title: Acetate limited chemostat D=0.1/h -3

source_name: Aerobic acetate limited chemostat

extract_protocol:
Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays were performed as described previously (6)
6- Piper, M. D. W., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S.,Nielsen, J., and Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008


title: Aerobic glucose limited chemostat culture with 79% CO2 D=0.1/h -2

status: Public on Aug 31 2007

type: RNA

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

hyb_protocol: One hundred millilitres of culture was sampled directly from the fermentor into a beaker containing 200–300 ml of liquid nitrogen and then processed . Total RNA was extracted with phenol/chloroform. mRNA extraction, cDNA synthesis and labelling, as well as array hybridisation against Affymetrix YG-S98 GeneChips® was performed as described in the Affymetrix user’s manual. Data acquisition was performed using the software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0 (Affymetrix, Santa Clara, CA, USA).

data_processing: MAS5.0 calculated intensity with global array targetting at 150

label: Biotinylated dUTP - streptavidine Phycoerythrin (SAPE)

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Steady state Aerobic glucose limited chemostat culture with 79% CO2

growth_protocol:
Cells were grown at 30 °C in laboratory fermenters (Applikon, Schiedam, The Netherlands) with a working volume of 1 l as described in . Cultures were fed with a defined synthetic medium that was designed to allow for steady-state growth limited by either carbon or nitrogen, with all other requirements in excess and at a constant residual concentration. The dilution rate was set to 0.10 h−1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2-M KOH with the use of an Applikon ADI 1030 Biocontroler. Stirrer speed was 800 rpm, and the gas flow was 0.5 l min−1.
Synthetic media were prepared as described [20] with the following modifications: for carbon-limited cultivation, the medium contained 5.0 g l−1 of (NH4)2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and either 7.5 g l−1 of glucose or 5.76 g l−1 of ethanol. For nitrogen-limited cultures, 1.0 g l−1 of (NH4)2SO4, 5,3 g l−1 of K2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and the necessary glucose to keep the residual glucose concentration at 18 g l−1 (59 and 62.2 g l−1 for the CO2-untreated and -treated cultures, respectively). This was done to avoid differences in the degree of glucose repression.
 For CO2-enriched aerobic cultivation, cultures were sparged with a defined gas mixture containing 79% CO2 and 21% O2 (HoekLoos, Schiedam, The Netherlands).

treatment_protocol: Liquid nitrogen quenching

tag: The prototrophic S. cerevisiae strain CEN.PK113-7D was used for this study


title: Polongued aerobic maltose limited chemostat culture D=0.1/h-1

hyb_protocol: The results for each growth condition were derived from three independently cultured replicates. Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays, as well as data acquisition and analysis, were performed as previously described (Daran-Lapujade  et al., 2004; Piper et al., 2002). Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277, 37001–37008. Daran-Lapujade, P., Jansen, M. L., Daran, J. M., Van Gulik, W., de Winde, J. H. & Pronk, J. T. (2004). Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae: a chemostat culture study. J Biol Chem 279, 9125–9138.

source_name: prolongued aerobic maltose chemostat culture 45 generation old

growth_protocol:
Aerobic chemostat cultivation was performed at a dilution rate of 0.10 h−1 at 30°C in 2.0-liter laboratory fermentors (Applikon, Schiedam, The Netherlands) with stirring at 800 rpm. The working volume of the cultures was kept at 1.0 liter by a peristaltic effluent pump coupled to an electrical level sensor. This setup ensured that under all growth conditions, biomass concentrations in samples taken directly from the culture differed by <1% from biomass concentrations in samples taken from the effluent line. The exact working volume was measured after each experiment. The pH was kept at 5.0 ± 0.1 by an ADI 1030 biocontroller via the automatic addition of 2 mol of KOH · liter−1. The fermentor was flushed with air at a flow rate of 0.5 liter · min−1 by using a Brooks 5876 mass flow controller. The dissolved oxygen concentration was continuously monitored with an oxygen electrode (model 34 100 3002; Ingold) and remained above 60% of air saturation. A steady state was defined as the situation in which at least five volume changes had passed after the last change in growth conditions and in which the biomass concentration and the specific rates of carbon dioxide production and oxygen consumption had remained constant (<2% variation) over two volume exchanges. In case of spontaneous oscillatory behavior, a pulse of ethanol (50 mM) was added to the culture to dampen out the oscillations. Chemostat cultures were routinely checked for purity by phase-contrast microscopy.
For chemostat cultivation, the maltose concentration in reservoir media was 7.5 g · liter−1 (0.25 mol of C · liter−1).

extract_protocol:
Cells were rapidly (within 3 s) transferred
from the chemostat culture into liquid nitrogen to immediately
quench the metabolism. The frozen cell suspension (about 40 g cell
broth) was thawed gently on ice. After complete thawing, the cell
suspension was centrifuged at 0 uC, 5000 g, for 5 min. Total RNA
extraction from the pellets was performed using the hot-phenol
method

tag: The haploid, prototrophic S. cerevisiae

tag: strain CEN.PK113-7D (MATa MAL2-8c SUC2) was obtained from

tag: Dr P. Ko¨tter, Frankfurt, Germany. Precultures were grown to stationary

tag: phase in shake-flask cultures of synthetic medium (Verduyn

tag: et al., 1992), adjusted to pH 6?0 and containing 2% (w/v) glucose.

tag: After adding sterile glycerol (30 %, v/v), 2 ml aliquots were stored

tag: in sterile vials at 280 uC. These frozen stock cultures were used to

tag: inoculate precultures for chemostat cultivation.

tag: Verduyn, C., Postma, E., Scheffers, W. A. & van Dijken, J. P. (1992).

tag: Effect of benzoic acid on metabolic fluxes in yeasts

value: a continuous study on regulation of respiration and alcoholic fermentation. Yeast 8, 501–517.


title: Anaerobic glucose limited chemostat culture with 100% CO2 D=0.1/h -2

scan_protocol: One hundred millilitres of culture was sampled directly from the fermentor into a beaker containing 200–300 ml of liquid nitrogen and then processed . Total RNA was extracted with phenol/chloroform. mRNA extraction, cDNA synthesis and labelling, as well as array hybridisation against Affymetrix YG-S98 GeneChips® was performed as described in the Affymetrix user’s manual. Data acquisition was performed using the software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0 (Affymetrix, Santa Clara, CA, USA).

source_name: steady state Anaerobic glucose limited chemostat culture with 100% CO2

growth_protocol:
Cells were grown at 30 °C in laboratory fermenters (Applikon, Schiedam, The Netherlands) with a working volume of 1 l as described in . Cultures were fed with a defined synthetic medium that was designed to allow for steady-state growth limited by either carbon or nitrogen, with all other requirements in excess and at a constant residual concentration. The dilution rate was set to 0.10 h−1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2-M KOH with the use of an Applikon ADI 1030 Biocontroler. Stirrer speed was 800 rpm, and the gas flow was 0.5 l min−1.
Synthetic media were prepared as described [20] with the following modifications: for carbon-limited cultivation, the medium contained 5.0 g l−1 of (NH4)2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and either 7.5 g l−1 of glucose or 5.76 g l−1 of ethanol. For nitrogen-limited cultures, 1.0 g l−1 of (NH4)2SO4, 5,3 g l−1 of K2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and the necessary glucose to keep the residual glucose concentration at 18 g l−1 (59 and 62.2 g l−1 for the CO2-untreated and -treated cultures, respectively). This was done to avoid differences in the degree of glucose repression.
 For CO2-enriched anaerobic cultivation, the nitrogen sparging gas was replaced by pure (>99.99%) CO2 (HoekLoos, Schiedam, The Netherlands).


title: Aerobic nitrogen limited chemostat culture with 79% CO2 D=0.1/h -2

source_name: Steady state Aerobic nitrogen limited chemostat culture with 79% CO2

label_protocol: One hundred millilitres of culture was sampled directly from the fermentor into a beaker containing 200–300 ml of liquid nitrogen and then processed . Total RNA was extracted with phenol/chloroform. mRNA extraction, cDNA synthesis and labelling, as well as array hybridisation against Affymetrix YG-S98 GeneChips® was performed as described in the Affymetrix user’s manual. Data acquisition was performed using the software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0 (Affymetrix, Santa Clara, CA, USA).

growth_protocol:
Cells were grown at 30 °C in laboratory fermenters (Applikon, Schiedam, The Netherlands) with a working volume of 1 l as described in . Cultures were fed with a defined synthetic medium that was designed to allow for steady-state growth limited by either carbon or nitrogen, with all other requirements in excess and at a constant residual concentration. The dilution rate was set to 0.10 h−1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2-M KOH with the use of an Applikon ADI 1030 Biocontroler. Stirrer speed was 800 rpm, and the gas flow was 0.5 l min−1.
Synthetic media were prepared as described by Verdyun (1992) with the following modifications: for carbon-limited cultivation, the medium contained 5.0 g l−1 of (NH4)2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and either 7.5 g l−1 of glucose or 5.76 g l−1 of ethanol. For nitrogen-limited cultures, 1.0 g l−1 of (NH4)2SO4, 5,3 g l−1 of K2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and the necessary glucose to keep the residual glucose concentration at 18 g l−1 (59 and 62.2 g l−1 for the CO2-untreated and -treated cultures, respectively). This was done to avoid differences in the degree of glucose repression.
 For CO2-enriched aerobic cultivation, cultures were sparged with a defined gas mixture containing 79% CO2 and 21% O2 (HoekLoos, Schiedam, The Netherlands).

tag: The prototrophic S. cerevisiae strain CEN.PK113-7D [18] was used for this study


title: Acetate limited chemostat culture D=0.1/h -2

hyb_protocol: Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays were performed as described previously (6) 6- Piper, M. D. W., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S.,Nielsen, J., and Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008

molecule: polyA RNA

source_name: Acetate limited aerobic chemostat culture

growth_protocol:
Strain and Growth Conditions Wild-type S. cerevisiae strain CEN.PK113-7D (MATa) (1) was grown at 30 Â°C in 2-liter chemostats (Applikon), with a working volume of 1.0 liter as described in Ref. 2.  Cultures were fed with a defined mineral medium that limited growth by glucose, ethanol, acetate, or maltose with all other growth requirements in excess. The dilution rate was set at 0.10 h-1. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH with the use of an Applikon ADI 1030 biocontroller. Stirrer speed was 800 rpm, and the airflow was 0.5 liters_min-1. Dissolved oxygen tension was measured online with an Ingold model 34-100-3002 probe, and was between 60 and 75% of air saturation. The off-gas was cooled by a condenser connected to a cryostat set at 2 Â°C and analyzed as previously described (3). Steady-state samples were taken after 10-14 volume changes to avoid strain adaptation caused by long term cu
 ltivation (4).
	Media The defined mineral medium composition was based on that described by Verduyn et al. (5). The carbon source was 256 mmol
of carbon/liter.
	1. Pronk, J. T., Wenzel, T. J., Luttik, M. A. H., Klaassen, C. C. M., Scheffers, W. A., and van Dijken, J. P. (1994) Microbiology 140, 601-610
	2. van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953-28959
	3. van Maris, A. J. A., Luttik, M. A. H., Winkler, A. A., van Dijken, J. P., and Pronk, J. T. (2003) Appl. Environ. Microbiol. 69, 2094-2099
	4. Ferea, T. L., Botstein, D., Brown, P. O., and Rosenzweig, R. F. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 9721-9726
	5- Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1992) Yeast 8, 501-517

treatment_protocol: liquid nitrogen quenching

tag: Prototrophic S. cerevisiae strain CEN.PK113â€“7D (MATa)


title: Prolongued aerobic maltose limited chemostat culture D=0.1/h -2

scan_protocol: The results for each growth condition were derived from three independently cultured replicates. Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays, as well as data acquisition and analysis, were performed as previously described (Daran-Lapujade  et al., 2004; Piper et al., 2002). Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277, 37001–37008. Daran-Lapujade, P., Jansen, M. L., Daran, J. M., Van Gulik, W., de Winde, J. H. & Pronk, J. T. (2004). Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae: a chemostat culture study. J Biol Chem 279, 9125–9138.

