+
4811636016_B


title: MDA_PR_Paclitaxel_Bexarotene_4

source_name: MDA cells resistant to paclitaxel were treated with 30 nM Paclitaxel + 1 µM Targretin

tag: Paclitaxel-sensitive


title: AML 2003 160 CD34+

description:
2003 160 CD34+
4809000056_F


title: AML 2003 152 CD34+

description:
2003 152 CD34+
4811636016_C


title: MDA_Parental_4

source_name: MDA-MB-231 parental cells


title: GAS_DIS_GC_YG52TV3_C1


title: GAS_DIS_GC_YG55T_C1


title: GAS_DIS_GC_YG51T_C2


title: AML 2002 197 CD34-

description:
2002 197 CD34-
4809000056_J


title: AML 2008 101 CD34+

description:
2008 101 CD34+
4809000056_E


title: AML 2005 049 CD34-

description:
2005 049 CD34-
4809000056_B


title: normal 2008 249 CD34+

description:
2008 249 CD34+
4809000055_L


title: GAS_DIS_GC_YG50T_C2


title: MDA_PR_Paclitaxel_Bexarotene_3


title: GAS_DIS_GC_YG49T_C1


title: MDA_PR_Paclitaxel_3


title: AML 2003 117 CD34-

description:
2003 117 CD34-
4809000056_H


title: AML 2005 165 CD34+

description:
2005 165 CD34+
4809000056_A


title: GAS_DIS_GC_YG48T_C1


title: normal 2008 255 CD34+

description:
2008 255 CD34+
4809000056_D


title: normal 2009 062 CD34+

description:
2009 062 CD34+
4809000055_B


title: MDA_PR_3


title: AML 2003 088 CD34-

description:
2003 088 CD34-
4809000055_H


title: MDA_Parental_3


title: AML 2005 289 CD34-

description:
2005 289 CD34-
4809000055_A


title: MDA_PR_Paclitaxel_Bexarotene_2


title: normal 2009 085 CD34+

description:
2009 085 CD34+
4809000042_K


title: MDA_PR_2


title: GAS_DIS_GC_YG44T_C2


title: AML 2003 114 CD34-

description:
2003 114 CD34-
4811636019_G


title: AML 2002 197 CD34+

description:
2002 197 CD34+
4809000042_J


title: normal 2009 096 CD34+

description:
2009 096 CD34+
4809000055_J


title: GAS_DIS_GC_YG47T_C2


title: AML 2003 163 CD34-

description:
2003 163 CD34-
4809000056_C


title: AML 2006 100 CD34+

description:
2006 100 CD34+
4809000042_D


title: MDA_PR_Paclitaxel_2


title: GAS_DIS_GC_YG46T_C2


title: AML 2003 022 CD34+

description:
2003 022 CD34+
4809000042_G


title: AML 2008 023 CD34-

description:
2008 023 CD34-
4809000042_E


title: GAS_DIS_GC_YG45T_C2


title: AML 2003 028 CD34+

description:
2003 028 CD34+
4809000041_I


title: MDA_Parental_2


title: GAS_DIS_GC_YG43T_C2


title: normal BM HC5 CD34+

description:
BM HC5 CD34+
4809000041_B


title: GAS_DIS_GC_YG41T_C1


title: GAS_DIS_GC_YG42T_C2


title: AML 2005 016 CD34-

description:
2005 016 CD34-
4809000041_L


title: AML 2005 016 CD34+

description:
2005 016 CD34+
4809000042_A


title: AML 2005 062 CD34-

description:
2005 062 CD34-
4809000041_G


title: AML 2003 119 CD34-

description:
2003 119 CD34-
4809000042_C


title: MDA_PR_1


title: AML 2005 165 CD34-

description:
2005 165 CD34-
4809000040_H


title: AML 2002 144 CD34+

description:
2002 144 CD34+
4809000041_E


title: MDA_Parental_1


title: AML 2005 251 CD34-

description:
2005 251 CD34-
4809000040_B


title: GAS_DIS_GC_YG39T_C1


title: MDA_PR_Paclitaxel_1


title: GAS_DIS_GC_YG40T_C1


title: AML 2001 054 CD34-

description:
2001 054 CD34-
4809000040_A


title: MDA_PR_Paclitaxel_Bexarotene_1


title: AML 2003 114 CD34+

description:
2003 114 CD34+
4809000035_G


title: AML 2004 032 CD34-

description:
2004 032 CD34-
4809000035_H


title: normal 2008 250 CD34+

description:
2008 250 CD34+
4809000035_F


title: GAS_DIS_GC_YG35T_C2


title: GAS_DIS_GC_YG38T_C1


title: AML 2005 051 CD34-

description:
2005 051 CD34-
4809000035_A


title: AML 2005 258 CD34+

description:
2005 258 CD34+
4809000035_D


title: S63-expanded islet, untreated

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: gene expression data of de-differentiated cells

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

data_processing: Gene-level analyses was performed. RMA normalization, summarization by mean and batch effect removal, all were done by Partek Genomics suite (version 6.5) Copyright.

source_name: expanded islet, UTR

growth_protocol: For expansion (de-differentiation), cells were trypsinized and seeded at 3.2X10^4/cm2 in ultra-low attachment plates (Corning). SFM consisted of CMRL 1066 containing 5.6 mM D-glucose and supplemented with 1% BSA fraction V (Sigma), ITS (Gibco-Invitrogen), penicillin (50 units/ml), and streptomycin (50 µg/ml).

