title: testis, sex-reversed, biological rep3

status: Public on Nov 05 2007

first: John

last: Malone

department: LCDB/NIDDK

institute: NIH

description: Gene expression data from sex-reversed sexually mature testis

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Xenopus laevis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: RMA normalized signal intensity using RMA Express

organism: Xenopus laevis x Xenopus muelleri

source_name: Xenopus laevis x X. muelleri sex-reversed sexually mature testis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Raised eggs to adulthood in standard conditions for Xenopus under 12L:12D photoperiod

extract_protocol: Ambion RiboPure using RNAWiz was used to extract total RNA and was performed according to the manufacturer's instructions.

treatment_protocol: Animals were killed by immersion in MS222 and testes were immediated extracted

tag: Mother

value: laevis (Cape of South Africa); Father:muelleri (Swaziland)

tag: Age:646 days


title: testis normal, biological rep3

type: RNA

city: Bethesda

state: MD

country: USA

description: Gene expression data from normal sexually mature testis

label: biotin

molecule: total RNA

source_name: Xenopus laevis x X. muelleri normal sexually mature testis

tag: Age:434 days


title: testis, sex-reversed, biological rep1

tag: Age:395 days


title: testis, sex-reversed, biological rep2


title: ovary, sex-reversed, biological rep1

description: Gene expression data from sex-reversed sexually mature ovary

treatment_protocol: Animals were killed by immersion in MS222 and ovary was immediated extracted

tag: Age:841 days


title: ovary, sex-reversed, biological rep2


title: testis normal, biological rep2


title: testis normal, biological rep1

tag: Age:524 days


title: ovary normal, biological rep4

description: Gene expression data from normal sexually mature ovary


title: ovary normal, biological rep1


title: ovary normal, biological rep2

tag: Age:526 days


title: ovary normal, biological rep3

tag: Age:509 days


title: Wild type mice on a high fat diet (CH 3)

status: Public on Nov 02 2007

city: Boston

first: Yasuhiro

last: Izumiya

state: MA

address: 715 Albany street

department: Molecular Cardiology

institute: Boston University School of Medicine

description: no additional information

hyb_protocol: For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases.  15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm.  Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).

scan_protocol: The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: MAS5.0, target intensity = 500

organism: Mus musculus

source_name: CH 3

label_protocol: Using a poly-dT primer incorporating a T7 promoter, double-stranded cDNA was synthesized from 10 micrograms total RNA using a cDNA synthesis kit (SuperScript double-stranded cDNA synthesis kit; Invitrogen, Carlsbad, CA).  Double-stranded cDNA was purified by phenol/chloroform extraction using a Phase-Lock Gel (PLG Heavy Brinkmann Instruments, Westbury, NY) followed by ethanol precipitation.  Biotin-labeled cRNA was generated from the double-stranded cDNA template though in-vitro transcription with T7 polymerase, and a nucleotide mix containing biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY).  The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).

extract_protocol: Total RNA was isolated by Qiagen RNeasy fibrous kit.

tag: genotype

value: wildtype

tag: diet

value: high fat

tag: muscle hypertrophy

tag: sex

value: male

tag: tissue

value: liver

tag: treatment

value: doxycycline 3wks


title: Wild type mice on a high fat diet (CH 1)

description: no additional information

source_name: CH 1


title: Wild type mice on a high fat diet (CH 4)

description: no additional information

source_name: CH 4


title: Wild type mice on a high fat diet (CH 2)

description: no additional information

source_name: CH 2


title: ovary, sex-reversed, biological rep3

tag: Age:754 days


title: Wild type mice on a normal diet (CN 3)

description: no additional information

source_name: CN 3

value: control


title: Akt1 double transgenic mice on a high fat diet (DH 4)

description: no additional information

source_name: DH 4

value: DTG


title: Akt1 double transgenic mice on a high fat diet (DH 1)

description: no additional information

source_name: DH 1


title: ovary, sex-reversed, biological rep4


title: E2F1 Serum #2

city: Minneapolis

first: Timothy

middle: C.

last: Hallstrom

state: MN

address: MMC 366

department: Pediatrics

institute: University of Minnesota

hyb_protocol: 10 µg of fragmented cRNA was hybridized for 16 hours at 45°C on rat RAE230a Affymetrix GeneChips.

scan_protocol: Gene Chips were scanned using the Molecular Devices GenePix 4000B scanner.

data_processing: MAS5 and RMA data were extracted from .CEL files using R software.

label: Biotin

organism: Rattus norvegicus

source_name: E2F1 Serum #2

label_protocol: The Duke microarray facility prepared biotinylated cRNA from 6 µg of total RNA following a standard Affymetrix protocol.

growth_protocol: REF52 cells were grown in DMEM containing 10% FBS, deprived of serum (0.25%) for 48 hrs prior to infection, Infected with control or E2F1 expressing adenovirus, and appropriate media added back without or with the PI3K inhibitor as designated.

extract_protocol: Total RNA was isolated using RNeasy midi kit according to manufacturer's protocol.

tag: REF52 cells


title: CMV Serum LY294002 #1

source_name: CMV Serum LY294002 #1


title: Akt1 double transgenic mice on a high fat diet (DH 3)

description: no additional information

source_name: DH 3


title: Akt1 double transgenic mice on a high fat diet (DH 2)

description: no additional information

source_name: DH 2


title: Wild type mice on a normal diet (CN 1)

description: no additional information

source_name: CN 1


title: E2F1 Serum LY294002 #2


title: CMV Serum LY294002 #2

source_name: CMV Serum LY294002 #2


title: DK1622 /(delta)DigR Exp.5, replica 1

city: Marburg

first: Lotte

last: Sogaard-Andersen

address: Karl-von-Frisch-Str.

department: Ecophysiology

country: Germany

institute: Max Planck Institute for Terrestrial Microbiology

description: standard protocol

hyb_protocol: Standard protocol see Overgaard et al. 2006, J. of Bact. Vol.188, No.12, p.4384-4394

scan_protocol: GenePix 6.0

data_processing: spot finding algorithm GenePix 6.0; ratio-normalized (mean ratio of medians = 1); local-background-subtracted median intensity value of Cy3 or Cy5 channel >= 500

organism: Myxococcus xanthus

source_name: veg. cells DK1622 (wt)

tag: veg. DK1622 (wt) Exp.5

source_name: veg. cells (delta)DigR

tag: veg. cells (delta)DigR Exp.5


title: Wild type mice on a normal diet (CN 2)

description: no additional information

source_name: CN 2


title: E2F1 Serum LY294002 #1


title: E2F1 Serum deprivation #2

source_name: E2F1 Serum deprivation #2


title: CMV Serum #1

source_name: CMV Serum #1


title: (delta)DigR / DK1622 Exp.4, replica 2

description: standard protocol

label_protocol: Standard protocol see Overgaard et al. 2006, J. of Bact. Vol.188, No.12, p.4384-4394

tag: veg. cells (delta)DigR Exp.4

source_name: veg. DK1622 (wt)

tag: veg. DK1622 (wt) Exp.4


title: (delta)DigR / DK1622 Exp.5, replica 2

description: standard protocol

growth_protocol: Standard protocol see Overgaard et al. 2006, J. of Bact. Vol.188, No.12, p.4384-4394


title: CMV Serum deprivation #1

source_name: CMV Serum deprivation #1


title: E2F1 Serum deprivation #1

source_name: E2F1 Serum deprivation #1


title: E2F1 Serum #1

source_name: E2F1 Serum #1


title: Transcriptional profiling of Loc1 knockout replicate #3

first: Suzanne

last: Komili

address: 44 Binney St.

institute: Harvard University

description: Replicate #3 of transcriptional profiling of Loc1- cells.

hyb_protocol: Sample was mixed with DIG Easy Hybe, salmon sperm DNA, and yeast tRNA, and incubated at 65oC for 2 minutes.  Sample was then hybridized to microarray and incubated at 37oC for 16 hours.  Arrays were washed three times for ten minutes each with 1xSSC, 0.1%SDS at 50oC. Arrays were then briefly rinsed with 1X SSC at 50oC and air-dried in a centrifuge.

scan_protocol: The Cy3 and Cy5 intensities at each spot were determined using a GenePix 4000B scanner.

data_processing: The ratio of 635/532 was determined at each pixel using Genepix.  Value is equal to the median of the ratios for a given spot.

organism: Saccharomyces cerevisiae

source_name: Wild-type cells grown in rich media at 30C

label_protocol: mRNA was reverse-transcribed using a poly-T probe, and then labeled with Cy5 using Klenow and random primers.

growth_protocol: 50mL cultures were grown in YPD to early log phase (OD600 0.2-0.4) at 30oC, centrifuged at room temeperature and flash-frozen using liquid nitrogen.

extract_protocol: mRNA was extracted from cell pellets using the hot phenol method and precipitated overnight in ethanol

tag: Strain

source_name: Loc1 deletion cells grown in rich media at 30C

label_protocol: mRNA was reverse-transcribed using a poly-T probe, and then labeled with Cy3 using Klenow and random primers.

tag: ura3 leu2-3,112 his3-11 trp1-1 ade2-1 ho can1-100 LOC1::KAN


title: DK1622 /(delta)DigR Exp.4, replica 1

description: standard protocol

extract_protocol: Standard protocol see Overgaard et al. 2006, J. of Bact. Vol.188, No.12, p.4384-4394


title: (delta)DigR / DK1622 Exp.2, replica 2

description: standard protocol

treatment_protocol: Standard protocol see Overgaard et al. 2006, J. of Bact. Vol.188, No.12, p.4384-4394

tag: veg. cells (delta)DigR Exp.2

tag: veg. DK1622 (wt) Exp.2


title: DK1622 /(delta)DigR Exp.3, replica 1

description: standard protocol

tag: veg. DK1622 (wt) Exp.3

tag: veg. cells (delta)DigR Exp.3


title: CMV Serum #2

source_name: CMV Serum #2


title: DK1622 /(delta)DigR Exp.2, replica 1

description: standard protocol


title: (delta)DigR / DK1622 Exp.3, replica 2

description: standard protocol


title: Transcriptional profiling of Loc1 knockout replicate #4

description: Replicate #4 of transcriptional profiling of Loc1- cells.