source_name: Prolongued aerobic maltose limited chemostat culture 45 generations old

growth_protocol: Aerobic chemostat cultivation was performed at a dilution rate of 0.10 h−1 at 30°C in 2.0-liter laboratory fermentors (Applikon, Schiedam, The Netherlands) with stirring at 800 rpm. The working volume of the cultures was kept at 1.0 liter by a peristaltic effluent pump coupled to an electrical level sensor. This setup ensured that under all growth conditions, biomass concentrations in samples taken directly from the culture differed by <1% from biomass concentrations in samples taken from the effluent line. The exact working volume was measured after each experiment. The pH was kept at 5.0 ± 0.1 by an ADI 1030 biocontroller via the automatic addition of 2 mol of KOH · liter−1. The fermentor was flushed with air at a flow rate of 0.5 liter · min−1 by using a Brooks 5876 mass flow controller. The dissolved oxygen concentration was continuously monitored with an oxygen electrode (model 34 100 3002; Ingold) and remained above 60% of air saturation. A steady state was defined as the situation in which at least five volume changes had passed after the last change in growth conditions and in which the biomass concentration and the specific rates of carbon dioxide production and oxygen consumption had remained constant (<2% variation) over two volume exchanges. In case of spontaneous oscillatory behavior, a pulse of ethanol (50 mM) was added to the culture to dampen out the oscillations. Chemostat cultures were routinely checked for purity by phase-contrast microscopy.

tag: The haploid, prototrophic S. cerevisiae strain CEN.PK113-7D (MATa MAL2-8c SUC2) was obtained from Dr P. KoÂ¨tter, Frankfurt, Germany. Precultures were grown to stationary phase in shake-flask cultures of synthetic medium (Verduyn et al., 1992), adjusted to pH 6?0 and containing 2% (w/v) glucose. After adding sterile glycerol (30 %, v/v), 2 ml aliquots were stored in sterile vials at 280 uC. These frozen stock cultures were used to inoculate precultures for chemostat cultivation.

tag: Verduyn, C., Postma, E., Scheffers, W. A. & van Dijken, J. P. (1992). Effect of benzoic acid on metabolic fluxes in yeasts

value: a continuous study on regulation of respiration and alcoholic fermentation. Yeast 8, 501-517.


title: AX4 - 300mM cis - biological replication 1 - technical replication4

city: Houston

first: Nancy

middle: E

last: Van Driessche

state: TX

address: One Baylor Plaza

country: USA

institute: Baylor college of medicine

hyb_protocol: Labeled cDNA in PerfectHybTM Plus Hybridization buffer (SIGMA H-7033) was hybridized to the arrays after heat treatment (95°C, 2 min) using a GeneTAC hybridization station (Genomic Solutions) according to the manufacturer’s recommended protocol. Labeled cDNA was hybridized to the arrays using a GeneTAC automatic hybridization station (Genomic Solutions) for 2 hours at 65C.  Arrays were sequentially washed with 3 solutions, 2x SSC, 0.5% SDS; 0.5x SSC, 0.5% SDS; 0.1x SSC, for 30 sec at room temperature twice each.

scan_protocol: The arrays were scanned with a ScanArray5000 scanner (GSI Lumonics) according to the manufacturer’s recommended protocol.  PMT and Laser settings were not recorded.

data_processing: All images were processed with the Imagene software package.

organism: Dictyostelium discoideum

source_name: Total RNA from AX4 cells, treated with 300mM cisplatin labeled with Alexa647

label_protocol: Total RNA (10 µg) was mixed with 1 µg of labeled [dT(18)] primer in 13 µl of water, incubated at 70°C for 10 minutes and on ice for 2-5 minutes.  Reaction buffer (Gibco-BRL), 0.1M DTT, 0.5 mM of each dNTP and 200U Superscript II (Gibco-BRL) were added and the reaction was incubated at 42°C for 2 hours.  Experimental RNA samples were labeled with Cy5 primers and the reference RNA sample was labeled with Cy3.  Both of the primers were HPLC-purified by the manufacturer (Operon Technologies).  Reverse transcription reactions were terminated with 0.1M EDTA.  RNA was degraded by adding 0.3 N NaOH and incubating at 60°C for 20 minutes.  The reaction was neutralized with 0.4 M Tris.HCl pH7.6.  Labeled cDNA was purified by ethanol precipitation, resuspended in 10 µl of DDW and mixed with 130 µl of PerfectHybTM Plus Hybridization buffer (SIGMA H-7033).

growth_protocol: Cells were grown in shaking suspension in HL5 medium, with the appropriate supplements for auxotrophy or drug selection.

extract_protocol: 2x106 cells/ml cells (treated or untreated) were collected, resuspended in 1 ml TRIZOL reagent (Life Technologies) and total RNA was extracted according to the manufacturer’s protocol.  The RNA was resuspended in 20 mM MOPS (pH7.0) and its concentration was determined by spectrophotometry and verified by Northern blot analysis and staining with methylene blue, which also tested RNA integrity.

treatment_protocol: Exponentially growing cells (2x106 cells/ml) were divided into twelve 50 ml aliquots in 500 ml flasks. The cells were shaken for 30 min, 300 µM cisplatin was added to 6 cultures (PT buffer was added to the 6 controls), and the cells were shaken for 3 hr at 22C in the dark. Samples (1 ml) were drawn and assayed for viability. The remaining cells were washed with phosphate buffered saline (PBS) and resuspended in 1.0 ml TRIzol reagent (Life Technologies, Gaithersburg, MD) and RNA was extracted.

tag: strain

source_name: Total RNA from developed AX4 cells (0,3,6,12,17 and 24hours) labeled with Cyanine3


title: AX4 - 300mM cis - biological replication 1 - technical replication2


title: AX4 - 300mM cis - biological replication 2 - technical replication1


title: AX4 - 300mM cis - biological replication 1 - technical replication1


title: AX4 - 300mM cis - biological replication 1 - technical replication5


title: AX4 - 300mM cis - biological replication 1 - technical replication3


title: AX4 - 300mM cis - biological replication 2 - technical replication3


title: Ethanol limited chemostat D=0.1/h -1

hyb_protocol: Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip® microarrays were performed as described previously (6) 6- Piper, M. D. W., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S.,Nielsen, J., and Pronk, J. T. (2002) J. Biol. Chem. 277, 37001–37008

source_name: Aerobic ethanol limited chemostat

growth_protocol:
Strain and Growth Conditions—Wild-type S. cerevisiae strain CEN.PK113–7D (MATa) (1) was grown at 30 °C in 2-liter chemostats (Applikon), with a working volume of 1.0 liter as described in Ref. 2.  Cultures were fed with a defined mineral medium that limited growth by glucose, ethanol, acetate, or maltose with all other growth requirements in excess. The dilution rate was set at 0.10 h-1. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH with the use of an Applikon ADI 1030 biocontroller. Stirrer speed was 800 rpm, and the airflow was 0.5 liters_min-1. Dissolved oxygen tension was measured online with an Ingold model 34-100-3002 probe, and was between 60 and 75% of air saturation. The off-gas was cooled by a condenser connected to a cryostat set at 2 °C and analyzed as previously described (3). Steady-state samples were taken after 10–14 volume changes to avoid strain adaptation caused by long term cultivation (4).
Media—The defined mineral medium composition was based on that described by Verduyn et al. (5). The carbon source was 256 mmol
of carbon/liter.
1. Pronk, J. T., Wenzel, T. J., Luttik, M. A. H., Klaassen, C. C. M., Scheffers, W. A., and van Dijken, J. P. (1994) Microbiology 140, 601–610
2. van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953–28959
3. van Maris, A. J. A., Luttik, M. A. H., Winkler, A. A., van Dijken, J. P., and Pronk, J. T. (2003) Appl. Environ. Microbiol. 69, 2094–2099
4. Ferea, T. L., Botstein, D., Brown, P. O., and Rosenzweig, R. F. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 9721–9726
5- Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1992) Yeast 8, 501–517

tag: Prototrophic S. cerevisiae strain CEN.PK113–7D (MATa)


title: Mouse old brain C30-Br-1

city: Boulder

first: Sang-Kyu

last: Park

state: CO

department: IBG

institute: University of Colorado at Boulder

description: We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples.

hyb_protocol: Total 10ug cRNA was placed in the gene chip. The gene chip I used for this study is the Affymetrix MOE 430 2.0 arrays (Affymetrix, Santa Clara, CA). The Affymetrix MOE 430 2.0 array has 45,037 probe sets. Hybridization was carried out at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. Following hybridization, the hybridization solutions were removed and the gene chips were be installed in a fluidics system for washes and staining.

scan_protocol: After staining, the gene chips were read at a resolution of 3 μm using a Hewlett Packard GeneArray Scanner (Affymetrix, Santa Clara, CA). The averaged images collected from two scanned images were used for the analysis.

data_processing: The GeneChip Operating Software (GCOS) version 1.2 was used to analyze the image data. GCOS determines the presence of mRNA in samples and computes the signals of probe sets using the differences and ratios between PM and MM signals. Signals in each image are normalized to minimize an overall variability in hybridization intensities by a global scaling method.

organism: Mus musculus

source_name: Old neocortex

label_protocol:
C: control diet
30: 30-month-old
Br: brain(neocortex)
1: sample number

growth_protocol: Male B6C3F1 mice were purchased from Harlan Sprague-Dawley at 6-7 weeks of age. Mice were housed singly in a pathogen-free facility and provided acidified water ad libitum.

extract_protocol: Total RNA was extracted from frozen tissue using the TRIZOL reagent (Life Technologies, Grand Island, NY) and mRNA was purified from the total RNA with oligo-dT-linked oligotex resin (Qiagen, Valencia, CA). Then, double-stranded cDNA was synthesized from 1ug of mRNA using the SuperScript Choice System (Life Technologies, Grand Island, NY) with an oligo-dT primer containing a T7 RNA polymerase promoter (Genset, La Jolla, CA), purified with phenol-chloroform-isoamyl alcohol, and precipitated with pellet paint co-precipitant (Novagen, Madison, WI). Purified double-stranded cDNA was used to synthesize biotin-labeled cRNA using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY). The biotin-labeled antisense cRNA was then purified with the RNeasy affinity column (Qiagen, Valencia, CA). After purification, biotin-labeled cRNA was fragmented randomly to sizes ranging from 35 to 200 bases.

