title: C-lim aerobic chemostat with methionine as N-source 1

status: Public on Feb 28 2007

source_name: chemostat culture with methionine as N-source

growth_protocol:
The prototrophic S. cerevisiae strain CEN.PK113-7D (MATa) (1,2) was grown at 30°C in 1.0-liter working volume chemostats (3). Cultures were fed with a synthetic medium (4) that supported glucose-limited growth. The glucose concentration in the reservoir medium was 7.5 g·l-1. The nitrogen source was used, at the following concentration: L-methionine, 11.3 g·l-1. When an amino acid served as nitrogen source, the synthetic medium was supplemented with 6.6 g·l-l K2SO4. The dilution rate was set at 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 biocontroller. Stirrer speed was 800 rpm and the airflow was 0.5 l.min-1. Dissolved oxygen tension was measured online with an Ingold model 34 100 3002 probe, and was above 50% air saturation. A condenser connected to a cryostat set at 2 °C cooled the off-gas, and oxygen and carbon dioxide were measured off-line. Steady-state samples for arrays were taken after 10 to 14 volume changes to minimize the impact of evolutionary adaptation that occurs after long term cultivation (5,6). Dry weight, metabolite-, and gas profiles were constant over at least 3 volume changes prior to sampling for RNA extraction.
(1) van Dijken et al. 2000. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb Technol 26(9,10): 706-714.
(2) Daran-Lapujade P et al. 2003. Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays. FEMS Yeast Res 4: 285-296.
(3) van den Berg et al. 1996. The two acetyl-coenzyme A synthetases of Saccharomyces cerevisiae differ with respect to kinetic properties and transcriptional regulation. J Biol Chem 271: 28953-28959.
(4) Verduyn et al. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-17.
(5) Ferea et al. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci U S A 96: 9721-9726.
(6) Jansen et al. 2004. Prolonged maltose-limited cultivation of Saccharomyces cerevisiae selects for cells with improved maltose affinity and hypersensitivity. Appl Environ Microbiol 70: 1956-1963.

treatment_protocol: Sampling of cells from chemostats, probe preparation and hybridization to Affymetrix GeneChip® Microarrays was performed as described by Piper et al (Piper et al., 2002).


title: C-lim aerobic chemostat with leucine as N-source 3

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: [Fluidics] Protocol	EukGE-WS2v4

scan_protocol: [Scanner] Pixel Size	3 Filter	570 Number of Scans	2 Scanner Type	HP

data_processing: MAS 5.1

label: SAPE

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: chemostat culture with leucine as N-source

label_protocol: Sampling of cells from chemostats, probe preparation and hybridization to Affymetrix GeneChip® Microarrays was performed as described by Piper et al (Piper et al., 2002).

growth_protocol:
The prototrophic S. cerevisiae strain CEN.PK113-7D (MATa) (1,2) was grown at 30°C in 1.0-liter working volume chemostats (3). Cultures were fed with a synthetic medium (4) that supported glucose-limited growth. The glucose concentration in the reservoir medium was 7.5 g·l-1. The nitrogen source was used, at the following concentration: L-leucine, 10.0 g·l-1. When an amino acid served as nitrogen source, the synthetic medium was supplemented with 6.6 g·l-l K2SO4. The dilution rate was set at 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 biocontroller. Stirrer speed was 800 rpm and the airflow was 0.5 l.min-1. Dissolved oxygen tension was measured online with an Ingold model 34 100 3002 probe, and was above 50% air saturation. A condenser connected to a cryostat set at 2 °C cooled the off-gas, and oxygen and carbon dioxide were measured off-line. Steady-state samples for arrays were taken after 10 to 14 volume changes to minimize the impact of evolutionary adaptation that occurs after long term cultivation (5,6). Dry weight, metabolite-, and gas profiles were constant over at least 3 volume changes prior to sampling for RNA extraction.
(1) van Dijken et al. 2000. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb Technol 26(9,10): 706-714.
(2) Daran-Lapujade P et al. 2003. Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays. FEMS Yeast Res 4: 285-296.
(3) van den Berg et al. 1996. The two acetyl-coenzyme A synthetases of Saccharomyces cerevisiae differ with respect to kinetic properties and transcriptional regulation. J Biol Chem 271: 28953-28959.
(4) Verduyn et al. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-17.
(5) Ferea et al. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci U S A 96: 9721-9726.
(6) Jansen et al. 2004. Prolonged maltose-limited cultivation of Saccharomyces cerevisiae selects for cells with improved maltose affinity and hypersensitivity. Appl Environ Microbiol 70: 1956-1963.

tag: The prototrophic S. cerevisiae strain CEN.PK113-7D (MATa) (1)


title: C-lim aerobic chemostat with methionine as N-source 3

extract_protocol: Sampling of cells from chemostats, probe preparation and hybridization to Affymetrix GeneChip® Microarrays was performed as described by Piper et al (Piper et al., 2002).

tag: (1) van Dijken et al. 2000. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb Technol 26(9,10)


title: C-lim aerobic chemostat with methionine as N-source 2


title: Dicer T00312750_15773_5

status: Public on Mar 24 2007

city: Houston

first: Ankang

last: Li

state: TX

address: 2121 West Holcombe

department: CMDD

country: USA

institute: IBT

description: Dicer mutant experimental group

hyb_protocol: CodeLink Expression Assay protocol

scan_protocol: CodeLink Expression Assay protocol

data_processing: GeneSpring analysis

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Dicer mutant embryonic heart

label_protocol: CodeLink Expression Assay protocol

extract_protocol: For RNA isolation, embryonic heart was dissected out and lysed using QiaShredder. RNA was isolated using RNeasy micro columns following the manufacturer's instructions, and including an on-column DNase digestion step.