title: DK1622 /(delta)DigR Exp.1, replica 1

description: standard protocol

tag: veg. DK1622 (wt) Exp.1

tag: veg. cells (delta)DigR Exp.1


title: Transcriptional profiling of Loc1 knockout replicate #2

description: Replicate #2 of transcriptional profiling of Loc1- cells.


title: (delta)DigR / DK1622 Exp.1, replica 2

description: standard protocol


title: gif1 7 DAF, biological replicate 2

city: Shanghai

first: Li

last: Qun

state: Shanghai

address: 300 Fenglin Road

department: National Key Laboratory of Plant Molecular Genetics

country: China

institute: Institute of plant physiology & ecology, SIBS, CAS

description: Gene expression data of mutant gif1 caryopsis, 7 DAF

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The data were analyzed with Affymetrix GeneChip® Operating Software (GCOS, Version 1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Oryza sativa

source_name: Oryza sativa mutant_gif1 Caryopsis, 7 DAF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol with GeneChip IVT Labeling Kit and Genechip Sample Cleanup Module (Affymetrix)

extract_protocol: Total RNA was extracted from caryopsis using the Trizol method (Invitrogen) and purified with RNeasy MiniKit (Qiagen). cDNA was synthesized and purified with one-cycle cDNA Synthesis Kit (Affymetrix) and GeneChip Sample Cleanup Module (Affymetrix), respectively.

tag: Genotype

value: gif1, mutant, Age:7 DAF, Tissue:caryopsis


title: gif1 7 DAF, biological replicate 3


title: Zhonghua11 7 DAF, biological replicate 2

description: Gene expression data of wild type Zhonghua11 caryopsis, 7 DAF

source_name: Oryza sativa_Zhonghua11 Caryopsis, 7 DAF

value: Zhonghua11, wild-type, Age:7 DAF, Tissue:caryopsis


title: gif1 7 DAF, biological replicate 1


title: Zhonghua11 7 DAF, biological replicate 3


title: Transcriptional profiling of Loc1 knockout replicate #1

description: Replicate #1 of transcriptional profiling of Loc1- cells.

source_name: Loc1 knockout cells grown in rich media at 30C


title: Zhonghua11 7 DAF, biological replicate 1


title: Thorium 3rd H

status: Public on Nov 01 2007

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from high power scanning. Data with flag value 0 were used for LOWESS normalization processing, although original raw data were remaining in this table. Merging high and low scanned data were done on the GeneSpring and represented as “AVG_VALUE”.

hyb_protocol: Hybridized for 16-18 h at 65 C

scan_protocol: Scan Array 4000 (PerkinElmer Japan Co., Ltd) was used for scanning. Array images were analyzed with Gene Pix Pro 4.0 (Axon Instrument).

data_processing: GeneSpring ver 7.3.1 (Agilent Technologies Inc.)

molecule: polyA RNA

source_name: Thorium treated for 2 h, Cy5

label_protocol: Cyscribe first-strand cDNA labelling kit (Amersham Biosciences)

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 5 mM (final concentration) then the yeast cells were exposed for 2 h.

extract_protocol: Hot-phenol and oligotex dt mRNA purification kit (TaKaRa)

treatment_protocol: Thorium (Nakarai Teque. Inc. (Kyoto, Japan))

tag: strain S288C

source_name: control (without treatment for 2 h), Cy3

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 2 h without any treatment.

treatment_protocol: without treatment


title: Thorium 2nd L

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from low power scanning. Data with flag value 0 were used for LOWESS normalization processing, although original raw data were remaining in this table. Merging high and low scanned data were done on the GeneSpring and represented as “AVG_VALUE”.


title: Thorium 2nd H


title: Thorium 1st H


title: Fast Neutron 20.3 Gy 1st L

source_name: Fast Neutron 20.3 Gy exposed, Cy5

growth_protocol: 50 ml of Saccharomyces cerevisiae strain S288C (OD=1) cells were harvested and washed with ice-cold salin (0.9 % NaCl), and resuspended in 2 ml ice-cold salin and transferred into cuvettes. The cells were exposed with heavy ion radiation for 19 h, that was corresponding to 20.3 Gy of fast neutron. During the irradiation procedure, yeast cells were kept at low temperature in a resting state as much as possible and irradiated cells were kept on ice until a recovery growth. The cells were resuspended in fresh YPD medium (50 ml) and allowed to grow for 40 min at 25 C.

treatment_protocol: Fast neutron irradiation was performed with a neutron irradiating system, the Hiroshima University Radiobiological Research Accelerator (HIRRAC) (Nisshin-High Voltage, Kyoto, Japan) in the Research Institute for Radiation Biology and Medicine of Hiroshima University (RIRBM). HIRRAC was operated at an average proton beam current of 73 μA. Fast neutrons were produced with the 7 Li (p, n) 7 Be reaction. Cells were exposed to total doses of 21.4 Gy in 336 min with dose rates of 0.064 Gy/min. Consequently the contribution of net fast neutrons was 20.3 Gy.

source_name: control (without irradiation), Cy3

growth_protocol: 50 ml of Saccharomyces cerevisiae strain S288C (OD=1) cells were harvested and washed with ice-cold salin (0.9 % NaCl), and resuspended in 2 ml ice-cold salin and transferred into tissue culture flasks. For 19 h, yeast cells were kept at low temperature in a resting state as much as possible, after that cells were kept on ice until a recovery growth. The cells were resuspended in fresh YPD medium (50 ml) and allowed to grow for 40 min at 25 C.

treatment_protocol: without irradiation


title: Fast Neutron 20.3 Gy 2nd H


title: Fast Neutron 20.3 Gy 3rd H


title: 1910-42-5 Paraquat, 35 ppm 2nd L

source_name: Paraquat 35 ppm treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in 50 ml YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 35 ppm (final concentration).

treatment_protocol: Methyl viologen dichloride hydrate 98 % (Aldrich, 856177)

source_name: control (without treatment), Cy3


title: Thorium 3rd L


title: 1910-42-5 Paraquat, 35 ppm 1st L


title: Fast Neutron 20.3 Gy 3rd L


title: Thorium 1st L


title: 1910-42-5 Paraquat, 35 ppm 3rd H


title: 1910-42-5 Paraquat, 35 ppm 3rd L


title: 1910-42-5 Paraquat, 35 ppm 2nd H


title: Fast Neutron 20.3 Gy 1st H


title: Fast Neutron 20.3 Gy 2nd L


title: 88-75-5 o-Nitrophenol 3rd H

source_name: o-Nitrophenol treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 3 mM (final concentration) then the yeast cells were exposed for 2 h.

treatment_protocol: o-Nitrophenol (Wako 142-02212)

source_name: control (before treatment for 2 h), Cy3

growth_protocol: Saccharomyces cerevisiae strain S288C cells at OD=1.

treatment_protocol: before treatment


title: 88-75-5 o-Nitrophenol 2nd L


title: 88-75-5 o-Nitrophenol 1st L


title: 88-75-5 o-Nitrophenol 2nd H


title: 88-75-5 o-Nitrophenol 3rd L


title: 88-75-5 o-Nitrophenol 1st H


title: 554-84-7 m-Nitrophenol 1st L

source_name: m-Nitrophenol treated for 2 h, Cy5

treatment_protocol: m-Nitrophenol (Wako 143-04202)


title: 40465-66-5 Round up hi-load herbicide 3rd

description: Data with flag value 0 were used for LOWESS normalization processing.

source_name: Round up treated for 2 h, Cy5

label_protocol: At least 4 µg of mRNA and a 0.4 µM oligo dT12-17 primer (GIBCO BRL; Life Technologies) were denatured at 70 ºC for 5 min, and the labeled cDNA was synthesized.  The reaction mixture contained 0.5 mM each of dATP, dGTP, and dCTP; 0.2 mM dTTP (GIBCO BRL; Life Technologies); 15 mM Cy5-labeled dUTP (PE Applied Biosystems); 200 units of PowerScript Reverse Transcriptase (CLONTEC, Palo Alto, CA); and an appropriate buffer and RNase inhibiter (GIBCO BRL; Life Technologies).  The reactions were performed at 42 ºC for 1h and 30 min.  Another 200 units of transcriptase was added in the tubes 40 min after the beginning of reverse transcription.  The template mRNA was dissolved by the addition of 0.5 N NaOH for 1 h at 65 ºC.  After neutralization with 1 M Tris-HCl, Cy3- and Cy5-labeled cDNA solution was mixed and filtered on Microcon 30 (AMICON).

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture with 1500 times dilution then the yeast cells were exposed for 2 h.

treatment_protocol: Round up hi-loadTM herbicide (Monsanto company, MON77692)

label_protocol: At least 4 µg of mRNA and a 0.4 µM oligo dT12-17 primer (GIBCO BRL; Life Technologies) were denatured at 70 ºC for 5 min, and the labeled cDNA was synthesized.  The reaction mixture contained 0.5 mM each of dATP, dGTP, and dCTP; 0.2 mM dTTP (GIBCO BRL; Life Technologies); 15 mM Cy3-labeled dUTP (PE Applied Biosystems); 200 units of PowerScript Reverse Transcriptase (CLONTEC, Palo Alto, CA); and an appropriate buffer and RNase inhibiter (GIBCO BRL; Life Technologies).  The reactions were performed at 42 ºC for 1h and 30 min.  Another 200 units of transcriptase was added in the tubes 40 min after the beginning of reverse transcription.  The template mRNA was dissolved by the addition of 0.5 N NaOH for 1 h at 65 ºC.  After neutralization with 1 M Tris-HCl, Cy3- and Cy5-labeled cDNA solution was mixed and filtered on Microcon 30 (AMICON).


title: 1910-42-5 Paraquat, 35 ppm 1st H


title: 554-84-7 m-Nitrophenol 2nd H


title: 554-84-7 m-Nitrophenol 3rd H


title: 127-18-4 Tetrachloroethylene 1st L

source_name: PCE treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 3.3 mM (final concentration) then the yeast cells were exposed for 2 h.

treatment_protocol: Tetrachloroethylene (Wako 203-00356).

source_name: control (before treatment), Cy3


title: 107-20-0 Chloroacetaldehyde 2nd L

source_name: CAA treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 25 ppm (final concentration) then the yeast cells were exposed for 2 h.

