title: wt SF8300 grown in TSB media to exponential phase biological replicate 1

description: gene expression data from_wtSF8300 grown in TSB media to exponential phase biological rep 1

source_name: wt8300 TSB log rep1


title: PVL mutant in MW2 grown in CCY media to stationary phase biological replicate 2

status: Public on Sep 12 2008

type: RNA

city: Hamilton

first: Amy

middle: M

last: Palazzolo-Ballance

state: MT

address: 903 S. 4th Street

department: Rocky Mountain Laboratory

country: USA

institute: NIH/NIAID

description: gene expression data from_mutMW2 grown in CCY media to stationary phase biological rep 2

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Staphylococcus aureus

source_name: mutMW2 CCY sta rep2

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Overnight cultures of bacteria were diluted 1:200 into 20 ml of either TSB or CCY media and cultured to exponential (exp, OD600 = 1.0) or stationary (sta, OD600 = 2.0) phases of growth

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

treatment_protocol: no treatments were performed


title: wt MW2 grown in CCY media to stationary phase biological replicate 2

description: gene expression data from_wtMW2 grown in CCY media to stationary phase biological rep 2

source_name: wtMW2 CCY sta rep2


title: PVL mutant in MW2 grown in TSB media to stationary phase biological replicate 2

description: gene expression data from_mutMW2 grown in TSB media to stationary phase biological rep 2

source_name: mutMW2 TSB sta rep2


title: PVL mutant in SF8300 grown in CCY media to stationary phase biological replicate 1

description: gene expression data from_mutSF8300 grown in CCY media to stationary phase biological rep 1

source_name: mut8300 CCY sta rep1


title: PVL mutant in MW2 grown in TSB media to stationary phase biological replicate 3

description: gene expression data from_mutMW2 grown in TSB media to stationary phase biological rep 3

source_name: mutMW2 TSB sta rep3


title: PVL mutant in MW2 grown in CCY media to stationary phase biological replicate 1

description: gene expression data from_mutMW2 grown in CCY media to stationary phase biological rep 1

source_name: mutMW2 CCY sta rep1


title: wt MW2 grown in CCY media to stationary phase biological replicate 1

description: gene expression data from_wtMW2 grown in CCY media to stationary phase biological rep 1

source_name: wtMW2 CCY sta rep1


title: wt MW2 grown in CCY media to stationary phase biological replicate 3

description: gene expression data from_wtMW2 grown in CCY media to stationary phase biological rep 3

source_name: wtMW2 CCY sta rep3


title: wt MW2 grown in TSB media to stationary phase biological replicate 2

description: gene expression data from_wtMW2 grown in TSB media to stationary phase biological rep 2

source_name: wtMW2 TSB sta rep2


title: wt MW2 grown in TSB media to stationary phase biological replicate 3

description: gene expression data from_wtMW2 grown in TSB media to stationary phase biological rep 3

source_name: wtMW2 TSB sta rep3


title: wt MW2 grown in TSB media to stationary phase biological replicate 1

description: gene expression data from_wtMW2 grown in TSB media to stationary phase biological rep 1

source_name: wtMW2 TSB sta rep1


title: YeastMHY100_[Heme+]_rep1

status: Public on Sep 10 2008

city: NEW YORK CITY

first: ANSHUL

middle: BHARAT

last: KUNDAJE

state: NY

address: 110 MORNINGSIDE DRIVE, APT. 31A

department: COMPUTER SCIENCE

institute: COLUMBIA UNIVERSITY

description: MHY100 cells grown in medium containing 250 microg/ml (heme-sufficient) 5-aminolevulinic acid. Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.

hyb_protocol: The yeast Saccharomyces cerevisiae genome 2.0 arrays were purchased from Affymetrix, Inc. Probe hybridization and data collection were carried out by the Columbia University Affymetrix GeneChip processing center. Specifically, the Affymetrix GeneChip Hybridization Oven 640 and the next generation GeneChip Fluidics Station 450 were used for hybridization and chip processing. Chip scanning was performed by using the GeneChip scanner 3000. Initial data acquisition, analysis was performed by using the Affymetrix Microarray suite. By using GCOS1.2 with the advanced PLIER (probe logarithmic intensity error) algorithm, we calculated and examined the parameters reflecting the image quality of the arrays. Arrays with a high background level in any region were discarded and replaced. The average noise or background level was limited to less than 5%. The average intensity for those genes judged to be present was at least 10-fold higher than those judged to be absent. Also, arrays that deviated considerably in the percentage of present and absent genes from the majority of the arrays were replaced. Arrays with a beta-actin 3’/5’ ratio greater than 2 were replaced.