tag: embryonic day 11.5 heart


title: Dicer T00312746_15605_2

description: Dicer mutant experimental group


title: 275_p_1

status: Public on Apr 30 2007

city: Chiba

first: Shuhei

last: Noda

state: Chiba

address: Anagawa 4-9-1

department: Frontier research center

country: Japan

institute: National institute of radiological sciences

description: prior to treatment, radiotherapy alone

data_processing: global median normalization

organism: Homo sapiens

source_name: biopsy

tag: female, cervical cancer


title: 1988_p_2

description: prior to treatment, radiotherapy alone


title: Dicer T00312746_15452_3

description: Dicer mutant experimental group


title: 1988_p_1

description: prior to treatment, radiotherapy alone


title: Dicer T00312746_15452_5

description: control group

source_name: embryonic heart control group


title: C-lim aerobic chemostat with leucine as N-source 2


title: 2030_p_1

description: prior to treatment, chemoradiotherapy


title: 1842_p_1

description: prior to treatment, radiotherapy alone


title: Dicer T00312749_15605_6

description: control group


title: 2314_d_2

description: during treatment, radiotherapy alone


title: 783_p_1

description: prior to treatment, chemoradiotherapy


title: 2030_d_1

description: during treatment, chemoradiotherapy


title: C-lim aerobic chemostat with proline as N-source 2

source_name: chemostat culture with Proline as N-source

growth_protocol:
The prototrophic S. cerevisiae strain CEN.PK113-7D (MATa) (1,2) was grown at 30°C in 1.0-liter working volume chemostats (3). Cultures were fed with a synthetic medium (4) that supported glucose-limited growth. The glucose concentration in the reservoir medium was 7.5 g·l-1. The nitrogen source was used, at the following concentration: L-proline, 8.8 g·l-1. When an amino acid served as nitrogen source, the synthetic medium was supplemented with 6.6 g·l-l K2SO4. The dilution rate was set at 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 biocontroller. Stirrer speed was 800 rpm and the airflow was 0.5 l.min-1. Dissolved oxygen tension was measured online with an Ingold model 34 100 3002 probe, and was above 50% air saturation. A condenser connected to a cryostat set at 2 °C cooled the off-gas, and oxygen and carbon dioxide were measured off-line. Steady-state samples for arrays were taken after 10 to 14 volume changes to minimize the impact of evolutionary adaptation that occurs after long term cultivation (5,6). Dry weight, metabolite-, and gas profiles were constant over at least 3 volume changes prior to sampling for RNA extraction.
(1) van Dijken et al. 2000. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb Technol 26(9,10): 706-714.
(2) Daran-Lapujade P et al. 2003. Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays. FEMS Yeast Res 4: 285-296.
(3) van den Berg et al. 1996. The two acetyl-coenzyme A synthetases of Saccharomyces cerevisiae differ with respect to kinetic properties and transcriptional regulation. J Biol Chem 271: 28953-28959.
(4) Verduyn et al. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-17.
(5) Ferea et al. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci U S A 96: 9721-9726.
(6) Jansen et al. 2004. Prolonged maltose-limited cultivation of Saccharomyces cerevisiae selects for cells with improved maltose affinity and hypersensitivity. Appl Environ Microbiol 70: 1956-1963.


title: C-lim aerobic chemostat with proline as N-source 3


title: C-lim aerobic chemostat with Proline as N-source 1


title: C-lim Anaerobic Acetate 3

status: Public on Feb 27 2007

hyb_protocol: According to manufacturer’s procedures

scan_protocol: Data acquisition was performed using the Affymetrix scanner 3000, quantification of array images and data filtering were performed with the Affymetrix software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0.

data_processing: Chip file GCOS (Affymetrix - version 1.2.0.037)

source_name: Chemostat sample

label_protocol:
Sampling of chemostat cultures, probe preparation and hybridization to Affymetrix GeneChip microarrays was performed as described previously (Piper et al., 2002), but with the following modifications.  Double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix).  The double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix).  Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA.
Piper MDW, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J & Pronk JT (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277: 37001-37008.

growth_protocol:
The laboratory reference strain CEN.PK 113-7D (MATa) was grown at 30 °C in 2-L chemostat fermentors (Applikon, Schiedam, The Netherlands) with a working volume of 1-L using an electronic level sensor to maintain a constant volume.  All cultures, including the reference, were fed with minimal medium as described by Verduyn et al. (1992) with 25 g L-1 glucose as the limiting nutrient and 0.15 ml L-1 silicone antifoam (BDH, Poole, England) to prevent excessive foaming.  The dilution rate was set to 0.10 h-1 and the pH was controlled at 5.0 with the automatic addition (ADI 1031 bio controller, Applikon) of 2 M KOH.  The stirrer speed was set at 800 RPM and anaerobicity was maintained by sparging the fermentor with N2 gas at 500 ml min-1.  To prevent diffusion of oxygen, the fermentor was equipped with Norprene tubing and Viton O-rings and the medium vessel was also flushed with N2 gas.  A comparable degree of weak acid uncoupling was ensured by decreasing the biomass yield to approximately 50% of the reference condition (no organic acids added) with the addition of the appropriate concentration of acetic acid, sodium benzoate, propionic acid or potassium sorbate to the reservoir media.
Verduyn C, Postma E, Scheffers WA & van Dijken JP (1992) Effect of benzoic acid on metabolic fluxes in yeast: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-517.

extract_protocol:
Sampling of chemostat cultures and probe preparation was performed as described previously (Piper et al., 2002).
Piper MDW, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J & Pronk JT (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277: 37001-37008.

treatment_protocol: N2 quenching

tag: Saccharomyces cerevisiae CENPK1137D (Mata)


title: C-lim Anaerobic Propionate 2

tag: Saccharomyces cerevisiae CENPK113-7D (MATa)


title: C-lim Anaerobic Benzoate 2


title: C-lim aerobic chemostat with ASN as N-source 2

source_name: chemostat culture with ASN as N-source

growth_protocol:
The prototrophic S. cerevisiae strain CEN.PK113-7D (MATa) (1,2) was grown at 30°C in 1.0-liter working volume chemostats (3). Cultures were fed with a synthetic medium (4) that supported glucose-limited growth. The glucose concentration in the reservoir medium was 7.5 g·l-1. The nitrogen source was used, at the following concentration: L-asparagine, 5.0 g·l-1. When an amino acid served as nitrogen source, the synthetic medium was supplemented with 6.6 g·l-l K2SO4. The dilution rate was set at 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 biocontroller. Stirrer speed was 800 rpm and the airflow was 0.5 l.min-1. Dissolved oxygen tension was measured online with an Ingold model 34 100 3002 probe, and was above 50% air saturation. A condenser connected to a cryostat set at 2 °C cooled the off-gas, and oxygen and carbon dioxide were measured off-line. Steady-state samples for arrays were taken after 10 to 14 volume changes to minimize the impact of evolutionary adaptation that occurs after long term cultivation (5,6). Dry weight, metabolite-, and gas profiles were constant over at least 3 volume changes prior to sampling for RNA extraction.
(1) van Dijken et al. 2000. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb Technol 26(9,10): 706-714.
(2) Daran-Lapujade P et al. 2003. Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays. FEMS Yeast Res 4: 285-296.
(3) van den Berg et al. 1996. The two acetyl-coenzyme A synthetases of Saccharomyces cerevisiae differ with respect to kinetic properties and transcriptional regulation. J Biol Chem 271: 28953-28959.
(4) Verduyn et al. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-17.
(5) Ferea et al. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci U S A 96: 9721-9726.
(6) Jansen et al. 2004. Prolonged maltose-limited cultivation of Saccharomyces cerevisiae selects for cells with improved maltose affinity and hypersensitivity. Appl Environ Microbiol 70: 1956-1963.


title: C-lim Anaerobic Acetate 1

scan_protocol: Data acquisition, quantification of array images and data filtering were performed with the Affymetrix software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0.

tag: Saccharomyces cerevisiae CENPK113-7D (Mata)


title: C-lim aerobic chemostat with ASN as N-source 1


title: C-lim Anaerobic Sorbate 2


title: C-lim Anaerobic Sorbate 3


title: C-lim Anaerobic Benzoate 1


title: C-lim Anaerobic Acetate 2


title: C-lim aerobic chemostat with ASN as N-source 3


title: C-lim Anaerobic Propionate 3

tag: Sacccharomyces cerevisiae CENPK113-7D (MATa)


title: C-lim Anaerobic Benzoate 3

source_name: chemostat sample


title: MPTP at day 25, biological rep3

status: Public on Feb 13 2007

city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

description: Prefrontal cortex of MPTP treated macaque at 25 days, replicate 3.