treatment_protocol: 40% Chloroacetaldehyde Solution (Wako 031-10722)


title: 127-18-4 Tetrachloroethylene 2nd L


title: 107-20-0 Chloroacetaldehyde 3rd L


title: 127-18-4 Tetrachloroethylene 2nd H


title: 100-02-7 p-Nitrophenol 3rd L

source_name: p-Nitrophenol treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 1.5 mM (final concentration) then the yeast cells were exposed for 2 h.

treatment_protocol: p-Nitrophenol (Wako 143-02242).


title: 127-18-4 Tetrachloroethylene 1st H


title: 554-84-7 m-Nitrophenol 1st H


title: 554-84-7 m-Nitrophenol 3rd L


title: 554-84-7 m-Nitrophenol 2nd L


title: 127-18-4 Tetrachloroethylene 3rd L


title: 107-20-0 Chloroacetaldehyde 1st H


title: 107-20-0 Chloroacetaldehyde 3rd H


title: 100-02-7 p-Nitrophenol 3rd H


title: 127-18-4 Tetrachloroethylene 3rd H


title: 100-02-7 p-Nitrophenol 2nd L


title: 100-02-7 p-Nitrophenol 1st L


title: 107-20-0 Chloroacetaldehyde 2nd H


title: 107-20-0 Chloroacetaldehyde 1st L


title: Supiculisporic Acid 6th

source_name: Supiculisporic Acid treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture (final concentration; 0.16 %) then the yeast cells were exposed for 2 h.

treatment_protocol: Supiculisporic Acid (Made by Dr. Ishigami).


title: 100-02-7 p-Nitrophenol 2nd H


title: 100-02-7 p-Nitrophenol 1st H

scan_protocol: Scan Array 4000 (PerkinElmer Japan Co., Ltd ) was used for scanning. Array images were analyzed with Gene Pix Pro 4.0 (Axon Instrument).


title: Supiculisporic Acid 2nd


title: Supiculisporic Acid 1st


title: 67-68-5 Dimethylsulfoxide 6th

scan_protocol: Scan Array 4000 (PerkinElmer Japan Co., Ltd) was used for scanning. Array images were analyzed with Gene Pix Pro 4.0 (Axon Instrument). NOTE: Original, complete .gpr files unavailable.

source_name: DMSO treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture (final concentration; 10 %=1.41 M) then the yeast cells were exposed for 2 h.

treatment_protocol: dimethylsulfoxide (Wako, 043-07216)


title: Supiculisporic Acid 4th


title: Supiculisporic Acid 3rd


title: 67-68-5 Dimethylsulfoxide 5th


title: 59-02-9 Vitamin E 1st

source_name: Vitamin E treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture then the yeast cells were exposed for 2 h.

treatment_protocol: Vitamin E (made by Dr. Noguchi (Tokyo univ.))


title: Supiculisporic Acid 5th


title: 79622-59-6 Fluazinam 3rd

source_name: Fluazinam treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 150 ul of 1 mM chemical stock solution were added into 100 ml OD=1 (exponential growing) culture (final concentration; 1.5 uM) then the yeast cells were exposed for 2 h.

treatment_protocol: Fluazinam Standard (Wako 068-02861)


title: 59-02-9 Vitamin E 3rd


title: 79622-59-6 Fluazinam 1st


title: 79622-59-6 Fluazinam 2nd


title: 59-02-9 Vitamin E 2nd


title: 934-32-7 2-Aminobenzimidazole 3rd

source_name: ABI treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 1 ml of 500 mM chemical stock solution were added into 100 ml OD=1 (exponential growing) culture (final concentration; 5 mM) then the yeast cells were exposed for 2 h.

treatment_protocol: 2-Aminobenzimidazole (Wako 011-08711)


title: 7553-56-2 Iodine, 0.5 mM 2 h (dose-response) 1st H

source_name: Iodine treated with 0.5 mM for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 0.5 mM (final concentration) then the yeast cells were exposed for 2 h.

treatment_protocol: Iodine (Wako 095-00392). An iodine solution (0.5 M) was prepared just before use as 12.7 g iodine and 25 g iodide in 100 ml solution


title: 934-32-7 2-Aminobenzimidazole 2nd

treatment_protocol: without treatment


title: 7553-56-2 Iodine, 1 mM 2 h (dose-response) 1st

source_name: Iodine treated with 1 mM for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 1 mM (final concentration) then the yeast cells were exposed for 2 h.


title: H2O2 slide 3 lower

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

description: Slide images were analyzed using the SoftWorx Tracker package (Applied Precision, Inc.), acquiring mean spot intensity and median background intensity for each spot. Spot signals were corrected for background by subtracting the median background intensity from the mean spot intensity. The natural logarithms of these background-corrected signals were adjusted by an additive constant to give a common median to each scan of the same array-dye combination. The data from both dye channels on a given array were normalized by locally weighted scatterplot smoother (LOWESS) normalization. These normalized data sets were then adjusted by an additive constant to make each median the same across all arrays. The triplicate spots were averaged together to produce one normalized measurement for each probe on the array.

hyb_protocol: After the purification of the cDNA targets, they were hybridized to the array using the previously described protocol [Madsen, M. L., D. Nettleton, E. L. Thacker, R. Edwards, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect. Immun. 74:160-166.]. Slides were washed using the Corning UltraGAPS slide wash protocol and dried by centrifugation at 1500 x g for two minutes.

scan_protocol: After hybridization and washing, the arrays were scanned using a ScanArray Express laser scanner (Applied Biosystems) three times with varying photomultiplier tube gain settings to encompass the dynamic range of the signal intensities [Dudley, A. M., J. Aach, M. A. Steffen, and G. M. Church. 2002. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. USA 99:7554-7559.].

data_processing:
We fit a mixed linear model with the normalized signal intensity as the response.

intensity = mu + trt + part + dye + slide + slide*part

where part refers to the upper or lower portion of the slide.

organism: Mesomycoplasma hyopneumoniae

source_name: Strain 232 H2O2 treated

label_protocol: Fluorescently labeled cDNA targets were generated and purified using a modified protocol as described in [Boyce, J. D., I. Wilkie, M. Harper, M. L. Paustian, V. Kapur, and B. Adler. 2004. Genomic-scale analysis of Pasteurella multocida gene expression during growth within liver tissue of chickens with fowl cholera. Microbes Infect. 6:290-298.] with a 129 hexamer primer set specific for M. hyopneumoniae open reading frames used in previous studies [Madsen, M. L., D. Nettleton, E. L. Thacker, R. Edwards, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect. Immun. 74:160-166.].

extract_protocol: RNA was isolated from frozen cell pellets using the Versagene RNA purification System (Qiagen, Valencia, Calif.). The manufacturer’s protocol was followed with the exception of the DNase treatment, which was extended to thirty minutes. The filter cutoff of 150 base pairs prevented small RNA fragments from interfering in subsequent manipulations.

tag: Strain 232 culture grown in friis media to mid-log phase.

tag: 250 ml flask containing 150 ml of culture were grown to early exponential phase as determined by color changing units. Hydrogen peroxide was added to flask to a concentration of 0.5%, and flask were incubated at 37˚C for 15 minutes.

source_name: Strain 232 control


title: H2O2 slide 3 upper

tag: Strain 232 culture grown in friis media to mid-log phase. 250 ml flask containing 150 ml of culture were grown to early exponential phase as determined by color changing units. Hydrogen peroxide was added to flask to a concentration of 0.5%, and flask were incubated at 37˚C for 15 minutes.


title: 934-32-7 2-Aminobenzimidazole 1st H

source_name: control (without treatment), Cy3

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 2 h without any treatment.


title: 7553-56-2 Iodine, 0.75 mM 2 h (dose-response) 1st

source_name: Iodine treated with 0.75 mM for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 0.75 mM (final concentration) then the yeast cells were exposed for 2 h.


title: H2O2 slide 1 upper

hyb_protocol: AAfter the purification of the cDNA targets, they were hybridized to the array using the previously described protocol [Madsen, M. L., D. Nettleton, E. L. Thacker, R. Edwards, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect. Immun. 74:160-166.]. Slides were washed using the Corning UltraGAPS slide wash protocol and dried by centrifugation at 1500 x g for two minutes.

tag: Strain 232 culture grown in friis media to mid-log phase. 250 ml flask containing 150 ml of culture were grown to early exponential phase as determined by color changing units.


title: H2O2 slide 2 upper


title: H2O2 slide 2 lower

tag: 250 ml flask containing 150 ml of culture were grown to early exponential phase as determined by color changing units.


title: skin_patient_M66

first: Jessica

last: Shin

address: 221 Longwood Avenue

institute: Brigham and Women's Hospital

description: Gene expression data from 6mm punch biopsies of skin

hyb_protocol: 5ug of cRNA were hybridized for 16 hours at 48 deg C using an HT Human Genome U133A array plate.

scan_protocol: The plate was scanned on a Genechip HT scanner.

data_processing: Gene expression data was processed using Robust Multi-Chip Average (RMA), as implemented in the R statistical package provided by Bioconductor.  RMA data processing includes background correction, quantile normalization, and expression summarization.  Genes were filtered in order to eliminate those with cross-sample variation, using a variation filter estimated on 14 HeLa cell lines and 5 Strategene samples.

label: SAPE

organism: Homo sapiens

source_name: Human skin biopsies

label_protocol: RNA was then labeled using the standard Affymetrix (Affymetrix Inc., Santa Clara, CA) in vitro transcription labeling protocol.

extract_protocol: 6 mm punch skin biopsies of CTCL skin lesions were obtained and immediately snap frozen in liquid nitrogen.  Tissue was powdered in liquid nitrogen (Cryo-Press, Microtec Co., Chiba, Japan) and total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

tag: Stage IB

tag: Cluster 2


title: skin_patient_M67

tag: Cluster 1


title: skin_patient_M65

tag: Stage III


title: H2O2 slide 1 lower


title: skin_patient_M63


title: skin_patient_M64

tag: Stage IA


title: skin_patient_M61


title: skin_patient_M60


title: skin_patient_T1

tag: Stage IIB


title: skin_patient_M62


title: skin_patient_M59


title: skin_patient_M53


title: skin_patient_M56


title: skin_patient_M57


title: skin_patient_M52


title: skin_patient_M51

tag: Cluster 0


title: skin_patient_M49


title: skin_patient_M55


title: skin_patient_M54


title: skin_patient_M58


title: skin_patient_M48


title: skin_patient_M50a


title: Human Ntera2, SUZ12 Promoter 1 Array, 98344

type: genomic

city: Davis

first: Kimberly

middle: Rose

last: Blahnik

state: CA

address: GBSF 1 Shields Ave

department: Genome and Biomedical Sciences

institute: University of California Davis

description: Human Ntera2 cells

hyb_protocol: The hybridization of DNA samples for ChIP-ChIP analysis was performed by NimbleGen Systems, Inc. Briefly, 13ug of the Cy5-labeled ChIP sample and 13ug of the Cy3-labeled total sample were mixed, dried down, and resuspended in 40 ul of NimbleGen Hybridization Buffer (NimbleGen Systems) plus 1.5 ug of human COT1 DNA. After denaturation, hybridization was carried out in a MAUI Hybridization System (BioMicro Systems) for 18 h at 42°C. The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems), dried by centrifugation.

