title: 10%sugar_HS_1

status: Public on Feb 23 2007

type: RNA

city: Tsukuba

first: Jun

last: Shima

state: Ibaraki

address: 1-2-12 Kannondai

department: Applied Microbiology

country: Japan

institute: National Food Research Institute

description: After 60min fermentation using 10% sucrose LF medium.

data_processing: Affymetrix GeneChip Operating Software Version 1.2

label: Biotin

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: mRNA

label_protocol: Labeling was done according to the Affymetrix GeneChip® Expression Analysis Technical Manual.

extract_protocol: Each samples of total RNA were extracted using the hot phenol method. Poly (A)+ RNA was isolated from the total RNA by using an Oligotex® dt30 (super) mRNA purification kit (Takara, Japan) according to the manufacturer’s instructions.

tag: Commercial baker's yeast specilized for use in high-sugar dough.


title: 50%sugar_HS_2

description: After 60min fermentation using 50% sucrose LF medium.


title: 20%sugar_HS_2

description: After 60min fermentation using 20% sucrose LF medium.


title: 50%sugar_LS_1

tag: Commercial baker's yeast specilized for use in unsugared dough.


title: 50%sugar_HS_1


title: 0%sugar_HS_2

description: After 60min fermentation using 0% sucrose LF medium.


title: 40%sugar_HS_1

description: After 60min fermentation using 40% sucrose LF medium.


title: 30%sugar_HS_1

description: After 60min fermentation using 30% sucrose LF medium.


title: 30%sugar_LS_2


title: 5%sugar_HS_1

description: After 60min fermentation using 5% sucrose LF medium.


title: 0%sugar_HS_1


title: 20%sugar_HS_1


title: 5%sugar_HS_2


title: 30%sugar_HS_2


title: 30%sugar_LS_1

extract_protocol: Each time samples of total RNA were extracted using the hot phenol method. Poly (A)+ RNA was isolated from the total RNA by using an Oligotex® dt30 (super) mRNA purification kit (Takara, Japan) according to the manufacturer’s instructions.


title: 50%sugar_LS_2


title: 10%sugar_HS_2


title: 40%sugar_HS_2


title: 20%sugar_LS_2


title: 40%sugar_LS_2


title: 40%sugar_LS_1


title: 10%sugar_LS_2


title: 10%sugar_LS_1


title: 20%sugar_LS_1


title: 5%sugar_LS_1


title: 0%sugar_LS_2


title: 5%sugar_LS_2


title: CD34+ Treated 10 uM UTP at 1 hour

status: Public on Feb 14 2007

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: The biotin-labeled target synthesis reactions, as well as the Affymetrix HG-U133A GeneChip arrays hybridization, staining, and scanning, were performed, starting from 2ug of total cellular RNA, using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNAs (20ug) were then hybridized to an identical lot of Affymetrix HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification. GeneChip were finally scanned using the GA2500 Affymetrix GeneChip scanner.

data_processing: GeneChip Operating Software (GCOS)

label: biotin-labeled

molecule: total RNA

organism: Homo sapiens

source_name: CD34+ progenitors cells

growth_protocol: Highly purified CD34+ cells from 6 healthy donors were seeded at 1000000 cells/ml in serum free medium (EX vivo 15) w/o cytokines and treated with 10 mM UTP  for 1 hour.

extract_protocol: Total RNA was isolated 1000000 cells using a modification of the guanidinium isothiocyanate procedure and ultracentrifugation on cesium chloride gradient. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 bioanalyzer. RNAs originating from the 6 donors were pooled in order to obtain at least 2ug per sample.

tag: CD34+ hemopoietic progenitors purified from peripheral blood.


title: Mouse live RNA, Ath1w

status: Public on Feb 20 2007

city: Singapore

first: Chew-Kiat

last: Heng

address: 5, Lower Kent Ridge Road, Singapore 119074

country: Singapore

institute: National University of Singapore

description: Gene expression data from Ath1w mouse livers.

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

scan_protocol: GeneChips were scanned using the Agilent G2500A Gene Array scanner.

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

label: biotin

organism: Mus musculus

source_name: C57B/L mice fed standard chow for 1 week.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: C57B/L mice aged 8 weeks maintained for 2 weeks and then fed atherogenic for 1week.

extract_protocol: Livers were pooled to isolate RNA using Trizol and clean up by RNAeasy Mini kit.

treatment_protocol: C57B/L mice aged 8 weeks maintained for 2 weeks and then fed atherogenic diet for 1 week.

tag: C57B/L female, inbred

tag: Age

value: 8 week-aged


title: Mouse live RNA, C10w

description: Gene expression data from C10w mouse livers.

source_name: C57B/L mice fed Standard Chow for 10 weeks

treatment_protocol: C57B/L mice aged 8 weeks maintained for 2 weeks and then  fed Standard Chow for 10 weeks.


title: Mouse live RNA, C1w

description: Gene expression data from C1w mouse livers.

growth_protocol: C57B/L mice aged 8 weeks maintained for 2 weeks and then fed standard chow for 1week.

treatment_protocol: C57B/L mice aged 8 weeks maintained for 2 weeks and then fed standard chow for 1 week.


title: Mouse live RNA, Ath10w

description: Gene expression data from Ath10w mouse livers.

source_name: C57B/L mice fed atherogenic diet for 10 weeks

treatment_protocol: C57B/L mice aged 8 weeks maintained for 2 weeks and then fed atherogenic diet for 10 weeks.


title: CD34+ Untreated at 6 hours

growth_protocol: Highly purified CD34+ cells from 6 healthy donors were seeded at 1000000 cells/ml in serum free medium (EX vivo 15) w/o cytokines and maintened in this culture conditions for 6 hours.


title: CD34+ Treated 10 uM UTP at 24 hours

growth_protocol: Highly purified CD34+ cells from 6 healthy donors were seeded at 1000000 cells/ml in serum free medium (EX vivo 15) w/o cytokines and treated with 10 mM UTP for 24 hours.


title: CD34+ Untreated at 24 hours

growth_protocol: Highly purified CD34+ cells from 6 healthy donors were seeded at 1000000 cells/ml in serum free medium (EX vivo 15) w/o cytokines and maintened in this culture conditions for 24 hours.


title: CD34+ Treated 10 uM UTP at 6 hours

growth_protocol: Highly purified CD34+ cells from 6 healthy donors were seeded at 1000000 cells/ml in serum free medium (EX vivo 15) w/o cytokines and treated with 10 mM UTP  for 6 hours.


title: Mouse live RNA, ST

description: Gene expression data from ST mouse livers.

source_name: C57B/L mice fed atherogenic diet for 10 week, with 3 weeks of atorvastatin treatment

growth_protocol: C57B/L mice aged 8 weeks maintained for 2 weeks and then fed atherogenic diet for 10 weeks, with final 3 weeks of atovastatin treatment.


title: C Fast Rep 2

status: Public on Feb 09 2007

city: Cambridge

first: Keira

last: Curtis

address: Box 232, Addenbrooke's Hospital, Hills Road

department: Clinical Biochemistry

country: United Kingdom

institute: University of Cambridge

hyb_protocol: GE Amersham Protocol

scan_protocol: Scanned on an Agilent G2565 scanner. Raw image data were extracted using Codelink Expression Software v4.0

data_processing: Data transformation: Set measurements <0.01 to 0.01; Per Chip: Normalize to 50th centile; Per Gene: Normalize to median expression value of fed samples.

label: Biotin Streptavidin Cy5

source_name: Cerebellum Fast

label_protocol: GE Amersham Protocol

tag: Strain

tag: Gender

value: Female

value: 10 weeks

tag: Treatment

value: Fasted 16 hours


title: C Fast Rep 1


title: C Fed Rep 1

source_name: Cerebellum Fed

tag: Tissue

value: Cerebellum


title: H Fast Rep 3

source_name: Hypothalamus Fast

value: Hypothalamus


title: H Fast Rep 2


title: CD34+ Untreated at 1 hour

growth_protocol: Highly purified CD34+ cells from 6 healthy donors were seeded at 1000000 cells/ml in serum free medium (EX vivo 15) w/o cytokines and maintened in this culture conditions for 1 hour.


title: H Fed Rep 2

source_name: Hypothalamus Fed


title: Arabidopsis_0.5mM_BTH_5h_rep2

status: Public on Feb 08 2007

city: Kaga-gun, Okayama

first: Yoshihiro

last: Narusaka

address: 7549-1, Kibityuo-town Yoshikawa

institute: Research Institute for Biological Sciences

description: Leaves were harvested and then snap-frozen in liquid nitrogen. Samples were stored at -80 ℃ until RNA extraction. To ensure biological reproducibility of the microarray results, the experiment was replicated three to four times with between thirty and seventy plants per sample. To obtain sufficient material for the experiments, samples from replicate experiments were pooled prior to RNA extraction. In addition, we conducted two to three independent microarray analyses with the same RNA for reproducibility of handling. The results demonstrated a high degree of correlation in fold change values between the different data sets. Total RNA was prepared using a TRIZOL Reagent (Invitrogen. Corp., Carlsbad, CA, USA), and subsequent mRNA was prepared using an oligotex mRNA isolation kit (Takara, Shiga, Japan). Labeling of the mRNA sample was carried out as reported previously (Seki et al.(2002) Plant J. 31:279-292). Labeled cDNA was dissolved in 15 ul hybridization buffer (3.4 x SSC, 0.3% SDS), denatured at 100 ℃ heat block for 2 min, left at room temperature for 5 min, and applied directly to the slides. Microarrays were covered with a 22 x 24 mm cover slip and hybridized in a 65 ℃ water bath for 16 to 20 h. Post-hybridization washing was performed 2 x SSC, 0.03% SDS for 2 min, then in 1 x SSC for 2 min, and finally in 0.06 x SSC for 2 min. Then, the slides were immediately dried by centrifugation (1 min at 2500 g). Slides were scanned with a ScanArray Lite (PerkinElmer, Wellesley, MA, USA) and signal calculation for each spot was processed with ScanArray Express Ver.3(PerkinElmer, Wellesley, MA, USA) .

hyb_protocol: The probe samples were denatured by placing them in a 100 ℃ heat block for 2 min, left at room temperature for 5 min, and then used for hybridization. The slides were placed in a sealed hybridization cassette (Telechem International Inc., Sunnyvale, CA) and submerged in a 65 ℃ water bath for 16 to 20 h.

scan_protocol: Slides were scanned with a ScanArray Lite (PerkinElmer, Wellesley, MA, USA) and signal calculation for each spot processed with ScanArray Express Ver.3(PerkinElmer, Wellesley, MA, USA) .

data_processing: log(2) ratio of intensity, defined as CH2 divided by CH1 (treated/untreated)

organism: Arabidopsis thaliana

source_name: Untreated plant (control)

label_protocol: Labeling of the mRNA sample was carried out as reported previously (Seki et al. (2002) Plant J. 31:279-292). Each mRNA sample was reverse-transcribed in the presence of Cy3-dUTP (Amersham Pharmacia, Piscataway, NJ).