hyb_protocol: According to the manufacturer's instructions.

scan_protocol: At 3-Am resolution using the GeneChip System confocal scanner (Hewlett-Packard, Santa Clara, CA) with a 488-nm emission and detection at 70 nm, controlled by Affymetrix Microarray Suite 5.0 (Affymetrix).

data_processing: Raw

label: Biotin

organism: Macaca fascicularis

source_name: MPTP treated macaque prefrontal cortex

label_protocol: According to the standard protocol outlined in the Affymetrix GeneChip Expression Analysis Technical Manual

growth_protocol: Animals were housed in individual primate cages under controlled conditions of humidity (50 F 5%), temperature (24 F 18C) and light (12h light/12h dark cycles, time lights on 8:00 am), food and water were available ad libitum and animal care was supervised by veterinarians skilled in the healthcare and maintenance of nonhuman primates. Experiments were carried out in accordance with European Communities Council Directive of 24 November 1986 (86/609/EEC) for care of laboratory animals.

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

treatment_protocol: Treated daily (9:00 am) with MPTP hydrochloride (0.2 mg/kg, i.v., Sigma, St. Louis, MO) dissolved in saline.  Sacrificed in ketamine anesthesia by sodium pentobarbital overdose

tag: State

value: Symptomatic

tag: Tissue

value: Prefrontal cortex

tag: Treatment

value: daily MPTP injections


title: MPTP at day 25, biological rep2

description: Prefrontal cortex of MPTP treated macaque at 25 days, replicate 2.


title: Saline, replicate 2

description: Prefrontal cortex of macaque, saline treatment, replicate 2.

source_name: Saline treated macaque prefrontal cortex

value: Presymptomatic

value: Saline


title: Saline, replicate 3

description: Prefrontal cortex of macaque, saline treatment, replicate 3.


title: C-lim Anaerbic Sorbate 1

tag: Saccharomyces cerevisie CENPK113-7D (MATa)


title: Control, replicate 1

description: Prefrontal cortex of macaque, replicate 1.

source_name: Untreated macaque prefrontal cortex


title: Control, replicate 2

description: Prefrontal cortex of macaque, replicate 2.

value: Untreated


title: C-lim aerobic chemostat with leucine as N-source 1


title: Saline, replicate 1

description: Prefrontal cortex of macaque, saline treatment, replicate 1.


title: Control, replicate 3

description: Prefrontal cortex of macaque, replicate 3.


title: MPTP at day 6, biological rep2

description: Prefrontal cortex of MPTP treated macaque at 6 days, replicate 2.

source_name: MPTP treated macaque


title: MPTP at day 12, biological rep4

description: Prefrontal cortex of MPTP treated macaque at 12 days, replicate 4.


title: MPTP at day 25, biological rep1

description: Prefrontal cortex of MPTP treated macaque at 25 days, replicate 1.


title: MPTP at day 6, biological rep1

description: Prefrontal cortex of MPTP treated macaque at 6 days, replicate 1.


title: MPTP at day 6, biological rep4

description: Prefrontal cortex of MPTP treated macaque at 6 days, replicate 4.


title: MPTP at day 12, biological rep1

description: Prefrontal cortex of MPTP treated macaque at 12 days, replicate 1.


title: C-lim Anaerobic Propionate 1


title: 12C anaerobic N-lim chemostat 0.03h-1 (2)

status: Public on Jan 20 2007

hyb_protocol: Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip® microarrays were preformed as described previously in {Piper, 2002}. RNA quality was determined using the Agilent 2100 Bioanalyser. The results for each growth condition were derived from three independently cultured replicates. Data acquisition and analysis as well as statistical analysis were performed as described previously in {Tai, 2005}. Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008. Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.

scan_protocol: Affymetrix scanner 3000

data_processing: GCOS

source_name: 12C anaerobic N-lim chemostat

growth_protocol:
The S. cerevisiae prototrophic haploid reference strain CEN.PK113-7D (MATa) was grown at a dilution rate (D) of 0.03 h-1 at 12oC in 2-liter chemostats (Applikon, Schiedam, The Netherlands) with a working volume of 1.0 liter as described in {van den Berg, 1996;Tai, 2005}. A temperature probe connected to a cryostat controlled cultures grown at 12oC. Cultures were grown in a defined synthetic medium that was limited by nitrogen with all other growth requirements in excess as described by {Tai, 2005}. The dilution rate was set at 0.03 hr-1 with pH measured online and kept constant at 5.0 by automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The stirrer speed was set to 600 rpm. Anaerobic growth and steady state conditions were maintained as described {Tai, 2005}. Biomass dry weight, metabolite, dissolved oxygen, and gas profiles were constant at least three volume changes prior to sampling.
Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.
van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T. & Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953-28959.

treatment_protocol: Culture quenched in liquid nitrogen


title: MPTP at day 12, biological rep2

description: Prefrontal cortex of MPTP treated macaque at 12 days, replicate 2.


title: 30C anaerobic N-lim chemostat 0.03h-1 (3)

source_name: 30C anaerobic N-lim chemostat

label_protocol:
Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip® microarrays were preformed as described previously in {Piper, 2002}. RNA quality was determined using the Agilent 2100 Bioanalyser. The results for each growth condition were derived from three independently cultured replicates. Data acquisition and analysis as well as statistical analysis were performed as described previously in {Tai, 2005}.
Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008.
Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.

growth_protocol:
The S. cerevisiae prototrophic haploid reference strain CEN.PK113-7D (MATa) was grown at a dilution rate (D) of 0.03 h-1 at 30oC in 2-liter chemostats (Applikon, Schiedam, The Netherlands) with a working volume of 1.0 liter as described in {van den Berg, 1996;Tai, 2005}. A temperature probe connected to a cryostat controlled cultures grown at 30oC. Cultures were grown in a defined synthetic medium that was limited by nitrogen with all other growth requirements in excess as described by {Tai, 2005}. The dilution rate was set at 0.03 hr-1 with pH measured online and kept constant at 5.0 by automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The stirrer speed was set to 600 rpm. Anaerobic growth and steady state conditions were maintained as described {Tai, 2005}. Biomass dry weight, metabolite, dissolved oxygen, and gas profiles were constant at least three volume changes prior to sampling.
Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.
van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T. & Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953-28959.


title: 12C anaerobic C-lim chemostat 0.03h-1 (3)

source_name: 12C anaerobic C-lim chemostat

growth_protocol:
The S. cerevisiae prototrophic haploid reference strain CEN.PK113-7D (MATa) was grown at a dilution rate (D) of 0.03 h-1 at both 12oC in 2-liter chemostats (Applikon, Schiedam, The Netherlands) with a working volume of 1.0 liter as described in {van den Berg, 1996;Tai, 2005}. A temperature probe connected to a cryostat controlled cultures grown at 12oC. Cultures were grown in a defined synthetic medium that was limited by carbon with all other growth requirements in excess as described by {Tai, 2005}. The dilution rate was set at 0.03 hr-1 with pH measured online and kept constant at 5.0 by automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The stirrer speed was set to 600 rpm. Anaerobic growth and steady state conditions were maintained as described {Tai, 2005}. Biomass dry weight, metabolite, dissolved oxygen, and gas profiles were constant at least three volume changes prior to sampling.
Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.
van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T. & Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953-28959.