scan_protocol: The arrays were scanned at 5-um resolution using the GenePix 4000B scanner (Axon Instruments).

data_processing: log base 2 ratios

molecule: genomic DNA

source_name: Ntera2 cells

label_protocol: The labeling of DNA samples for ChIP-ChIP analysis was performed by NimbleGen Systems, Inc. Briefly, each DNA sample (1 ug) was denatured in the presence of 5'-Cy3- or Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1 mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reactions were terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.

extract_protocol: Performed following the 'Chromatin Immunoprecipitation Assay (ChIPs)' protocol provided at http://genomics.ucdavis.edu/farnham

label_protocol: see labeling protocol for channel 1

extract_protocol: see extract protocol for channel 1

tag: control total input


title: skin_patient_M45


title: skin_patient_M46


title: skin_patient_M47


title: 7553-56-2 Iodine, 1 mM 2 h (time course) 1st L


title: Human Ntera2, KAP1 Promoter 1 Array, 100206

description: Human Ntera2 cells


title: Human Ntera2, SUZ Promoter 1 Array, 90787

description: Human Ntera2 cells


title: skin_patient_M44


title: skin_patient_M42


title: skin_patient_M41


title: 7553-56-2 Iodine, 1 mM 1.5 h (time course) 1st H

source_name: Iodine treated with 1 mM for 1.5 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 1 mM (final concentration) then the yeast cells were exposed for 1.5 h.


title: 7553-56-2 Iodine, 1 mM 1 h (time course) 1st L

source_name: Iodine treated with 1 mM for 1 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 1 mM (final concentration) then the yeast cells were exposed for 1 h.

source_name: control (before treatment), Cy3


title: skin_patient_M43


title: skin_patient_M40


title: 7553-56-2 Iodine, 1 mM 2 h (time course) 1st H


title: 7553-56-2 Iodine, 1 mM 1 h (time course) 1st H


title: Human Ntera, Kap1 Promoter 1 Array, 94527

description: Human Ntera2 cells

tag: KAP1 antibody immunoprecipitated DNA


title: 7553-56-2 Iodine, 1 mM 0.5 h (time course) 1st L

source_name: Iodine treated with 1 mM for 0.5 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 1 mM (final concentration) then the yeast cells were exposed for 0.5 h.


title: skin_patient_M38


title: Human Ntera, me3K9 Promoter 1 Array, 100154

description: Human Ntera2 cells

tag: me3K9 antibody immunoprecipitated DNA


title: skin_patient_M36


title: Human Ntera, me3K27 Promoter 1 Array, 100163

description: Human Ntera2 cells

tag: me3K27 antibody immunoprecipitated DNA


title: 7553-56-2 Iodine, 1 mM 0.5 h (time course) 1st H

tag: strain S288C

growth_protocol: Saccharomyces cerevisiae strain S288C cells at OD=1.


title: Human Ntera2, me3K9 Promoter 1 Array, 94920

description: Human Ntera2 cells


title: 7553-56-2 Iodine, 1 mM 1.5 h (time course) 1st L


title: Human Ntera2, me3K9 Promoter 1 Array, 100209

description: Human Ntera2 cells


title: Human Foreskin, me3K27 Promoter 1 Array, 92159

description: Human foreskin

source_name: Human foreskin


title: Human Foot, Kap1 Promoter 1 Array, 104073

description: Human foot

source_name: Human foot


title: Human foot, me3K9 Promoter 1 Array, 99599

description: Human foot

source_name: Human Foot


title: Human Lung, 3meK27 Promoter 1 Array, 95742

description: Human lung

source_name: Human lung


title: skin_patient_M37


title: Human Ntera2, KAP1 Promoter 1 Array, 94917

description: Human Ntera2 cells


title: Human Ntera2, me3K27 Promoter 1 Array, 91209

description: Human Ntera2 cells


title: Human Ntera2, me3K27 Promoter 1 Array, 91211

description: Human Ntera2 cells


title: 12427-38-2 Maneb 2nd

source_name: Maneb treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 20 ul of 2 % chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 2 ppm) then the yeast cells were exposed for 2 h.

treatment_protocol: Maneb Standard (Wako, 136-06533)


title: Human Foreskin, me3K9 Promoter 1 Array, 90492

description: Human Foreskin

source_name: Human Foreskin


title: Human Foot, me3K27 Promoter 1 Array, 90060

description: Human foot


title: Human Lung, me3K9 Promoter 1 Array, 99607

description: Lung

source_name: Lung


title: skin_patient_M35


title: 12427-38-2 Maneb 1st


title: Supress under 40 MPa 25 C 1st

source_name: Supress under 40 MPa 25 C, Cy5

growth_protocol: For the pressure shock treatment, 200 ml of yeast culture, at an exponential growth phase (A660=1.0), was transferred into a 30 or 50 ml syringe. These syringes were pressed with 40 MPa in the 30-11HF4 (High Pressure Equipment Co.) at 25 C for 2 h. After decompression, the cells were harvested by centrifugation.

treatment_protocol: Growing cell under 40 MPa 25 C

source_name: control (before pressure treatment), Cy3

growth_protocol: 200 ml of yeast culture, at an exponential growth phase (A660=1.0), was harvested by centrifugation.

treatment_protocol: before pressure treatment


title: skin_patient_M34


title: Recovery from 40 MPa 4C 2nd

source_name: Recovery from 40 MPa 4C, Cy5

growth_protocol: For the pressure shock treatment, 200 ml of yeast culture, at an exponential growth phase (A660=1.0), was centrifuged and resuspended in 10 ml YPD medium in a 10 ml syringe. These syringes were pressed with 40 MPa for 16 h. To achieve pressurization, we used the 30-11HF4 (High Pressure Equipment Co.). During the treatment, the temperature was maintained by an ice-water bath. After decompression, the cells were resuspended in 200 ml fresh YPD medium and incubated for 1 h at 25°C. The yeast cells were then centrifuged and washed in distilled water before storage at −80°C.

treatment_protocol: Recovery from 40 MPa 4C

source_name: control (without pressure treatment), Cy3

growth_protocol: For the control cells, 200 ml of yeast culture, at an exponential growth phase (A660=1.0), was centrifuged and resuspended in 10 ml YPD medium in a 10 ml syringe. These syringes were kept under 0.1 MPa in ice-water bath for 16 h. The cells were resuspended in 200 ml fresh YPD medium and incubated for 1 h at 25°C. The yeast cells were then centrifuged and washed in distilled water before storage at −80°C.

treatment_protocol: without pressure treatment


title: skin_patient_M31

source_name: Human skin biopsies


title: Recovery from 40 MPa 4C 3rd


title: 12122-67-7 Zineb 3rd

source_name: Zineb treated for 2 h, Cy5

treatment_protocol: Zineb Standard (Wako, 266-00783)

source_name: control (without treatment), Cy3


title: 1897-45-6 TPN 2nd

source_name: TPN treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 40 ul of 50 mM chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 10 uM) then the yeast cells were exposed for 2 h.

treatment_protocol: TPN Standard (Wako 200-06581)


title: skin_patient_M25


title: skin_patient_M30


title: skin_patient_M23


title: 137-26-8 Thiuram, 75 uM 2 h 3rd

source_name: Thiuram treatment with 75 uM for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 300 ul of 50 mM chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 75 uM) then the yeast cells were exposed for 2 h.

treatment_protocol: Thiuram Standard (Wako 204-11371)


title: skin_patient_M27


title: skin_patient_M24


title: skin_patient_M22


title: 23513-14-6 Gingerol 1st

source_name: Gingerol treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture (final concentration; 400 ppm) then the yeast cells were exposed for 2 h.

treatment_protocol: Gingerol (Nacalai tesque, 16739-86)


title: skin_patient_M29


title: skin_patient_M28


title: skin_patient_M21


title: skin_patient_M20


title: Supress under 40 MPa 25 C 2nd


title: 12122-67-7 Zineb 2nd


title: skin_patient_M19


title: skin_patient_M18


title: skin_patient_M17


title: skin_patient_M14


title: skin_patient_M13


title: skin_patient_M16


title: skin_patient_M9


title: skin_patient_M8


title: skin_patient_M12


title: skin_patient_M15


title: skin_patient_M11


title: skin_patient_M5E


title: skin_patient_M5a


title: skin_patient_M10


title: skin_patient_M1


title: skin_patient_M2


title: Thermal Neutron 20.8 Gy 3rd L

source_name: Thermal Neutron 20.8 Gy exposed, Cy5

growth_protocol: 50 ml of Saccharomyces cerevisiae strain S288C (OD=1) cells were harvested and washed with ice-cold salin (0.9 % NaCl), and resuspended in 2 ml ice-cold salin and transferred into cuvettes. The cells were exposed with heavy ion radiation for 20 h, that was corresponding to 20.8 Gy. During the irradiation procedure, yeast cells were kept at low temperature in a resting state as much as possible and irradiated cells were kept on ice until a recovery growth. The cells were resuspended in fresh YPD medium (50 ml) and allowed to grow for 40 min at 25 C.

treatment_protocol: The Heavy Water Neutron Irradiation Facility (HWNIF) of the Kyoto University Research Reactor (KUR) was used for thermal neutron irradiation.  The dose rate of global irradiation was 17 mGy/min, and the dose rate of thermal neutrons was 1.0-2.0 mGy/min.  The net thermal neutrons and net fast neutrons were measured by gold foil activation analysis.  Net dose of gamma rays including net secondary gamma rays were measured with a thermo luminescence dosimeter.