extract_protocol: according to the manufacturer's protocol (Trizol, Sigma-Aldrich)

tag: sample origin

value: Pancreatic Islets from individual donors

value: de-differentiated beta-cells

tag: experiment batch


title: S66-expanded islet, untreated

scan_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)


title: I34-expanded islet, RC treatment

description: gene expression data of re-differentiation cells

source_name: expanded islet, RC treatment

label_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Redifferentiation Cocktail (RC) treatment consisted of 6 days in SFM supplemented with 25 mM D-glucose, N2 and B27 supplements (Stem Cell Technologies), 10 mM nicotinamide (Sigma), 8 nM exendin-4 (Acris), and 8 nM activin A (Peprotech), followed by 2 days in the same medium lacking activin A and containing a reduced glucose concentration (5.6 mM).

value: re-differentiated beta-cells


title: GAS_DIS_GC_YG32T_C2


title: S68-expanded islet, untreated


title: I34-expanded islet, untreated


title: GAS_DIS_GC_YG33TV3_C1


title: GAS_DIS_GC_YG30T_C2


title: Uncultured Islets- donor-I18

description: gene expression data of intact islet cells

source_name: Uncultured Islets

growth_protocol: For preparation of islet cells : according to Ouziel-Yahalom L., et al.,  Biochem Biophys Res Commun (2006) 341:291-298

value: islet cells


title: GAS_DIS_GC_YG31T_C1


title: Uncultured Islets- donor-G31


title: GIST_YG28T_C3_GIST


title: GAS_DIS_GC_YG36T_C1


title: S68_expanded islet, RC treatment


title: GAS_DIS_GC_YG34T_C2


title: GAS_DIS_GC_YG27T_C2


title: Uncultured Islets- donor-S64


title: GAS_DIS_GC_YG29T_C1


title: GAS_DIS_GC_YG26T_C2


title: Embryonic Stem Cell line - rep4

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

country: Spain

institute: CMRB

description: Three hESC lines were used: ES[2], ES[3], and ES[4]. All lines were derived as published (Aran et al., ; Raya et al., 2008) at the CMR[B]. One vial for each line at low passage was thawed and cultured for one passage over a feeder layer of human foreskin fibroblasts (HFFs; CCD1112Sk ATCC, Manassas, USA) in hES medium at 37°C and 5% CO2. The composition of hES medium is: KO-DMEM (Invitrogen, Carsbad, USA), 20% KO serum replacement (Invitrogen, Carsbad, USA), Glutamax (2 mmol/l; Invitrogen, Carsbad, USA), penicillin-streptomycin, non essential amino acids (Lonza, Verviers, Belgium), 2-mercaptoethanol (0.05 mmol/l, Invitrogen, Carsbad, USA), and basic fibroblast growth factor (bFGF, 10 ng/m; Invitrogen, Carsbad, USA). To avoid contamination of the cell ES sample by HFFs by whole colony trypsinization, a clump of approximately 50-100 ES cells was mechanically dislodged from a colony and processed as described.

hyb_protocol: Hybridization, washing, staining and scanning of Affymetrix Human Gene ST 1.0 arrays were performed following the manufacturer’s recommendations.

scan_protocol: Scanned images (DAT files) were transformed into intensities (CEL files) by GCOS (Affymetrix, Santa Clara, USA).

data_processing: Statistical analysis of the data was performed using the affy package in R (Gautier et al., 2004). Briefly, raw CEL files (which will be submitted to the GEO database upon manuscript acceptance) were imported with gene annotation from NetAffix and data was normalized with GCRMA and summarized at the gene level (32,321 genes). We performed gene expression profiles in 2 batches, and corrected for batch effect using the ComBat algorithm in R (Johnson et al., 2007).

source_name: Embryonic Stem Cell line

label_protocol: 10 µg cDNA was subsequently fragmented by DNAseI and biotinylated by terminal transferase (Affymetrix, Santa Clara, USA).

extract_protocol: RNA from single oocytes and embryos was purified using RNA Clean XP bead suspension (Agencourt Bioscience, Beckman Coulter, Danvers, USA). Genomic DNA is bound by the beads but released in only a small percentage as long as it is not sheared (data not shown). Therefore, every effort was made to minimize shearing. RNA was eluted in 20 µl water. Different percentages of the RNA isolations were used for amplification, according to the expected RNA content of embryos. From MII, 2-cell, 4-cell, 6-cell and 8-10 cell embryos, the entire RNA preparation was used (20µl); from morulas, 6 µl were used; from blastocycsts 3 µl; from ESC, 4 µl. Library preparation were performed following the distributor’s (Sigma-Aldrich, St.Louis, USA) recommendations for WTA2. SYBR Green (Sigma-Aldrich, St.Louis, USA) was added to the amplification reaction, which was performed in a CFX Real-time instrument (Bio-Rad), to monitor yield. When the SYBR Green signal reached a plateau after 21 cycles, the reaction was stopped. Amplified cDNA was purified and quantified.

value: Embryonic Stem Cell lines

tag: cell line

value: 3 embryonic stem cell lines (see Raya et al. 2008)


title: PGK12.1ES_PolIIS5p_rep2

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description: ChIP-chip PGK12.1 ES cells treated by negative control siRNAs PolII S5p

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Standard NimbleGen protocol

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed. The supplementary GFF files contain the bi-weight mean adjusted log base 2 ratios in MM8 coordinates

source_name: PolIIS5p ChIP DNA from mouse female PGK12.1 ES cells treated by negative control siRNAs (Invitrogen).