treatment_protocol: control diet

value: B6/C3H F1 hybrid

tag: gender

value: male

tag: age


title: Mouse young brain C5-Br-5

source_name: Young neocortex

label_protocol:
C: control diet
5: 5-month-old
Br: brain(neocortex)
5: sample number


title: Mouse young brain C5-Br-4

label_protocol:
C: control diet
5: 5-month-old
Br: brain(neocortex)
4: sample number


title: AX4 - 300mM cis - biological replication 2 - technical replication4


title: Mouse old brain C30-Br-2

label_protocol:
C: control diet
30: 30-month-old
Br: brain(neocortex)
2: sample number


title: Mouse young brain C5-Br-3

label_protocol:
C: control diet
5: 5-month-old
Br: brain(neocortex)
3: sample number


title: Mouse old heart w/ a- & g-tocopherol agT-Ht-1

hyb_protocol: Total 10ug cRNA was placed in the gene chip. The gene chip I used for this study is the Affymetrix Murine Genome U74Av2 chips (Affymetrix, Santa Clara, CA), which covers 12,422 transcripts. Hybridization was carried out at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. Following hybridization, the hybridization solutions were removed and the gene chips were be installed in a fluidics system for washes and staining.

data_processing: GeneChip Analysis Suite 5.0 was used to analyze the image data. The Affymetrix Mouse Genome U74Av2 chip is derived from selected genes and ESTs. Each gene is represented by the use of 16 perfectly matched and mismatched (MM) control probes. The MM probes acts as specificity controls that allows the direct subtraction of both background and cross-hybridization signals. To determine the quantitative RNA abundance, the average of the differences representing PM minus MM for each gene-specific probe family is calculated, after discarding the maximum, the minimum and any outliers beyond 3 standard deviations. To minimize variability in hybridization, the global scaling method normalizes signals of each chip. The global scaling method is computational technique in which the average signal of all probe sets in one chip is scaled to a target average intensity by multiplying a scaling factor. This scaling factor is multiplied to each probe set signal to give the raw expression.

source_name: Old heart

label_protocol:
agT: 30-month-old a- & g-tocopherol supplemented mouse
Ht: heart
1: sample number

treatment_protocol: This group received a diet containing 500mg/kg of α- and γ-tocopherol each since the age of 15 months.


title: Mouse old brain C30-Br-3

label_protocol:
C: control diet
30: 30-month-old
Br: brain(neocortex)
3: sample number


title: Acetate limited chemostat culture D=0.1/h -1

scan_protocol: Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip® microarrays were performed as described previously (6) 6- Piper, M. D. W., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S.,Nielsen, J., and Pronk, J. T. (2002) J. Biol. Chem. 277, 37001–37008

source_name: acetate limited aerobic chemostat


title: Mouse old brain C30-Br-4

label_protocol:
C: control diet
30: 30-month-old
Br: brain(neocortex)
4: sample number


title: Mouse young brain C5-Br-2

label_protocol:
C: control diet
5: 5-month-old
Br: brain(neocortex)
2: sample number


title: Mouse old heart C30-Ht-5

label_protocol:
C: control diet
30: 30-month-old
Ht: heart
5: sample number


title: Mouse old heart w/ a-tocopherol aT-Ht-4

label_protocol:
aT: 30-month-old a-tocopherol supplemented mouse
Ht: heart
4: sample number

treatment_protocol: This group received a diet supplemented with 1000mg/kg of α-tocopherol since the age of 15 months.


title: Mouse old heart w/ a-tocopherol aT-Ht-3

label_protocol:
aT: 30-month-old a-tocopherol supplemented mouse
Ht: heart
3: sample number


title: Mouse young brain C5-Br-1

label_protocol:
C: control diet
5: 5-month-old
Br: brain(neocortex)
1: sample number


title: Mouse old heart C30-Ht-4

label_protocol:
C: control diet
30: 30-month-old
Ht: heart
4: sample number

value: B6/C3H hybrid


title: Mouse old heart w/ a-tocopherol aT-Ht-1

label_protocol:
aT: 30-month-old a-tocopherol supplemented mouse
Ht: heart
1: sample number


title: Mouse old brain C30-Br-5

label_protocol:
C: control diet
30: 30-month-old
Br: brain(neocortex)
5: sample number


title: Mouse old heart C30-Ht-3

label_protocol:
C: control diet
30: 30-month-old
Ht: heart
3: sample number


title: Mouse old heart w/ a- & g-tocopherol agT-Ht-5

label_protocol:
agT: 30-month-old a- & g-tocopherol supplemented mouse
Ht: heart
5: sample number


title: Mouse old heart w/ a- & g-tocopherol agT-Ht-4

label_protocol:
agT: 30-month-old a- & g-tocopherol supplemented mouse
Ht: heart
4: sample number


title: Mouse old heart w/ a- & g-tocopherol agT-Ht-3

label_protocol:
agT: 30-month-old a- & g-tocopherol supplemented mouse
Ht: heart
3: sample number


title: Mouse young heart C5-Ht-5

source_name: Young heart

label_protocol:
C: control diet
5: 5-month-old
Ht: heart
5: sample number


title: Mouse old heart C30-Ht-2

label_protocol:
C: control diet
30: 30-month-old
Ht: heart
2: sample number


title: Mouse old heart w/ a-tocopherol aT-Ht-2

label_protocol:
aT: 30-month-old a-tocopherol supplemented mouse
Ht: heart
2: sample number


title: Mouse young heart C5-Ht-4

label_protocol:
C: control diet
5: 5-month-old
Ht: heart
4: sample number


title: Mouse young heart C5-Ht-3

label_protocol:
C: control diet
5: 5-month-old
Ht: heart
3: sample number


title: Mouse young heart C5-Ht-1

label_protocol:
C: control diet
5: 5-month-old
Ht: heart
1: sample number


title: Mouse old heart C30-Ht-1

label_protocol:
C: control diet
30: 30-month-old
Ht: heart
1: sample number


title: slide 3000070252A

status: Public on Aug 30 2007

city: Seattle

first: John

last: Leigh

state: WA

department: Microbiology

institute: University of Washington

description: Biological replicate 2 of 4. Cultures grown under leucine limitation where compated to those grown under phosphate limitation

hyb_protocol: 100-120 pmol of Cy3 and Cy5 labeled cDNA where mixed, dried, resuspended in hybridization buffer (Agilent), boiled 3 min, 30 sec on ice, placed on the slide, covered with a coverslip and incubated at 42 C for 14-16 hours in the dark. Slides where washed in 1xSSC + 0.2% SDS then 0.1xSSC + 0.2% SDS at 54 C, washed with 0.1xSSC at room temp then rinsed with water and dried under nitrogen gas.

scan_protocol: Scanned on a Molecular Dynamics Gen III array scanner Images where quantified using TIGR spotfinder

data_processing: Background subtraction followed by LOESS normalization using S+ array analyzer

organism: Methanococcus maripaludis

source_name: Total RNA from Methanococcus maripaludis grown with 15 mM leucine

label_protocol: A variation of aminoallyl cDNA labeling (Ambion), 5-10 ug of total RNA was incubated with 4 ug of random decamers at 75 C for 7 min, reverse transcibed in the presence of 0.15mM aminoallyl UTP for 2 hours at 42 C,the RNA hydrolyzed by NaOH at 65 C for 15 min, neutralized with HEPES, percipitated and resuspended in coupling buffer, NHS-Cy5 was used to couple Cy5 to the aminoallyl UTP, and the reaction cleaned up with minelute columns

growth_protocol: cells were grown in chemostats in McCas media with 15 mM leucine

extract_protocol: Qiagen RNeasy

tag: grown under leucine limitation

source_name: Total RNA from Methanococcus maripaludis grown under 15 mM phosphate

label_protocol: A variation of aminoallyl cDNA labeling (Ambion), 5-10 ug of total RNA was incubated with 4 ug of random decamers at 75 C for 7 min, reverse transcibed in the presence of 0.15mM aminoallyl UTP for 2 hours at 42 C,the RNA hydrolyzed by NaOH at 65 C for 15 min, neutralized with HEPES, percipitated and resuspended in coupling buffer, NHS-Cy3 was used to couple Cy3 to the aminoallyl UTP, and the reaction cleaned up with minelute columns

growth_protocol: cells were grown in chemostats in McCas media with 15 mM phosphate

tag: grown under phosphate limitation


title: slide 3000070243B

description: Biological replicate 3 of 4. Cultures grown under leucine limitation where compated to those grown under phosphate limitation


title: slide 3000070243A


title: slide 3000070252B


title: Mouse old heart w/ a-tocopherol aT-Ht-5

label_protocol:
aT: 30-month-old a-tocopherol supplemented mouse
Ht: heart
5: sample number


title: slide 3000070256A

description: Biological replicate 1 of 4. Cultures grown under leucine limitation where compated to those grown under phosphate limitation


title: slide 3000070031A

description: Biological replicate 4 of 4. Cultures grown under leucine limitation where compated to those grown under phosphate limitation


title: slide 3000070251B


title: slide 3000070257B


title: slide 3000070030B


title: Mouse old heart w/ a- & g-tocopherol agT-Ht-2

label_protocol:
agT: 30-month-old a- & g-tocopherol supplemented mouse
Ht: heart
2: sample number


title: Mouse young heart C5-Ht-2

label_protocol:
C: control diet
5: 5-month-old
Ht: heart
2: sample number


title: slide 3000070257A


title: slide 3000070256B


title: slide 3000070244B


title: slide 3000070244A


title: slide 3000070030A


title: slide 3000070251A


title: slide 3000070031B


title: Hindlimb_Muscle_Knockout 3 vs Control_array version 33.1

status: Public on Aug 29 2007

city: Vienna

first: J. Andrew

last: Pospisilik

address: Dr. Bohr-gasse 3

country: Austria

institute: IMBA

description: Biological Replicate 3

hyb_protocol: Hybridization was performed on a TECAN HS4800, according to protocol attached (TECAN HS4800 Hybridization Program.txt)

scan_protocol: Scanner: GenePix 4000B Image Analysis: GenPix Pro 6.0

data_processing: Print-tip Lowess Normalization, R package marray

source_name: Control hindlimb muscle

label_protocol: Labeling was done according to standard Protocol attached (Linear Amplification and Labeling for Microarray Application.txt)

growth_protocol: All mice were housed normally and sacrificed at 8 weeks of age

extract_protocol: Total RNA extracted using Qiagen RNAeasy following manufacturer's instructions

treatment_protocol: No treatment

tag: Strain

value: C57Bl/6, Age:8 weeks, Sex:Male, Tissue:hindlimb muscle

source_name: Muscle-specific AIF knockout hindlimb muscle


title: Liver Knockout 4 vs Control_array version 38.1

description: 3 Technical Replicates of Biological Replicate 4

data_processing: LIMMA processing,  default parameters, Background correction: RMA; normalizeWithinArrays, lmFit,  eBayes, topTable (adjust = fdr)