extract_protocol:
Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip® microarrays were preformed as described previously in {Piper, 2002}. RNA quality was determined using the Agilent 2100 Bioanalyser. The results for each growth condition were derived from three independently cultured replicates. Data acquisition and analysis as well as statistical analysis were performed as described previously in {Tai, 2005}.
Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008.
Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.


title: 12C anaerobic N-lim chemostat 0.03h-1 (3)

tag: S. cerevisiae prototrophic haploid reference strain CEN.PK113-7D (MATa)


title: 30C anaerobic C-lim chemostat 0.03 h-1 (3)

source_name: 30C anaerobic C-lim chemostat

growth_protocol:
The S. cerevisiae prototrophic haploid reference strain CEN.PK113-7D (MATa) was grown at a dilution rate (D) of 0.03 h-1 at 30oC in 2-liter chemostats (Applikon, Schiedam, The Netherlands) with a working volume of 1.0 liter as described in {van den Berg, 1996;Tai, 2005}. A temperature probe connected to a cryostat controlled cultures grown at 30oC. Cultures were grown in a defined synthetic medium that was limited by carbon with all other growth requirements in excess as described by {Tai, 2005}. The dilution rate was set at 0.03 hr-1 with pH measured online and kept constant at 5.0 by automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The stirrer speed was set to 600 rpm. Anaerobic growth and steady state conditions were maintained as described {Tai, 2005}. Biomass dry weight, metabolite, dissolved oxygen, and gas profiles were constant at least three volume changes prior to sampling.
Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.
van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T. & Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953-28959.


title: 30C anaerobic C-lim chemostat 0.03h-1 (2)


title: 30C Anaerobic C-lim chemostat 0.03h-1 (1)

source_name: 30C Anaerobic C-lim chemostat


title: 12C anaerobic N-limitation chemostat 0.03h-1 (1)

source_name: 12C anaerobic N-limitation chemostat


title: 30C anaerobic N-lim chemostat 0.03h-1 (1)


title: 30C anaerobic N-lim chemostat 0.03h-1 (2)


title: 12C C-im anaerobic chemostat 0.03h-1 (2)

source_name: 12 degree C-lim anaerobic chemostat culture

growth_protocol:
The S. cerevisiae prototrophic haploid reference strain CEN.PK113-7D (MATa) was grown at a dilution rate (D) of 0.03 h-1 at both 12oC in 2-liter chemostats (Applikon, Schiedam, The Netherlands) with a working volume of 1.0 liter as described in {van den Berg, 1996;Tai, 2005}. A temperature probe connected to a cryostat controlled cultures grown at 12oC. Cultures were grown in a defined synthetic medium that was limited by carbon with all other growth requirements in excess as described by {Tai, 2005}. The dilution rate was set at 0.03 hr-1 with pH measured online and kept constant at 5.0 by automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The stirrer speed was set to 600 rpm. Anaerobic growth and steady state conditions were maintained as described {Tai, 2005}. Biomass dry weight, metabolite, dissolved oxygen, and gas profiles were constant at least three volume changes prior to sampling.
Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.
van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T. & Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953-28959

treatment_protocol: Culture Sample quenched in liquid nitrogen


title: 12C Chemostat anaerobic C-lim 0.03h-1 (1)

hyb_protocol: Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip® microarrays were preformed as described previously in {Piper, 2002}. RNA quality was determined using the Agilent 2100 Bioanalyser. The results for each growth condition were derived from three independently cultured replicates. Data acquisition and analysis as well as statistical analysis were performed as described previously in {Tai, 2005}. Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447. Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008.

scan_protocol: Array was scanned with the Affymetrix Scanner 3000

source_name: 12C carbon limited anaerobic Chemostat sample

label_protocol:
Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip® microarrays were preformed as described previously in {Piper, 2002 }. RNA quality was determined using the Agilent 2100 Bioanalyser. The results for each growth condition were derived from three independently cultured replicates. Data acquisition and analysis as well as statistical analysis were performed as described previously in {Tai, 2005 }.
Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.
Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008.

growth_protocol:
The S. cerevisiae prototrophic haploid reference strain CEN.PK113-7D (MATa)  was grown at a dilution rate (D) of 0.03 h-1 at both 12oC in 2-liter chemostats (Applikon, Schiedam, The Netherlands) with a working volume of 1.0 liter as described in {van den Berg, 1996;Tai, 2005}. A temperature probe connected to a cryostat controlled cultures grown at 12oC. Cultures were grown in a defined synthetic medium that was limited by carbon with all other growth requirements in excess as described by {Tai, 2005}. The dilution rate was set at 0.03 hr-1 with pH measured online and kept constant at 5.0 by automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The stirrer speed was set to 600 rpm. Anaerobic growth and steady state conditions were maintained as described {Tai, 2005}. Biomass dry weight, metabolite, dissolved oxygen, and gas profiles were constant at least three volume changes prior to sampling.
Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.
van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T. & Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953-28959.

treatment_protocol: Culture sample quenched in liquid nitrogen


title: Prostate_03-055H_GL4

status: Public on Jul 14 2006

city: Seattle

first: Denise

last: Mauldin

state: WA

address: 1100 Fairview Ave N D4-100

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: Human prostate cancer patient 03-055H with Gleason Score 4+5 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA).  The image intensity data were gridded and extracted using GenePix Pro 4.1 software.

data_processing: Log-Ratios: For each spot and in each channel (Cy3 and Cy5); the median background intensity was subtracted from the median foreground intensity. Log-ratios of cancer expression to benign expression were created by first dividing the background subtracted intensities (CaP/Benign) and then taking the log base 2. If the median background intensity was greater than the median foreground intensity, the spot was considered missing. Removal of Control Genes: The array contained approximately 400 clones used only for quality control purposes (i.e. yeast sequences or blank spots). These clones were removed from the dataset. Lowess Normalization: For each array, the log-ratio data were centered using a print-tip specific Lowess curve (Y. H. Yang, S. Dudoit, P. Luu and T. P. Speed. Normalization for cDNA Microarray Data. SPIE BiOS 2001, San Jose, California, January 2001). This curve was fit to the log intensity versus log-ratio plot using the neighboring 20.0% of the data to calculate the fit at each spot. The Lowess fit at each point was subtracted from the observed log-ratio for that spot, resulting in a normalized log-ratio. Assessing Spot Quality: Spots of poor quality, as determined by both visual inspection and GenePix Pro 4.1 quality flags were considered missing. In addition, spots with background subtracted intensity levels less than 300 were considered missing due to poorly hybridized cDNAs. Clones which were missing on > 20% of arrays were removed from the analysis. Imputation: Missing values were imputed using k-nearest neighbors imputation (k = 10) (2). The dataset was split by Gleason pattern (Grades 3, 4 and 5) and imputation was performed separately for each pattern. Average Replicated Clones: Log-ratios from the replicated cDNA spots on each PEDB chip were averaged after normalization and imputation. These average expression values were used for comparative analysis.