label_protocol: Amplified ChIP or input DNA were labeled by Cy5 or Cy3 respectively using standard NimbleGen protocol.

growth_protocol: ES cells were maintained in standard ES medium with 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on MEF feeders. ES cells were incubated on 1% gelatin coated dishes for 30min to deplete MEF feeders and transferred to fresh gelatin coated plates for culture for experiments and cell collection.

extract_protocol: 1x10E7 cells were fixed with 1% formaldehyde and lysed in 1 ml of IP buffer (150mM NaCl, 50 mM Tris pH7.5, 5 mM EDTA, 0.5% NP-40, 1.0% Triton X-100). The nuclear pellet was sheared to an average size of 0.5-1 kb by sonication. A 10% of chromatin was saved as the input fraction. ChIP was performed using 5ug rabbit anti-RNA polymerase II phosphorylated at serine 5 polyclonal antibody (PolII S5p, Abcam). Pull-down chromatin by protein A sepharose beads and input were treated with 0.2M NaCl at 65°C overnight to remove crosslinks. DNA was purified using Qiaquick® PCR purification kit (Qiagen) and amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma) prior to labeling.

treatment_protocol: Negative control siRNA treatment.

tag: genotype

value: Wild type XX

value: PGK12.1 ES

value: Derived from blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

tag: chip antibody

value: RNA PolII S5p

tag: vendor

value: Abcam

source_name: Input DNA from PGK12.1 ES cells treated by negative control siRNAs

value: none, input DNA


title: PGK12.1ES_PolIIS5p_rep1

description: ChIP-chip PGK12.1 ES cells PolII S5p

source_name: PolIIS5p ChIP DNA from mouse female PGK12.1 ES cells

treatment_protocol: No treatment

source_name: Input DNA from PGK12.1 ES cells

tag: PGK12.1 ES cell line


title: GAS_DIS_GC_YG21T_GIST-like_C3

source_name: Primary gastric cancer


title: Embryonic Stem Cell line - rep2


title: S66-expanded islet, RC treatment


title: GAS_DIS_GC_YG23T_C1


title: Embryonic Stem Cell line - rep3


title: Blastocyst stage human embryo - rep3

description:
All embryos were frozen at the pronuclear stage, 18 to 20 h after insemination. After thawing, embryos were allowed to develop until the required stage in a sequential culture system (G1/G2, Vitrolife AB, Goteborg, Sweden) system, at 37°C and 6% CO2. Embryos were monitored every 12 h to detect developmental progression. Once the embryos reached the appropriate stage of development, their zona pellucida (ZP) was removed by exposure to pronase (5mg/ml; Roche, Basel, Switzerland) at 37°C.
Dezoned oocytes and embryos were immediately plunged in 45 µl of Lysis Buffer (20 mM DTT, 10 mM TrisHCl, 0.5% SDS, 1 mg/ml Proteinase K) preheated at 65°C. The tube was maintained at 65°C for 15 minutes and placed at -80°C for later processing.

source_name: blastocyst stage human embryo

tag: developmental stage

value: blastocyst stage human embryo

value: preimplantation embryo


title: Morula stage human embryo - rep3

source_name: morula stage human embryo

value: morula stage human embryo


title: GAS_DIS_GC_YG18T_C2


title: Embryonic Stem Cell line - rep1


title: Blastocyst stage human embryo - rep2


title: Blastocyst stage human embryo - rep1


title: GAS_DIS_GC_YG24T_C1


title: GAS_DIS_GC_YG17T_C2


title: GAS_DIS_GC_YG20T_C1


title: 8 to 10-cell stage human embryo - rep1

source_name: 8 to 10-cell stage human embryo

value: 8 to 10-cell stage human embryo


title: Morula stage human embryo - rep1


title: GAS_DIS_GC_YG16T_C2


title: Morula stage human embryo - rep2


title: GAS_DIS_GC_YG15T_C2


title: GAS_DIS_GC_YG14T_GIST-like_C3


title: 8 to 10-cell stage human embryo - rep2


title: 6-cell stage human embryo - rep3

source_name: 6-cell stage human embryo

value: 6-cell stage human embryo


title: GAS_DIS_GC_YG19T_C1


title: GIST_YG11T_C3_GIST


title: GAS_DIS_GC_YG12T_C1


title: GIST_YG10T_C3_GIST


title: 6-cell stage human embryo - rep2


title: 4-cell stage human embryo - rep2

source_name: 4-cell stage human embryo

value: 4-cell stage human embryo


title: 6-cell stage human embryo - rep1


title: GAS_DIS_GC_YG09T_C1


title: GAS_DIS_GC_YG13T_C1


title: 4-cell stage human embryo - rep3


title: 2-cell stage human embryo - rep1

source_name: 2-cell stage human embryo

value: 2-cell stage human embryo


title: 4-cell stage human embryo - rep1


title: GAS_DIS_GC_YG07T_GIST-like_C3


title: GAS_DIS_GC_YG06T_C2


title: GAS_DIS_GC_YG04T_C2


title: Metaphase II Oocyte - rep2

description:
Oocytes were collected from preovulatory follicle by follicular punction after controlled ovarian hyperstimulation, and the cumulus oocytes complexes were allowed to recover for 2 h in collection medium G.1 (Vitrolife AB, Goteborg, Sweden) at 37 °C and 6% CO2. Subsequently, cumulus cells were removed by exposure to hyaluronidase (80Ui/ml; Hyase, Vitrolife AB, Goteborg, Sweden) and mild pipetting. Denuded oocytes were visually evaluated, and those arrested in the metaphase of the second meiotic division (MII) were allocated to this study.
Dezoned oocytes and embryos were immediately plunged in 45 µl of Lysis Buffer (20 mM DTT, 10 mM TrisHCl, 0.5% SDS, 1 mg/ml Proteinase K) preheated at 65°C. The tube was maintained at 65°C for 15 minutes and placed at -80°C for later processing.