data_processing: For each microarray, we converted the .DAT image files into .CEL files using the Affymetrix GCOS software. These raw .CEL files were further processed into expression values using the RMA express software by Bolstad. This software uses the robust multiarray average method by Irrizary et al. which involves a background correction and a quantile-based normalization scheme.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae, MHY100, heme sufficient, replicate 3

label_protocol: The synthesis of cDNA and biotin-labeled cRNA were carried out exactly as described in the Affymetrix GeneChip Expression Analysis Technical Manual (2000).

extract_protocol: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.]. RNA samples were prepared from MHY100 cells grown in medium containing 250 microg/ml (heme-sufficient) 5-aminolevulinic acid. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.

tag: Yeast strains used MHY100 (MATa, ura3-52, leu2-3, 112, his4-519, ade1-100, hem1-delta100). MHY100 was used for studies of heme regulation. MHY100 cells were grown in medium containing 250 microg/ml (heme-sufficient) 5-aminolevulinic acid. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.


title: YeastL51_[air+Hap1+Co+]_rep3

description: L51 yeast cells bearing the empty expression plasmid in the presence of 400 microM cobalt chloride for 6 hours. Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.

scan_protocol: The yeast Saccharomyces cerevisiae genome 2.0 arrays were purchased from Affymetrix, Inc. Probe hybridization and data collection were carried out by the Columbia University Affymetrix GeneChip processing center. Specifically, the Affymetrix GeneChip Hybridization Oven 640 and the next generation GeneChip Fluidics Station 450 were used for hybridization and chip processing. Chip scanning was performed by using the GeneChip scanner 3000. Initial data acquisition, analysis was performed by using the Affymetrix Microarray suite. By using GCOS1.2 with the advanced PLIER (probe logarithmic intensity error) algorithm, we calculated and examined the parameters reflecting the image quality of the arrays. Arrays with a high background level in any region were discarded and replaced. The average noise or background level was limited to less than 5%. The average intensity for those genes judged to be present was at least 10-fold higher than those judged to be absent. Also, arrays that deviated considerably in the percentage of present and absent genes from the majority of the arrays were replaced. Arrays with a beta-actin 3’/5’ ratio greater than 2 were replaced.

source_name: Saccharomyces cerevisiae L51 (HAP1), Cobalt induced, aerobic conditions, replicate 3

extract_protocol: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.]. RNA samples were prepared from L51 yeast cells bearing the empty expression plasmid in the presence of 400 microM cobalt chloride for 6 hours. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.

tag: Yeast strains used were L51 (MATa, ura3-52, leu2-3, 112, his4-519, ade1-100, trp1::HisG, hap1::LEU2). L51 was used for studies of oxygen regulation. To avoid variations from the differences accumulated after many generations of growth of strains, we transformed the L51 strain with the HAP1 gene deleted for studies of Hap1 function. Hap1 protein was expressed in L51 cells by transforming an ARS-CEN plasmid bearing the complete HAP1 genomic sequence. For comparison with cells without Hap1 expressed, an empty vector was transformed into L51 cells. The use of Hap1 expression plasmid generated much more reproducible results than the use of different strains. Yeast cells with or without Hap1 expressed grew at similar rates under both anaerobic and aerobic conditions. The UAS1/CYC1-lacZ reporter plasmid was transformed into yeast cells to confirm the expression of Hap1 and the oxygen levels. Cells were grown in yeast synthetic complete media. Co2+-induced cells were grown in the presence of 400 microM cobalt chloride for 6 hours.


title: YeastMHY100_[Heme-]_rep3

description: MHY100 cells grown in medium containing 2.5 microg/ml (heme-deficient) 5-aminolevulinic acid. Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.

source_name: Saccharomyces cerevisiae, MHY100, heme deficient, replicate 3

extract_protocol: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.]. RNA samples were prepared from MHY100 cells grown in medium containing 2.5 microg/ml (heme-deficient) 5-aminolevulinic acid. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.

tag: Yeast strains used MHY100 (MATa, ura3-52, leu2-3, 112, his4-519, ade1-100, hem1-delta100). MHY100 was used for studies of heme regulation. MHY100 cells were grown in medium containing 2.5 microg/ml (heme-deficient) 5-aminolevulinic acid. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.