source_name: control (without irradiation), Cy3

growth_protocol: 50 ml of Saccharomyces cerevisiae strain S288C (OD=1) cells were harvested and washed with ice-cold salin (0.9 % NaCl), and resuspended in 2 ml ice-cold salin and transferred into tissue culture flasks. For 20 h, yeast cells were kept at low temperature in a resting state as much as possible, after that cells were kept on ice until a recovery growth. The cells were resuspended in fresh YPD medium (50 ml) and allowed to grow for 40 min at 25 C.

treatment_protocol: without irradiation


title: Thermal Neutron 20.8 Gy 2nd H


title: Thermal Neutron 20.8 Gy 1st L


title: Thermal Neutron 20.8 Gy 3rd H


title: Thermal Neutron 20.8 Gy 1st H


title: skin_patient_M33


title: skin_patient_M7


title: Thermal Neutron 20.8 Gy 2nd L


title: Human Lung, 3meK27 Promoter 2 Array, 95631

description: Human lung

tag: 3meK27 antibody immunoprecipitated DNA


title: Heavy ion radiation 25 Gy 1st H

source_name: Heavy ion radiation 25 Gy exposed, Cy5

growth_protocol: 50 ml of Saccharomyces cerevisiae strain S288C (OD=1) cells were harvested and washed with ice-cold salin (0.9 % NaCl), and resuspended in 5 ml ice-cold salin and transferred into tissue culture flasks. The cells were exposed with heavy ion radiation for 10 min, that was corresponding to 25 Gy. During the irradiation procedure, yeast cells were kept at low temperature in a resting state as much as possible and irradiated cells were kept on ice until a recovery growth. The cells were resuspended in fresh YPD medium (50 ml) and allowed to grow for 40 min at 25 C.

treatment_protocol: An experiment was carried out at a physics/general beam line (PH2) at Heavy Ion Medical Accelerator (HIMAC) in the International Space Radiation Laboratory (NIRS). Carbon-12 ions (C) were accelerated by HIMAC up to a mono-energetic 290 MeV/u.  Exposure was conducted using horizontal carbon beams with a dose rate of 3 Gy/min.

growth_protocol: 50 ml of Saccharomyces cerevisiae strain S288C (OD=1) cells were harvested and washed with ice-cold salin (0.9 % NaCl), and resuspended in 5 ml ice-cold salin and transferred into tissue culture flasks. For 10 min, yeast cells were kept at low temperature in a resting state as much as possible and irradiated cells were kept on ice until a recovery growth. The cells were resuspended in fresh YPD medium (50 ml) and allowed to grow for 40 min at 25 C.


title: Gamma ray 17 Gy 2nd

source_name: Gamma ray 17 Gy exposed, Cy5

growth_protocol: 50ml of Saccharomyces cerevisiae strain S288C (OD=1) cells were harvested and washed with ice-cold salin (0.9%NaCl), and resuspended in 2ml ice-cold salin and transferred into cuvettes. The cells were exposed with gamma ray for about 20.5 hr, that was corresponding to 17 Gy of gamma ray. During the irradiation procedure, yeast cells were kept at low temperature in a resting state as much as possible and irradiated cells were kept on ice until a recovery growth. The cells were resuspended in fresh YPD medium (50 ml) and allowed to grow for 40 min at 25 C.

treatment_protocol: A Cs-137 g-ray source (Sangyo Kagaku, Tokyo, Japan) was used for gamma ray irradiation in RIRBM.  The dose rate was 1.4 Gy/min.

growth_protocol: 50ml of Saccharomyces cerevisiae strain S288C (OD=1) cells were harvested and washed with ice-cold salin(0.9%NaCl), and resuspended in 2ml ice-cold salin and transferred into cuvettes. For about 20.5 hr, yeast cells were kept at low temperature in a resting state as much as possible. After that, the cells were kept on ice until a recovery growth, and the cells were resuspended in fresh YPD medium (50 ml) and allowed to growth for 40 min at 25 C.


title: Heavy ion radiation 25 Gy 2nd H


title: Heavy ion radiation 25 Gy 2nd L


title: 7758-99-8 Copper(II) Sulfate 10mM 3rd L

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from low power scanning. Data with flag value 0 were used for LOWESS normalization processing, although original raw data were remaining in this table. Merging high and low scanned data were done on the GeneSpring and represented as “AVG_VALUE”. However, this data was eliminated from further analysis.

source_name: CuSO4 treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 10 mM (final concentration) then the yeast cells were exposed for 2 h.

treatment_protocol: Copper(2) Sulfate Pentahydrate (Nacalai tesque 09604-85)

source_name: control (without treatment for 2 h), Cy3

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 2 h without any treatment.


title: Gamma ray 17 Gy 1st


title: Heavy ion radiation 25 Gy 1st L


title: Heavy ion radiation 25 Gy 3rd L


title: Gamma ray 17 Gy 3rd


title: Heavy ion radiation 25 Gy 3rd H


title: 251390210290K27_MET24-16

city: Chicago

first: Jindan

last: Yu

state: IL

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

description:
H3K27me3 binding in prostate cancer metastatic to liver 1, array 1
Biological replicate 1 of 3. H3K27me3 antibody

hyb_protocol: human Cot DNA was added to labelled cDNA and hybridized in Agilent blocking and hybridization buffer to arrays in Agilent hybridization chamber and Oven at 65C for 72hrs.

scan_protocol: Scanned on an Agilent scanner Images were quantified using Agilent Feature Extraction Software

data_processing: median normalized, background subtracted data obtained

source_name: ChIP-enriched, H3K27me3  antibody; labeled with Cyanine-5 (red).

label_protocol: 30ul of ChIP product was LM-PCR amplified, labeled using Invitrogen BioPrimer Array CGH genomic labeling system.

extract_protocol: ChIP performed using corresponding antibodies against SUZ12 and H3K27me3 respectively.

tag: H3K27me3 antibody

tag: metastatic prostate cancer to liver

tag: patient 1

tag: ChIP-enriched genomic DNA

source_name: whole cell extract DNA

tag: sheared genomic DNA


title: Human Foot, me3K27 Promoter 2 Array, 98035

description: Human foot

source_name: Human foot


title: 251390210224-SUZ12-MET26-5

description:
SUZ12 binding in prostate cancer metastatic to liver 2, array 1
Biological replicate 2 of 3. SUZ12 antibody

source_name: ChIP-enriched, SUZ12 antibody; labeled with Cyanine-5 (red).

tag: SUZ12 antibody

tag: patient 2


title: Human Ntera, Kap1 Promoter 2 Array, 94180

description: Human Ntera2 cells

source_name: Ntera2 cells


title: 251390210223-K27-MET26-5

description:
H3K27me3 binding in prostate cancer metastatic to liver 2, array 1
Biological replicate 2 of 3. H3K27me3 antibody


title: 7758-99-8 Copper(II) Sulfate 10mM 2nd L


title: 7758-99-8 Copper(II) Sulfate 10mM 3rd H

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from high power scanning. Data with flag value 0 were used for LOWESS normalization processing, although original raw data were remaining in this table. Merging high and low scanned data were done on the GeneSpring and represented as “AVG_VALUE”. However, the data in “AVG_VALUE” was not used for further analysis.


title: 251390210222-K27-MET25-51

description:
H3K27me3 binding in prostate cancer metastatic to lung, array 1
Biological replicate 3 of 3. H3K27me3 antibody

tag: metastatic prostate cancer to lung

tag: patient 3


title: 7758-99-8 Copper(II) Sulfate 10mM 1st

description: Data with flag value 0 were used for LOWESS normalization processing, although original raw data were remaining in this table. To give the same format, this file has also “AVG_VALUE” column.

source_name: control (without exposure), Cy3


title: 7758-99-8 Copper(II) Sulfate 10mM 2nd H


title: Human Foot, Kap1 Promoter 2 Array, 101926

description: Human foot


title: Human Ntera, me3K9 Promoter 2 Array, 94173

description: Human Ntera2 cells


title: 67-56-1 Methanol 5 % 3rd H

source_name: MeOH treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 5 % (final concentration) then the yeast cells were exposed for 2 h.

treatment_protocol: Methanol (Wako 131-01826)


title: 50-00-0 Formaldehyde 1.8mM 3rd L

source_name: FAH treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 1.8 mM (final concentration) then the yeast cells were exposed for 2 h.

treatment_protocol: Formaldehyde Solution (Wako 064-00406)


title: Human Foreskin, me3K27 Promoter 2 Array, 92019

description: Human foreskin

source_name: Human foreskin


title: 67-56-1 Methanol 5 % 2nd L

treatment_protocol: without treatment


title: Human Ntera, me3K27 Promoter 2 Array, 100189

description: Human Ntera2 cells


title: Human Foreskin, me3K9 Promoter2 Array, 92056

description: Human Foreskin

source_name: Human Foreskin


title: Human Lung, me3K9 Promoter 2 Array, 99032

description: Human Lung

source_name: Human Lung

source_name: Human lung


title: 67-56-1 Methanol 5 % 3rd L


title: 67-56-1 Methanol 5 % 1st L


title: 50-00-0 Formaldehyde 1.8mM 3rd H


title: 67-56-1 Methanol 5 % 2nd H


title: 50-00-0 Formaldehyde 1.8mM 2nd H


title: 50-00-0 Formaldehyde 1.8mM 2nd L


title: Human Ntera, Kap1 ENCODE Array, 83201

description: Human Ntera2 cells


title: 67-56-1 Methanol 5% 1st H


title: 251390210221Suz12-MET24-16

description:
SUZ12 binding in prostate cancer metastatic to liver 1, array 1
Biological replicate 1 of 3. SUZ12 antibody


title: Human Ntera, Kap1 ENCODE Array, 87645

description: Human Ntera2 cells


title: Human Foot, me3K9 Promoter 2 Array, 90387

description: Human Foot

source_name: Human Foot


title: 50-00-0 Formaldehyde 1.8mM 1st L


title: 13463-41-7 Zinc pyrithione 2nd H

source_name: ZnPT treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 12.6 uM (final concentration) then the yeast cells were exposed for 2 h.