source_name: Metaphase II Oocyte

value: Metaphase II Oocyte

value: oocyte


title: Metaphase II Oocyte - rep3


title: 2-cell stage human embryo - rep3


title: GAS_DIS_GC_YG03T_C1


title: 2-cell stage human embryo - rep2


title: GAS_DIS_ST_YG55N

tag: normal surrounding gastric tissue


title: GAS_DIS_GC_YG05T_C1


title: GAS_DIS_ST_YG53N


title: GAS_DIS_ST_YG48N


title: GAS_DIS_ST_YG73N


title: GAS_DIS_ST_YG51N


title: GAS_DIS_ST_YG50N


title: GAS_DIS_ST_YG54N


title: GAS_DIS_GC_YG08T_C1


title: Metaphase II Oocyte - rep1


title: GAS_DIS_ST_YG34N


title: Uncultured Islets- donor-F14

value: Pancreatic Islets from individual donors

value: islet cells


title: GAS_DIS_ST_YG35N


title: 6HR-A

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with GeneChip 3000.

data_processing: Affymetrix Mouse 430 v2 arrays were analyzed in R, version 2.11.1, using the packages affy (Gautier et al. 2004), version 1.26.1, and limma (Smyth et al., 2005), version 3.4.3. Normalization was done using rma.

source_name: KH2 mES

label_protocol: Biotin labelling was done with 200 ng total RNA with the Ambion MessageAmp III kit.

growth_protocol: One day before of thawing, T25 plates with feeders were prepared. Aseptically the cell suspension was transferred into a sterile centrifuge tube containing several ml of warm FCS-ES media. Cells were pelleted by centrifuging at 1000 rpm for 5 minutes. Supernatant was aspirated and cells were resuspended into required quantity of fresh media. Cells were distributed evenly by tilting plates several times and then were placed in incubator (at 370 C and 5% CO2).    Passage/expand of ES cells: Media was changed 3 hours before passaging them. Media was aspirated and washed twice with PBS. 800l of pre warmed Trypsin/EDTA solution were added and placed in incubator at 370 C for 1minute. During this period colonies float off when flicking the plate. Trypsin activity was stopped by adding 5ml of FCS-ES medium to flask. Colonies were dissociated into single cells by pipetting up and down for several times and pelleting the cells by centrifugation at 1000 rpm for 5 minutes. Media was aspirated and the cells were resuspended in appropriate volume of fresh ES cell medium and cells were seeded in 1:6 ratio into T75 flask. Plate was tilted several times to distribute the cells evenly and placed in the incubator.

extract_protocol: RNA for microarray analysis was isolated from ES cells grown on feeder cells. After induction, cells were washed in PBS, trypsinized, and replated onto a fresh gelatinized plate for 30 minutes. Media and unbound cells were aspirated. Adhered cells were resuspended in Trizol, aliquoted and flash frozen until needed. RNA were isolated as described per manufacture’s instruction and cleaned using RNAeasy Kit ( Quiagen). Quality and quantity of RNA were analyzed by Agilent Bioanlayzer 2100.

treatment_protocol: Media was changed 3 hours before passaging them. Media was aspirated and washed twice with PBS. 2 ml of pre warmed Trypsin/EDTA solution were added and placed in incubator at 370 C for 1minute. During this period colonies float off when flicking the plate. Trypsin activity was stopped by adding 5ml of FCS-ES medium to flask. Colonies were dissociated into single cells by pipetting up and down for several times and pelleting the cells by centrifugation at 1000 rpm for 5 minutes. Media was aspirated and the cells were resuspended in appropriate volume of fresh ES cell medium and cells were seeded in 1:6. ratio into fresh  T75 flask with feeders. Plate was tilted several times to distribute the cells evenly and placed in the incubator. Next day media was changed. Cells treated for 2, 4 and and 6  hours with RA  were supplemented with differentiation media ( DMEM + 10% Serum + NAA+ 0.3uM  RA) . After required period of induction, Media was aspirated and washed twice with PBS. 2 ml of pre warmed Trypsin/EDTA solution were added and placed in incubator at 370 C for 1minute. During this, period colonies float off when flicking the plate. Trypsin activity was stopped by adding 5ml of FCS-ES medium to flask. Colonies were dissociated into single cells by pipetting up and down for several times. Additional 15 ml of Differentiation media (without RA) was added and plated into freshly gelatinized plates. For gelatinized plates, Culture plates were treated half an hour before seeding with 0.1% Gelatin. Gelatin was later aspirated just before seeding of cells. After half an hour media was aspirated and centrifuged for 5 min at 1000 rpm. Pellets were dislodged by gentle tapping and 2 ml trizol were added.   These tubes were stored at -80 until RNA isolation.