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a12 h light/12 h dark cycle. The samples were frozen in liquid nitrogen.

extract_protocol: Total RNA was prepared using a TRIZOL Reagent (Invitrogen. Corp., Carlsbad, CA, USA), and then mRNA was prepared using an oligotex mRNA isolation kit (Takara, Shiga, Japan).

treatment_protocol: Untreated plants were used.

tag: Ecotype

value: Columbia, Age:28 days, Sample:whole plant (except for root)

source_name: Treatment with 0.5 mM BTH for 5 h

label_protocol: Labeling of the mRNA sample was carried out as reported previously (Seki et al. (2002) Plant J. 31:279-292). Each mRNA sample was reverse-transcribed in the presence of Cy5-dUTP (Amersham Pharmacia, Piscataway, NJ).

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to BTH treatment for 5 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 0.5 mM BTH. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 5 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: H Fed Rep 3


title: Arabidopsis_0.1mM_JA_24h_rep1

source_name: Treatment with 0.1 mM MeJA for 24 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to MeJA treatment for 24 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 0.1 mM MeJA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 24 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_10mM_BABA_10h_rep1

source_name: Treatment with 10 mM BABA for 10 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to BABA treatment for 10 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 10 mM BABA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 10 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_0.1mM_JA_5h_rep1

source_name: Treatment with 0.1 mM MeJA for 5 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to MeJA treatment for 5 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 0.1 mM MeJA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 5 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: C Fed Rep 2


title: H Fed Rep 1


title: Arabidopsis_10mM_BABA_5h_rep1

source_name: Treatment with 10 mM BABA for 5 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to BABA treatment for 5 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 10 mM BABA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 5 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: H Fast Rep 1


title: Arabidopsis_0.1mM_JA_10h_rep1

source_name: Treatment with 0.1 mM MeJA for 10 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to MeJA treatment for 10 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 0.1 mM MeJA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 10 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_0.5mM_BTH_24h_rep1

source_name: Treatment with 0.5 mM BTH for 24 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to BTH treatment for 24 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 0.5 mM BTH. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 24 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: C Fed Rep 3


title: Arabidopsis_0.5mM_BTH_10h_rep1

source_name: Treatment with 0.5 mM BTH for 10 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to BTH treatment for 10 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 0.5 mM BTH. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 10 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_0.5mM_BTH_5h_rep1


title: Arabidopsis_0.5mM_BTH_2h_rep1

source_name: Treatment with 0.5 mM BTH for 2 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to BTH treatment for 2 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 0.5 mM BTH. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 2 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_1mM_INA_10h_rep2

extract_protocol: Total RNA was prepared using a TRIZOL Reagent (Invitrogen. Corp., Carlsbad, CA, USA), and then mRNA was prepared using an oligotex mRNA isolation kit (Takara, Shiga, Japan)

source_name: Treatment with 1 mM INA for 10 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to INA treatment for 10 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 1 mM INA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 10 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.

value: Columbia, Age:28 days, Samples:whole plant (except for root)


title: Arabidopsis_5mM_SA_24h_rep1

source_name: Treatment with 5 mM SA for 24 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to SA treatment for 24 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 5 mM SA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 24 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_10mM_BABA_24h_rep1

source_name: Treatment with 10 mM BABA for 24 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to BABA treatment for 24 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 10 mM BABA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 24 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_1mM_INA_2h_rep1

source_name: Treatment with 1 mM INA for 2 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to INA treatment for 2 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 1 mM INA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 2 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_1mM_ET_24h_rep1

source_name: Treatment with 1 mM ethephon for 24 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to ET treatment for 24 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 1 mM ethephon (ET). Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 24 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_1mM_INA_10h_rep1


title: Arabidopsis_10mM_BABA_2h_rep1

source_name: Treatment with 10 mM BABA for 2 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to BABA treatment for 2 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 10 mM BABA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 2 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_5mM_SA_5h_rep1

source_name: Treatment with 5 mM SA for 5 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to SA treatment for 5 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 5 mM SA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 5 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_5mM_SA_10h_rep1

source_name: Untreated plant (control)

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The samples were frozen in liquid nitrogen.

treatment_protocol: Untreated plants were used.

source_name: Treatment with 5 mM SA for 10 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to SA treatment for 10 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 5 mM SA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 10 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_1mM_INA_24h_rep2

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a12 h light/12 h dark cycle. The samples were frozen in liquid nitrogen.

source_name: Treatment with 1 mM INA for 24 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to INA treatment for 24 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 1 mM INA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 24 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_5mM_SA_2h_rep1

growth_protocol:
The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a12 h light/12 h dark cycle. The samples were frozen in liquid nitrogen.
Channel Molecule

source_name: Treatment with 5 mM SA for 2 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to SA treatment for 2 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 5 mM SA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 2 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_1mM_INA_24h_rep1


title: Arabidopsis_1mM_ET_5h_rep1

value: Columbia,

value: 28 days,

tag: Sample

value: whole plant (except for root)

source_name: Treatment with 1 mM ethephon for 5 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to ET treatment for 5 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 1 mM ethephon (ET). Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 5 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_1mM_INA_5h_rep1

source_name: Treatment with 1 mM INA for 5 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to INA treatment for 5 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 1 mM INA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 5 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_1mM_ET_10h_rep1

source_name: Treatment with 1 mM ethephon for 10 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to ET treatment for 10 h and then frozen in liquid nitrogen.

tag: The 28- day-old plants were sprayed with 1 mM ethephon (ET). Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 10 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_0.1mM_JA_2h_rep1

source_name: Treatment with 0.1 mM MeJA for 2 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to MeJA treatment for 2 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 0.1 mM MeJA. Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 2 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.


title: Arabidopsis_1mM_ET_2h_rep1

description:
Leaves were harvested and then snap-frozen in liquid nitrogen. Samples were stored at -80 ℃ until RNA extraction. To ensure biological reproducibility of the microarray results, the experiment was replicated three to four times with between thirty and seventy plants per sample. To obtain sufficient material for the experiments, samples from replicate experiments were pooled prior to RNA extraction. In addition, we conducted two to three independent microarray analyses with the same RNA for reproducibility of handling. The results demonstrated a high degree of correlation in fold change values between the different data sets. Total RNA was prepared using a TRIZOL Reagent (Invitrogen. Corp., Carlsbad, CA, USA), and subsequent mRNA was prepared using an oligotex mRNA isolation kit (Takara, Shiga, Japan). Labeling of the mRNA sample was carried out as reported previously (Seki et al.(2002) Plant J. 31:279-292). Labeled cDNA was dissolved in 15 ul hybridization buffer (3.4 x SSC, 0.3% SDS), denatured at 100 ℃ heat block for 2 min, left at room temperature for 5 min, and applied directly to the slides. Microarrays were covered with a 22 x 24 mm cover slip and hybridized in a 65 ℃ water bath for 16 to 20 h. Post-hybridization washing was performed  2 x SSC, 0.03% SDS for 2 min, then in 1 x
SSC for 2 min, and finally in 0.06 x SSC for 2 min. Then, the slides were immediately dried by centrifugation (1 min at 2500 g). Slides were scanned with a ScanArray Lite (PerkinElmer, Wellesley, MA, USA) and signal calculation for each spot was processed with ScanArray Express Ver.3(PerkinElmer, Wellesley, MA, USA) .

source_name: Treatment with 1 mM ethephon for 2 h

growth_protocol: The plants were grown in soil for 28 days in a growth chamber at 22 ℃ and 50-60 % humidity under a 12 h light/12 h dark cycle. The plants were subjected to ET treatment for 2 h and then frozen in liquid nitrogen.

treatment_protocol: The 28- day-old plants were sprayed with 1 mM ethephon (ET).  Plants were then returned to the growth chamber and maintained at a high humidity. Leaves were harvested 2 h after the treatment and then frozen immediately in liquid nitrogen. The sample was stored at -80 ℃ for isolation of the RNA.

tag: Samples


title: #149303 Soybean seed coat, OX951 & OX736, 2005 rep4 time course

status: Public on Jan 01 2007

city: London

first: Mark

last: Gijzen

state: ON

address: 1391 Sandford St

department: Agriculture & AgriFood Canada

country: Canada

institute: SCPFRC London

description: Seed coat comparison between cultivars OX951, impermeable to water and OX736, permeable to water

data_processing: Arrayvision LRGC scanner layout, background subtracted intensity

organism: Glycine max

source_name: OX951 Early 2005 rep4

tag: OX951, soybean cultivar, seed coat impermeable to water

source_name: OX736 Early 2005 rep4

tag: OX736, soybean cultivar, seed coat permeable to water


title: #149302 Soybean seed coat, OX951 & OX736, 2005 rep3 time course

source_name: OX736 Late 2005 rep3

source_name: OX951 Late 2005 rep3


title: #149308 Soybean seed coat, OX951 & OX736, 2005 rep4 time course

source_name: OX736 Late 2005 rep4

source_name: OX951 Late 2005 rep4


title: #149304 Soybean seed coat, OX951 & OX736, 2005 rep4 time course


title: #149306 Soybean seed coat, OX951 & OX736, 2005 rep4 time course

source_name: OX736 Mid 2005 rep4

source_name: OX951 Mid 2005 rep4


title: #149307 Soybean seed coat, OX951 & OX736, 2005 rep4 time course


title: #149301 Soybean seed coat, OX951 & OX736, 2005 rep3 time course


title: #149305 Soybean seed coat, OX951 & OX736, 2005 rep4 time course


title: #148950 Soybean seed coat, OX951 & OX736, 2005 rep3 time course

source_name: OX736 Early 2005 rep3

source_name: OX951 Early 2005 rep3


title: #148941 Soybean seed coat, OX951 & OX736, 2004 rep2 time course

source_name: OX951 Late 2004 rep2

source_name: OX736 Late 2004 rep2


title: #148942 Soybean seed coat, OX951 & OX736, 2004 rep2 time course


title: #148939 Soybean seed coat, OX951 & OX736, 2004 rep2 time course

source_name: OX951 Mid 2004 rep2

source_name: OX736 Mid 2004 rep2


title: #148948 Soybean seed coat, OX951 & OX736, 2005 rep3 time course

source_name: OX736 Mid 2005 rep3

source_name: OX951 Mid 2005 rep3


title: #148947 Soybean seed coat, OX951 & OX736, 2005 rep3 time course


title: #148937 Soybean seed coat, OX951 & OX736, 2004 rep2 time course

source_name: OX951 Early 2004 rep2

source_name: OX736 Early 2004 rep2


title: #148949 Soybean seed coat, OX951 & OX736, 2005 rep3 time course


title: #148929 Soybean seed coat, OX951 & OX736, 2004 rep1 time course

source_name: OX736 Late 2004 rep1

source_name: OX951 Late 2004 rep1


title: #148940 Soybean seed coat, OX951 & OX736, 2004 rep2 time course


title: isoeugenol_18month_rat_405_liver

status: Public on Dec 31 2006

city: Durham

first: Joel

last: Parker

state: NC

address: 2605 Meridian Parkway

country: USA

institute: Constella Group

data_processing: Loess normalized with Rosetta Resolver error weighted model

organism: Rattus norvegicus

source_name: isoeugenol_18month_rat_405_liver - all samples are UNTREATED - chemical names are for study association only