label_protocol: The protocol used for indirect labeling of cDNAs was a modification of a protocol described elsewhere (http://cmgm.stanford.edu/pbrown/protocols/aadUTPCouplingProcedure.htm). In brief, cDNA probes were made from 2 µg of amplified RNA in a reaction volume of 30 µl containing 5 µg random hexamer primers, 0.2 mM 5-(3-aminoallyl)-2_-deoxyuridine-5_-triphosphate (amino acid-dUTP; Sigma-Aldrich), 0.3 mM dTTP, 0.5 mM each dATP, dCTP, and dGTP, and 380 units of Superscript II reverse transcriptase (Invitrogen) incubated at 42oC for 120 minutes. After RNA hydrolysis, purified cDNA was combined with either Cy3 or Cy5 monoreactive fluors (Amersham) that covalently couple to the cDNA-incorporated aminoallyl linker in the presence of 50 mM NaHCO3 (pH 9.0). Samples were randomly labeled with either Cy3 or Cy5 dye to account for dye-bias. The coupling reaction was quenched with hydroxylamine.

extract_protocol: Following LCM, captured cells were lysed in RNA extraction buffer (Arcturus). RNA was isolated using the PicoPure RNA Isolation Kit (Arcturus) and the samples were DNAse treated using RNase-Free DNase (Qiagen). Each slide capture session lasted no longer than 20 minutes to minimize RNA degradation. The laser capture settings were: 55 mW beam, 1.5 ms pulse, 15 µm spot size. Subsequently, RNA was amplified through two rounds of linear amplification using the MessageAmp aRNA Kit (Ambion, Inc). Sample quality and quantification was assessed by agarose gel electrophoresis and absorbance at A260.

tag: Prostate Cancer patient 03-055H Gleason_Score:4+5 LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:60-69 PSA:14.0 Volume:4 Margin_Status:positive Treatment:Vit E

tag: Prostate normal adjacent from cancer patient 03-055H


title: Prostate_03-116C_GL5

description: Human prostate cancer patient 03-116C with Gleason Score 3+4 (tertiary pattern 5) prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 03-116C

tag: Prostate Cancer patient 03-116C Gleason_Score:3+4 (tertiary pattern 5)

tag: LCM_Gleason_Pattern:5 Gleason_Pattern:5 Age:60-69 PSA:6.6 Volume:5.5 Margin_Status:negative Treatment:none


title: Prostate_03-063A_GL3

description: Human prostate cancer patient 03-063A with Gleason Score 3+3 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 03-063A

tag: Prostate Cancer patient 03-063A Gleason_Score:3+3 LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:60-69 PSA:6.5 Volume:1.6 Margin_Status:negative Treatment:none


title: Control, replicate 4

description: Prefrontal cortex of macaque, replicate 4.


title: Prostate_03-115E_GL5

description: Human prostate cancer patient 03-115E with Gleason Score 4+3 (tertiary pattern 5) prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 03-115E Gleason_Score:4+3 (tertiary pattern 5)

tag: LCM_Gleason_Pattern:5 Gleason_Pattern:5 Age:70-79 PSA:5.2 Volume:4 Margin_Status:negative Treatment:none

tag: Prostate normal adjacent from cancer patient 03-115E


title: Prostate_02-209C_GL3

description: Human prostate cancer patient 02-209C with Gleason Score 3+4 (tertiary pattern 5 ) prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 02-209C Gleason_Score:3+4 (tertiary pattern 5 ) LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:50-59 PSA:8.5 Volume:5 Margin_Status:probable negative Treatment:none

tag: Prostate normal adjacent from cancer patient 02-209C


title: Prostate_03-207C_GL4

description: Human prostate cancer patient 03-207C with Gleason Score 3+4 (tertiary pattern 2) prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 03-207C Gleason_Score:3+4 (tertiary pattern 2) LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:60-69 PSA:6.9 Volume:4.8 Margin_Status:negative Treatment:fish oil

tag: Prostate normal adjacent from cancer patient 03-207C


title: Prostate_03-140B_GL3

description: Human prostate cancer patient 03-140B with Gleason Score 3+3 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 03-140B Gleason_Score:3+3 LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:50-59 PSA:5.2 Volume:0.1 Margin_Status:negative Treatment:fish oil

tag: Prostate normal adjacent from cancer patient 03-140B


title: Prostate_03-089D_GL5

description: Human prostate cancer patient 03-089D with Gleason Score 4+3 (tertiary pattern 5) prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 03-089D

tag: Prostate Cancer patient 03-089D Gleason_Score:4+3 (tertiary pattern 5)

tag: LCM_Gleason_Pattern:5 Gleason_Pattern:5 Age:60-69 PSA:13.7 Volume:1 Margin_Status:negative Treatment:selenium


title: Prostate_03-093D_GL4

description: Human prostate cancer patient 03-093D with Gleason Score 4+3 (tertiary pattern 5) prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 03-093D Gleason_Score:4+3 (tertiary pattern 5)

tag: LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:50-59 PSA:6.0 Volume:11 Margin_Status:positive Treatment:none

tag: Prostate normal adjacent from cancer patient 03-093D


title: Prostate_03-068D_GL3

description: Human prostate cancer patient 03-068D with Gleason Score 4+5 (tertiary pattern 3) prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 03-068D

tag: Prostate Cancer patient 03-068D Gleason_Score:4+5 (tertiary pattern 3) LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:60-69 PSA:5.3 Volume:8 Margin_Status:positive Treatment:no neoadjuvant


title: Prostate_03-141C_GL4

description: Human prostate cancer patient 03-141C with Gleason Score 4+3 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 03-141C

tag: Prostate Cancer patient 03-141C Gleason_Score:4+3 LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:60-69 PSA:5.7 Volume:2.3 Margin_Status:positive Treatment:none


title: Prostate_03-119D_GL3

description: Human prostate cancer patient 03-119D with Gleason Score 3+4 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 03-119D Gleason_Score:3+4 LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:70-79 PSA

value: Volume:5 Margin_Status:probable positive Treatment:none

tag: Prostate normal adjacent from cancer patient 03-119D


title: Prostate_02-053C_GL4

description: Human prostate cancer patient 02-053C with Gleason Score 3+4 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 02-053C Gleason_Score:3+4 LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:60-69 PSA:1.0 Volume:<0.1 Margin_Status:negative Treatment:none

tag: Prostate normal adjacent from cancer patient 02-053C


title: Prostate_02-003E_GL3

description: Human prostate cancer patient 02-003E with Gleason Score 3+4 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 02-003E

tag: Prostate Cancer patient 02-003E Gleason_Score:3+4 LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:60-69 PSA:5.0 Volume:1.3 Margin_Status:negative Treatment:none


title: Prostate_03-066C_GL4

description: Human prostate cancer patient 03-066C with Gleason Score 3+4 (tertiary pattern 5) prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 03-066C

tag: Prostate Cancer patient 03-066C Gleason_Score

value: 3+4 (tertiary pattern 5) LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:70-79 PSA:10.4 Volume:9 Margin_Status:positive Treatment:none