tag: ra exposure

value: 6 hours


title: GAS_DIS_ST_YG42N


title: GAS_DIS_ST_YG40N


title: GAS_DIS_ST_YG33N


title: knockout sample 3

city: Rostock

first: Markus

last: Krohn

address: Gehlsheimer Str. 20

country: Germany

institute: University of Rostock

hyb_protocol: Array hybridization was performed according to the supplier’s instructions using the “Ambion WT Expression Kit” (Ambion, Applied Biosystems, Invitrogen) plus the “GeneChip WT Terminal Labeling and Hybridization Kit” and the “GeneChip Sample Cleanup Module” (Affymetrix). For signal enhancement, an antibody amplification was carried out using a biotinylated antistreptavidin antibody (Vector Laboratories.), which was cross-linked by goat IgG (Sigma) followed by a second staining with streptavidin-phycoerythrin conjugate (Molecular Probes, Invitrogen).

scan_protocol: G7 upgraded GeneChip Scanner 3000 (Affymetrix) at 0.7 micron resolution

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. Scaled Log2.

source_name: mouse brain

growth_protocol: normal mouse growth

value: brain


title: 4HR-A

value: 4 hours


title: MIGR1 CD34+ cells rep3

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files. Chp fies are generated with Affymetrix expression console using MAS5.0.

source_name: CD34+ cells infected with MIGR1

label_protocol: 200 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: 20% BIT IMEM media with human SCF, TPO, Flt3L and IL6, 37 degree 5% CO2 incubator

extract_protocol: RNA extraction plus kit was used to isolate RNA.

treatment_protocol: Human CD34+ cord blood cells were infected with retrovirus expressing MIGR1, AML1-ETO and AML1-ETO∆NHR1.  CD34+GFP+ cells were isolated by FACS.

value: CD34+ cord blood cells

tag: infection


title: GAS_DIS_ST_YG45N


title: MIGR1 CD34+ cells rep2

tag: cell type


title: MIGR1 CD34+ cells rep1


title: GAS_DIS_ST_YG38N


title: 2HR-B

value: 2 hours


title: 6HR-B


title: 4HR-B


title: 4HR-C


title: 2HR-C


title: 6HR-C


title: GAS_DIS_ST_YG30N


title: WT-C


title: AML1-ETO∆NHR1 CD34+ cells rep3

source_name: CD34+ cells infected with MIGR1-AML1-ETO∆NHR1


title: GAS_DIS_ST_YG31N


title: knockout sample 2

label_protocol: GeneChip WT Terminal Labeling and Hybridization Kit” and the “GeneChip Sample Cleanup Module” (Affymetrix)

tag: tissue


title: 2HR-A


title: control sample 3


title: knockout sample 1


title: AML1-ETO∆NHR1 CD34+ cells rep2


title: AML1-ETO∆NHR1 CD34+ cells rep1


title: Y4507_143_berlin_stein_pmt800_112806

status: Public on Jul 18 2011

city: Berlin

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

institute: Charité-Universitätsmedizin Berlin

hyb_protocol: The microarrays were hybridized in 6× SSPE (0.9 M sodium chloride/60 mM sodium phosphate/8 mM EDTA, pH 7.4)/30% formamide at 25°C for 18 h, washed in 0.75× TNT (Tris·HCl/sodium chloride/Tween 20) at 37°C for 40 min, and processed by using direct detection of the biotin-containing transcripts by Streptavidin-Alexa647 conjugate.

scan_protocol: The hybridized chips were washed, stained with streptavidin-Alexa647 conjugate (Invitrogen, USA) and the fluorescence intensity was assessed with an Axon 4000B microarray scanner (Axon Instruments, USA).

data_processing: Microarray images were analyzed using GENEPIX PRO 6.0 (Axon Instruments, USA). Average values of the replicate spots of each miRNA were background subtracted, thresholded to 75 and normalized using the quantiles method as implemented in the Bioconductor package/function Affymetrix/normalization. Micro RNAs showing low expression variation among all samples were excluded from further analysis. Statistical analysis (ANOVA, q-value cut off 0.05) and hierarchical clustering (Pearson correlation, average linkage, standardized intensities by mean) were performed using Partek Genomics Suite 6.5 beta (Partek, USA).

source_name: Burkitt Lymphoma

label_protocol: Briefly, 5 µg of total RNA were reverse transcribed using Biotin-labeled random octamers. The labeled targets were then hybridized to Ohio State University custom miRNA microarray chips, which contain probes for 602 human miRNAs spotted in duplicate.

extract_protocol: Total RNA was isolated from formalin-fixed and paraffin-embedded (FFPE) tissue sections with the RecoverALL Kit (Ambion, USA) according to the manufacturer’s recommendations and quantified using the Nanodrop ND-1000 UV-vis spectrophotometer (Nanodrop Technologies, USA).

tag: diagnosis

value: HIV-BL

tag: myc translocation

value: positive

tag: epstein barr virus infection

value: pos

tag: hans classifier

value: nd


title: Y4518_155_berlin_stein_pmt800_113006

value: neg


title: control sample 2


title: WT-A


title: WT-B


title: GAS_DIS_ST_YG7N


title: GAS_DIS_ST_YG23N


title: Diclofenac rep1

city: Tampa

first: James

middle: T

last: Riordan

address: 4202 E Fowler Ave

department: CMMB

institute: University of South Florida

hyb_protocol: Arrays were blocked in 1% SDS, 5 X SSC and 1 mg/ml BSA at 42C for 1 h.  Arrays were then washed 2X for 5 min in 0.1X SSC and 2X for 30 sec in sterile double-distilled water.  Arrays were hybirdized to Cy-labeled cDNAs denatured at 05C in 10 mM EDTA for 5 min and mixed with 40 ul hybridization buffer (Ambion) before loading under a caverslip on the array and sealing in hybridization cassettes.  Hybridization was carried out at 47C for 18 h.  Afterwards, array slides were washed in 2X SSC, 0.5% SDS at 37C for 5 min, followed by stringency washes 2X in 0.1X SSC at 37C for 2.5 min each, and 2X in 0.1X SSC at room temperature for 2.5 min each.