extract_protocol: Paradigm Array Labs (Icoria, Inc., A Clinical Data Inc. Company, RTP, NC)

source_name: Equal amounts of RNA from sixty-three male sentinel rats (25 rats at 32 weeks of age, 25 rats at 58 weeks of age and 13 rats at 84 weeks of age) were used to form a composite control pool


title: isoeugenol_18month_rat_406_liver

source_name: isoeugenol_18month_rat_406_liver - all samples are UNTREATED - chemical names are for study association only

tag: Equal amounts of RNA from sixty-three male sentinel rats (25 rats at 32 weeks of age, 25 rats at 58 weeks of age and 13 rats at 84 weeks of age) were used to form a composite control pool


title: isoeugenol_18month_rat_408_liver

source_name: isoeugenol_18month_rat_408_liver - all samples are UNTREATED - chemical names are for study association only


title: #148936 Soybean seed coat, OX951 & OX736, 2004 rep1 time course

source_name: OX736 Mid 2004 rep1

source_name: OX951 Mid 2004 rep1


source_name: 5-hydroxymethyl-2-furfural_18month_rat_409_liver - all samples are UNTREATED - chemical names are for study association only


source_name: 5-hydroxymethyl-2-furfural_18month_rat_408_liver - all samples are UNTREATED - chemical names are for study association only


title: #148934 Soybean seed coat, OX951 & OX736, 2004 rep1 time course

source_name: OX736 Early 2004 rep1

source_name: OX951 Early 2004 rep1


title: #148930 Soybean seed coat, OX951 self test, 2004 rep1 time course


title: #148933 Soybean seed coat, OX951 & OX736, 2004 rep1 time course


title: #148938 Soybean seed coat, OX951 & OX736, 2004 rep2 time course


title: #148928 Soybean seed coat, OX951 & OX736, 2004 rep1 time course


title: #148935 Soybean seed coat, OX951 & OX736, 2004 rep1 time course

data_processing: Arrayvision LRGC scanner layout, background subtracted intensity"


source_name: 5-hydroxymethyl-2-furfural_18month_rat_407_liver - all samples are UNTREATED - chemical names are for study association only


title: #148931 Soybean seed coat, OX736 self test, 2004 rep1 time course


source_name: 5-hydroxymethyl-2-furfural_18month_rat_413_liver - all samples are UNTREATED - chemical names are for study association only


source_name: 5-hydroxymethyl-2-furfural_18month_rat_410_liver - all samples are UNTREATED - chemical names are for study association only


title: beta-myrcene_18month_rat_414_liver

source_name: beta-myrcene_18month_rat_414_liver - all samples are UNTREATED - chemical names are for study association only


title: beta-myrcene_18month_rat_406_liver

source_name: beta-myrcene_18month_rat_406_liver - all samples are UNTREATED - chemical names are for study association only


title: beta-myrcene_18month_rat_408_liver

source_name: beta-myrcene_18month_rat_408_liver - all samples are UNTREATED - chemical names are for study association only


source_name: "1,2-dibromo-2,4-dicyanobutane_12month_rat_408_liver" - all samples are UNTREATED - chemical names are for study association only


source_name: bis_2-chloroethoyl_methane_12month_rat_415_liver - all samples are UNTREATED - chemical names are for study association only


title: beta-myrcene_18month_rat_404_liver

source_name: beta-myrcene_18month_rat_404_liver - all samples are UNTREATED - chemical names are for study association only

source_name: Equal amounts of RNA from sixty-three male sentinel rats (25 rats at 32 weeks of age, 25 rats at 58 weeks of age and 13 rats at 84 weeks of age) were used to form a composite control pool


title: pulegone_6month_rat_409_liver

source_name: pulegone_6month_rat_409_liver - all samples are UNTREATED - chemical names are for study association only


title: pulegone_6month_rat_413_liver

source_name: pulegone_6month_rat_413_liver - all samples are UNTREATED - chemical names are for study association only


title: pulegone_6month_rat_414_liver

source_name: pulegone_6month_rat_414_liver - all samples are UNTREATED - chemical names are for study association only


title: Pyrogallol_6M_Rat_408_Liver

source_name: Pyrogallol_6M_Rat_408_Liver - all samples are UNTREATED - chemical names are for study association only


title: beta-myrcene_18month_rat_405_liver

source_name: beta-myrcene_18month_rat_405_liver - all samples are UNTREATED - chemical names are for study association only


title: Pyrogallol_6M_Rat_407_Liver

source_name: Pyrogallol_6M_Rat_407_Liver - all samples are UNTREATED - chemical names are for study association only


title: DMPT_6M_Rat_494_Liver

source_name: DMPT_6M_Rat_494_Liver - all samples are UNTREATED - chemical names are for study association only


title: Pyrogallol_6M_Rat_413_Liver

source_name: Pyrogallol_6M_Rat_413_Liver - all samples are UNTREATED - chemical names are for study association only


source_name: bis_2-chloroethoyl_methane_12month_rat_403_liver - all samples are UNTREATED - chemical names are for study association only


source_name: bis_2-chloroethoyl_methane_12month_rat_409_liver - all samples are UNTREATED - chemical names are for study association only


title: DMPT_6M_Rat_485_Liver

source_name: DMPT_6M_Rat_485_Liver - all samples are UNTREATED - chemical names are for study association only


source_name: bis_2-chloroethoyl_methane_12month_rat_411_liver - all samples are UNTREATED - chemical names are for study association only


title: pulegone_6month_rat_405_liver

source_name: pulegone_6month_rat_405_liver - all samples are UNTREATED - chemical names are for study association only


source_name: bis_2-chloroethoyl_methane_12month_rat_401_liver - all samples are UNTREATED - chemical names are for study association only


source_name: "1,2-dibromo-2,4-dicyanobutane_12month_rat_409_liver" - all samples are UNTREATED - chemical names are for study association only


source_name: "1,2-dibromo-2,4-dicyanobutane_12month_rat_410_liver" - all samples are UNTREATED - chemical names are for study association only


source_name: "1,2-dibromo-2,4-dicyanobutane_12month_rat_407_liver" - all samples are UNTREATED - chemical names are for study association only

source_name: Equal amounts of RNA from sixty-three male sentinel rats (25 rats at 32 weeks of age, 25 rats at 58 weeks of age and 13 rats at 84 weeks of age) were used to form a composite control pool


title: HBEC_9F_Control_48h_rep3

status: Public on Dec 25 2006

city: Albquerque

first: Susan

middle: Esther

last: Boggs

state: NM

address: 2425 Ridgecrest Dr SE

institute: Lovelace Respiratory Research Institute

description: Total RNA was extracted and treated with DNase I before enriching for poly A+ RNA using biotynylated oligo(dT) and streptavidin-coated magnetic beads.  P-32 labeled probes were synthesized directly on the magnetic beads with Powerscript RT.

hyb_protocol: Hybridization was performed per manufacturer's recommendations.

scan_protocol: Images were scanned at a 100 micron resolution with a phosphorimager (BioRad).  TIFF images were analyzed with Atlas Image (v 2.7).

data_processing: Background was subtracted and values were globally normalized to the sum of all transcripts on the array

source_name: Primary human bronchial epithelial cells, donor 9F, 48h control

label_protocol: Probe synthesis was carried out per manufacturer's recommendations except Powerscript RT was used.

extract_protocol: Total RNA was extracted using the Atlas Pure Total RNA Labeling System.

treatment_protocol: Samples were treated with either phosphate buffered saline as vehicle control or environmental tobacco smoke condensate for 4 or 48 h.

tag: Cell type

value: primary human bronchial epithelial cells

value: male

tag: Catalog number


source_name: "1,2-dibromo-2,4-dicyanobutane_12month_rat_406_liver" - all samples are UNTREATED - chemical names are for study association only


title: HBEC_9F_Treated_48h_rep1

source_name: Primary human bronchial epithelial cells, donor 9F, 48h treated


title: HBEC_9F_Control_48h_rep2


title: control day 5 (#19) vs. 400 mg/kg day 5 BECM (#54)

data_processing: Loess normalized, and combined dye flip replicates with Rosetta Resolver error weighted model

source_name: control day 5 (#19)

extract_protocol: QIAGEN Rneasy kit (QIAGEN, Valencia, CA)

tag: Total cardiac RNA from control day 5 (#19)

source_name: 400 mg/kg day 5 BECM (#54)

tag: Total cardiac RNA from 400 mg/kg day 5 BECM (#54)


title: control day 5 (#9) vs. 400 mg/kg day 5 BECM (#54)

source_name: control day 5 (#9)

tag: Total cardiac RNA from control day 5 (#9)


title: control day 2 (#7) vs. 400 mg/kg day 2 BECM (#50)

source_name: control day 2 (#7)

tag: Total cardiac RNA from control day 2 (#7)

source_name: 400 mg/kg day 2 BECM (#50)

tag: Total cardiac RNA from 400 mg/kg day 2 BECM (#50)


title: control day 5 (#9) vs. 400 mg/kg day 5 BECM (#49)

source_name: 400 mg/kg day 5 BECM (#49)

tag: Total cardiac RNA from 400 mg/kg day 5 BECM (#49)


title: Pyrogallol_6M_Rat_414_Liver

source_name: Pyrogallol_6M_Rat_414_Liver - all samples are UNTREATED - chemical names are for study association only


title: HBEC_9F_Treated_4h_rep3

source_name: Primary human bronchial epithelial cells, donor 9F, 4h treated

tag: Gender

tag: Age


title: control day 2 (#22) vs. 400 mg/kg day 2 BECM (#52)

source_name: control day 2 (#22)

tag: Total cardiac RNA from control day 2 (#22)

source_name: 400 mg/kg day 2 BECM (#52)

tag: Total cardiac RNA from 400 mg/kg day 2 BECM (#52)


title: control day 5 (#19) vs. 400 mg/kg day 5 BECM (#57)

source_name: 400 mg/kg day 5 BECM (#57)

tag: Total cardiac RNA from 400 mg/kg day 5 BECM (#57)


title: Pyrogallol_6M_Rat_409_Liver

source_name: Pyrogallol_6M_Rat_409_Liver - all samples are UNTREATED - chemical names are for study association only