title: Prostate_04-023C_GL5

description: Human prostate cancer patient 04-023C with Gleason Score 4+3 (tertiary pattern 5) prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 04-023C

tag: Prostate Cancer patient 04-023C Gleason_Score:4+3 (tertiary pattern 5)

tag: LCM_Gleason_Pattern:5 Gleason_Pattern:5 Age:60-69 PSA:14.0 Volume:24 Margin_Status:positive Treatment:none


title: Prostate_03-068D_GL5

tag: Prostate Cancer patient 03-068D Gleason_Score:4+5 (tertiary pattern 3)

tag: LCM_Gleason_Pattern:5 Gleason_Pattern:5 Age:60-69 PSA:5.3 Volume:8 Margin_Status:positive Treatment:no neoadjuvant


title: Prostate_03-029B_GL3

description: Human prostate cancer patient 03-029B with Gleason Score 3+4 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 03-029B Gleason_Score:3+4 LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:50-59 PSA:3.7 Volume:2.6 Margin_Status:negative Treatment:none

tag: Prostate normal adjacent from cancer patient 03-029B


title: Prostate_03-184C_GL5

description: Human prostate cancer patient 03-184C with Gleason Score 5+4 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 03-184C

tag: Prostate Cancer patient 03-184C Gleason_Score:5+4 LCM_Gleason_Pattern:5 Gleason_Pattern:5 Age:50-59 PSA:6.5 Volume:4 Margin_Status:negative Treatment:none


title: Prostate_03-115E_GL4

tag: Prostate normal adjacent from cancer patient 03-115E

tag: Prostate Cancer patient 03-115E Gleason_Score:4+3 (tertiary pattern 5)

tag: LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:70-79 PSA:5.2 Volume:4 Margin_Status:negative Treatment:none


title: Prostate_03-152A_GL5

description: Human prostate cancer patient 03-152A with Gleason Score 5+4 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 03-152A

tag: Prostate Cancer patient 03-152A Gleason_Score:5+4 LCM_Gleason_Pattern:5 Gleason_Pattern:5 Age:60-69 PSA:9.0 Volume:8 Margin_Status:positive Treatment:Vit E


title: Prostate_03-015F_GL3

description: Human prostate cancer patient 03-015F with Gleason Score 3+3 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 03-015F

tag: Prostate Cancer patient 03-015F Gleason_Score:3+3 LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:50-59 PSA:7.1 Volume:4.5 Margin_Status:positive Treatment:no neoadjuvant


title: Prostate_03-159_GL4

description: Human prostate cancer patient 03-159 with Gleason Score 3+4 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 03-159 Gleason_Score:3+4 LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:60-69 PSA:4.7 Volume:3 Margin_Status:positive Treatment:none

tag: Prostate normal adjacent from cancer patient 03-159


title: Prostate_04-030A_GL4

description: Human prostate cancer patient 04-030A with Gleason Score 3+4 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 04-030A

tag: Prostate Cancer patient 04-030A Gleason_Score:3+4 LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:60-69 PSA:15.9 Volume:2.6 Margin_Status:negative Treatment:none


title: Prostate_03-021F_GL3

description: Human prostate cancer patient 03-021F with Gleason Score 3+4 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 03-021F Gleason_Score:3+4 LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:40-49 PSA:9.3 Volume:3.5 Margin_Status:positive Treatment:selenium

tag: Prostate normal adjacent from cancer patient 03-021F


title: Prostate_03-060A_GL3

description: Human prostate cancer patient 03-060A with Gleason Score 4+3 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 03-060A Gleason_Score:4+3 LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:70-79 PSA:6.9 Volume:2.5 Margin_Status:positive Treatment:none

tag: Prostate normal adjacent from cancer patient 03-060A


title: Prostate_03-066C_GL3

tag: Prostate normal adjacent from cancer patient 03-066C

tag: Prostate Cancer patient 03-066C Gleason_Score:3+4 (tertiary pattern 5)

tag: LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:70-79 PSA:10.4 Volume:9 Margin_Status:positive Treatment:none


title: Prostate_03-143C_GL5

description: Human prostate cancer patient 03-143C with Gleason Score 4+3 (tertiary pattern 5) prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 03-143C Gleason_Score:4+3 (tertiary pattern 5)

tag: LCM_Gleason_Pattern:5 Gleason_Pattern:5 Age:40-49 PSA:3.7 Volume:2.2 Margin_Status:negative Treatment:none

tag: Prostate normal adjacent from cancer patient 03-143C


title: Prostate_03-155C_GL4

description: Human prostate cancer patient 03-155C with Gleason Score 4+4 (tertiary pattern 3) prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 03-155C

tag: Prostate Cancer patient 03-155C Gleason_Score:4+4 (tertiary pattern 3)

tag: LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:60-69 PSA:6.2 Volume:4.5 Margin_Status:negative Treatment:low-fat diet (study patient)


title: Anaerobic sulfur limited 1

status: Public on Sep 03 2004

description:
S2
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

hyb_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner..

data_processing:
Data Acquisition and Primary Analysis—Acquisition and quantification
of array images as well as primary data analysis were performed using the Affymetrix software packages: Microarray Suite version 4.0.1, MicroDB version 2.0, and Data Mining Tool version 2.0. Microsoft Excel was used for further statistical analyses. All arrays were globally scaled to a target value of 150 using the average signal from all gene features using Microarray Suite version 4.0.1. When pairwise comparisons were performed (using Microarray Suite version 4.0.1), a transcript was considered “changed” when a call of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.

label: Biotinylated-UTP SAPE-Phycoerythrin

source_name: chemostat culture

growth_protocol:
Chemostat Cultivation—
Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [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]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0. For anaerobic cultivation, the reservoir medium was supplemented with Tween 80 and ergosterol as described previously. Anaerobic conditions were maintained by sparging the medium reservoir and the fermentor with pure nitrogen gas (0.5 liter_min_1). Furthermore, Norprene tubing and butyl rubber septa were used to minimize oxygen of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.
Media—
The defined mineral medium composition was based on that described by Verduyn et al [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The residual glucose concentration was targeted to 17 g_liter_1 to sustain glucose repression at the same level . For sulfur-limited cultivation: 4.0 g of NH4Cl, 0.05 g of MgSO4.7H2O, 3.0 g of KH2PO4, 0.4 g of MgCl2 and 59 g of glucose.

extract_protocol:
Sampling and RNA Isolation—
Samples from the chemostat cultures were taken as rapidly as possible to limit any potential changes in transcript profiles during the procedure. 40–60 ml of culture broth was sampled directly from the chemostat into a beaker containing 200 ml of liquid nitrogen. With vigorous stirring, the sample froze instantly. The frozen sample was then broken into small fragments and transferred to a 50-ml centrifuge tube. The sample was then thawed at room temperature, ensuring that it remained as close to zero as possible. Cells were pelleted (5000 rpm at 0 °C for 4 min), resuspended in 2 ml of ice-cold AE buffer (50 mM sodium acetate, 10 mM EDTA, pH 5.0) and aliquoted into 5 Eppendorf tubes. This corresponded to _20 mg of dry weight per tube. For each array, total RNA was extracted from a single tube using the hot-phenol method (32) or the FastRNA kit, Red (BIO 101, Inc., Vista, CA).