treatment_protocol: Zinc Pyrithione Standard (Wako 264-01541) dissolved in DMSO


title: 13463-41-7 Zinc pyrithione 2nd L


title: 50-00-0 Formaldehyde 1.8 mM 1st H


title: RWPE cell treated with EZH2 adenovirus for 72 hours

description: time-course 6 of 6 of EZH2-overexpression

hyb_protocol: human Cot DNA and yeast tRNA were added to labelled cDNA and hybridized in SSC/SDS buffer to arrays

scan_protocol: Scanned on an Affymetrix Axon scanner Images were quantified using Genepix6.0

source_name: Total RNA from EZH2-adenovirus infected cells, labelled with Cy5

label_protocol: 30µg of total RNA were primed with 6 µl of poly-dT primers for 10min, then reverse-transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dCTP, dGTP, with 25 µM dTTP, 25 µM aadUTP; the reaction mix were then cleaned and concentrated by Microcon filter, and labelled with Cy3 or Cy5 dyes at RT for 1hour

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

tag: RWPE

tag: EZH2 adenovirus-infected

tag: Age

source_name: Total RNA from vector adenovirus-infected cells labelled with Cy3

tag: vector-adenovirus-infected


title: 13463-41-7 Zinc pyrithione 1st H

source_name: control (without treatment for 2 h), Cy3


title: 13463-41-7 Zinc pyrithione 3rd L


title: 13463-41-7 Zinc pyrithione 3rd H


title: RWPE cell treated with EZH2 adenovirus for 24 hours

description: time-course 4 of 6 of EZH2-overexpression


title: 13463-41-7 Zinc pyrithione 1st L


title: H16N2 cell treated with EZH2 adenovirus for 72 hours

description: time-course 5 of 5 of EZH2-overexpression


title: RWPE cell treated with EZH2 adenovirus for 48 hours

description: time-course 5 of 6 of EZH2-overexpression


title: RWPE cell treated with EZH2 adenovirus for 3 hours

description: time-course 1 of 6 of EZH2-overexpression


title: H16N2 cell treated with EZH2 adenovirus for 48 hours

description: time-course 4 of 5 of EZH2-overexpression


title: RWPE cell treated with EZH2 adenovirus for 12 hours

description: time-course 3 of 6 of EZH2-overexpression


title: RWPE cell treated with EZH2 adenovirus for 6 hours

description: time-course 2 of 6 of EZH2-overexpression


title: RWPE cell treated with EZH2 siRNA Replicate  2

description: Biological replicate 2 of 3. EZH2-siRNA-treated  vs. luciferase siRNA-treated control

source_name: Total RNA from EZH2 siRNA-treated RWPE cells labeled with Cyanine-5 (red).

tag: EZH2 siRNA-transfected

value: day 2

source_name: Total RNA from luciferase siRNA-treated RWPE cells labeled with Cyanine-3 (green).

tag: luciferase siRNA-transfected


title: H16N2 cell treated with EZH2 adenovirus for 12 hours

description: time-course 2 of 5 of EZH2-overexpression


title: RWPE cell treated with EZH2 siRNA Replicate  3

description: Biological replicate 3 of 3. EZH2-siRNA-treated  vs. luciferase siRNA-treated control


title: H16N2 cell treated with EZH2 adenovirus for 24 hours

description: time-course 3 of 5 of EZH2-overexpression


title: H16N2 cell treated with EZH2 siRNA Replicate  3

source_name: Total RNA from EZH2 siRNA-treated H16N2 cells labeled with Cyanine-5 (red).

source_name: Total RNA from luciferase siRNA-treated H16N2 cells labeled with Cyanine-3 (green).


title: RWPE cell treated with EZH2 siRNA Replicate  1

description: Biological replicate 1 of 3. EZH2-siRNA-treated  vs. luciferase siRNA-treated control


title: H16N2 cell treated with EZH2 siRNA Replicate  1


title: RWPE cell treated with control siRNA Replicate 1

description: Biological replicate 1 of 3. luciferase siRNA-treated control vs. luciferase siRNA-treated control, self-self hybridization

source_name: Total RNA from control siRNA-treated RWPE cells labeled with Cyanine-5 (red).

tag: control siRNA-transfected


title: H16N2 cell treated with luciferase siRNA Replicate 1

source_name: Total RNA from luciferase siRNA-treated H16N2 cells labeled with Cyanine-5 (red).


title: H16N2 cell treated with luciferase siRNA Replicate  2

description: Biological replicate 2 of 3. luciferase siRNA-treated control vs. luciferase siRNA-treated control, self-self hybridization


title: RWPE cell treated with control siRNA Replicate  2


title: H16N2 cell treated with EZH2 adenovirus for 6 hours

description: time-course 1 of 5 of EZH2-overexpression


title: H16N2 cell treated with luciferase siRNA Replicate  3

description: Biological replicate 3 of 3. luciferase siRNA-treated control vs. luciferase siRNA-treated control, self-self hybridization


title: mock IP, replicate 1

city: Worcester

first: Marcus

last: Johansson

address: 55 Lake Avenue North

department: Molecular Genetics and Microbiology

institute: University of Massachusetts Medical School

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Yeast Genome S98 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix GCOS using global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250

source_name: mock IP RNA

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

growth_protocol: Cells were grown in YEPD medium at 30ºC.

extract_protocol: Cells were lysed by manual grinding for 30 minutes with intermittent addition of liquid nitrogen while keeping the mortar on dry ice. Ground cells were thawed on ice in 2 ml of buffer B (buffer A containing 0.5 mM DTT, 1X protease inhibitor cocktail (complete EDTA free, Roche Applied Science), 25 U/ml Protector RNase inhibitor (Roche Applied Science), 10 mM ribonucleoside-vanadyl complex (New England Biolabs)) per gram material. The crude extracts were cleared by centrifugation at 3,000 g for 5 minutes. Following a second centrifugation at 10,000 g for 30 minutes, the extracts were incubated at 4ºC for 2 hours in the presence of 200 μl of buffer A pre-washed IgG Sepharose (GE Healthcare) suspension. The remaining steps of the IgG immunopurification protocol were performed essentially as described (Puig et al., Methods, 24, 218-229, 2001). The buffers used were; 10 mM Tris-HCl pH 8.0, 140 mM KCl, 0.1% NP-40 (wash buffer) and 10 mM Tris-HCl pH 8.0, 140 mM KCl , 0.1% NP-40, 0.5 mM EDTA, 1 mM DTT (TEV cleavage buffer). RNA in the TEV (AcTEV, Invitrogen) eluates was isolated by phenol/chloroform extraction followed by isopropanol precipitation. The precipitated RNA was dissolved in RNase free water. An equivalent amount of RNA from the Upf1p-TAP and mock samples was further purified using the RNeasy Micro Kit (Qiagen).


title: RWPE cell treated with control siRNA Replicate  3


title: mock IP, replicate 4


title: mock IP, replicate 2


title: H16N2 cell treated with EZH2 siRNA Replicate  2


title: Upf1p-TAP IP, replicate 2

source_name: Upf1p-TAP IP RNA

tag: Strain MJY11 (MATα ura3-1 leu2-3,112 his3-11,15 trp1-1 ade2-1 can1-100 UPF1::TAP-K. lactis TRP1)


title: Upf1p-TAP IP, replicate 1


title: Upf1p-TAP IP, replicate 3


title: mock IP, replicate 3


title: D-nmd2D-time 60 min, biological replicate 4

first: Feng

last: He

address: 368 Plantation Street

department: Microbiology and Physiological Systems

description: a nmd2::HIS3 strain harboring an empty URA3 vector

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast YG-S98 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

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

growth_protocol: Cells were grown in SC medium containing galatocse but lacking uracile at 30°C

extract_protocol: Hot phenol

tag: Genotype, nmd2::HIS3


title: Upf1p-TAP IP, replicate 4


title: D-GAL-NMD2-time 0 min, biological replicate 4

description: a nmd2::HIS3 strain harboring the GAL-NMD2 on a plasmid

tag: Genotype, GAL-NMD2


title: D-GAL-NMD2-time 10 min, biological replicate 4


title: D-nmd2D-time 10 min, biological replicate 4


title: D-GAL-NMD2-time 20 min, biological replicate 4


title: D-GAL-NMD2-time 60 min, biological replicate 4


title: D-nmd2D-time 0 min, biological replicate 4


title: D-GAL-NMD2-time 40 min, biological replicate 4


title: C-nmd2D-time 20 min, biological replicate 3


title: C-nmd2D-time 0 min, biological replicate 3


title: C-nmd2D-time 10 min, biological replicate 3


title: C-nmd2D-time 60 min, biological replicate 3


title: C-GAL-NMD2-time 60 min, biological replicate 3


title: C-nmd2D-time 40 min, biological replicate 3


title: D-nmd2D-time 20 min, biological replicate 4


title: C-GAL-NMD2-time 40 min, biological replicate 3


title: C-GAL-NMD2-time 20 min, biological replicate 3


title: D-nmd2D-time 40 min, biological replicate 4


title: C-GAL-NMD2-time 10 min, biological replicate 3


title: C-GAL-NMD2-time 0 min, biological replicate 3


title: B-nmd2D-time 60 min, biological replicate 2


title: 251390310269-K27-MET26-5

description:
H3K27me3 binding metastatic to liver 2, array 2
Biological replicate 2 of 3. H3K27me3 antibody

source_name: ChIP-enriched, H3K27me3  antibody; labeled with Cyanine-5 (red).

tag: H3K27me3 antibody

tag: metastatic prostate cancer to liver

source_name: whole cell extract DNA


title: 251390310266K27_MET24-16

description:
H3K27me3 binding metastatic to liver 1, array 2
Biological replicate 1 of 3. H3K27me3 antibody

tag: patient 1

tag: ChIP-enriched genomic DNA

tag: sheared genomic DNA


title: 251390310270-SUZ12-MET26-5

description:
SUZ12 binding metastatic to liver 2, array 2
Biological replicate 2 of 3. SUZ12 antibody

source_name: ChIP-enriched, SUZ12 antibody; labeled with Cyanine-5 (red).

tag: SUZ12 antibody

tag: patient 2


title: B-nmd2D-time 40 min, biological replicate 2


title: 251390310267Suz12-MET24-16

description:
SUZ12 binding metastatic to liver 1, array 2
Biological replicate 1 of 3. SUZ12 antibody


title: 251390310268-K27-MET25-51

description:
H3K27me3 binding metastatic to lung, array 2
Biological replicate 3 of 3. H3K27me3 antibody

tag: metastatic prostate cancer to lung

tag: patient 3


title: Human Ntera2 cells, Nimblegen Expression Array, replicate 1

description: Human Ntera2 cells, replicate 1

hyb_protocol: The RNA was hybridized to human whole genome expression microarrays from Nimblegen, which contain probes for every human gene based on genome build HG18 from the UCSC database (more details at http://www.nimblegen.com). 10 ug total RNA were used to synthesize cDNA using the SuperScript Double-Stranded cDNA synthesis kit (Invitrogen).