title: HBEC_9F_Control_4h_rep3

source_name: Primary human bronchial epithelial cells, donor 9F, 4h control


title: DMPT_6M_Rat_493_Liver

source_name: DMPT_6M_Rat_493_Liver - all samples are UNTREATED - chemical names are for study association only

source_name: Equal amounts of RNA from sixty-three male sentinel rats (25 rats at 32 weeks of age, 25 rats at 58 weeks of age and 13 rats at 84 weeks of age) were used to form a composite control pool


title: HBEC_9F_Treated_4h_rep2


title: HBEC_9F_Treated_4h_rep1


title: pulegone_6month_rat_404_liver

source_name: pulegone_6month_rat_404_liver - all samples are UNTREATED - chemical names are for study association only


title: DMPT_6M_Rat_489_Liver

source_name: DMPT_6M_Rat_489_Liver - all samples are UNTREATED - chemical names are for study association only


title: HBEC_7F_Treated_48h_rep2

source_name: Primary human bronchial epithelial cells, donor 7F, 48h treated


title: HBEC_7F_Control_48h_rep3

source_name: Primary human bronchial epithelial cells, donor 7F, 48h control


title: HBEC_7F_Control_48h_rep1


title: HBEC_7F_Control_48h_rep2


title: HBEC_7F_Treated_4h_rep3

source_name: Primary human bronchial epithelial cells, donor 7F, 4h treated


title: HBEC_7F_Treated_48h_rep3


title: HBEC_7F_Treated_4h_rep2


title: control day 5 (#9) vs. 400 mg/kg day 5 BECM (#57)

source_name: control day 5 (#9)


title: control day 5 (#19) vs. 400 mg/kg day 5 BECM (#49)

source_name: control day 5 (#19)


title: control day 2 (#7) vs. 400 mg/kg day 2 BECM (#52)

source_name: control day 2 (#7)


title: DMPT_6M_Rat_484_Liver

source_name: DMPT_6M_Rat_484_Liver - all samples are UNTREATED - chemical names are for study association only


title: HBEC_9F_Treated_48h_rep3

source_name: Primary human bronchial epithelial cells, donor 9F, 48h treated


title: control day 2 (#7) vs. 400 mg/kg day 2 BECM (#59)

source_name: 400 mg/kg day 2 BECM (#59)

tag: Total cardiac RNA from 400 mg/kg day 2 BECM (#59)


title: HBEC_9F_Control_48h_rep1

source_name: Primary human bronchial epithelial cells, donor 9F, 48h control


title: HBEC_9F_Treated_48h_rep2


title: Field 2005 Shipyard Creek S14

status: Public on Sep 01 2006

city: Ocean Springs

first: Jonathan

last: Roling

state: MS

address: 703 East Beach Dr

department: Department of Coastal Sciences

institute: University of Southern Mississippi

description: liver from adult male Fundulus heteroclitus

hyb_protocol: Probes are heated to 100C for 10 minutes, and then chilled on ice. Arrays are prehybridized with 5 mL of ExpressHyb Hybridization Solution (Clontech, Palo Alto, CA) and 1 mg sheared salmon sperm (denatured at 95C for 10 minutes then chilled on ice) at 68C for greater than 4 hours. Arrays were hybridized overnight at 68C. The blots were washed four times for 15 minutes at 64C using 2x SSC/0.5% SDS, then four times for 15 minutes at 64C using 0.5x SSC/0.5% SDS.

scan_protocol: Blots are wrapped in plastic wrap and exposed to a phosphoscreen at room temperature, visualized on BioRad FX Imager (Hercules, CA), and quantified with Invitrogen ResGen Pathways software (Carlsbad, CA).

data_processing: Data normalized to immediate background using ResGen Pathways software.

label: radioactive phosphorus 33 - [33P] dATP

organism: Fundulus heteroclitus

source_name: Fundulus heteroclitus adult male liver

label_protocol: 2 ug RNA is diluted into 10 uL of DEPC water. 10 uL of 0.5 uM poly T primers are added and incubated at 65C for 5 minutes and cooled to room temperature for two minutes. Radiolabelled cDNA is made by adding 30 uL of a mix containing 10 uL 5x reverse transcription buffer, 6 uL 10 mM dNTPs (without dATP), 10 uCi [33P]dATP, and 200 units MMLV-RT and incubating for 2 hours at 37C. Probes are cleaned of short nucleotide sequences through ProbeQuant G-50 Micro Columns (Amersham Biosciences, Piscataway, NJ) and counted on scintillation counter.

extract_protocol: RNA isolation performed by TriReagent according to manufactures protocols, followed by DNAse treatment.

treatment_protocol: Mummichogs were captured at the Shipyard Creek site using baited minnow traps.  Shipyard Creek is adjacent to a chromium contaminated Superfund site.  Livers were excised and frozen at -80C.

tag: Adult (>4cm in length) male liver excised immediately upon euthanasia


title: WT(YHT652)-YPD37deg60min

status: Public on Oct 01 2006

city: Baltimore

first: Hidekazu

last: Takahashi

state: Maryland

address: 339 Broadway Research Building, 733 North Broadway

department: High Throughput Biology Center

institute: Johns Hopkins University School of Medicine

description: This is a special situation where scaling or quantile normalization cannot be used because of global change in expression. Thus, we took the mean signal (although we knew GEO does not recommend this for individual samples), normalized with controls, and assessed the data significance by comparing with null set.

hyb_protocol: Affymetrix standard protocol (overnight).

scan_protocol: Affymetrix standard protocol using Affymetirix Fluidics 450 and Scanner 3000.

data_processing: Background correct with RMA, take the mean of two replicates and normalize with controls defined by Affymetrix using lowess curve.

label_protocol: Affymetrix sample processing protocol

growth_protocol: Culture in YPD

extract_protocol: Acid-phenol(Ausubel., 1994) followed by RNeasy Mini(Qiagen)

treatment_protocol: Heat shock at 37deg for 60min

tag: Strain background

tag: Genotype

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 acs2::HygMX [pHT215, acs2-Ts1-CEN-URA3]


title: Field 2005 Shipyard Creek S10


title: control day 2 (#22) vs. 400 mg/kg day 2 BECM (#59)

source_name: control day 2 (#22)


title: control day 2 (#22) vs. 400 mg/kg day 2 BECM (#50)

source_name: 400 mg/kg day 2 BECM (#50)


title: Synthetic Lethality/slow growth with acs2-Ts8

type: genomic

description: See above.

hyb_protocol: Labeled extracts were hybridized overnight to microarray slides at 42 degrees C. See PubMed ID 15994458.

scan_protocol: Images were acquired with a GenePix 4000B scanner.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when F635-B635 were less than 150. UpTag and DnTag ratios were multiplied by the normalization factors 1.8169 and 1.0615 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values.

molecule: genomic DNA

source_name: Control

label_protocol: UpTag and DnTag sequences were amplified from genomic DNA by asymmetric PCR using labeled primers. See PubMed ID 15994458.

growth_protocol: Cells were grown at 33 degrees C to confluence on "Magic Marker" selection plates with G418 without uracil, histidine and clonNat. See PubMed ID 15525520.

extract_protocol: Genomic DNA was prepared by extraction with phenol-chloroform and ethanol-precipitated. See PubMed ID 15525520.

tag: Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and selected to yield MATa haploid progeny. The parental strain was BY4743 (from S288C), with modifications resulting in the following genotype

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX [pHT217, acs2-Ts8-CEN-URA3]. The second-site ("query") mutation had the genotype acs2::natMX.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1 selection).

source_name: Experiment -- acs2-Ts8

label_protocol: As in Channel 1.

growth_protocol: Cells were grown at 33 degrees C to confluence on "Magic Marker" selection plates with G418 and cloNat without uracil and histidine. The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.

extract_protocol: As in Channel 1.

tag: As in Channel 1.


title: Field 2005 Shipyard Creek S4


title: HBEC_9F_Control_4h_rep2

source_name: Primary human bronchial epithelial cells, donor 9F, 4h control

tag: Cell type

tag: Catalog number


title: HBEC_9F_Control_4h_rep1


title: Field 2005 NERR G10

treatment_protocol: Mummichogs were captured at the NERR site using baited minnow traps.  NERR is relatively pristine and is used as the reference site in this study.  Livers were excised and frozen at -80C.


title: Field 2005 NERR G15


title: Field 2005 NERR G3


title: Field 2003 Shipyard Creek CS18


title: HBEC_7F_Treated_48h_rep1


title: Field 2003 Shipyard Creek CS17


title: Field 2003 Shipyard Creek CS16


title: Field 2005 Shipyard Creek S7


title: Field 2003 Shipyard Creek CS8


title: Field 2003 Shipyard Creek CS2


title: HBEC_7F_Control_4h_rep3

source_name: Primary human bronchial epithelial cells, donor 7F, 4h control


title: HBEC_7F_Control_4h_rep2


title: Field 2003 NERR CG18


title: WT(YHT651)-YPD37deg60min

hyb_protocol: Affymetrix standard protocol (overnight)

scan_protocol: Affymetrix standard protocol using Affymetirix Fluidics 450 and Scanner 3000

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 acs2::HygMX [pHT112-1, ACS2-CEN-URA3]


title: Field 2005 NERR G19


title: HBEC_7F_Treated_4h_rep1


title: HBEC_7F_Control_4h_rep1


title: Field 2003 NERR CG16


title: Field 2003 NERR CG3


title: Field 2003 NERR CG2


title: Field 2003 NERR CG19


title: Field 2005 Shipyard Creek S15


title: Field 2005 Shipyard Creek S12


title: Field 2005 NERR G14


title: Field 2000 Shipyard Creek S6


title: Field 2005 NERR G8


title: Field 2000 Shipyard Creek S4


title: Field 2005 NERR G5


title: Field 2005 Shipyard Creek S3


title: Field 2003 Shipyard Creek CS13


title: Field 2003 Shipyard Creek CS3


title: Field 2005 NERR G2


title: Field 2000 NERR G11


title: Field 2000 NERR G610


title: Field 2003 NERR CG15


title: wt 50 rep3

status: Public on Aug 31 2006

city: Madison

first: Michael

last: Culbertson

state: WI

address: 1525 Linden Drive

department: Genetics

institute: University of Wisconsin

description: Yeast cultures were grown to mid-log phase and harvested at 50 minutes after transcription inhibition by 10ug/ml thiolutin.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Robust Multiarray Average

source_name: upf1- cell at time point 50

label_protocol: cDNA was synthesized from 15ug total RNA from all samples using oligo(dT) primer. 5ul out of 12ul RnaseH-puriÞed cDNA samples were used to synthesize biotinylated cRNA.

extract_protocol: hot phenol protocol

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 50 minutes after transcription inhibition.


title: wt 60 rep3

description: Yeast cultures were grown to mid-log phase and harvested at 60 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 60

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 60 minutes after transcription inhibition.