source_name: Control liver sample pooled from 4 mice

value: C57Bl/6, Age:8 weeks, Sex:Male, Tissue:liver

source_name: Liver-specific AIF knockout liver


title: Liver Knockout 2 vs Control_array version 38.1

description: 3 Technical Replicates of Biological Replicate 2


title: Hindlimb_Muscle_Knockout 3 vs Control_array version 30.1

description: Biological Replicate 3


title: Hindlimb_Muscle_Knockout 2 vs Control_array version 33.1

description: Biological Replicate 2


title: Hindlimb_Muscle_Knockout 1 vs Control_array version 33.1

description: Biological Replicate 1


title: H2126 parental cell line-21% oxygen

status: Public on Aug 28 2007

city: boston

first: kwok-kin

last: wong

state: MA

address: 44 binney street

department: medical oncology

institute: dana farber cancer institute

description: Agilent

hyb_protocol: Agilent

scan_protocol: Agilent

data_processing: Lowess Normalization

label: H2126 parental cell line-21% oxygen

organism: Homo sapiens

source_name: H2126 parental cell line-21% oxygen

label_protocol: Agilent

extract_protocol: H2126 parental cell line-21% oxygen

tag: H2126 parental cell line-21% oxygen

label: Common Reference

source_name: Common Reference

extract_protocol: Common Reference

tag: common reference


title: Liver Knockout 3 vs Control_array version 38.1

description: 3 Technical Replicates of Biological Replicate 3


title: H2126 LKB1-WT2-21% oxygen

description: Agilent

label: H2126 LKB1-WT2-21% oxygen

source_name: H2126 LKB1-WT2-21% oxygen

extract_protocol: H2126 LKB1-WT2-21% oxygen

tag: H2126 LKB1-WT2-21% oxygen


title: Liver Knockout 3 vs Control_array version 37.1


title: Liver Knockout 4 vs Control_array version 37.1


title: H2126 parental cell line-3% oxygen

description: Agilent

source_name: H2126 parental cell line-3% oxygen

tag: H2126 parental cell line-3% oxygen


title: A549 parental cell line-3% oxygen

description: Agilent

label: A549 parental cell line-3% oxygen

source_name: A549 parental cell line-3% oxygen

extract_protocol: A549 parental cell line-3% oxygen

tag: A549 parental cell line-3% oxygen


title: Liver Knockout 1 vs Control_array version 37.1

description: 3 Technical Replicates of Biological Replicate 1


title: Liver Knockout 1 vs Control_array version 38.1


title: Liver Knockout 2 vs Control_array version 37.1


title: p770bis sample_Ovarian tumor

status: Public on Aug 25 2007

city: Milan

first: Pietro

last: Mariani

address: Via La Masa 19

country: Italy

institute: Mario Negri Institute

hyb_protocol: Microarray hybridization: Add to each Sample 2.5 ul Cot-1 DNA and 12.50 ul 2X Hybridization Buffer. Heat samples for 2 min at 65 C. Centrifuge. Pipet the cDNA array and 22 ul of sample. Incubate for 16 hr at 65 C. Used Atlas Glass Microarray User Manual PT3453-1 instructions for post-hybridization wash.

scan_protocol: Arrays were scanned using a laser-scanner Axon 4000-B, (Axon Instruments, Union City, CA), using 5-micron resolution. Within the GenePix program were chosen photo-multiplier parameters that defined the quanta intensity density distribution of the array to give a Cy3/Cy5 ratio close to 1.0 and produced not too much saturated signals for each array. Separate 16-bit images were acquired for Cy3 and Cy5.

data_processing: Images were analysed using the GenePix Pro software (Axon Instruments) version 3.0. GenePix Result files (GPR) and the related scan images, together with the Agilent cDNA pattern file and information on the hybridised samples and labelling signs (positive for normal labelling and negative for dye-swap labelling), were then loaded into the Rosetta Resolver SE software. The Axon GenePix error model was applied to transform data and then duplicate ratio profiles were combined to obtain one ratio experiment for each patient. Log ratios, log ratio errors and p-values were thus available for the non flagged sequences of each ratio experiment.

source_name: Total RNA extracted from frozen biopsies of ovarian tumors

label_protocol: RNA amplification for array analysis was performed using Ambion MessageAmp aRNA Kit, cat 1750. cDNA labeling was performed using Amino Allyl cDNA Labeling Kit - cat 1705 by Ambion.

extract_protocol: Total RNA purification from human biopsies were performed using the SV Total RNA Isolation System -cat:#z3100 from Promega.

tag: Gender

value: Female

tag: Status:alive no evidence of disease

tag: FIGO Stage:1

tag: FIGO Substage:b

tag: Overall Survival(days):0

tag: Progression Free Survival(days):0

source_name: Clontech Universal Reference

extract_protocol: see the producer web site: http//clontech.com/products/detail.asp?tabno=2&catalog_id=636538&page=all&faq_id=153665

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p597bis sample_Ovarian tumor

tag: FIGO Substage:a

tag: Overall Survival(days):1136

tag: Progression Free Survival(days):1136


title: H2126 LKB1-WT1-21% oxygen

description: Agilent

label: H2126 LKB1-WT1-21% oxygen

source_name: H2126 LKB1-WT1-21% oxygen

extract_protocol: H2126 LKB1-WT1-21% oxygen

tag: H2126 LKB1-WT1-21% oxygen


title: Hindlimb_Muscle_Knockout 2 vs Control_array version 30.1

description: Biological Replicate 2

tag: Strain


title: p646bis sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):1196

tag: Progression Free Survival(days):1196


title: Hindlimb_Muscle_Knockout 1 vs Control_array version 30.1

description: Biological Replicate 1


title: A549 parental cell line-21% oxygen

description: Agilent

label: A549 parental cell line-21% oxygen

source_name: A549 parental cell line-21% oxygen

extract_protocol: A549 parental cell line-21% oxygen

tag: A549 parental cell line-21% oxygen

tag: common reference


title: H2126 LKB1-WT2-3% oxygen

description: Agilent

source_name: H2126 LKB1-WT2-3% oxygen

tag: H2126 LKB1-WT2-3% oxygen


title: A549 LKB-KD-21% oxygen

description: Agilent

label: A549 LKB-KD-21% oxygen

source_name: A549 LKB-KD-21% oxygen

extract_protocol: A549 LKB-KD-21% oxygen

tag: A549 LKB-KD-21% oxygen


title: H2126 LKB1-WT1-3% oxygen

description: Agilent

label: H2126 LKB1-WT1-3% oxygen

source_name: H2126 LKB1-WT1-3% oxygen

extract_protocol: H2126 LKB1-WT1-3% oxygen

tag: H2126 LKB1-WT1-3% oxygen


title: p462bis sample_Ovarian tumor

tag: Gender

tag: Status:alive no evidence of disease

tag: FIGO Stage:1

tag: Overall Survival(days):1745

tag: Progression Free Survival(days):1745


title: p549bis sample_Ovarian tumor

tag: FIGO Substage:a

tag: Overall Survival(days):1189

tag: Progression Free Survival(days):1189

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p209bis sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):2669

tag: Progression Free Survival(days):2669


title: p433bis sample_Ovarian tumor

tag: Overall Survival(days):1839

tag: Progression Free Survival(days):1839


title: p540bis sample_Ovarian tumor

tag: Overall Survival(days):1507

tag: Progression Free Survival(days):1507


title: p502bis sample_Ovarian tumor

tag: Overall Survival(days):178

tag: Progression Free Survival(days):178


title: p616bis sample_Ovarian tumor

tag: Gender

tag: Status:alive no evidence of disease

tag: Histotype:clear cells

tag: Overall Survival(days):1220

tag: Progression Free Survival(days):1220


title: p141bis sample_Ovarian tumor

tag: Status:death unrelated to cancer

tag: FIGO Stage:1

tag: Overall Survival(days):2861

tag: Progression Free Survival(days):2861


title: p448bis sample_Ovarian tumor

tag: FIGO Substage:a

tag: Overall Survival(days):2095

tag: Progression Free Survival(days):2095

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p775bis sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):490

tag: Progression Free Survival(days):490


title: p39bis sample_Ovarian tumor

tag: Overall Survival(days):3452

tag: Progression Free Survival(days):3452


title: p310bis sample_Ovarian tumor

tag: Gender

tag: Status:alive no evidence of disease

tag: Overall Survival(days):2451

tag: Progression Free Survival(days):2451


title: p690bis sample_Ovarian tumor

tag: Overall Survival(days):1084

tag: Progression Free Survival(days):1084


title: p429bis sample_Ovarian tumor

tag: Status:death related to cancer

tag: FIGO Stage:1

tag: Overall Survival(days):429

tag: Progression Free Survival(days):429


title: p398bis sample_Ovarian tumor

tag: Histotype:clear cells

tag: Overall Survival(days):1076

tag: Progression Free Survival(days):1076


title: p17bis sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):4404

tag: Progression Free Survival(days):4404

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p90bis sample_Ovarian tumor

tag: Gender

tag: FIGO Substage:a

tag: Overall Survival(days):3395

tag: Progression Free Survival(days):3395


title: p541bis sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):2705

tag: Progression Free Survival(days):2705


title: p793bis sample_Ovarian tumor

tag: FIGO Stage:1

tag: Overall Survival(days):427

tag: Progression Free Survival(days):427


title: p212bis sample_Ovarian tumor

tag: Histotype:clear cells

tag: Overall Survival(days):2926

tag: Progression Free Survival(days):2926


title: p0103bis sample_Ovarian tumor

tag: Overall Survival(days):5824

tag: Progression Free Survival(days):5824


title: p455bis sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):1974

tag: Progression Free Survival(days):1974


title: p692bis sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):887

tag: Progression Free Survival(days):887

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p760bis sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):381

tag: Progression Free Survival(days):381


title: p573bis sample_Ovarian tumor

tag: FIGO Stage:1

tag: Overall Survival(days):1393

tag: Progression Free Survival(days):1393


title: p79bis sample_Ovarian tumor

tag: Status:death related to cancer

tag: Overall Survival(days):2267

tag: Progression Free Survival(days):2267


title: p772bis sample_Ovarian tumor

tag: Histotype:clear cells

tag: Overall Survival(days):482

tag: Progression Free Survival(days):482


title: p725bis sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):531

tag: Progression Free Survival(days):531


title: p586bis sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):1111

tag: Progression Free Survival(days):1111


title: p336bis sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):2497

tag: Progression Free Survival(days):2497

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p388bis sample_Ovarian tumor

tag: FIGO Stage:1

tag: FIGO Substage:b

tag: Overall Survival(days):2234

tag: Progression Free Survival(days):2234


title: p414bis sample_Ovarian tumor

tag: Overall Survival(days):1800

tag: Progression Free Survival(days):1800


title: p246bis sample_Ovarian tumor

tag: Overall Survival(days):2814

tag: Progression Free Survival(days):2814


title: p057bis sample_Ovarian tumor

tag: FIGO Substage:a

tag: Histotype:clear cells

tag: Overall Survival(days):4324

tag: Progression Free Survival(days):4324


title: p56bis sample_Ovarian tumor

tag: Gender

tag: FIGO Substage:c

tag: Overall Survival(days):3516

tag: Progression Free Survival(days):3516


title: p567bis sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):1266

tag: Progression Free Survival(days):1266

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p66bis sample_Ovarian tumor

tag: FIGO Stage:1

tag: Overall Survival(days):3459

tag: Progression Free Survival(days):3459


title: p497bis sample_Ovarian tumor

tag: Status:death related to cancer

tag: Overall Survival(days):695

tag: Progression Free Survival(days):695


title: p375bis sample_Ovarian tumor

tag: FIGO Substage:a

tag: Overall Survival(days):2287

tag: Progression Free Survival(days):2287


title: p139bis sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):3050

tag: Progression Free Survival(days):3050


title: p68bis sample_Ovarian tumor

tag: FIGO Substage:c

tag: Histotype:clear cells

tag: Overall Survival(days):3473

tag: Progression Free Survival(days):3473


title: p550bis sample_Ovarian tumor

tag: Overall Survival(days):1369

tag: Progression Free Survival(days):1369

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p284bis sample_Ovarian tumor