scan_protocol: Arrays were scanned using an Axon 4000b, and images analyzed using Spotfinder.

data_processing: Array intensity data was log2-transformed, and normalized using the Lowess algorithm.  Statistical analysis was performed using a significance analysis of microarrays (SAM, MultiExperiment Viewer, ver. 4.0) unpaired contrast.  A d-statistic was calculated for each gene based on repeated permutations, and a false discovery rate FDR of 0.01 was used to assign a critical cutoff for significance.

organism: Staphylococcus aureus subsp. aureus COL

source_name: Control

label_protocol: Amino-allyl labeled cDNA was dried and then suspended in 0.1 M sodium carbonate (pH 9.3) and coupled with Cy3.  Uncoupled dye was removed by column purification (Qiagen).

growth_protocol: Cultures were initiated from overnight cultures in LB into fresh LB at 1:100 and grown to OD600=0.5

extract_protocol: Samples were added to RNA Protect (Qiagen, Valencia, CA) and processed according to the manufacturer's instructions.  Cells were harvested by centrifugation (8,000 X g, 20 min, 4C) and then resuspended in 1 ml Trizol (Invitrogen, Carlsbad, CA) and processed in an FP120 FastPrep cell disruptor (MP Biomedicals, Irvine, CA).  Chloroform was subsequently added to the lysates, followed by centrifugation (16,000 X g, 15 min, 4C) and RNA was precipitated 1:1 (vol/vol) in 100% ethyl alcohol.  The RNA was then purified using the RNeasy™ kit (Qiagen) according to the manufacturer's instructions. Contaminating DNA was removed from purified RNA using DNAfree (Ambion, Austin, TX).  cDNA was produced using SuperScript II Reverse Transcriptase (Invitrogen) from 2 µg of total RNA combined with random hexamers, 0.25 mM deoxynucleoside triphosphate, and 0.25 mM aminoallyl-dUTP.

treatment_protocol: No Diclofenac treatment

tag: strain

value: COL

tag: treatment

source_name: Treatment

label_protocol: Amino-allyl labeled cDNA was dried and then suspended in 0.1 M sodium carbonate (pH 9.3) and coupled with Cy5.  Uncoupled dye was removed by column purification (Qiagen).

treatment_protocol: Diclofenac treated (80 ug/ml) for 15 min.

value: Diclofenac


title: Diclofenac rep1 dye-swap

data_processing: Array intensity data was log2-transformed, and normalized using the Lowess algorithm. Duplicates were averaged and ratio was calculated as Treatment/Control. Statistical analysis was performed using a significance analysis of microarrays (SAM, MultiExperiment Viewer, ver. 4.0) unpaired contrast.  A d-statistic was calculated for each gene based on repeated permutations, and a false discovery rate FDR of 0.01 was used to assign a critical cutoff for significance.

label_protocol: Amino-allyl labeled cDNA was dried and then suspended in 0.1 M sodium carbonate (pH 9.3) and coupled with Cy3. Uncoupled dye was removed by column purification Qiagen).

growth_protocol: Cultures were initiated from overnight cultures in LB into fresh LB at 1:100 and grown to OD600=0.5.

label_protocol: Amino-allyl labeled cDNA was dried and then suspended in 0.1 M sodium carbonate (pH 9.3) and coupled with Cy5. Uncoupled dye was removed by column purification Qiagen).


title: Diclofenac rep2

value: control


title: AML1-ETO CD34+ cells rep3

source_name: CD34+ cells infected with MIGR1-AML1-ETO


title: Y4503_138_berlin_stein_pmt800_112806


title: P4220 IDCC 653 pmt800 09262008


title: P4214 IDCC 647 pmt800 09262008

value: negative


title: P3496  629  pmt800  06262008


title: P4204 IDCC 637 pmt800 09262008


title: Y4504_139_berlin_stein_pmt800_112806


title: Control

description:
Gene expression data from ASCL1 knock-down control DMS79 cells.
DMS79_SiCont

hyb_protocol: 10μg cRNA, 45 degree C, 16 hours.

scan_protocol: Affymetrix GeneChip® scanner 3000 7G.

data_processing: Affymetrix Microarray Suite v5.0 (MAS5.0). Target intensity = 100.

source_name: control, 72 hours

label_protocol: 1 ug cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics).

extract_protocol: After cells were cultured for 72 hours, total RNA was extracted using TRIzol (Invitrogen).

treatment_protocol: DMS79 cells were transfected with 20nM siRNA using Lipofectamine2000 (Invitrogen).