title: Field 2000 Shipyard Creek S2


title: wt 40 rep3

description: Yeast cultures were grown to mid-log phase and harvested at 40 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 40

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 40 minutes after transcription inhibition.


title: wt 30 rep3

description: Yeast cultures were grown to mid-log phase and harvested at 30 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 30

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 30 minutes after transcription inhibition.


title: Field 2000 NERR G8


title: Field 2000 Shipyard Creek S8


title: Field 2000 NERR G6


title: Field 2000 Shipyard Creek S7


title: Field 2003 NERR CG8


title: wt 45 rep3

description: Yeast cultures were grown to mid-log phase and harvested at 45 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 45

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 45 minutes after transcription inhibition.


title: wt 25 rep3

description: Yeast cultures were grown to mid-log phase and harvested at 25 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 25

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 25 minutes after transcription inhibition.


title: wt 20 rep3

description: Yeast cultures were grown to mid-log phase and harvested at 20 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 20

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 20 minutes after transcription inhibition.


title: Field 2000 NERR G9


title: wt 35 rep3

description: Yeast cultures were grown to mid-log phase and harvested at 35 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 35

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 35 minutes after transcription inhibition.


title: wt 12 rep3

description: Yeast cultures were grown to mid-log phase and harvested at 12 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 12

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 12 minutes after transcription inhibition.


title: wt 10 rep3

description: Yeast cultures were grown to mid-log phase and harvested at 10 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 10

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 10 minutes after transcription inhibition.


title: wt 8 rep3

description: Yeast cultures were grown to mid-log phase and harvested at 8 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 8

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 8 minutes after transcription inhibition.


title: wt 6 rep2

description: Yeast cultures were grown to mid-log phase and harvested at 6 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 6

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 6 minutes after transcription inhibition.


title: wt 35 rep2


title: wt 50 rep2


title: wt 15 rep2

description: Yeast cultures were grown to mid-log phase and harvested at 15 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 15

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 15 minutes after transcription inhibition.


title: wt 8 rep2


title: wt 30 rep2


title: wt 25 rep2


title: wt 20 rep2


title: wt 4 rep3

description: Yeast cultures were grown to mid-log phase and harvested at 4 minutes after transcription inhibition by 14ug/ml thiolutin.

source_name: upf1- cell at time point 4

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 4 minutes after transcription inhibition.


title: wt 6 rep3


title: wt 2 rep2

description: Yeast cultures were grown to mid-log phase and harvested at 2 minutes after transcription inhibition by 10ug/ml thiolutin.

source_name: upf1- cell at time point 0

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 2 minutes after transcription inhibition.


title: wt 60 rep1


title: wt 60 rep2


title: wt 0 rep2

description: Yeast cultures were grown to mid-log phase and harvested at 0 minutes after transcription inhibition by 10ug/ml thiolutin.

tag: Yeast strain S288C with wild type UPF1 ORF. Cells harvested at 0 minutes after transcription inhibition.


title: wt 2 rep3


title: wt 50 rep1


title: wt 0 rep3


title: wt 45 rep2


title: wt 30 rep1


title: wt 45 rep1


title: wt 25 rep1


title: wt 40 rep2


title: wt 20 rep1


title: wt 12 rep2


title: wt 15 rep3


title: wt 10 rep1


title: wt 4 rep1


title: wt 40 rep1


title: wt 4 rep2


title: mut 60 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 60 minutes after transcription inhibition.


title: wt 0 rep1


title: wt 10 rep2


title: wt 2 rep1


title: wt 35 rep1


title: mut 40 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 40 minutes after transcription inhibition.


title: mut 30 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 30 minutes after transcription inhibition.


title: mut 15 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 15 minutes after transcription inhibition.


title: mut 45 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 45 minutes after transcription inhibition.


title: mut 6 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 6 minutes after transcription inhibition.


title: wt 12 rep1


title: wt 6 rep1


title: wt 15 rep1


title: mut 2 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 2 minutes after transcription inhibition.


title: mut 4 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 4 minutes after transcription inhibition.


title: mut 50 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 50 minutes after transcription inhibition.


title: wt 8 rep1


title: mut 8 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 8 minutes after transcription inhibition.


title: mut 0 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 0 minutes after transcription inhibition.


title: mut 25 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 25 minutes after transcription inhibition.


title: mut 12 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 12 minutes after transcription inhibition.


title: mut 35 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 35 minutes after transcription inhibition.


title: mut 20 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 20 minutes after transcription inhibition.


title: mut 40 rep2


title: mut 10 rep3

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 10 minutes after transcription inhibition.


title: mut 25 rep2


title: mut 45 rep2


title: mut 50 rep2


title: mut 12 rep2


title: mut 20 rep2


title: mut 15 rep2


title: mut 10 rep2


title: mut 35 rep2


title: mut 60 rep2


title: mut 30 rep2


title: mut 6 rep2


title: mut 8 rep2


title: mut 30 rep1


title: mut 2 rep2


title: mut 40 rep1


title: mut 45 rep1


title: mut 8 rep1


title: mut 0 rep2


title: mut 10 rep1


title: mut 35 rep1


title: mut 25 rep1


title: mut 4 rep2


title: mut 20 rep1


title: mut 15 rep1


title: mut 12 rep1


title: mut 60 rep1


title: mut 50 rep1


title: mut 4 rep1


title: alveolar septal tips experiment 1 replicate 1

status: Public on Aug 19 2006

city: Iowa City

first: Jeanne

middle: M

last: Snyder

state: IA

address: 51 Newton Road

department: Anatomy and Cell Biology

institute: University of Iowa

description: Whole lung tissue from day 6 C57/Bl6 neonatal mice

data_processing: Affymetrix Microarray Suite version 5.0

source_name: tips of secondary alveolar septae in day 6 neonatal lung tissue

label_protocol: Approximately 50 ng of total RNA was processed to

extract_protocol: Total RNA was extracted from lung tissue using a PicoPure RNA isolation kit (Arcturus). The RNA was amplified two times using a RiboAmp RNA Amplification kit(Arcturus)

tag: secondary alveolar septae harvested from neonatal day 6 lung tissue by laser capture microscopy


title: alveolar septal tips experiment 1 replicate 2


title: alveolar septal tips experiment 2 replicate 2


title: lung experiment 1 replicate 1

source_name: day 6 neonatal lung tissue

label_protocol: Approximately 50 ng of total RNA was processed to produce biotinylated cRNA targets using the standard Affymetrix two-cycle target labelling kit.

extract_protocol: Total RNA was extracted from lung tissue using a PicoPure RNA isolation kit (Arcturus). Two micrograms of RNA were amplified two times using a RiboAmp RNA Amplification kit (Arcturus).

tag: neonatal day 6 whole lung tissue


title: lung experiment 1 replicate 2

extract_protocol: Total RNA was extracted from lung tissue using a PicoPure RNA isolation kit (Arcturus).


title: mut 0 rep1


title: lung experiment 2 replicate 1


title: 12781299_Sce28cy5_Sce15cy3Chip2

status: Public on Jul 15 2006

city: Mississauga

first: James

middle: B

last: Anderson

state: Ontario

address: 3359 Mississauga Road N.

department: Biology

institute: University of Toronto

description:
12781299_Sce28cy5_Sce15cy3Rep2.
Generation 400 hyb group

data_processing: Log 2 ratio of signal intensity of experimental over the reference strain. Lowess subgrid normalization method.

tag: Sce15. Reference strain

tag: Sce28. Experimental strain. Generation 400


title: mut 2 rep1


title: 12735294_Sce27cy5_Sce14cy3Chip4

description: 12735294_Sce27cy5_Sce14cy3Rep4. Generation 400 hyb group

tag: Sce14. Reference strain

tag: Sce27. Experimental strain. Generation 400


title: 12709764_Sce14cy5_Sce27cy3Chip3

description:
12709764_Sce14cy5_Sce27cy3Rep3.
Generation 400 hyb group


title: alveolar septal tips experiment 2 replicate 1


title: 12759648_Sce100cy3_Sce509cy5Chip2

description:
12759648_Sce100cy3_Sce509cy5.Rep2.
One step mutant hyb group

tag: Sce100. Reference strain.

tag: Sce509. Experimental strain. One step mutant.


title: 12709773_Sce13cy5_Sce26cy3Chip3

description:
12709773_Sce13cy5_Sce26cy3Rep3
Generation 400 hyb group

tag: Sce13. Reference strain

tag: Sce26. Experimental strain. Generation 400.


title: lung experiment 2 replicate 2


title: 12709704_Sce26cy5_Sce13cy3Chip1

description: 12709704_Sce26cy5_Sce13cy3Rep1. Generation 400 hyb group

tag: Sce13.Reference strain

tag: Sce26. Experimental strain. Generation400


title: 12781294_Sce14cy5_Sce27cy3Chip1

description: 12781294_Sce14cy5_Sce27cy3Rep1 Generation 400 hyb group


title: 12759581_Sce509cy3_Sce100cy5Chip1

description:
12759581_Sce509cy3_Sce100cy5Rep1.
One step mutant hyb group.

tag: Sce100. Reference strain

tag: Sce509. Experimental strain. One step mutant


title: 12709710_Sce15cy5_Sce19cy3Chip1

description: 12709710_Sce15cy5_Sce19cy3Rep1. Generation 100 hyb group


title: 12778054_Sce27cy5_Sce14cy3Chip2

description: 12778054_Sce27cy5_Sce14cy3Rep2. Generation 400 hyb group


title: 12709705_Sce13cy5_Sce17cy3Chip1

description: 12709705_Sce13cy5_Sce17cy3Rep1. Generation 100 hybridization group

tag: Sce13.Reference strain.

tag: Sce17.Generation 100 experimental


title: 12709711_Sce17cy5_Sce13cy3Chip2

description:
12709711_Sce17cy5_Sce13cy3Rep2.
Generation 100 hybridization group

tag: Sce13cy3.Reference strain

tag: Sce17.Generation 100. Experimental strain


title: 12709775_Sce26cy5_Sce13cy3Chip2

description:
12709775_Sce26cy5_Sce13cy3Rep2
Generation 400 hyb group.

tag: Sce26. Experimental strain. Generation 400


title: 12709774_Sce13cy5_Sce26cy3Chip4

description: 12709774_Sce13cy5_Sce26cy3Rep4. Generation 400 hyb group.


title: 12781277_Sce19cy5_Sce15cy3Chip2

description: 12781277_Sce19cy5_Sce15cy3Rep2 Generation 100 hyb group

tag: Sce15. Reference strain

tag: Sce19. Experimental strain. Generation100


title: 12709771_Sce14cy5_Sce18cy3Chip1

description:
12709771_Sce14cy5_Sce18cy3Rep1
Generation 100 hyb group

tag: Sce14. Reference strain

tag: Sce18. Experimental strain. Generation 100


title: 12759573_Sce1113cy5_sce100cy3Chip1

description:
12759573_Sce1113cy5_sce100cy3Rep1.
Double Mutant hybridization group

tag: Sce1113.Experimental strain.  Double mutant


title: 12709776b_Sce13cy5_Sce17cy3Chip3

description: 12709776b_Sce13cy5_Sce17cy3Rep3. Generation 100 hyb group

data_processing: Log2 ratio of signal intensity of experimental over the reference strain. Lowess subgrid normalization method.