tag: Status:in progression

tag: FIGO Stage:1

tag: Overall Survival(days):1053

tag: Progression Free Survival(days):1053


title: p350bis sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: FIGO Substage:a

tag: Overall Survival(days):2528

tag: Progression Free Survival(days):2528


title: p0188bis sample_Ovarian tumor

tag: Gender

tag: Status:death related to cancer

tag: Overall Survival(days):716

tag: Progression Free Survival(days):716


title: p482bis sample_Ovarian tumor

tag: Overall Survival(days):1742

tag: Progression Free Survival(days):1742


title: p0112bis sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):4366

tag: Progression Free Survival(days):4366


title: p382bis sample_Ovarian tumor

tag: Overall Survival(days):1864

tag: Progression Free Survival(days):1864

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p243bis sample_Ovarian tumor

tag: FIGO Stage:1

tag: Overall Survival(days):2702

tag: Progression Free Survival(days):2702


title: p386bis sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: FIGO Substage:a

tag: Overall Survival(days):2032

tag: Progression Free Survival(days):2032


title: p070bis sample_Ovarian tumor

tag: Gender

tag: Status:death related to cancer

tag: Histotype:clear cells

tag: Overall Survival(days):609

tag: Progression Free Survival(days):609


title: p293bis sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):2199

tag: Progression Free Survival(days):2199


title: p13bis sample_Ovarian tumor

tag: Overall Survival(days):3766

tag: Progression Free Survival(days):3766


title: p261bis sample_Ovarian tumor

tag: FIGO Stage:1

tag: FIGO Substage:b

tag: Overall Survival(days):2281

tag: Progression Free Survival(days):2281

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p73bis sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: FIGO Substage:a

tag: Overall Survival(days):2997

tag: Progression Free Survival(days):2997


title: p383bis sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):2093

tag: Progression Free Survival(days):2093


title: p0128bis sample_Ovarian tumor

tag: Status:death related to cancer

tag: FIGO Substage:c

tag: Overall Survival(days):689

tag: Progression Free Survival(days):689


title: p84bis sample_Ovarian tumor

tag: Histotype:clear cells

tag: Overall Survival(days):3500

tag: Progression Free Survival(days):3500


title: p487bis sample_Ovarian tumor

tag: FIGO Stage:1

tag: Overall Survival(days):1794

tag: Progression Free Survival(days):1794


title: p0210bis sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):4615

tag: Progression Free Survival(days):4615

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p63bis sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):3359

tag: Progression Free Survival(days):3359


title: p459bis sample_Ovarian tumor

tag: FIGO Substage:a

tag: Overall Survival(days):1891

tag: Progression Free Survival(days):1891


title: p401bis sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):2178

tag: Progression Free Survival(days):2178


title: p213bis sample_Ovarian tumor

tag: Overall Survival(days):2910

tag: Progression Free Survival(days):2910


title: p331bis sample_Ovarian tumor

tag: FIGO Stage:1

tag: Histotype:clear cells

tag: Overall Survival(days):2682

tag: Progression Free Survival(days):2682


title: p0146bis sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):3561

tag: Progression Free Survival(days):3561


title: p091bis sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):4673

tag: Progression Free Survival(days):4673

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p31bis sample_Ovarian tumor

tag: FIGO Substage:a

tag: Overall Survival(days):3656

tag: Progression Free Survival(days):3656


title: p171bis sample_Ovarian tumor

tag: Status:death related to cancer

tag: FIGO Substage:c

tag: Overall Survival(days):743

tag: Progression Free Survival(days):743


title: p421bis sample_Ovarian tumor

tag: FIGO Stage:1

tag: Histotype:clear cells

tag: Overall Survival(days):787

tag: Progression Free Survival(days):787


title: p183bis sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):3045

tag: Progression Free Survival(days):3045


title: p0125bis sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):4176

tag: Progression Free Survival(days):4176


title: p080bis sample_Ovarian tumor

tag: Overall Survival(days):2810

tag: Progression Free Survival(days):2810

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p166bis sample_Ovarian tumor

tag: Overall Survival(days):3006

tag: Progression Free Survival(days):3006


title: p0143bis sample_Ovarian tumor

tag: FIGO Substage:b

tag: Overall Survival(days):4478

tag: Progression Free Survival(days):4478


title: p0217bis sample_Ovarian tumor

tag: Status:death related to cancer

tag: FIGO Stage:1

tag: Overall Survival(days):2248

tag: Progression Free Survival(days):2248


title: p0114bis sample_Ovarian tumor

tag: Status:in progression

tag: FIGO Substage:c

tag: Overall Survival(days):3592

tag: Progression Free Survival(days):3592


title: p0208bis sample_Ovarian tumor

tag: Gender

tag: Status:death unrelated to cancer

tag: Overall Survival(days):2788

tag: Progression Free Survival(days):2788


title: p320bis sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):2541

tag: Progression Free Survival(days):2541

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p0102bis sample_Ovarian tumor

tag: Overall Survival(days):3903

tag: Progression Free Survival(days):3903


title: p462 sample_Ovarian tumor

data_processing: Image addressing and segmentation was performed using CSIRO Spot software, and data analysis occurred with R statistical software package. For each found array dataset two distinct classes of log2 ratio have been computed. The first (MA=(FR BGR)/(FG BGG)) was the classic log ratio of the two net fluorescence signal (F-BG) determined by subtraction of the local background (BG) from the spot median intensity (F). The second (MB=(FR/BGR)/(FG/BGG)) instead was the log ratio of the two relative intensities (F/BG) of each channel fluorescence (F) of spot in respect to its own local background (BG). The log2 geometric mean intensities and log ratios of both classes were arbitrarily set to 0 if a spot had not a net fluorescence signal greater than 0 in both channels (i. e. is a unreliable spot). Both kind of M-values were normalised and corrected from possible biases using the LOWESS. In order to evaluate which genes have probably modified their expression level an intensity-dependent Z-score calculation has been performed for each microarray data set and log ratio class (MA and MB).

tag: FIGO Stage:1

tag: FIGO Substage:a

tag: Overall Survival(days):1745

tag: Progression Free Survival(days):1745


title: p770 sample_Ovarian tumor

tag: FIGO Substage:b

tag: Overall Survival(days):0

tag: Progression Free Survival(days):0


title: p646 sample_Ovarian tumor

tag: Gender

tag: FIGO Substage:c

tag: Overall Survival(days):1196

tag: Progression Free Survival(days):1196


title: p310 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):2451

tag: Progression Free Survival(days):2451


title: p541 sample_Ovarian tumor

tag: Overall Survival(days):2705

tag: Progression Free Survival(days):2705

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p540 sample_Ovarian tumor

tag: FIGO Stage:1

tag: Overall Survival(days):1507

tag: Progression Free Survival(days):1507


title: p209 sample_Ovarian tumor

tag: Overall Survival(days):2669

tag: Progression Free Survival(days):2669


title: p141 sample_Ovarian tumor

tag: Status:death unrelated to cancer

tag: Overall Survival(days):2861

tag: Progression Free Survival(days):2861


title: p39 sample_Ovarian tumor

tag: Gender

tag: FIGO Substage:a

tag: Overall Survival(days):3452

tag: Progression Free Survival(days):3452


title: p793 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Histotype:clear cells

tag: Overall Survival(days):427

tag: Progression Free Survival(days):427


title: p775 sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):490

tag: Progression Free Survival(days):490

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p549 sample_Ovarian tumor

tag: FIGO Stage:1

tag: Overall Survival(days):1189

tag: Progression Free Survival(days):1189


title: p690 sample_Ovarian tumor

tag: Overall Survival(days):1084

tag: Progression Free Survival(days):1084


title: p17 sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):4404

tag: Progression Free Survival(days):4404


title: p692 sample_Ovarian tumor

tag: Overall Survival(days):887

tag: Progression Free Survival(days):887


title: p597 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: FIGO Substage:a

tag: Overall Survival(days):1136

tag: Progression Free Survival(days):1136


title: p433 sample_Ovarian tumor

tag: Overall Survival(days):1839

tag: Progression Free Survival(days):1839


title: p502 sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):178

tag: Progression Free Survival(days):178

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p616 sample_Ovarian tumor

tag: FIGO Stage:1

tag: Histotype:clear cells

tag: Overall Survival(days):1220

tag: Progression Free Survival(days):1220


title: p0103 sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):5824

tag: Progression Free Survival(days):5824


title: p90 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):3395

tag: Progression Free Survival(days):3395


title: p455 sample_Ovarian tumor

tag: Overall Survival(days):1974

tag: Progression Free Survival(days):1974


title: p760 sample_Ovarian tumor

tag: Overall Survival(days):381

tag: Progression Free Survival(days):381


title: p212 sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):2926

tag: Progression Free Survival(days):2926


title: p79 sample_Ovarian tumor

tag: Status:death related to cancer

tag: FIGO Stage:1

tag: Overall Survival(days):2267

tag: Progression Free Survival(days):2267

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p057 sample_Ovarian tumor

tag: Gender

tag: FIGO Substage:a

tag: Histotype:clear cells

tag: Overall Survival(days):4324

tag: Progression Free Survival(days):4324


title: p398 sample_Ovarian tumor

tag: Overall Survival(days):1076

tag: Progression Free Survival(days):1076


title: p429 sample_Ovarian tumor

tag: Overall Survival(days):429

tag: Progression Free Survival(days):429


title: p586 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: FIGO Substage:c

tag: Overall Survival(days):1111

tag: Progression Free Survival(days):1111


title: p336 sample_Ovarian tumor

tag: FIGO Stage:1

tag: Overall Survival(days):2497

tag: Progression Free Survival(days):2497


title: p448 sample_Ovarian tumor

tag: Overall Survival(days):2095

tag: Progression Free Survival(days):2095

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p725 sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):531

tag: Progression Free Survival(days):531


title: p573 sample_Ovarian tumor

tag: Histotype:clear cells

tag: Overall Survival(days):1393

tag: Progression Free Survival(days):1393


title: p772 sample_Ovarian tumor

tag: Overall Survival(days):482

tag: Progression Free Survival(days):482


title: p550 sample_Ovarian tumor

tag: Status:death related to cancer

tag: FIGO Substage:c

tag: Overall Survival(days):1369

tag: Progression Free Survival(days):1369


title: p246 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: FIGO Stage:1

tag: Overall Survival(days):2814

tag: Progression Free Survival(days):2814


title: p567 sample_Ovarian tumor

tag: Overall Survival(days):1266

tag: Progression Free Survival(days):1266

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p497 sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):695