treatment_protocol: Liquid nitrogen quenching

tag: Strain and Maintenance—

tag: This study was performed with the prototrophic laboratory strain S. cerevisiae CEN.PK113-7D (MATa) [van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heinen, J. J., Hoare, M., Lange, H. C., Madden, E. A., Niederberger, P., Nielsen, J., Parrou, J. L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H. Y., Verrips, C. T., Vindelov, J., and

tag: Pronk, J. T. (2000) Enz. Microb. Technol. 26, 706–714]


title: Anaerobic sulfur limited 2

description:
S3
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

label_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner..


title: Aerobic sulfur limited 1

description:
M53
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

hyb_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner.

label: Biotinylated dUTP - streptavidine Phycoerythrin (SAPE)

growth_protocol:
Chemostat Cultivation—
Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [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]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0. Aerobic conditions were maintained by sparging the cultures with air (0.5 liter_min_1). The dissolved oxygen concentration, which was continuously monitored with an Ingold model 34-100-3002 probe, remained above 80% of air saturation.
Media—
The defined mineral medium composition was based on that described by Verduyn et al [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The residual glucose concentration was targeted to 17 g_liter_1 to sustain glucose repression at the same level . For sulfur-limited, the composition was 4.0 g of NH4Cl, 0.05 g of MgSO4_7H2O, 3.0 g of KH2PO4, 0.4g of MgCl2, and 42 g of glucose.

tag: This study was performed with the prototrophic laboratory strain S. cerevisiae CEN.PK113-7D (MATa) [van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heinen, J. J., Hoare, M., Lange, H. C., Madden, E. A., Niederberger, P., Nielsen, J., Parrou, J. L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H. Y., Verrips, C. T., Vindelov, J., and Pronk, J. T. (2000) Enz. Microb. Technol. 26, 706–714]


title: Anaerobic nitrogen limited 1

description:
JM1
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitationon

scan_protocol: scanning with the Affymetrix GeneArray Scanner

growth_protocol:
Chemostat Cultivation—
Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [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]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0. For anaerobic cultivation, the reservoir medium was supplemented with Tween 80 and ergosterol as described previously. Anaerobic conditions were maintained by sparging the medium reservoir and the fermentor with pure nitrogen gas (0.5 liter_min_1). Furthermore, Norprene tubing and butyl rubber septa were used to minimize oxygen of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.
Media—
The defined mineral medium composition was based on that described by Verduyn et al [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The residual glucose concentration was targeted to 17 g_liter_1 to sustain glucose repression at the same level . For nitrogen-limited cultivation: 0.65 g of (NH4)2SO4, 5.75 g of K2SO4, 3.0 g of KH2PO4, 0.5 g of MgSO4.7H2O and 46 g of glucose.


title: Prostate_03-138A_GL3

description: Human prostate cancer patient 03-138A with Gleason Score 3+3 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 03-138A Gleason_Score:3+3 LCM_Gleason_Pattern:3 Gleason_Pattern:3 Age:60-69 PSA:4.3 Volume:0.5 Margin_Status:negative Treatment:prednisone

tag: Prostate normal adjacent from cancer patient 03-138A


title: Aerobic sulfur limited 3

description:
M55
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

growth_protocol:
Chemostat Cultivation—
Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [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]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0. Aerobic conditions were maintained by sparging the cultures with air (0.5 liter_min_1). The dissolved oxygen concentration, which was continuously monitored with an Ingold model 34-100-3002 probe, remained above 80% of air saturation.

Media—
The defined mineral medium composition was based on that described by Verduyn et al [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The residual glucose concentration was targeted to 17 g_liter_1 to sustain glucose repression at the same level . For sulfur-limited, the composition was 4.0 g of NH4Cl, 0.05 g of MgSO4_7H2O, 3.0 g of KH2PO4, 0.4g of MgCl2, and 42 g of glucose.


title: Anaerobic nitrogen limited 3

description:
S8
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation


title: Aerobic sulfur limited 2

description:
M54
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

label_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner.


title: Anaerobic nitrogen limited 2

description:
JM3
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

scan_protocol: scanning with the Affymetrix GeneArray Scanner..


title: ADHC4

status: Public on Apr 07 2005

city: Washington

first: Indira

last: Poola

state: DC

address: 520 W Street, NW

department: Biochemistry and MOlecular Biology

institute: Howard University College of Medicine

description:
Fresh Atypical ductal hyperplasia (ADH) tissue collected from breast of a women who had cancer before ADH, or had cancer at the time as ADH or developed cancer after ADH diagnosis
Keywords = Homo sapiens, Atypical Ductal Hyperplasia

source_name: breast precancerous tissue


title: Aerobic phosphorus limited 2

description:
M47
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

growth_protocol:
Chemostat Cultivation—
Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [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]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0. Aerobic conditions were maintained by sparging the cultures with air (0.5 liter_min_1). The dissolved oxygen concentration, which was continuously monitored with an Ingold model 34-100-3002 probe, remained above 80% of air saturation.
Media—
The defined mineral medium composition was based on that described by Verduyn et al [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The residual glucose concentration was targeted to 17 g_liter_1 to sustain glucose repression at the same level . For phosphorus-limited, the composition was 5.0 g of (NH4)2SO4, 1.9 g of K2SO4, 0.12 g of KH2PO4, 0.5 g of MgSO4_7H2O, and 59 g of glucose .

treatment_protocol: Liquid N2 quenching


title: Anaerobic phosphorus limited 3

description:
S7
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

hyb_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and. scanning with the Affymetrix GeneArray Scanner.

growth_protocol:
Chemostat Cultivation—
Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [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]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0. For anaerobic cultivation, the reservoir medium was supplemented with Tween 80 and ergosterol as described previously. Anaerobic conditions were maintained by sparging the medium reservoir and the fermentor with pure nitrogen gas (0.5 liter_min_1). Furthermore, Norprene tubing and butyl rubber septa were used to minimize oxygen of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.
Media—
The defined mineral medium composition was based on that described by Verduyn et al [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The residual glucose concentration was targeted to 17 g_liter_1 to sustain glucose repression at the same level . For phosphorus-limited cultivation: 5.0 g of (NH4)2SO4, 1.9 g of K2SO4, 0.12 g KH2PO4, 0.5 g of MgSO4.7H2O, and 66 g of glucose.


title: Anaerobic sulfur limited 3

description:
S4
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation


title: Aerobic phosphorus limited 1

description:
M46
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

scan_protocol: scanning with the Affymetrix GeneArray Scanner.


title: Aerobic nitrogen limited 3

description:
V1
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

growth_protocol:
Chemostat Cultivation—
Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [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]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0. Aerobic conditions were maintained by sparging the cultures with air (0.5 liter_min_1). The dissolved oxygen concentration, which was continuously monitored with an Ingold model 34-100-3002 probe, remained above 80% of air saturation.
Media—
The defined mineral medium composition was based on that described by Verduyn et al [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The residual glucose concentration was targeted to 17 g_liter_1 to sustain glucose repression at the same level.. For nitrogen-limited, the composition was 1.0 g of (NH4)2SO4, 5.3 g of K2SO4, 3.0 g of KH2PO4, 0.5 g of MgSO4_7H2O, and 59 g of glucose.