tag: Sce17. Experimental strain generation100.


title: 12759655_Sce1060cy5_Sce13Cy3Chip1

description:
12759655_Sce1060cy5vsSce13Cy3rep1.
Double Mutant hyb group

tag: Sce1060.Experimental strain. Double Mutant


title: Control Brain C3

status: Public on Jul 01 2006

city: Basel

first: Lydia

last: Michaut

address: Klingelbergstrasse 70

department: Cell Biology

country: Switzerland

institute: Biozentrum

description:
Strain: CantonS
Gender: female
Developmental Stage:adult
Tissue: Brain
Treatment: none

data_processing: MAS5 acquisition and normalization

organism: Drosophila melanogaster

source_name: Brain of CantonS adult females

growth_protocol: Standard corn meal food at 25C.

extract_protocol: Trizol

tag: Strain

value: CantonS

tag: Gender

value: female

tag: Developmental Stage:adult

tag: Tissue

value: Brain

tag: Treatment


title: MB-ablated Brain HU6

description:
Strain: CantonS.
Gender: female.
Developmental Stage:adult.
Tissue: Brain.
Treatment: hydroxyurea.

source_name: Mushroom-body-ablated brain of CantonS adult females

treatment_protocol: Ablation of MBs with hydroxyurea (HU) was performed as described in deBelle et al., (1994): newly hatched larvae were fed for 4 hours with heat-inactivated yeast paste containing 25 mg/ml HU, rinsed and transfered back on standard corn meal food until adulthood.

value: CantonS.

value: female.

tag: Developmental Stage:adult.

value: Brain.

value: hydroxyurea.


title: MB-ablated Brain HU5

description:
Strain: CantonS
Gender: female
Developmental Stage:adult
Tissue: Brain
Treatment: hydroxyurea

treatment_protocol: Ablation of MBs with hydroxyurea(HU) was done as described in de Belle et al., (1994): newly hatched larvae were fed for 4 hours with heat-inactivated yeast paste containing 25 mg/ml HU, rinsed and transfered back on standard corn meal food until adulthood.


title: Control Brain C2


title: 12759616_Sce100cy5_Sce1113cy3Chip2

description:
12759616_Sce100cy5_Sce1113cy3Rep2.
Double Mutant hybridization group

tag: Sce100.Reference strain

tag: Sce1113. Double Mutant experimental strain


title: 12754793_Sce13cy5_Sce1060cy3Chip2

description:
12754793_Sce13cy5_Sce1060cy3Rep2.
Double mutant hyb group

tag: Sce13 reference strain


title: 12709706_Sce17cy5_Sce13cy3Chip4

description:
12709706_Sce17cy5_Sce13cy3Rep4.
Generation 100 hybridization group

tag: Sce13. Reference strain

tag: Sce17. Experimental strain. Generation 100


title: 12735240_Sce18cy5_Sce14cy3Chip2

description: 12735240_Sce18cy5_Sce14cy3Rep2. Generation 100 hyb group

tag: Sce14.Reference strain


title: MB-ablated Brain HU4

treatment_protocol: Ablation of MBs with hydroxyurea(HU) was performed as described in deBelle et al., (1994): newly hatched larvae were fed for 4 hours with heat-inactivated yeast paste containing 25 mg/ml HU, rinsed and transfered back on standard corn meal food until adulthood.


title: 12759643_Sce13cy5_Sce1089cy3Chip1

description:
12759643_Sce13cy5_Sce1089cy3Rep1.
Double Mutant hyb group

tag: Sce1089.Experimental strain. Double Mutant


title: Control Brain C1


title: PBMCs from an HIV negative mother in Botswana (20)

city: Boston

first: Monty

last: Montano

state: MA

address: 650 Albany Street, Bldg X, room 640

department: Medicine

institute: Boston Medical Center

description: HIV seronegative

data_processing: No processing, these data are unscaled

source_name: Human peripheral blood mononuclear cells (PBMCs) from an HIV negative Batswana woman

tag: Botswana mother between 18 and 38 years old.  HIV negative.


title: 12759582_Sce1089cy5_Sce13cy3Chip2

description: 12759582_Sce1089cy5_Sce13cy3Rep2. Double Mutant hyb group

tag: Sce1089. Experimental strain.Double Mutant


title: TC Pro_B pre_ex

status: Public on Jun 16 2006

city: Jena

first: Sandy

last: Mosig

address: Bachstrasse 18

department: Molecular Hemostaseology - Institute of Vascular Medicine

country: Germany

institute: University Hospital Jena

description:
cRNA from T lymphocytes from proband B
before exhaustive exercise

data_processing: GCOS 1.2 and Agilent GeneSpring 7.2

source_name: T lymphocytes

tag: T lymphocytes from proband B pre exercise


title: TC Pro_C post_ex

description: cRNA from T lymphocytes from proband C after exhaustive exercise

tag: cRNA from T lymphocytes from proband C

tag: after exhaustive exercise


title: TC Pro_C pre_ex

description: cRNA from T lymphocytes from proband C before exhaustive exercise

tag: pre exhaustive exercise


title: PBMC Pro_C pre_ex

description: cRNA from Peripheral Blood Mononuclear Cells from proband C before exhaustive exercise

source_name: Peripheral Blood Mononuclear Cells

label_protocol: standard Affymetrix procedures

tag: Peripheral Blood Mononuclear Cells from proband C pre exercise


title: TC Pro_A post_ex

description: cRNA from T lymphocytes from proband A after exhaustive exercise

tag: T lymphocytes from proband A post exercise


title: PBMC Pro_A pre_ex

description: cRNA from Peripheral Blood Mononuclear Cells from proband A before exhaustive exercise

tag: Peripheral Blood Mononuclear Cells from proband A pre exercise


title: PBMC Pro_B post_ex

description: cRNA from Peripheral Blood Mononuclear Cells from proband B after exhaustive exercise

tag: Peripheral Blood Mononuclear Cells from proband B post exercise


title: WBC Pro_B pre_ex

description:
cRNA from White blood cells from proband B
before exhaustive exercise

source_name: White blood cells

tag: White blood cells from proband B pre exercise


title: PBMC Pro_C post_ex

description: cRNA from Peripheral Blood Mononuclear Cells from proband C after exhaustive exercise

tag: Peripheral Blood Mononuclear Cells from proband C post exercise


title: PBMC Pro_A post_ex

description: cRNA from Peripheral Blood Mononuclear Cells from proband A after exhaustive exercise

tag: Peripheral Blood Mononuclear Cells from proband A post exercise


title: WBC Pro_A pre_ex

description:
cRNA from White blood cells from proband A
before exhaustive exercise

tag: White blood cells from proband A pre exercise


title: WBC Pro_C post_ex

description:
cRNA from White blood cells from proband C
after exhaustive exercise

tag: White blood cells from proband C post exercise


title: rTreg

status: Public on Jun 15 2006

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: Peripheral blood was obtained from 8 healthy adult donors. Human PBL were purified from peripheral blood by bicoll gradient centrifugation  followed by plastic adherence to deplete monocytes. Adult peripheral CD4+CD25+ cells were first enriched using MACS beads (Miltenyi Biotech) and subsequently CD4+CD25high CD45RO(low)CD31(high)cells were sorted with a FACS-Diva™ cell sorter (BD Biosciences).

data_processing: MAS 5.0

label: Biotin-SA-PE

source_name: CD95L mediated cell death resistant Treg

tag: CD4+CD25+CD45RO(low) CD31(high) sorted T-Lymphocytes from PBL are resistent to CD95L-mediated cell death (AICD resisent group)


title: WBC Pro_B post_ex

description:
cRNA from White blood cells from proband B
after exhaustive exercise

tag: White blood cells from proband B post exercise


title: TC Pro_B post_ex

description: cRNA from T lymphocytes from proband B after exhaustive exercise

tag: T lymphocytes from proband B post exercise


title: PBMC Pro_B pre_ex

description: cRNA from Peripheral Blood Mononuclear Cells from proband B before exhaustive exercise

tag: Peripheral Blood Mononuclear Cells from proband B pre exercise


title: TC Pro_A pre_ex

description: cRNA from T lymphocytes from proband A before exhaustive exercise

tag: T lymphocytes from proband A pre exercise


title: WBC Pro_C pre_ex

description:
cRNA from White blood cells from proband C
before exhaustive exercise

tag: White blood cells from proband C pre exercise


title: Treg control

description: Peripheral blood was obtained from healthy adult donors. Human PBL were purified from peripheral blood by bicoll gradient centrifugation  followed by plastic adherence to deplete monocytes. Adult peripheral CD4+CD25+ cells were first enriched using MACS beads (Miltenyi Biotech) and subsequently CD4+CD25high cells were sorted with a FACS-Diva™ cell sorter (BD Biosciences).

tag: CD4+CD25high T-Lymphocytes derived from human PBL (control group)


title: Resistant_2_NF639

status: Public on Jun 01 2006

first: Gail

middle: E

last: Sonenshein

address: 715 Albany Street

department: Biochemistry

institute: Boston University Medical School

description:
Green Tea Polyhenol Epigallocatechin 3-Gallate (EGCG) resistant pool of NF639 Cells
Replicate 2

label: Standard Affymetrix protocol

source_name: NF639 breast cancer cell line EGCG-resistant population

tag: Tissue

value: breast cancer cell line

tag: Population


title: WBC Pro_A post_ex

description:
cRNA from White blood cells from proband A
after exhaustive exercise

tag: White blood cells from proband A post exercise


title: F8 broiler by Fayoumi cross spleen day 8 high SE load verse non-SE replicate 2

city: Ames

middle: J

last: Lamont

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

description: spleen total RNA were amplified into aRNA. Two high SE load pooled samples were hybridized one non-SE sample

data_processing: LOWESS normalization, mixed model analysis by SAS

organism: Gallus gallus

source_name: High SE load total RNA

tag: Two high SE load spleen total RNA were pooled

source_name: Non-SE total RNA

tag: one non-SE spleen total RNA


title: F8 broiler by Fayoumi spleen day 8 low SE load verse non-SE replicate 2

description: spleen total RNA were amplified into aRNA. Two low SE load pooled samples were hybridized one non-SE sample

source_name: Low SE total RNA

tag: Two low SE spleen total RNA were pooled


title: F8 broiler by Fayoumi spleen day 8 high SE load verse low SE load replicate 2

description: spleen total RNA were amplified into aRNA. Two high SE load pooled samples were hybridized two low SE load samples