tag: Progression Free Survival(days):695


title: p414 sample_Ovarian tumor

tag: Overall Survival(days):1800

tag: Progression Free Survival(days):1800


title: p139 sample_Ovarian tumor

tag: FIGO Substage:a

tag: Overall Survival(days):3050

tag: Progression Free Survival(days):3050


title: p284 sample_Ovarian tumor

tag: Status:in progression

tag: FIGO Substage:c

tag: Overall Survival(days):1053

tag: Progression Free Survival(days):1053


title: p375 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: FIGO Stage:1

tag: Overall Survival(days):2287

tag: Progression Free Survival(days):2287


title: p56 sample_Ovarian tumor

tag: Overall Survival(days):3516

tag: Progression Free Survival(days):3516

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p388 sample_Ovarian tumor

tag: Gender

tag: FIGO Substage:b

tag: Overall Survival(days):2234

tag: Progression Free Survival(days):2234


title: p13 sample_Ovarian tumor

tag: FIGO Substage:a

tag: Overall Survival(days):3766

tag: Progression Free Survival(days):3766


title: p482 sample_Ovarian tumor

tag: Overall Survival(days):1742

tag: Progression Free Survival(days):1742


title: p68 sample_Ovarian tumor

tag: FIGO Substage:c

tag: Histotype:clear cells

tag: Overall Survival(days):3473

tag: Progression Free Survival(days):3473


title: p66 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: FIGO Stage:1

tag: Overall Survival(days):3459

tag: Progression Free Survival(days):3459


title: p243 sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):2702

tag: Progression Free Survival(days):2702

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p382 sample_Ovarian tumor

tag: Overall Survival(days):1864

tag: Progression Free Survival(days):1864


title: L62

type: genomic

city: Heidelberg

first: Stefan

middle: M

last: Pfister

address: INF 580

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center

description: Comparison of tumor DNA (Cy3-labeled) vs. normal DNA (Cy5-labeled). Whole-genome screening of DNA copy-number aberrations using array-CGH

hyb_protocol: Ten micrograms each of tumor and reference DNA were combined with 300µg of human Cot-1 DNA (Roche Diagnostics, Mannheim, Germany) and suspended in 125µl of UltrahybTM hybridization buffer (Ambion, Bad Soden, Germany). Denaturation of combined DNA was performed at 75°C for 10 min, followed by preannealing at 37°C for 30 min. Hybridization was carried out in a GeneTAC Hybridization Station (Genomic Solutions, Oberhaching, Germany) for 36 hr at 37°C. Slides were washed with 2× SSC/0.05% Tween-20 at 37°C for 1 cycle, 2× SSC/0.05% Tween-20 at 44°C for 2 cycles, 50% formamide/2× SSC/0.1% Tween-20 at 44°C for 3 cycles, 2× SSC/0.05% Tween-20 at 44°C for 2 cycles, and finally 1× PBS/0.05% Tween-20 at 25°C for 2 cycles. Slides were dried by centrifugation at 54 g for 1 min, followed by centrifugation at 216 g for 1 min in a clinical centrifuge.

scan_protocol: Arrays were scanned at a 5µm resolution with an Axon 4000B scanner (Axon Instruments, Burlingame, USA) and images analyzed using GenePix Pro 6.0 software (Axon Instruments). Results files containing all relevant raw data were processed by use of ChipYard microarray analysis platform software (developed in-house), the statistical programming language R (http://www.r-project.org), and packages of the Bioconductor project (http://bioconductor.org; Ihaka and Gentleman, 1996).

data_processing: Fluorescence intensities of all spots were filtered consistently (intensity/local background >3; mean/median intensity <1.3; standard deviation of clone log2 ratios <0.2) and globally normalized using the printtip-loess algorithm (Smyth and Speed, 2003).

molecule: genomic DNA

source_name: tumor DNA

label_protocol: Genomic DNA (300-500 ng) was labeled with Cy3-labeled dCTP (tumor) or Cy5-conjugated dCTP (control) by use of a BioPrime DNA Labeling Kit (Invitrogen, Karlsruhe, Germany). Unincorporated nucleotides, random primers, and dyes were removed by use of MicroCon YM30 Spin Columns (Millipore, Schwalbach, Germany). Incorporation of dyes into the labeled DNA was determined by UV spectrophotometry.

extract_protocol: Genomic DNA from tumor tissue was isolated using the Blood and Cell Culture Kit (Qiagen,Hilden, Germany) following the instructions of the suppliers.  Genomic DNA from peripheral blood mononuclear cells of healthy donors was isolated by use of the Quiagen DNA Blood Midi-Kit (Hilden, Germany).

tag: male patient, good prednisone response, MRD N/A, NOTCH wild-type, no relapse within follow-up period

source_name: Pooled lymphocyte DNA from 10 healthy individuals (age 25-40 years)

tag: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: p386 sample_Ovarian tumor

tag: FIGO Substage:a

tag: Overall Survival(days):2032

tag: Progression Free Survival(days):2032


title: p84 sample_Ovarian tumor

tag: FIGO Substage:c

tag: Histotype:clear cells

tag: Overall Survival(days):3500

tag: Progression Free Survival(days):3500


title: L51

tag: female patient, poor prednisone response, MRD N/A, NOTCH wild-type, no relapse within follow-up period


title: p0188 sample_Ovarian tumor

tag: Status:death related to cancer

tag: FIGO Stage:1

tag: Overall Survival(days):716

tag: Progression Free Survival(days):716


title: L48

tag: male patient, good prednisone response, MRD N/A, NOTCH mutation, no relapse within follow-up period


title: L64

tag: male patient, poor prednisone response, MRD N/A, NOTCH wild-type, no relapse within follow-up period


title: p0112 sample_Ovarian tumor

tag: Gender

tag: Overall Survival(days):4366

tag: Progression Free Survival(days):4366

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: L65

tag: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: L47

tag: female patient, good prednisone response, MRD N/A, NOTCH mutation, no relapse within follow-up period


title: L66

tag: male patient, good prednisone response, MRD N/A, NOTCH wild-type, no relapse within follow-up period


title: L52

tag: female patient, poor prednisone response, MRD N/A, NOTCH wild-type,  relapse within follow-up period


title: L46

tag: male patient, poor prednisone response, MRD N/A, NOTCH wild-type,  relapse within follow-up period


title: p350 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: FIGO Substage:a

tag: Overall Survival(days):2528

tag: Progression Free Survival(days):2528


title: L45


title: L49


title: L50


title: p293 sample_Ovarian tumor

tag: FIGO Stage:1

tag: FIGO Substage:c

tag: Overall Survival(days):2199

tag: Progression Free Survival(days):2199


title: L44

tag: male patient, good prednisone response, MRD N/A, NOTCH mutation,  relapse within follow-up period


title: L43


title: L39


title: L42

tag: male patient, good prednisone response, MRD N/A, NOTCH mutation, no relapse within follow-up period


title: L41


title: p0128 sample_Ovarian tumor

tag: Gender

tag: Status:death related to cancer

tag: Overall Survival(days):689

tag: Progression Free Survival(days):689


title: p0146 sample_Ovarian tumor

tag: Overall Survival(days):3561

tag: Progression Free Survival(days):3561

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: L37

tag: male patient, good prednisone response, MRD N/A, NOTCH wild-type, no relapse within follow-up period

tag: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: p0210 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):4615

tag: Progression Free Survival(days):4615


title: L38

tag: female patient, good prednisone response, MRD N/A, NOTCH mutation, no relapse within follow-up period


title: p261 sample_Ovarian tumor

tag: FIGO Stage:1

tag: FIGO Substage:b

tag: Overall Survival(days):2281

tag: Progression Free Survival(days):2281


title: p487 sample_Ovarian tumor

tag: Gender

tag: FIGO Substage:c

tag: Histotype:clear cells

tag: Overall Survival(days):1794

tag: Progression Free Survival(days):1794


title: p63 sample_Ovarian tumor

tag: Overall Survival(days):3359

tag: Progression Free Survival(days):3359


title: p070 sample_Ovarian tumor

tag: Status:death related to cancer

tag: Overall Survival(days):609

tag: Progression Free Survival(days):609

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p73 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: FIGO Substage:a

tag: Overall Survival(days):2997

tag: Progression Free Survival(days):2997


title: 1750

tag: female patient, poor prednisone response, unfavorable MRD, NOTCH wild-type, no relapse within follow-up period

tag: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: p383 sample_Ovarian tumor

tag: Gender

tag: FIGO Stage:1

tag: Overall Survival(days):2093

tag: Progression Free Survival(days):2093


title: 1723


title: 1753

tag: male patient, prednisone response N/A, favorable MRD, NOTCH wild-type, no relapse within follow-up period


title: p421 sample_Ovarian tumor

tag: FIGO Substage:c

tag: Histotype:clear cells

tag: Overall Survival(days):787

tag: Progression Free Survival(days):787


title: p091 sample_Ovarian tumor

tag: Overall Survival(days):4673

tag: Progression Free Survival(days):4673


title: p459 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):1891

tag: Progression Free Survival(days):1891

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: L35

tag: male patient, poor prednisone response, MRD N/A, NOTCH wild-type,  relapse within follow-up period


title: L36

tag: male patient, good prednisone response, MRD N/A, NOTCH mutation,  relapse within follow-up period

tag: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: p401 sample_Ovarian tumor

tag: Gender

tag: FIGO Stage:1

tag: Overall Survival(days):2178

tag: Progression Free Survival(days):2178


title: 1757

tag: female patient, good prednisone response, favorable MRD, NOTCH mutation, no relapse within follow-up period


title: p320 sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):2541

tag: Progression Free Survival(days):2541


title: 1694

tag: female patient, prednisone response N/A, unfavorable MRD, NOTCH wild-type, no relapse within follow-up period


title: p331 sample_Ovarian tumor

tag: Histotype:clear cells

tag: Overall Survival(days):2682

tag: Progression Free Survival(days):2682


title: 1713

tag: male patient, good prednisone response, favorable MRD, NOTCH mutation, no relapse within follow-up period


title: 1678


title: p31 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: FIGO Substage:a

tag: Overall Survival(days):3656

tag: Progression Free Survival(days):3656

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p213 sample_Ovarian tumor

tag: Gender

tag: FIGO Stage:1

tag: Overall Survival(days):2910

tag: Progression Free Survival(days):2910


title: 1670

tag: male patient, poor prednisone response, favorable MRD, NOTCH mutation, no relapse within follow-up period

tag: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: 1640

tag: male patient, good prednisone response, MRD N/A, NOTCH wild-type, no relapse within follow-up period


title: p0114 sample_Ovarian tumor

tag: Status:in progression

tag: FIGO Substage:c

tag: Overall Survival(days):3592

tag: Progression Free Survival(days):3592


title: 1651


title: p080 sample_Ovarian tumor

tag: Status:death related to cancer

tag: Overall Survival(days):2810

tag: Progression Free Survival(days):2810


title: 1634

tag: male patient, poor prednisone response, unfavorable MRD, NOTCH wild-type, no relapse within follow-up period