tag: cell line

tag: sirna


title: Diclofenac rep2 dye-swap


title: P3484  617  pmt800  06262008


title: P3479  612  pmt800  06262008


title: P3478  611  pmt800  06262008


title: siASCL1_2

description:
Gene expression data from ASCL1 knock-down DMS79 cells.
DMS79_SiASCL1_2

source_name: ASCL1 siRNA, 72 hours


title: AML1-ETO CD34+ cells rep1


title: AML1-ETO CD34+ cells rep2


title: P3362  573  pmt800 05302008


title: siASCL1_1

description:
Gene expression data from ASCL1 knock-down DMS79 cells.
DMS79_SiASCL1_1


title: control sample 1

tag: genotype


title: GAS_DIS_ST_YG29N

source_name: Primary gastric cancer


title: P3361  572  pmt800 05302008


title: Y4523_160_berlin_stein_pmt800_113006

value: sBL


title: P3480  613  pmt800  06262008


title: Y4520_157_berlin_stein_pmt800_113006


title: P3360  571  pmt800 05302008


title: Y4521_158_berlin_stein_pmt800_113006


title: Y4522_159_berlin_stein_pmt800_113006


title: Y4516_153_berlin_stein_pmt800_113006


title: Y4510_146_berlin_stein_pmt800_113006

value: eBL


title: Y4519_156_berlin_stein_pmt800_113006


title: Y4517_154_berlin_stein_pmt800_113006


title: Y4502_137_berlin_stein_pmt800_112806


title: Y4509_144_berlin_stein_pmt800_112806


title: Y4506_142_berlin_stein_pmt800_112806


title: Y4508_145_berlin_stein_pmt800_112806


title: P4222 IDCC 655 pmt800 09262008


title: Y4501_136_berlin_stein_pmt800_112806


title: P4208 IDCC 641 pmt800 09262008


title: P4211 IDCC 644 pmt800 09262008


title: Y4500_135_berlin_stein_pmt800_112806


title: P4201 IDCC 634 pmt800 09262008


title: P3500  633  pmt800  07012008


title: P4205 IDCC 638 pmt800 09262008


title: P3593  140-2  pmt800  07012008


title: P3499  632  pmt800  07012008


title: P3497  630  pmt800  07012008


title: P3498  631  pmt800  07012008


title: P3495  628  pmt800  06262008


title: Y4505_141_berlin_stein_pmt800_112806


title: P3491  624  pmt800  06262008


title: P3492  625  pmt800  06262008


title: P3493  626  pmt800  06262008


title: P3494  627  pmt800  06262008


title: P3490  623  pmt800  06262008


title: Y4499_134_berlin_stein_pmt800_112806


title: P3489  622  pmt800  06262008


title: P3488  621  pmt800  06262008


title: P3487  620  pmt800  06262008


title: P3486  619  pmt800  06262008


title: P3485  618  pmt800  06262008


title: P3483  616  pmt800  06262008


title: P3481  614  pmt800  06262008


title: P3482  615  pmt800  06262008


title: P3476  609  pmt800  06262008


title: P3475  608  pmt800  06262008


title: P3371  582  pmt800 05302008


title: P3474  607  pmt800  06262008


title: P3473  606  pmt800  06262008


title: P3364  575  pmt800 05302008


title: P3370  581  pmt800 05302008


title: P3369  580  pmt800 05302008


title: Y4487_121_berlin_stein_pmt800_112806

source_name: diffuse large B-cell lymphoma

value: DLBCL

value: GCB


title: Y4488_122_berlin_stein_pmt800_112806

value: non-GCB


title: Y4524_5r_berlin_stein_pmt800_113006


title: Y4489_123_berlin_stein_pmt800_112806


title: P3477  610  pmt800  06262008


title: Y4485_119_berlin_stein_pmt800_112106


title: Y4477_111_berlin_stein_pmt800_112106


title: Y4479_113_berlin_stein_pmt800_112106


title: Y4484_118_berlin_stein_pmt800_112106


title: Y4481_115_berlin_stein_pmt800_112106


title: Y4482_116_berlin_stein_pmt800_112106


title: Y4471_105_berlin_stein_pmt800_112106


title: Y4483_117_berlin_stein_pmt800_112106


title: Y4474_108_berlin_stein_pmt800_112106


title: Y4466_100_berlin_stein_pmt800_112106


title: Y4469_103_berlin_stein_pmt800_112106


title: Y4470_104_berlin_stein_pmt800_112106


title: Y4464_98_berlin_stein_pmt800_112106


title: Y4465_99_berlin_stein_pmt800_112106


title: Y4525_29r_berlin_stein_pmt800_113006


title: Y4460_94_berlin_stein_pmt800_111706


title: Y4459_93_berlin_stein_pmt800_111706


title: Y4461_95_berlin_stein_pmt800_111706


title: Y4456_90_berlin_stein_pmt800_111706


title: Y4458_92_berlin_stein_pmt800_111706


title: Y4480_114_berlin_stein_pmt800_112106


title: Y4453_87_berlin_stein_pmt800_111706


title: Y4454_88_berlin_stein_pmt800_111706


title: Y4455_89_berlin_stein_pmt800_111706


title: Y4452_86_berlin_stein_pmt800_111706


title: Y4445_79_berlin_stein_pmt800_111706


title: Y4462_96_berlin_stein_pmt800_112106


title: Y4450_84_berlin_stein_pmt800_111706


title: Y4446_80_berlin_stein_pmt800_111706


title: Y4438_72_berlin_stein_pmt800_111706


title: Y4439_73_berlin_stein_pmt800_111706


title: Y4444_78_berlin_stein_pmt800_111706


title: Y4443_77_berlin_stein_pmt800_111706


title: Y4442_76_berlin_stein_pmt800_111706


title: Y4422_56_berlin_stein_pmt800_111606


title: Y4427_61_berlin_stein_pmt800_111606


title: Y4435_69_berlin_stein_pmt800_111606


title: Y4419_54_berlin_stein_pmt800_111606


title: Y4436_70_berlin_stein_pmt800_111606


title: Y4421_55_berlin_stein_pmt800_111606


title: Y4418_53_berlin_stein_pmt800_111606


title: Y4415_50_berlin_stein_pmt800_111606