source_name: Low SE load total RNA

tag: Two low SE load spleen total RNA were pooled


title: Original_2_NF639

description:
Original population of NF639 Cells
Replicate 2

source_name: NF639 breast cancer cell line original population

value: original population


title: Resistant_1_NF639

description:
Green Tea Polyhenol Epigallocatechin 3-Gallate (EGCG) resistant pool of NF639 Cells
Replicate 1


title: Original_1_NF639

description:
Original population of NF639 Cells
Replicate 1


title: F8 broiler by Fayoumi cross spleen day 8 low SE load verse non-SE replicate 1


title: F8 broiler by Fayoumi cross spleen day 7 high SE load verse low SE load replicate 1

description: spleen total RNA were amplified into aRNA. Two high SE load pooled samples were hybridized two low SE load pooled sample


title: F8 broiler by Fayoumi cross spleen day 7 low SE load verse non-SE replicate 2

tag: One non-SE spleen total RNA


title: F8 broiler by Fayoumi cross spleen day 8 high SE verse low SE load replicate 1


title: F8 broiler by Fayoumi cross spleen day 7 high SE load verse low SE load replicate 2


title: F8 broiler by Fayoumi day 8 spleen high SE load vs non-SE replicate 1


title: F8 broiler by Fayoumi cross spleen day 7 high SE load verse non-SE load replicate 2


title: F8 broiler by Leghorn cross spleen day 8 low SE load verse non-SE replicate 2

source_name: non-SE total RNA


title: F8 broiler by Fayoumi spleen day 7 high SE load verse non-SE

tag: Two high SE load total RNA were pooled


title: F8 broiler by Leghorn spleen day 8 high SE load verse low SE load replicate 1

source_name: high SE load spleen total RNA

source_name: Low SE load spleen total RNA


title: F8 broiler by Leghorn cross spleen day 8 low SE load verse non-SE replicate 1

source_name: non-SE spleen total RNA


title: F8 broiler by Leghorn spleen day 8 high SE load verse non-SE replicate 2

tag: two high SE load spleen total RNA were pooled

source_name: Non-SE spleen total RNA


title: F8 broiler by Leghorn spleen day 8 high SE load verse low SE load replicate 2

source_name: low SE spleen total RNA

source_name: High SE total RNA


title: F8 broiler by Fayoumi cross spleen day 7 low SE load verse non-SE


title: F8 broiler by Leghorn cross spleen day 7 high SE verse low SE load replicate 2

source_name: Low SE spleen

source_name: High SE load spleen total RNA


title: F8 broiler by Leghorn day 7 spleen low SE load verse non-SE replicate 2

tag: Two SE load spleen total RNA were pooled


title: F8 broiler by Leghorn cross spleen day 7 high SE load verse non_SE replicate 2


title: F8 broiler by Leghorn spleen day 7 low SE load verse non-SE replicate 1

source_name: Low SE load spleen

tag: two low SE load spleen total RNA were pooled

source_name: Non-SE spleen


title: F8 broiler by Leghorn spleen day 8 high SE load verse non-SE replicate 1

source_name: High SE load spleen RNA


title: F8 broiler by Leghorn cross spleen day 7 high SE verse low SE load replicate 1

source_name: High SE load spleen

source_name: low SE load spleen


title: Staphylococcus aureus_peracetic acid_20min_replicate3

status: Public on May 31 2006

first: Matthew

middle: Wook

last: Chang

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

institute: Nanyang Technological University

description: peracetic acid treatment

hyb_protocol: Standard Affymetrix procedures

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

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.2

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_peracetic acid

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

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

extract_protocol: Total RNA was isolated after 20 min incubation with peracetic acid using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.

treatment_protocol: peracetic acid (1mM)

tag: NCTC 8325 Wild type


title: Staphylococcus aureus_peracetic acid_20min_replicate2

description: peracetic acid treatment


title: Staphylococcus aureus_peracetic acid_10min_replicate1

description: peracetic acid treatment

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


title: FW_1a_BN1544

city: Berlin

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

institute: Max Planck Institute for Molecular Genetics

description: inflammatory cardiomyopathy

hyb_protocol: After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment (40 mmol/L Trisacetate (pH 8.2), 100 mmol//L potassium acetate, and 50 mmol//L magnesium acetate) at 94°C for 35 minutes. 15 µg of each cRNA sample was hybridized for 16 hours at 45°C to an Affymetrix Human Genome U133 Plus 2.0 GeneChip Array. Chips were washed and stained with streptavidin-phycoerythrin using a fluidics station according to protocolsrecommended by Affymetrix.

scan_protocol: Affymetrix scanner 3000

data_processing: Affymetrix GeneChip Operating Software (GCOS)

label: biotin labeled

source_name: inflammatory Cardiomyopathy

label_protocol: Starting with amounts below 1 µg, cRNA targets were generated using the small sample protocol (Affymetrix, vers. II). Briefly, in vitro transcribed unlabeled cRNA from the first round of amplification was subjected to a second round of amplification. cRNA was transcribed into cDNA using random primers. After RNAse H mediated removal of surplus cRNA a second strand was synthesized using a T7 primer. In detail, total RNA amounts of 50-200ng were used for first strand synthesis. cDNA was synthesized starting with the annealing to 5pmol/ul of a T7- (dT)24 primer that contains a promotor for DNA dependent RNA polymerase (TIB Molbiol, Berlin, Germany) at 70°C for 6 min. Reverse transcription (RT) was performed at 42°C for 1 hr in first strand buffer containing 50mM TRIS-HCl (pH=8.3), 75mM KCl, 3mM MgCl2, 10 mM dithiothreitol, 500 µM each dATP, dCTP, dGTP, and dTTP, and 20,000 U/ml of Superscript II reverse transcriptase (Invitrogen, Karlsruhe, Germany). Second-strand synthesis was carried out in 20-µl solutions, using the complete cDNA reaction mix and the MgCl2-, dNTP and enzyme solutions of the two cycle synthesis kit (Affymetrix) The mixture was incubated at 16°C for 2 hours, followed by a further incubation at 75°C for 10 minutes. Double strand cDNA was directly subjected to the first round of amplification using the MEGAScript T7 Kit (Ambion). Incubation was carried out at 37°C for 16hrs The amplified cRNA was purified with an affinity resin column (RNeasy, Qiagen, Hilden, Germany). 50-600ng of the yielded cRNA was used for the second round. For first strand synthesis random primers (final concentration 0.2 µg/µl) were used. After incubation at 42°C for 1h RNAse H was added at 37°C for 20min.and the reaction was stopped by heating at 95°C. After addition of 5pmol/ul of a T7- (dT)24-primer, the mix was heated at 70°C for 6 min. Then the second strand reaction mix was added. The mixture was incubated at 16°C for 2 h followed by a further incubation with 2 µl of T4 DNA polymerase (5 U/µl) (Invitrogen, Karlsruhe, Germany) for 10 min. The reaction was terminated by addition of 10 µl of 0.5 M EDTA. Cleanup of double stranded cDNA was performed using the cDNA-clean-up-modul of Affymetrix. Synthesis of biotin-labeled cRNA was performed using the GeneChip IVT labeling kit (Affymetrix, Santa  Clara, CA). The amplified cRNA was purified with an affinity resin column (RNeasy, Qiagen, Hilden, Germany) and fragmented by incubation at 94°C for 35 min. cRNA amounts were determined by UV-spectroscopy and distribution of cRNA fragment sizes of both, cRNA and fragmentation products, was checked by analyzing the samples on a LabChip (BioAnalyzer, AGILENT Technologies, Santa Clara, CA).

extract_protocol: standard protocol TRIzol (Invitrogen)

treatment_protocol: endomyocardial biopsy from the right ventricle

tag: age

tag: gender

tag: ejection fraction

tag: left ventricular end diastolic diameter

value: positive


title: Staphylococcus aureus_peracetic acid_10min_replicate3

city: Singapore

description: peracetic acid treatment


title: F8 broiler by Leghorn cross day 7 spleen high SE load verse non_SE replicate 1

source_name: Non-SE

tag: F8 broiler by Leghorn cross non-SE sample

source_name: High SE burden

tag: F8 broiler by Leghorn cross high SE load sample


title: FW_18c_BV3965

description: healthy endomyocardial control

source_name: healthy control

value: negative


title: Staphylococcus aureus_peracetic acid_20min_replicate1

description: peracetic acid treatment


title: ANA1_PA_1

status: Public on May 17 2006

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

institute: Istiuto Giannina Gaslini

description: Labelling, hybridization and scanning were performed at NCI-Frederick/LMT Microarray Research Facility according to the facility protocols.

data_processing: Normalization Method:Precalculated 50th Percentile (Median); Signal calculation: Mean Intensity minus Median Background; VALUE was calculated as log2 of the Ratio of Signal. The data were generated by NCI mAdb web tool.

source_name: ANA1_picolinic acid

tag: ANA-1 cell line treated with 4 mM picolinic acid

tag: ANA-1 cell line in normal condition


title: FW_5a_BV8411

description: inflammatory cardiomyopathy


title: FW_4a_BV4281

description: inflammatory cardiomyopathy


title: FW_15c_BV5830

description: healthy endomyocardial control


title: FW_14c_BV5933

description: healthy endomyocardial control

hyb_protocol: After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment (40 mmol/L Trisacetate (pH 8.2), 100 mmol//L potassium acetate, and 50 mmol//L magnesium acetate) at 94°C for 35 minutes. 15 µg of each cRNA sample was hybridized for 16 hours at 45°C to an Affymetrix Human Genome U133 Plus 2.0 GeneChip Array. Chips were washed and stained with streptavidin-phycoerythrin using a fluidics station according to protocols recommended by Affymetrix.


title: FW_2a_BV8343

description: inflammatory cardiomyopathy


title: FW_8a_BV8865

description: inflammatory cardiomyopathy


title: Staphylococcus aureus_peracetic acid_10min_replicate2

description: peracetic acid treatment


title: ANA1_PA_2


title: FW_3a_BV8771

description: inflammatory cardiomyopathy


title: CCAT Full Length Rep B1

status: Public on May 05 2006

city: Stanford

first: Ricardo

last: Dolmetsch

state: CA

address: 299 Campus Drive, D227

department: Neurobiology

institute: Ricardo Dolmetsch

description: The goal of these experiments was to identify the genes that are regulated by CCAT, a novel transcription factor derived from the C-terminus of CaV1.2. Neuro2A neuroblastoma cells were transfected with the last 503 AA of CaV1.2 which is full length CCAT (CCAT FL) or with the last 280 AA of CaV1.2, a form of CCAT that lacks the transcriptional activation domain (CCAT DTA). The mRNA from either CCAT FL or CCAT DTA expressing cells was hybridized to Agilent mouse genome microarrays along with mRNA from untransfected neuro2A cells. The microarray data was subsequently analyzed with the Rossetta Luminator gene expression data analysis system. Subsequent investigation revealed that CCAT DTA can still activate transcription albeit at much lower levels than CCAT FL.