title: 1599

tag: male patient, good prednisone response, favorable MRD, NOTCH mutation, no relapse within follow-up period


title: p166 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):3006

tag: Progression Free Survival(days):3006

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p171 sample_Ovarian tumor

tag: Gender

tag: FIGO Stage:1

tag: Histotype:clear cells

tag: Overall Survival(days):743

tag: Progression Free Survival(days):743


title: 1612

tag: male patient, poor prednisone response, favorable MRD, NOTCH mutation,  relapse within follow-up period

tag: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: 1650

tag: male patient, good prednisone response, favorable MRD, NOTCH wild-type, no relapse within follow-up period


title: 1618


title: 1669

tag: male patient, good prednisone response, unfavorable MRD, NOTCH mutation, no relapse within follow-up period


title: 1569


title: p0143 sample_Ovarian tumor

tag: FIGO Substage:b

tag: Overall Survival(days):4478

tag: Progression Free Survival(days):4478


title: p0102 sample_Ovarian tumor

tag: FIGO Substage:c

tag: Overall Survival(days):3903

tag: Progression Free Survival(days):3903


title: 1568

tag: male patient, poor prednisone response, favorable MRD, NOTCH wild-type, no relapse within follow-up period


title: p183 sample_Ovarian tumor

tag: Status:alive no evidence of disease

tag: Overall Survival(days):3045

tag: Progression Free Survival(days):3045

tag: Human Atlas high pure control total RNA extracted from a pool of 60 human cell lines (BD Biosciences)


title: p0217 sample_Ovarian tumor

tag: Gender

tag: Status:death related to cancer

tag: FIGO Stage:1

tag: Overall Survival(days):2248

tag: Progression Free Survival(days):2248


title: 1514

tag: female patient, good prednisone response, unfavorable MRD, NOTCH wild-type, no relapse within follow-up period

tag: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: 1553

tag: female patient, poor prednisone response, unfavorable MRD, NOTCH wild-type, no relapse within follow-up period


title: p0208 sample_Ovarian tumor

tag: Status:death unrelated to cancer

tag: Overall Survival(days):2788

tag: Progression Free Survival(days):2788


title: 1523

tag: male patient, good prednisone response, unfavorable MRD, NOTCH wild-type, no relapse within follow-up period


title: p0125 sample_Ovarian tumor

tag: FIGO Substage:a

tag: Overall Survival(days):4176

tag: Progression Free Survival(days):4176


title: 1667

tag: male patient, good prednisone response, favorable MRD, NOTCH wild-type, no relapse within follow-up period


title: 1475

tag: male patient, poor prednisone response, unfavorable MRD, NOTCH wild-type, no relapse within follow-up period


title: 1489

tag: female patient, good prednisone response, MRD N/A, NOTCH wild-type, no relapse within follow-up period


title: 1474


title: 1521

tag: male patient, good prednisone response, favorable MRD, NOTCH mutation, no relapse within follow-up period


title: 1455

tag: male patient, good prednisone response, unfavorable MRD, NOTCH mutation, no relapse within follow-up period


title: 1447


title: 1435


title: 1473

tag: male patient, prednisone response N/A, favorable MRD, NOTCH wild-type, no relapse within follow-up period


title: 1402


title: 1381


title: 1429


title: 1410


title: 1405

tag: female patient, prednisone response N/A, favorable MRD, NOTCH mutation, no relapse within follow-up period


title: Staphylococcus aureus_Triclosan_60min_replicate4

city: ft. meade

first: Hyeung-Jin

last: Jang

state: MD

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

description: Triclosan treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 500)

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.2

label: Biotin

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_Triclosan

label_protocol: Approximately 12 µg of total RNA was processed to produce biotinylated cDNA targets.

growth_protocol: (i) we initiated S. aureus cultures at 37°C with shaking at 250 rpm using sterilized Luria-Bertani (LB) broth, (ii) after 17 hours, we diluted the overnight cultures 1:100 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm until OD600 reached the early logarithmic phase (~ 0.8), and (iii) we re-diluted the cells 1:10 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm.  Then, we added 0.045 mM triclosan immediately after OD600 reached 0.8.

extract_protocol: Total RNA was isolated after 60 min incubation with triclosan using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.

treatment_protocol: Triclosan (0.045 mM)

tag: NCTC 8325 Wild type


title: 1260

tag: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: Staphylococcus aureus_Triclosan_60min_replicate5

description: Triclosan treatment


title: 1430

tag: male patient, poor prednisone response, favorable MRD, NOTCH mutation, no relapse within follow-up period


title: 1434


title: 1449

tag: male patient, prednisone response N/A, unfavorable MRD, NOTCH wild-type,  relapse within follow-up period


title: 1253

tag: male patient, poor prednisone response, MRD N/A, NOTCH wild-type, no relapse within follow-up period


title: Staphylococcus aureus_Triclosan_10min_replicate5

description: Triclosan treatment

extract_protocol: Total RNA was isolated after 10 min incubation with triclosan using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.


title: 1295


title: 1262


title: 1170


title: Staphylococcus aureus_Triclosan_60min_replicate1

description: Triclosan treatment


title: Staphylococcus aureus_Triclosan_60min_replicate3

description: Triclosan treatment


title: 1178

tag: female patient, good prednisone response, favorable MRD, NOTCH wild-type, no relapse within follow-up period


title: 1201

tag: female patient, poor prednisone response, MRD N/A, NOTCH wild-type, no relapse within follow-up period


title: Staphylococcus aureus_Triclosan_10min_replicate4

description: Triclosan treatment


title: Staphylococcus aureus_Triclosan_60min_replicate2

description: Triclosan treatment


title: Staphylococcus aureus_Triclosan_10min_replicate3

description: Triclosan treatment


title: 1225


title: Staphylococcus aureus_Triclosan_10min_replicate1

description: Triclosan treatment


title: Staphylococcus aureus_Triclosan_10min_replicate2

description: Triclosan treatment


title: Staphylococcus aureus_no treatment_0min_replicate5

description: No treatment

source_name: Staphylococcus aureus_no treatment

growth_protocol: (i) we initiated S. aureus cultures at 37°C with shaking at 250 rpm using sterilized Luria-Bertani (LB) broth, (ii) after 17 hours, we diluted the overnight cultures 1:100 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm until OD600 reached the early logarithmic phase (~ 0.8), and (iii) we re-diluted the cells 1:10 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm.

extract_protocol: Total RNA was isolated at 0 min after OD600 reached 0.8 using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.


title: Staphylococcus aureus_no treatment_0min_replicate4

description: No treatment


title: Staphylococcus aureus_no treatment_0min_replicate3

description: No treatment


title: Staphylococcus aureus_no treatment_0min_replicate2

description: No treatment


title: 1134

tag: female patient, poor prednisone response, unfavorable MRD, NOTCH wild-type,  relapse within follow-up period


title: 1115


title: 1114


title: 1168

tag: female patient, good prednisone response, favorable MRD, NOTCH mutation, no relapse within follow-up period


title: 1162


title: Staphylococcus aureus_no treatment_0min_replicate1

description: No treatment


title: PASMC_atorvastatin_rep3

status: Public on Aug 23 2007

city: Little Rock

first: Marjan

last: Boerma

state: AR

address: 4301 West Markham, Slot 725

institute: University of Arkansas for Medical Sciences

description: This sample is number 3 of 3 repeats.

hyb_protocol: 1.5 μg of biotin-labeled aRNA was hybridized to Illumina Human Ref-6 v1 BeadChips at 58 °C overnight. BeadChips were incubated with Cy3 streptavidin and washed according to the manufacturer’s instructions.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina’s BeadStudio v1.5.1.3. aRNA synthesis, hybridization and scanning were performed by the Microarray Core Laboratory of the University of Texas Health Science Center.

data_processing: Initial analysis was done using Illumina’s Beadstudio v1.5.1.3. The array was normalized to sample GSM214810 by rank-invariant method.

label: biotin

source_name: Human Pulmonary Artery Smooth Muscle Cells, atorvastatin treated 24 h

label_protocol: 200 ng of total RNA was reverse transcribed and amplified overnight with T7 RNA polymerase and labeled with biotin following the manufacturer’s protocol.

growth_protocol: Human pulmonary artery smooth muscle cells (PASMC; CC-25841, Cambrex) were cultured in SmGM-2 BulletKit medium, containing smooth muscle basal medium, hEGF, hFGF-B, insulin, gentamicin, amphotericin-B, and 5% FBS and maintained at 37 ºC in a humidified atmosphere of 5% CO2 and 95% air.

extract_protocol: 24 hours after treatment with atorvastatin, cells were harvested and total RNA was isolated using Ultraspec RNA isolation reagent (Biotecx Laboratories), according to the manufacturer’s instructions.

treatment_protocol: PASMC at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing 10 μM atorvastatin.

tag: Primary culture of human pulmonary artery smooth muscle cells (CC-25841)


title: Fibroblasts_vehicle_rep3

description: This sample is number 3 of 3 repeats.

source_name: Normal Human Dermal Fibroblasts, vehicle treated 24 h

growth_protocol: Normal Human Dermal Fibroblasts (NHDF; CC-2511, Cambrex) were cultured in FGM-2 BulletKit medium, containing fibroblast basal medium, hFGF-B, insulin, gentamicin, amphotericin-B, and 2% FBS and maintained at 37 ºC in a humidified atmosphere of 5% CO2 and 95% air.

extract_protocol: 24 hours after treatment with vehicle, cells were harvested and total RNA was isolated using Ultraspec RNA isolation reagent (Biotecx Laboratories), according to the manufacturer’s instructions.

treatment_protocol: NHDF at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing vehicle (10 μl sterile PBS).

tag: Primary culture of normal human dermal fibroblasts (CC-2511)


title: 1069


title: PASMC_atorvastatin_rep2

description: This sample is number 2 of 3 repeats.


title: Fibroblasts_atorvastatin_mevalonate_rep2

description: This sample is number 2 of 3 repeats.

source_name: Normal Human Dermal Fibroblasts, atorvastatin and mevalonate treated 24 h

extract_protocol: 24 hours after treatment with atorvastatin and mevalonate, cells were harvested and total RNA was isolated using Ultraspec RNA isolation reagent (Biotecx Laboratories), according to the manufacturer’s instructions.

treatment_protocol: NHDF at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing a combination of 10 μM atorvastatin and 500 μM mevalonate.


title: PASMC_atorvastatin_mevalonate_rep2

description: This sample is number 2 of 3 repeats.

source_name: Human Pulmonary Artery Smooth Muscle Cells, atorvastatin and mevalonate treated 24 h

treatment_protocol: PASMC at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing a combination of 10 μM atorvastatin and 500 μM mevalonate.


title: Fibroblasts_atorvastatin_rep2

description: This sample is number 2 of 3 repeats.

source_name: Normal Human Dermal Fibroblasts, atorvastatin treated 24 h

treatment_protocol: NHDF at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing 10 μM atorvastatin.


title: Fibroblasts_SLx2119_rep3

description: This sample is number 3 of 3 repeats.

source_name: Normal Human Dermal Fibroblasts, SLx-2119 treated 24 h

extract_protocol: 24 hours after treatment with SLx-2119, cells were harvested and total RNA was isolated using Ultraspec RNA isolation reagent (Biotecx Laboratories), according to the manufacturer’s instructions.