title: Y4412_47_berlin_stein_pmt800_111406


title: Y4414_49_berlin_stein_pmt800_111606


title: Y4408_43_berlin_stein_pmt800_111406


title: Y4437_71_berlin_stein_pmt800_111606


title: Y4429_63_berlin_stein_pmt800_111606


title: Y4406_41_berlin_stein_pmt800_111406


title: Y4407_42_berlin_stein_pmt800_111406


title: Y4405_40_berlin_stein_pmt800_111406


title: Y4403_38_berlin_stein_pmt800_111406


title: Y4402_37_berlin_stein_pmt800_111406


title: Y4404_39_berlin_stein_pmt800_111406


title: Y4431_65_berlin_stein_pmt800_111606


title: Y4299_34_berlin_stein_pmt800_111406


title: Y4300_35_berlin_stein_pmt800_111406


title: Y4298_33_berlin_stein_pmt800_111406


title: Y4291_26_berlin_stein_pmt800_111406


title: Y4290_25_berlin_stein_pmt800_111406


title: Y4292_27_berlin_stein_pmt800_111406


title: Y4297_32_berlin_stein_pmt800_111406


title: Y4295_30_berlin_stein_pmt800_111406


title: Y4293_28_berlin_stein_pmt800_111406


title: Y4289_24_berlin_stein_pmt800_111406


title: Y4296_31_berlin_stein_pmt800_111406


title: Y4287_22_berlin_stein_pmt800_110906


title: Y4285_20_berlin_stein_pmt800_110906


title: Y4288_23_berlin_stein_pmt800_110906


title: Y4283_18_berlin_stein_pmt800_110906


title: Y4282_17_berlin_stein_pmt800_110906


title: Y4278_13_berlin_stein_pmt800_110906


title: Y4281_16_berlin_stein_pmt800_110906


title: Y4279_14_berlin_stein_pmt800_110906


title: Y4274_9_berlin_stein_pmt800_110906


title: Y4401_36_berlin_stein_pmt800_111406


title: Y4275_10_berlin_stein_pmt800_110906


title: Y4266_1_berlin_stein_pmt800_110906


title: Y4272_7_berlin_stein_pmt800_110906


title: Y4271_6_berlin_stein_pmt800_110906


title: Y4269_4_berlin_stein_pmt800_110906


title: Y4267_2_berlin_stein_pmt800_110906


title: Y4277_12_berlin_stein_pmt800_110906


title: 24h EGF versus Control replicate 3 (Operon)

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

description: 24h time point, biological replicate 3 of 3. Technical replicate 1 of 2. HeLa cells treated with EGF compared to untreated controls.

hyb_protocol: Three biological replicate experiments were performed, each comparing EGF treated with untreated control HeLa cells. Each experimental pair of labelled samples was co-hybridized on two separate microarrays with dye swapping to correct for dye bias effects. Thus, six microarray hybridizations were processed for each of three biological replicates for the two time points, totalling 12 array datasets.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor quality spots, followed by scaling across chips. Differentially expressed genes for each time point were chosen using as cut off criteria a SAM FDR of 5% and an average absolute fold change (|FC|) above 1.2 .

source_name: Cervical cancer cell line (HeLa)

label_protocol: First and second strand cDNA were synthesized from total RNA (1 ug) with the Aminoallyl Message Amp II Kit (Ambion). cDNA was purified and in vitro transcribed for aRNA synthesis. aRNA was purified and coupled to the Cy ester, and further purified, to remove unincorporated dye. Arrays were hybridized on a Maui hybridization station washed and dried following Operon’s instructions (2/7/2007 Oparray protocol).

growth_protocol: HeLa cells were cultured at 37ºC in a 95/5 Air/CO2 water saturated  atmosphere in Dulbecco’s  modified  Eagle’s medium (DMEM) containing 10% heat inactivated foetal bovine serum (FBS), 2 mM  L-glutamine and 100U/ml Penicilin/streptomycine (complete growth medium).

extract_protocol: Total RNA from HeLa cells was extracted using the RNeasy RNA Isolation kit (Qiagen) followed by treatment with RNase-free DNase I (Ambion, Austin, TX) following manufacturers instructions. RNA quantification was performed with a Nanodrop spectrophotometer, and the RNA integrity was assessed using the Bioanalyzer 2100 nanoelectrophoresis Lab-on-a–chip system (Agilent, Wilmington, DE). All RNAs used had RIN (RNA integrity number) ranging between 9.3 and 10, and 28S/18S ratios between 1.67 and 2.07.

treatment_protocol: For treatments, the cells were transferred  to 60 mm dishes and cultured for 48h in complete growth medium, after which they were starved for 24h in DMEM containing 2% FBS. After serum deprivation cells were stimulated with EGF (150 ng/ml) for the indicated times.

value: serum deprived for 24 hours, followed by exposure to EGF for 24 hours

value: HeLa

value: serum deprived for 24 hours, followed by culture without EGF addition into the medium for 24 additional hours


title: 24h EGF versus Control replicate 1 (Operon)

description: 24h time point, biological replicate 1 of 3. Technical replicate 1 of 2. HeLa cells treated with EGF compared to untreated controls.


title: 24h EGF versus Control replicate 1 dye swap (Operon)

description: 24h time point, biological replicate 1 of 3. Technical replicate 2 of 2. HeLa cells treated with EGF compared to untreated controls.