hyb_protocol: Gene Expression Hybridization Kit, Hybridization chamber-Surehyb and hybridization oven were used for the hybridization step followed by Gene Expression Wash buffers and Stabilization and drying solution (Agilent). All steps were performed according to manufacturer’s instructions. Two color RNA Spike-In kit (Agilent) was used to monitor microarray workflow.

scan_protocol: Microarrays were scanned using Agilent’s Microarray scanner. Feature extraction was performed using Agilent's feature extraction software 8.5.

data_processing: Microarray results were analyzed using the Rosetta LuminatorTM gene expression data analysis system.

label_protocol: In an ozone-free room, labeling and linear amplification was accomplished using Agilent’s low RNA Input Linear Amplification Kit PLUS, Two-Color. All steps were performed according to manufacturer’s instructions.

growth_protocol: Cell were maintained acording to the recomendations of ATCC. ATCC complete growth medium: Minimum essential medium (Eagle) with 2 mM L-glutamine and Earle's BSS adjusted to contain 1.5 g/L sodium bicarbonate, 0.1 mM non-essential amino acids, and 1.0 mM sodium pyruvate, 90%; fetal bovine serum, 10%; Temperature: 37.0C; Atmosphere: air, 95%; carbon dioxide (CO2), 5%

extract_protocol: Total RNA was extracted using RNAesay Mini kit (Qiagen). RNA sample quality assessment was performed using the Agilent 2100 bioanalyzer and RNA LabChip Kits.

treatment_protocol: For the mRNA in the green channel (SIG_1): Neuro2A Cells were transfected using Lipofoctamine 2000 transfection reagent with a PA1 plasmid containing CCAT (503AA C-term of CaV 1.2, Accesion# M67515). 24 hours after transfection, GFP expressing cells were selected using fluorescence activated cell sorting (FACS) and total RNA was extracted from these cells.

tag: Neuroblastoma cell line from ATCC (Cat# CCL-131) transfected with CCAT (503AA C-term of CaV 1.2, Accesion# M67515) for 24hrs

source_name: Neuroblastoma Neuro2A Cells from ATCC (Cat# CCL-131) transfected with empty PA1 Vector

treatment_protocol: For the mRNA in the green channel (SIG_1): Neuro2A Cells were transfected using Lipofoctamine 2000 transfection reagent with a empty PA1 plasmid. 24 hours after transfection, GFP expressing cells were selected using fluorescence activated cell sorting (FACS) and total RNA was extracted from these cells.

tag: Neuroblastoma cell line from ATCC (Cat# CCL-131) transfected with empty PA1 vector


title: FW_7a_BV8479

description: inflammatory cardiomyopathy


title: CCAT Full Length Rep B3

source_name: Neuroblastoma cell line from ATCC (Cat# CCL-131) transfected with CCAT (503AA C-term of CaV 1.2, Accesion# M67515)

growth_protocol: Cells were maintained acording to the recomendations of ATCC. ATCC complete growth medium: Minimum essential medium (Eagle) with 2 mM L-glutamine and Earle's BSS adjusted to contain 1.5 g/L sodium bicarbonate, 0.1 mM non-essential amino acids, and 1.0 mM sodium pyruvate, 90%; fetal bovine serum, 10%; Temperature: 37.0C; Atmosphere: air, 95%; carbon dioxide (CO2), 5%

treatment_protocol: For the mRNA in the red channel (SIG_2): Neuro2A Cells were transfected using Lipofoctamine 2000 transfection reagent with a empty PA1 plasmid. 24 hours after transfection, GFP expressing cells were selected using fluorescence activated cell sorting (FACS) and total RNA was extracted from these cells.


title: CCAT Full Length Rep B2

treatment_protocol: For the mRNA in the red channel (SIG_2): Neuro2A Cells were transfected using Lipofoctamine 2000 transfection reagent with an empty PA1 plasmid. 24 hours after transfection, GFP expressing cells were selected using fluorescence activated cell sorting (FACS) and total RNA was extracted from these cells.


title: FW_16c_BV7565

description: healthy endomyocardial control


title: CCAT DTS Rep A3

source_name: Neuroblastoma cell line from ATCC (Cat# CCL-131) transfected with CCAT DTS (280AA C-term of CaV 1.2, Accesion# M67515)

source_name: Untransfected Neuro2A Cells

treatment_protocol: Untransfected Neuro2A cells were grown under identical conditions to transfected cells and sorted using a fluorescence activated cell sorter to replicate the condition of cells expressing CCAT.


title: CCAT DTS Rep A2

treatment_protocol: For the mRNA in the green channel (SIG_1): Neuro2A Cells were transfected using Lipofoctamine 2000 transfection reagent with a PA1 plasmid containing CCAT DTA (280AA C-term of CaV 1.2, Accesion# M67515). 24 hours after transfection, GFP expressing cells were selected using fluorescence activated cell sorting (FACS) and total RNA was extracted from these cells.

tag: Neuroblastoma cell line from ATCC (Cat# CCL-131)


title: CCAT DTS Rep A1

treatment_protocol: For the mRNA in the green channel (SIG_1): Neuro2A Cells were transfected using Lipofoctamine 2000 transfection reagent with a PA1 plasmid containing CCAT DTS (280AA C-term of CaV 1.2, Accesion# M67515). 24 hours after transfection, GFP expressing cells were selected using fluorescence activated cell sorting (FACS) and total RNA was extracted from these cells.

tag: Neuroblastoma cell line from ATCC (Cat# CCL-131) transfected with CCAT DTA (280AA C-term of CaV 1.2, Accesion# M67515) for 24hrs


title: FW_6a_BV7625

description: inflammatory cardiomyopathy

source_name: inflammatory cardiomyopathy


title: CCAT Full Length Rep A3

growth_protocol:
Cell were maintained acording to the recomendations of ATCC.
ATCC complete growth medium: Minimum essential medium (Eagle) with 2 mM L-glutamine and Earle's BSS adjusted to contain 1.5 g/L sodium bicarbonate, 0.1 mM non-essential amino acids, and 1.0 mM sodium pyruvate, 90%; fetal bovine serum, 10%;
Temperature: 37.0C;
Atmosphere: air, 95%; carbon dioxide (CO2), 5%


title: CCAT Full Length Rep A1


title: CCAT Full Length Rep A2


title: RSV1-24H

status: Public on May 01 2006

first: Yuh-Chin

middle: Tony

last: Huang

address: Erwin Rd

institute: Duke University Medical Center

description: RSV treated (24 hours)

data_processing: Background subtracted

source_name: BEAS cells

tag: RSV 1.0 MOI 24 hours


title: RSV4-24H

description: RSV treated (24 hours)


title: Control 1

description: Vehicle treated (4 hours)

label: Control 1

tag: Vehicle treated 4 hours


title: RSV2-4H

description: RSV treated (4 hours)

tag: RSV 1.0 MOI 4 hours


title: Control 3

description: Vehicle treated (4 hours)

label: Control 3

tag: RSV gene expression


title: Control 2

description: Vehicle treated (4 hours)

label: Control 2


title: RSV1-4H

description: RSV treated (4 hours)


title: RSV4-4H

description: RSV treated (4 hours)


title: RSV3-24H

description: RSV treated (24 hours)


title: RSV3-4H

description: RSV treated (4 hours)


title: Control 4

description: Vehicle treated (4 hours)

label: Control 4


title: D7F(1)Cy3_I

status: Public on Apr 20 2006

city: Leiden

first: Ellen

last: Sterrenburg

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: OPMD, cell line, transfected, mutant pabpn1 high

source_name: Reference IM2


title: D7F(2)Cy3_I

description: OPMD, cell line, transfected mutant pabpn1 low


title: D7F(3)Cy5_II

description: OPMD experiment

data_processing: Rosetta Resolver Genepix error model

tag: Reference IM2


title: D7F(1)Cy3_II

description: OPMD experiment


title: D7F(3)Cy3_II

description: OPMD experiment


title: D7F(3)Cy3_I


title: D7F(2)Cy5_II

description: OPMD experiment


title: D7F(1)Cy5_I


title: D7F(2)Cy5_I


title: D7F(3)Cy5_I


title: D7E(3)Cy3_I

description: OPMD, cell line, transfected mutant pabpn1 high


title: D7F(2)Cy3_II

description: OPMD experiment


title: D7F(1)Cy5_II

description: OPMD experiment


title: D7E(3)Cy3_II

description: OPMD experiment


title: Viro3P10-064

city: San Francisco

first: Joe

last: DeRisi

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: amplified RNA from an ET aspirate sample from a patient with fulminant pneumonia

data_processing: Median feature intensity minus median background intensity

organism: Viruses

tag: Parainfluenza 4a


title: D7E(3)Cy5_I


title: D7E(2)Cy3_I


title: D7E(3)Cy5_II

description: OPMD experiment


title: D7E(1)Cy3_I


title: D7E(2)Cy3_II

description: OPMD experiment


title: D7E(2)Cy5_I


title: D7E(1)Cy5_II

description: OPMD experiment


title: WTD(3)Cy5_I

description: OPMD, cell line, transfected wildtype pabpn1 low


title: WTD(1)Cy3_I


title: WTD(2)Cy3_II

description: OPMD experiment


title: WTD(2)Cy3_I


title: WTD(1)Cy5_II

description: OPMD experiment


title: D7E(2)Cy5_II

description: OPMD experiment


title: WTD(1)Cy5_I


title: WTD(3)Cy3_II

description: OPMD experiment


title: WTD(2)Cy5_I


title: WTD(3)Cy3_I


title: WTA(3)Cy5_I

description: OPMD, cell line, transfected pabpn1 wildtype high


title: WTD(2)Cy5_II

description: OPMD experiment


title: WTA(3)Cy3_II

description: OPMD experiment


title: D7E(1)Cy3_II

description: OPMD experiment


title: D7E(1)Cy5_I


title: WTA(3)Cy5_II

description: OPMD experiment


title: WTD(3)Cy5_II

description: OPMD experiment


title: WTD(1)Cy3_II

description: OPMD experiment


title: RSV2-24H

city: Durham

description: RSV treated (24 hours)


title: WTA(2)Cy3_I


title: WTA(3)Cy3_I


title: WTA(2)Cy3_II

description: OPMD experiment


title: WTA(2)Cy5_I


title: WTA(2)Cy5_II

description: OPMD experiment


title: WTA(1)Cy3_II

description: OPMD experiment


title: IM2(3)Cy3_II

description: OPMD experiment


title: WTA(1)Cy3_I


title: WTA(1)Cy5_II

description: OPMD experiment


title: IM2(2)Cy5_I

description: OPMD, cell line, untransfected


title: WTA(1)Cy5_I