treatment_protocol: NHDF at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing 40 μM SLx-2119 (a small molecule ROCK-2 inhibitor).


title: HMVEC_atorvastatin_rep2

description: This sample is number 2 of 3 repeats.

source_name: Human Microvascular Endothelial Cells, atorvastatin treated 24 h

growth_protocol: Human microvascular EC (HMVEC; CC-2527, Cambrex) were cultured in EGM-2 MV BulletKit medium, containing endothelial cell basal medium-2, human epidermal growth factor (hEGF), hydrocortisone, human basal fibroblast growth factor (hFGF-B), vascular endothelial growth factor, recombinant insulin-like growth factor 1, ascorbic acid, gentamicin, amphotericin-B, and 5% fetal bovine serum (FBS) and maintained at 37 ºC in a humidified atmosphere of 5% CO2 and 95% air.

treatment_protocol: HMVEC at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing 10 μM atorvastatin.

tag: Primary culture of human lung microvascular endothelial cells (CC-2527)


title: Fibroblasts_vehicle_rep1

description: This sample is number 1 of 3 repeats.


title: Fibroblasts_SLx2119_rep1

description: This sample is number 1 of 3 repeats.


title: PASMC_SLx2119_rep1

description: This sample is number 1 of 3 repeats.

source_name: Human Pulmonary Artery Smooth Muscle Cells, SLx-2119 treated 24 h

extract_protocol: 24 hours after treatment with SLX-2119, cells were harvested and total RNA was isolated using Ultraspec RNA isolation reagent (Biotecx Laboratories), according to the manufacturer’s instructions.

treatment_protocol: PASMC at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing 40 μM SLX-2119 (ROCK-2 inhibitor).


title: PASMC_atorvastatin_mevalonate_rep3

description: This sample is number 3 of 3 repeats.


title: PASMC_SLx2119_rep3

description: This sample is number 3 of 3 repeats.

treatment_protocol: PASMC at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing 40 μM SLX-2119 (small molecule ROCK-2 inhibitor).


title: Fibroblasts_atorvastatin_rep3

description: This sample is number 3 of 3 repeats.


title: Fibroblasts_atorvastatin_mevalonate_rep1

description: This sample is number 1 of 3 repeats.


title: Fibroblasts_atorvastatin_mevalonate_rep3

description: This sample is number 3 of 3 repeats.


title: Fibroblasts_SLx2119_rep2

description: This sample is number 2 of 3 repeats.


title: PASMC_atorvastatin_mevalonate_rep1

description: This sample is number 1 of 3 repeats.


title: PASMC_vehicle_rep3

description: This sample is number 3 of 3 repeats.

source_name: Human Pulmonary Artery Smooth Muscle Cells, vehicle treated 24 h

label_protocol: 200 ng of total RNA was reverse transcribed and amplified overnight with T7 RNA polymerase and labeled with biotin following the manufacturer’s protocol

treatment_protocol: PASMC at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing vehicle (10 μl sterile PBS).


title: PASMC_atorvastatin_rep1

description: This sample is number 1 of 3 repeats.


title: Fibroblasts_atorvastatin_rep1

description: This sample is number 1 of 3 repeats.


title: Fibroblasts_vehicle_rep2

description: This sample is number 2 of 3 repeats.


title: PASMC_SLx2119_rep2

description: This sample is number 2 of 3 repeats.


title: PASMC_vehicle_rep1

description: This sample is number 1 of 3 repeats.


title: HMVEC_atorvastatin_mevalonate_rep3

description: This sample is number 3 of 3 repeats

source_name: Human Microvascular Endothelial Cells, atorvastatin and mevalonate treated 24h

growth_protocol: Human microvascular endothelial cells (HMVEC;CC-2527, Cambrex) were cultured in EGM-2 MV BulletKit medium, containing endothelial cell basal medium-2, human epidermal growth factor (hEGF), hydrocortisone, human basal fibroblast growth factor (hFGF-B), vascular endothelial growth factor, recombinant insulin-like growth factor 1, ascorbic acid, gentamicin, amphotericin-B, and 5% fetal bovine serum (FBS) and maintained at 37 ºC in a humidified atmosphere of 5% CO2 and 95% air.

treatment_protocol: HMVEC at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing a combination of 10 μM atorvastatin and 500 μM mevalonate.


title: Z138/rep2

city: Madrid

first: Antonio

last: Ruiz-Vela

state: Madrid

address: Melchor Fernández Almagro

country: Spain

institute: CNIO

description: The raw image was processed using Feature Extraction 9.1 (Agilent Technologies).

hyb_protocol: Hybridization was performed as indicated (in Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent Technologies) on single glass slides containing 41,000 human unique genes in high-density

scan_protocol: Slides were scanned on a microarray scanner (Agilent Technologies, model G2505B)

data_processing: Gene expression data were further pre-processed using GEPAS tools (http://gepas.bioinfo.cipf.es/).  Changes in gene expression were estimated using the Preprocessing tool by imputing missing values as zeros.

source_name: MCL1 over-expressing Z-138 B-cells

label_protocol: 2 μg of RNA was amplified, labeled and complimentary RNA (cRNA) generated according to manufacturer’s instructions (Low RNA Input Linear Amplification Kit, Agilent Technologies). Preparation of cyanine 3-CTP and cyanine 5-CTP labeled cRNA were purified according to manufacturer’s instructions (Two-Color Microarray-Based Gene Expression Analysis Protocol, http://www.chem.agilent.com/scripts/literaturepdf.asp?iWHID=48835) and quantified using an Agilent-2100 Bioanalyzer.

extract_protocol: Total RNA was extracted from frozen cell pellets following manufacturer’s instructions (RNeasy mini kit, Qiagen). Yields from 10E7 cells were in the range of 250 μg of total RNA. RNA quality was further evaluated using an Agilent-2100 Bioanalyzer (Agilent Technologies).

tag: MCL1 over-expressing

source_name: Empty vector/Z-138 B-cells

tag: Empty vector


title: PASMC_vehicle_rep2

description: This sample is number 2 of 3 repeats.


title: RAMOS RA-1/rep2

source_name: MCL1 over-expressing RAMOS RA-1

source_name: Empty vector/RAMOS RA-1


title: HMVEC_atorvastatin_rep1

description: This sample is number 1 of 3 repeats.


title: Z138/rep1


title: HMVEC_vehicle_rep3

description: This sample is number 3 of 3 repeats.

source_name: Human Microvascular Endothelial Cells, vehicle treated 24 h

treatment_protocol: HMVEC at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing vehicle (10 μl sterile PBS).


title: HMVEC_SLx2119_rep3

description: This sample is number 3 of 3 repeats.

source_name: Human Microvascular Endothelial Cells, SLx-2119 treated 24 h

treatment_protocol: HMVEC at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture medium containing 40 µM SLx-2119 (small molecule ROCK-2 inhibitor).


title: RAMOS RA-1/rep1


title: HMVEC_vehicle_rep2

description: This sample is number 2 of 3 repeats.


title: HMVEC_SLx2119_rep2

description: This sample is number 2 of 3 repeats.

tag: Primary cultures of human lung microvascular endothelial cells (CC-2527)


title: HMVEC_atorvastatin_rep3

description: This sample is number 3 of 3 repeats.


title: HMVEC_SLx2119_rep1

description:
This sample is number 1 of 3 repeats.
Please note: The background of this array was 5 times higher than the background of the other arrays in the series. After background subtraction, values are still more than twice as high as values of the other arrays. We therefore excluded this sample from our subsequent analyses.


title: HMVEC_atorvastatin_mevalonate_rep2

description: This sample is number 2 of 3 repeats

source_name: Human Microvascular Endothelial Cells, atorvastatin and mevalonate treated 24 h


title: HMVEC_atorvastatin_mevalonate_rep1

description: This sample is number 1 of 3 repeats


title: HMVEC_vehicle_rep1

description: This sample is the first of 3 replicates.

hyb_protocol: 1.5 microgram of biotin-labeled aRNA was hybridized to Illumina Human Ref-6 v1 BeadChips at 58 °C overnight. BeadChips were incubated with Cy3 streptavidin and washed according to the manufacturer’s protocol.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. aRNA synthesis, hybridization and scanning were performed by the Microarray Core Laboratory of the University of Texas Health Science Center.

data_processing: Initial analysis was done using Illumina’s Beadstudio version 1.5.1.3. This array was used as "reference array" for normalization by rank-invariant method.

label_protocol: Two hundred ng of total RNA was reverse transcribed and amplified overnight with T7 RNA polymerase and labeled with biotin following the manufacturer’s protocol.

extract_protocol: 24 hours after treatment with the vehicle cells were harvested and total RNA was isolated using Ultraspec RNA isolation reagent (Biotecx Laboratories), according to the manufacturer’s instructions.

treatment_protocol: HMVEC at passage 7 were plated in 6 cm culture dishes with 3 ml culture medium, at a density of 1,000,000 cells/dish. After 2 days (confluence 90%) the cells were incubated for 24 hours in 3 ml culture media containing vehicle (10 μl sterile PBS).


title: Human HeLaS3 cells, E2F4 Replicate C

status: Public on Aug 22 2007

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

description: Human HeLaS3 cells

hyb_protocol: Cy-labedled ChIP Samples

scan_protocol: NimbleScan

data_processing: log base 2 ratios

source_name: HeLaS3 cells

label_protocol: Cy5 dye

extract_protocol: ChIP-chip

tag: E2F4 antibody

label_protocol: Cy3 dye

tag: control total input


title: Human Ntera2 cells, H3me3K27 Replicate D

description: Human Ntera2 cells

source_name: Ntera2 cells

tag: H3me3K27 antibody


title: Human Ntera2 cells, E2F6 Replicate D

description: Human Ntera2 cells

tag: E2F6 antibody


title: Human MCF7 cells, IgG Replicate A

description: Human MCF7 cells

source_name: MCF7 cells

tag: IgG antibody


title: Human HeLaS3 cells, E2F1 Replicate B

description: Human HeLaS3 cells

tag: E2F1 antibody


title: Human Ntera2 cells, H3me3K9 Replicate D

description: Human Ntera2 cells

tag: H3me3K9 antibody


title: Human MCF7 cells, E2F1 Replicate A

description: Human MCF7 cells


title: Human HeLaS3 cells, IGG Replicate B

description: Human HeLaS3 cells

tag: IGG antibody


title: Human HeLaS3 cells, IgG Replicate C

description: Human HeLaS3 cells


title: Human HeLaS3 cells, IgG Replicate A

description: Human HeLaS3 cells


title: Human HeLaS3 cells, E2F1 Replicate C

description: Human HeLaS3 cells


title: Human HeLaS3 cells, IgG Replicate B

description: Human HeLaS3 cells


title: Human HeLaS3 cells, IGG Replicate C

description: Human HeLaS3 cells


title: Human Ntera2 cells, E2F4 Replicate B

description: Human Ntera2 cells


title: Human HeLaS3 cells, E2F4 Replicate B

description: Human HeLaS3 cells


title: Human HeLaS3 cells, E2F4 Replicate A

description: Human HeLaS3 cells