scan_protocol: Nimblegen technology

data_processing: ArrayStar v2.0 available through Nimblegen

label: bio-11-CTP and bio-16 UTP

source_name: Ntera2 cells

label_protocol: Labeling performed by Nimblegen

extract_protocol: Total RNA was prepared from 5x106 Ntera cells using RNAeasy Kit (Qiagen) following the manufacturerÕs instructions. RNA quality was ensured using the Agilent Systems Bioanalyzer. !Sample_label_protocol_ch1 = The labeling of RNA samples, array hybridization and preliminary RNA expression analysis (data normalization) was performed by NimbleGen Systems, Inc.

tag: Expression array using cell RNA extract from Ntera cell line


title: A-nmd2D-time 40 min, biological replicate 1


title: B-GAL-NMD2-time 60 min, biological replicate 2


title: B-nmd2D-time 20 min, biological replicate 2


title: B-nmd2D-time 0 min, biological replicate 2


title: A-nmd2D-time 10 min, biological replicate 1


title: A-nmd2D-time 20 min, biological replicate 1


title: B-GAL-NMD2-time 40 min, biological replicate 2


title: B-GAL-NMD2-time 20 min, biological replicate 2


title: B-nmd2D-time 10 min, biological replicate 2


title: B-GAL-NMD2-time 0 min, biological replicate 2


title: A-nmd2D-time 60 min, biological replicate 1


title: B-GAL-NMD2-time 10 min, biological replicate 2


title: A-GAL-NMD2-time 60 min, biological replicate 1


title: A-GAL-NMD2-time 0 min, biological replicate 1


title: A-GAL-NMD2-time 40 min, biological replicate 1


title: Human Ntera2 cells, Nimblegen Expression Array, replicate 2

description: Human Ntera2 cells, replicate 2


title: H69 tumor untreated, biological rep1

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

description: Early gene expression data from xenograft tumors following sensitizing and PDT treatment.

hyb_protocol: Following fragmentation, 10 micrograms of cRNA wer hybridized for 16 hr at 45C on GeneChip Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCOS Scanner 3000.

data_processing: Data was analyzed with Agilent Genespring GX v. 7.3.1 using Affymetrix GCOS generated flag data from scaled CHP files, and RMA-normalized CEL files.

source_name: NCI-H69 xenografts, PDT treated and control untreated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 micrograms total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed from flash frozed/pulverized samples according to the manufacturer's instructions.

treatment_protocol: Sample tumor (untreated) collected parallel to PDT treated sample

tag: NCI-H69 human small cell lung cancer


title: H69 tumor untreated, biological rep3


title: H69 tumor post-PDT, biological rep2

treatment_protocol: Sample tumor collected 4 hours after PDT treatment


title: A-GAL-NMD2-time 10 min, biological replicate 1


title: A-GAL-NMD2-time 20 min, biological replicate 1


title: A-nmd2D-time 0 min, biological replicate 1


title: H69 tumor untreated, biological rep2


title: H69 tumor post-PDT, biological rep1


title: H69 tumor post-PDT, biological rep3

data_processing:
Data was analyzed with Agilent Genespring GX v. 7.3.1 using Affymetrix GCOS generated flag data from scaled CHP files, and RMA-normalized CEL files.
Data was analyzed with Agilent Genespring GX v. 7.3.1 using Affymetrix GCOS generated flag data from scaled CHP files, and RMA-normalized CEL files.


title: CM774-U133A, biological rep2

city: Gainesville

first: bilian

last: jin

state: FL

address: 1601 SW Archer Road

institute: University of Florida

description: Gene expression data from CM774

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133A and U133B Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Homo Sapiens CM774

growth_protocol: ICF LCLs were grown in RPMI1640 media supplemented with 2 mM L-glutamine  and 20% heat-inactivated fetal bovine serum;Normal LCLs were grown in the same media except 10% fetal bovine serum was used.

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

treatment_protocol: Cells were harvested when 70-80% confluency.

tag: Genotype

value: DNMT 3B wild type and mutation

tag: normal


title: 10759-U133A, biological rep3

description: Gene expression data from 10759 LCL

source_name: Homo Sapiens 10759

tag: ICF


title: CM304-U133A, biological rep2

description: Gene expression data from CM304

source_name: Homo Sapiens CM304


title: 10759-U133A, biological rep1

description: Gene expression data from 10759 LCL


title: CM774-U133A, biological rep3

description: Gene expression data from CM774


title: 4088-U133A, biological rep1

description: Gene expression data from 4088 LCL

source_name: Homo Sapiens 4088


title: 7553-56-2 Iodine, 1 mM 2.5 h (time course) 1st H

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from high power scanning. Data with flag value 0 were used for LOWESS normalization processing, although original raw data were remaining in this table. Merging high and low scanned data were done on the GeneSpring and represented as “AVG_VALUE”.

source_name: Iodine treated with 1 mM for 2.5 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 1 mM (final concentration) then the yeast cells were exposed for 2.5 h.

treatment_protocol: Iodine (Wako 095-00392). An iodine solution (0.5 M) was prepared just before use as 12.7 g iodine and 25 g iodide in 100 ml solution

tag: strain S288C

source_name: control (before treatment), Cy3

growth_protocol: Saccharomyces cerevisiae strain S288C cells at OD=1.

treatment_protocol: before treatment


title: 4088-U133A, biological rep2

description: Gene expression data from 4088 LCL


title: 7553-56-2 Iodine, 1 mM 2 h (time course) 2nd L

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from low power scanning. Data with flag value 0 were used for LOWESS normalization processing, although original raw data were remaining in this table. Merging high and low scanned data were done on the GeneSpring and represented as “AVG_VALUE”.

source_name: Iodine treated with 1 mM for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 1 mM (final concentration) then the yeast cells were exposed for 2 h.


title: LCL1-U133A, biological rep1

description: Gene expression data from LCL1

source_name: Homo Sapiens LCL1


title: 7553-56-2 Iodine, 1 mM 2 h (time course) 2nd H


title: 10759-U133A, biological rep2

description: Gene expression data from 10759 LCL


title: CM304-U133A, biological rep1

description: Gene expression data from CM304


title: GM08729-U133A, biological rep2

description: Gene expression data from GM08729 LCL

source_name: Homo Sapiens GM08729


title: GM08714-U133A, biological rep2

description: Gene expression data from GM08714 LCL

source_name: Homo Sapiens GM08714


title: GM08714-U133A, biological rep1

description: Gene expression data from GM08714 LCL


title: LCL1-U133A, biological rep3

description: Gene expression data from LCL1


title: 7553-56-2 Iodine, 1 mM 1.5 h (time course) 2nd H

source_name: Iodine treated with 1 mM for 1.5 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 1 mM (final concentration) then the yeast cells were exposed for 1.5 h.


title: 7553-56-2 Iodine, 1 mM 1 h (time course) 2nd L

source_name: Iodine treated with 1 mM for 1 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 1 mM (final concentration) then the yeast cells were exposed for 1 h.


title: CM304-U133A, biological rep3

description: Gene expression data from CM304


title: 7553-56-2 Iodine, 1 mM 1.5 h (time course) 2nd L


title: GM08729-U133A, biological rep3

description: Gene expression data from GM08729 LCL


title: CM774-U133A, biological rep1

description: Gene expression data from CM774


title: GM08728-U133A, biological rep3

description: Gene expression data from GM08728 LCL

source_name: Homo Sapiens GM08728


title: GM08728-U133A, biological rep1

description: Gene expression data from GM08728LCL


title: GM08728-U133A, biological rep2

description: Gene expression data from GM08728 LCL


title: 7553-56-2 Iodine, 1 mM 2.5 h (time course) 1st L


title: 7553-56-2 Iodine, 1 mM 1 h (time course) 2nd H


title: LCL1-U133A, biological rep2

description: Gene expression data from LCL1


title: GM08729-U133A, biological rep1

description: Gene expression data from GM08729 LCL


title: 7553-56-2 Iodine, 1 mM 0.5 h (time course) 2nd L

source_name: Iodine treated with 1 mM for 0.5 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 1 mM (final concentration) then the yeast cells were exposed for 0.5 h.


title: 7553-56-2 Iodine, 1 mM 0.5 h (time course) 2nd H


title: 67-68-5 Dimethylsulfoxide 1st

description: Data with flag value 0 were used for LOWESS normalization processing.

source_name: DMSO treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture (final concentration; 10 %=1.41 M) then the yeast cells were exposed for 2 h.

treatment_protocol: dimethylsulfoxide (Wako, 043-07216)

source_name: control (without treatment), Cy3


title: 66-81-9 Cycloheximide 2nd

source_name: Cycloheximide treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 60 ul of 50 mM chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 15 uM) then the yeast cells were exposed for 2 h.

treatment_protocol: Cycloheximide, 95% (Wako, 038-11131)


title: 137-26-8 Thiuram, 75 uM 30 min 3rd

source_name: Thiuram treatment with 75 uM for 30 min, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 300 ul of 50 mM chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 75 uM) then the yeast cells were exposed for 30 min.

treatment_protocol: Thiuram Standard (Wako 204-11371)

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 30 min without any treatment.


title: 1897-45-6 TPN 1st

source_name: TPN treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 40 ul of 50 mM chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 10 uM) then the yeast cells were exposed for 2 h.

treatment_protocol: TPN Standard (Wako 200-06581)

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 2 h without any treatment.


title: 137-26-8 Thiuram, 75 uM 30 min 2nd


title: 67-68-5 Dimethylsulfoxide 2nd


title: Raji untreated (2)

city: Berlin

first: Anke

last: Ehlers

state: Berlin

address: Hindenburgdamm 30

department: Institute of Pathology

institute: Charité Universitätsmedizin

description: no

data_processing: GCOS TGT=2000

source_name: Cell line

label_protocol: Affymetrix standard protocol

growth_protocol: RPMI 1640 supplemented with 10% fetal bovine serum at 37°C and 5% CO2

extract_protocol: Qiagen

treatment_protocol: untreated

tag: Burkitt lymphoma


title: 58-89-9 Lindane 3rd

source_name: Lindane treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture (final concentration; 1.25 mM) then the yeast cells were exposed for 2 h.

treatment_protocol: Lindane, >99 % (Sigma, H4500)


title: 137-26-8 Thiuram, 75 uM 30 min 1st

source_name: Thiuram treated for 30 min with 75 uM, Cy5


title: 137-26-8 Thiuram, 75 uM 15 min 3rd

source_name: Thiuram treatment with 75 uM for 15 min, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 300 ul of 50 mM chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 75 uM) then the yeast cells were exposed for 15 min.