tag: Strain and Maintenance


title: Anaerobic phosphorus limited 1

description:
S5
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation


title: Anaerobic phosphorus limited 2

description:
S6
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

label_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and. scanning with the Affymetrix GeneArray Scanner.


title: Aerobic phosphorus limited 3

description:
M52.1
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

treatment_protocol: Liquid Nitrogen Quenching


title: ADH4

description:
Fresh Atypical ductal hyperplasia tissue collected from breast of a women who had no prior history of breast cancer and had not developed breast cancer in five years after diagnosis
Keywords = Homo sapiens, Atypical Ductal Hyperplasia


title: Aerobic nitrogen limited 1

description:
M40.1
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

hyb_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner

data_processing:
Data Acquisition and Primary Analysis—Acquisition and quantification
of array images as well as primary data analysis were performed using the Affymetrix software packages: Microarray Suite version 4.0.1, MicroDB version 2.0, and Data Mining Tool version 2.0. Microsoft Excel was used for further statistical analyses. All arrays were globally scaled to a target value of 150 using the average signal from all gene features using Microarray Suite version 4.0.1. When pairwise comparisons were performed (using Microarray Suite version 4.0.1), a transcript was considered “changed” when a call of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present

label: SAPE phycoerythrin


title: Prostate_03-135C_GL4

description: Human prostate cancer patient 03-135C with Gleason Score 4+3 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate Cancer patient 03-135C Gleason_Score:4+3 LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:50-59 PSA:5.0 Volume:2.3 Margin_Status:negative Treatment:none

tag: Prostate normal adjacent from cancer patient 03-135C


title: Prostate_03-158F_GL4

description: Human prostate cancer patient 03-158F with Gleason Score 4+3 prostate cancer hybridized against normal adjacent prostate tissue from the same patient through laser capture microdissection (LCM).

tag: Prostate normal adjacent from cancer patient 03-158F

tag: Prostate Cancer patient 03-158F Gleason_Score:4+3 LCM_Gleason_Pattern:4 Gleason_Pattern:4 Age:70-79 PSA:4.2 Volume:3.5 Margin_Status:negative Treatment:none


title: 24hpi_rep1

status: Public on Oct 04 2008

city: Brisbane

first: Elizabeth

middle: A

last: Williams

state: QLD

address: St Lucia campus

department: School of Integrative Biology

country: Australia

institute: University of Queensland

description: loop design

hyb_protocol: 4X SSC, 40% deionized formamide (Astral Scientific) and 0.1% SDS were added to the probe mix to create the hybridisation buffer. Following incubation at 95ºC for 5 min and 45ºC for 90 min, the labelled probe mix was loaded onto the microarray chip, and placed in a hybridisation chamber (Corning) with 10 μl H2O at each end in a 45 ºC oven for 16 h (as per Woods et al. 2004).

scan_protocol: Following hybridisation, chips were washed once in a 0.2X SSC, 0.05% SDS solution and twice in 0.2X SSC solution, then dried by low speed centrifugation. Washed slides were scanned using a GenePix 4000B Microarray Scanner (Molecular Devices). Spot intensities from raw scan data were quantified using GenePix Pro 6.0 software (Molecular Devices). Spots were flagged as present or absent based on circularity and diameter (circularity </= 70 and diameter < 100 = absent) or sum of means (Cy5 intensity/Cy3 intensity < 200 = absent).

data_processing: Quantified data was transferred as a one-colour analysis into Genespring version 7.0 (Silicon Genetics). Raw data was normalised per chip to the 50th percentile and per gene to the median, and measurements < 0.01 were set to 0.01. Median polishing was performed per chip and per gene.

organism: Haliotis asinina

source_name: pooled whole postlarvae

label_protocol: 2.5 μg total RNA was used to prepare labelled cDNA for each developmental stage. cDNA was transcribed with an oligo(dT)15 primer using a dNTP mix with a ratio of 4:1 aminoallyl-dUTP to dTTP (Sigma) and Superscript III Reverse Transcriptase (Invitrogen) according to manufacturers’ instructions. Aminoallyl-labelled cDNA (aa-cDNA) was purified, dried and redissolved in 100 mM sodium carbonate pH 9. Cy3 and Cy5 reactive dyes (Amersham) were added to their respective aa-cDNA samples and the coupling reaction allowed to proceed. After 1 h, 4.5 μl 4 M hydroxylamine was added to remove unincorporated dyes. Cy3- and Cy5-labeled cDNA were combined and purified with a PCR cleanup kit (Qiagen). To prevent non-specific binding, 10 μg human Cot1 DNA (Invitrogen) and 0.125 A260 units poly dA (Roche) were added to the purified probe mix. This solution was dehydrated in a speed-vac to a volume of 8 μl.

growth_protocol: Spawning of adult Haliotis asinina and larval culture were carried out at Heron Island Research Station on the Great Barrier Reef, Australia (23°27’S; 151°55’E) as previously described (Counihan et al. 2001; Jackson et al. 2005). Larval cultures were derived from gametic contributions from at least 3 females and 3 males, and were treated for 2 hours daily with 20 μg/L rifampicin to protect against bacterial invasion. Larvae were allowed to develop to 96 hours post fertilisation (hpf), at which time a subset were introduced into 0.5 L plastic chambers containing ~11.5 cm2 surface area of the encrusting coralline algae, Mastophora pacifica, previously shown to be an effective inducer of Haliotis asinina metamorphosis (Jackson et al. 2005). After 2 h, chambers were supplied with a gentle flow of seawater, such that any larvae not in constant contact with the coralline algae were washed out of the chamber. At 8 h after their introduction, the algal shards were removed from chambers and all attached larvae were washed into fresh 0.5 L plastic chambers using a jet of 0.22 μM filtered seawater (FSW). Once again, chambers were supplied with a gentle flow of seawater so that only larvae exhibiting constant crawling behaviour were maintained. Washed larvae were allowed to develop for a further 48 h, at which point the experiment ended. Throughout the induction experiment, postlarvae were treated with rifampicin as described above. A subset of larvae were maintained in the original culture chambers to act as an non-induced control.

extract_protocol: Abalone larvae were collected for RNA extraction at 66, 78, 90, 108, 120 and 144 hpf. Competent larvae were induced by exposure to coralline algae at 96 hpf (see above) and postlarval samples were collected at 12, 24 and 48 hpi. This meant that postlarvae 12, 24 and 48 hpi were actually the same age as larvae 108, 120 and 144 hpf. Total RNA was extracted using TRIreagent (Sigma) as described by the manufacturer. Quantity and quality of RNA was assessed using UV spectrophotometry (Nanodrop ND-1000) and agarose gel electrophoresis.

tag: SOURCE POP

value: Heron Island

tag: CHIP #

tag: HYB DATE


title: BCR-ABL-SNP-#21

status: Public on Oct 02 2008

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cryopreserved peripheral blood or bone marrow samples obtained at diagnosis

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

tag: B-progenitor ALL with BCR-ABL1 fusion