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 15 min without any treatment.


title: Namalwa untreated (1)

description: no


title: L1236 untreated (2)

description: no

tag: classical Hodgkin lymphoma


title: Raji + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h) (1)

description: no


title: Namalwa + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h) (2)

description: no


title: Raji untreated (1)

description: no


title: Namalva + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h) (1)

description: no


title: Raji + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h) (2)

description: no


title: L1236 + 5 µM 5-aza-dC (5 days) (2)

description: no

treatment_protocol: 5 µM 5-aza-dC (5 days)


title: L1236 untreated (1)

description: no


title: L1236 + 5 µM 5-aza-dC (5 days) (1)

description: no


title: L428 untreated (2)

description: no


title: 137-26-8 Thiuram, 75 uM 15 min 1st

source_name: Thiuram treated for 15 min with 75 uM, Cy5


title: 137-26-8 Thiuram, 75 uM 15 min 2nd


title: 58-89-9 Lindane 1st


title: L428 untreated (1)

description: no


title: 66-81-9 Cycloheximide 3rd


title: Namalwa untreated (2)

description: no


title: 151-21-3 Sodium dodecyl sulfate 1st

source_name: SDS treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture (final concentration; 0.01 %) then the yeast cells were exposed for 2 h.

treatment_protocol: Sodium dodecyl sulfate, >=98.5 % (Sigma, L4509)


title: 404-86-4 Capsaicin 2nd

source_name: Capsaicin treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture (final concentration; 250 ppm) then the yeast cells were exposed for 2 h.

treatment_protocol: Capsaicin (Wako, 033-15961)


title: 87-86-5 Pentachlorophenol 3rd

source_name: PCP treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 200 ul of 50 mM chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 50 uM) then the yeast cells were exposed for 2 h.

treatment_protocol: Pentachlorophenol (Nacalai tesque, 262-28)


title: 23513-14-6 Gingerol 3rd

source_name: Gingerol treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture (final concentration; 400 ppm) then the yeast cells were exposed for 2 h.

treatment_protocol: Gingerol (Nacalai tesque, 16739-86)

treatment_protocol: without treatment


title: 151-21-3 Sodium dodecyl sulfate 2nd


title: L428 + + 5 µM 5-aza-dC (5 days) (2)

description: no


title: KMH2 + 5 µM 5-aza-dC (5 days) (2)

description: no


title: 404-86-4 Capsaicin 3rd


title: KMH2 + 5 µM 5-aza-dC (5 days) (1)

description: no


title: 10759-U133B, biological rep3

description: Gene expression data from 10759 LCL

source_name: Homo Sapiens 10759

growth_protocol: ICF LCLs were grown in RPMI1640 media supplemented with 2 mM L-glutamine  and 20% heat-inactivated fetal bovine serum;Normal LCLs were grown in the same media except 10% fetal bovine serum was used.


title: Daudi untreated (2)

description: no


title: KMH2 untreated (2)

description: no


title: KMH2 untreated (1)

description: no


title: 12427-38-2 Maneb 3rd

source_name: Maneb treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 20 ul of 2 % chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 2 ppm) then the yeast cells were exposed for 2 h.

treatment_protocol: Maneb Standard (Wako, 136-06533)


title: GM08714-U133B, biological rep1

description: Gene expression data from GM08714 LCL

source_name: Homo Sapiens GM08714


title: Daudi + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h) (2)

description: no

tag: Burkitt Lymphoma


title: Daudi untreated (1)

description: no


title: 10759-U133B, biological rep2

description: Gene expression data from 10759 LCL


title: Daudi + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h) (1)

description: no

source_name: RNA


title: 10759-U133B, biological rep1

description: Gene expression data from 10759 LCL


title: GM08714-U133B, biological rep3

description: Gene expression data from GM08714 LCL


title: GM08714-U133B, biological rep2

description: Gene expression data from GM08714 LCL


title: 4088-U133B, biological rep2

description: Gene expression data from 4088 LCL

source_name: Homo Sapiens 4088


title: CM774-U133B, biological rep3

description: Gene expression data from CM774

source_name: Homo Sapiens CM774


title: 4088-U133B, biological rep1

description: Gene expression data from 4088 LCL


title: CM774-U133B, biological rep1

description: Gene expression data from CM774


title: CM774-U133B, biological rep2

description: Gene expression data from CM774


title: CM304-U133B, biological rep3

description: Gene expression data from CM304

source_name: Homo Sapiens CM304


title: 7553-56-2 Iodine, 1 mM 2 h (dose-response) 2nd L

source_name: Iodine treated with 1 mM for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 1 mM (final concentration) then the yeast cells were exposed for 2 h.

source_name: control (without treatment), Cy3


title: Recovery from 30 MPa 25 C 3rd

description: Data with flag value 0 were used for LOWESS normalization processing, although original raw data were remaining in this table.

source_name: Recovery from 30 MPa 25 C, Cy5

growth_protocol: Yeast culture at an exponential growth phase (A660=1.0) was transferred into 30 or 50 ml volumes of syringes. These syringes were pressed with 30 MPa for 16 h at 25 C. To achieve pressurization, we used the 30-11HF4 (High Pressure Equipment Co.). After decompression, the cells were allowed to grow for 2 h under 0.1 MPa then harvested by centrifugation.

treatment_protocol: Recovery from 30 MPa 25 C

source_name: Decompressed from 30 MPa 25 C, Cy3

growth_protocol: Yeast culture at an exponential growth phase (A660=1.0) was transferred into 30 or 50 ml volumes of syringes. These syringes were pressed with 30 MPa for 16 h at 25 C. To achieve pressurization, we used the 30-11HF4 (High Pressure Equipment Co.). After decompression, the cells were harvested by centrifugation (0 h).

treatment_protocol: Decompressed from 30 MPa 25 C


title: CM304-U133B, biological rep2

description: Gene expression data from CM304

treatment_protocol: Cells were harvested when 70-80% confluency.


title: Recovery from 30 MPa 25 C 1st H


title: Recovery from 30 MPa 25 C 2nd L


title: L428 + 5 µM 5-aza-dC (5 days) (1)

description: no

source_name: Cell line

treatment_protocol: 5 µM 5-aza-dC (5 days) (1)


title: CM304-U133B, biological rep1

description: Gene expression data from CM304


title: LCL1-U133B, biological rep2

description: Gene expression data from LCL1

source_name: Homo Sapiens LCL1


title: Recovery from 30 MPa 25 C 2nd H


title: LCL1-U133B, biological rep3

description: Gene expression data from LCL1


title: GM08728-U133B, biological rep3

description: Gene expression data from GM08728 LCL

source_name: Homo Sapiens GM08728


title: LCL1-U133B, biological rep1

description: Gene expression data from LCL1


title: 7553-56-2 Iodine, 1 mM 2 h (dose-response) 2nd H

treatment_protocol: Iodine (Wako 095-00392). An iodine solution (0.5 M) was prepared just before use as 12.7 g iodine and 25 g iodide in 100 ml solution


title: 7553-56-2 Iodine, 0.75 mM 2 h (dose-response) 2nd L

source_name: Iodine treated with 0.75 mM for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 0.75 mM (final concentration) then the yeast cells were exposed for 2 h.


title: Recovery from 30 MPa 25 C 1st L


title: GM08728-U133B, biological rep2

description: Gene expression data from GM08728 LCL


title: 7553-56-2 Iodine, 0.75 mM 2 h (dose-response) 2nd H


title: 58-89-9 Lindane 2nd

source_name: Lindane treated for 2 h, Cy5


title: 151-21-3 Sodium dodecyl sulfate 3rd

source_name: SDS treated for 2 h, Cy5


title: GM08728-U133B, biological rep1

description: Gene expression data from GM08728 LCL


title: Recovery from freezing (60 min) 3rd

source_name: Recovery from freezing (60 min), Cy5

growth_protocol: Yeast strain S288C was grown until the exponential phase (A660, 1.0) in 600 ml YPD medium in a 3 L Erlenmeyer flask at 30 °C. An aliquot of 400 ml in a 3 L Erlenmeyer flask was frozen at −80 C without the addition of a cryoprotectant, and stored for 1 week. The frozen cell culture was then thawed at 30 °C in a water-bath for 25 min. The thawed cells were further incubated and an aliquot of 100 ml was sampled from the culture at 60 min after complete thawing.

treatment_protocol: Recovery from freezing (60 min)

source_name: control (before freezing treatment), Cy3

growth_protocol: Yeast strain S288C was grown until the exponential phase (A660, 1.0) in 600 ml YPD medium in a 3 L Erlenmeyer flask at 30 °C. An aliquot of 200 ml was taken from the cell culture and used as the control without freezing.

treatment_protocol: before freezing treatment


title: 7553-56-2 Iodine, 0.5 mM 2 h (dose-response) 2nd H

source_name: Iodine treated with 0.5 mM for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 0.5 mM (final concentration) then the yeast cells were exposed for 2 h.

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 2 h without any treatment.


title: GM08729-U133B, biological rep2

description: Gene expression data from GM08729 LCL

source_name: Homo Sapiens GM08729


title: GM08729-U133B, biological rep3

description: Gene expression data from GM08729 LCL


title: 40465-66-5 Round up hi-load herbicide 2nd

source_name: Round up treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture with 1500 times dilution then the yeast cells were exposed for 2 h.

treatment_protocol: Round up hi-loadTM herbicide (Monsanto company, MON77692)


title: 67-68-5 Dimethylsulfoxide 3rd

source_name: DMSO treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture (final concentration; 10 %=1.41 M) then the yeast cells were exposed for 2 h.

treatment_protocol: dimethylsulfoxide (Wako, 043-07216)