title: YeastMHY100_[Heme+]_rep2

source_name: Saccharomyces cerevisiae, MHY100, heme sufficient, replicate 2


title: HighDepression 5

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

description: Affymetrix U133A

hyb_protocol: Standard Affymetrix hybridization protocol for gene expression profiling (carried out in UCLA DNA Microarray Core).

scan_protocol: Standard Affymetrix scan protocol for gene expression profiling (carried out in UCLA DNA Microarray Core).

data_processing: RMA (RMAExpress) processing of Affymetrix .CEL files generated by UCLA DNA Microarray Core.

organism: Homo sapiens

source_name: Primary ovarian carcinoma from patients with high depression

label_protocol: Standard Affymetrix probe synthesis for gene expression profiling (carried out in UCLA DNA Microarray Core).

extract_protocol: Primary ovarian carcinoma tissues were homogenized and total RNA was extracted using Qiagen RNEasy.

tag: HighDepression


title: YeastMHY100_[Heme-]_rep2

source_name: Saccharomyces cerevisiae, MHY100, heme deficient, replicate 2


title: LowDepression 4

description: Affymetrix U133A

source_name: Primary ovarian carcinoma from patients with low depression

tag: LowDepression


title: YeastMHY100_[Heme+]_rep3


title: LowDepression 5

description: Affymetrix U133A


title: HighDepression 1

description: Affymetrix U133A


title: YeastMHY100_[Heme-]_rep1

source_name: Saccharomyces cerevisiae, MHY100, heme deficient, replicate 1

tag: Yeast strains used MHY100 (MATa, ura3-52, leu2-3, 112, his4-519, ade1-100, hem1-delta100). MHY100 was used for studies of heme regulation. MHY100 cells were grown in medium containing 2.5 microg/ml (heme-deficient) 5-aminolevulinic acid.  For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.


title: YeastL51_[air+Hap1+]_rep3

description: L51 cells bearing the Hap1 expression were grown under normoxic conditions. The UAS1/CYC1-lacZ reporter plasmid was transformed into yeast cells to confirm the expression of Hap1 and the oxygen levels. Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.

source_name: Saccharomyces cerevisiae L51 (HAP1) aerobic conditions, replicate 3

extract_protocol: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.]. RNA samples were prepared from L51 yeast cells bearing the Hap1 expression plasmid maintained under aerobic conditions. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.

tag: Yeast strains used were L51 (MATa, ura3-52, leu2-3, 112, his4-519, ade1-100, trp1::HisG, hap1::LEU2). L51 was used for studies of oxygen regulation. To avoid variations from the differences accumulated after many generations of growth of strains, we transformed the L51 strain with the HAP1 gene deleted for studies of Hap1 function. Hap1 protein was expressed in L51 cells by transforming an ARS-CEN plasmid bearing the complete HAP1 genomic sequence. For comparison with cells without Hap1 expressed, an empty vector was transformed into L51 cells. The use of Hap1 expression plasmid generated much more reproducible results than the use of different strains. Yeast cells with or without Hap1 expressed grew at similar rates under both anaerobic and aerobic conditions.


title: YeastL51_[anaerobic_Hap1-]_6hrs_rep3

description: L51 yeast cells bearing the empty expression plasmid maintained under anaerobic conditions for 6 hours. Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.

source_name: Saccharomyces cerevisiae L51 (\delta HAP1) anaerobic conditions 6 hours, replicate 3

extract_protocol: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.]. RNA samples were prepared from L51 yeast cells bearing the empty expression plasmid maintained under anaerobic conditions for 6 hours. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.

tag: Yeast strains used were L51 (MATa, ura3-52, leu2-3, 112, his4-519, ade1-100, trp1::HisG, hap1::LEU2). L51 was used for studies of oxygen regulation. To avoid variations from the differences accumulated after many generations of growth of strains, we transformed the L51 strain with the HAP1 gene deleted for studies of Hap1 function. Hap1 protein was expressed in L51 cells by transforming an ARS-CEN plasmid bearing the complete HAP1 genomic sequence. For comparison with cells without Hap1 expressed, an empty vector was transformed into L51 cells. The use of Hap1 expression plasmid generated much more reproducible results than the use of different strains. Yeast cells with or without Hap1 expressed grew at similar rates under both anaerobic and aerobic conditions. We chose to use a low oxygen level (~10 ppb) in this study, in order to identify all oxygen-regulated genes. Previous studies have shown that most, if not all, oxygen-regulated genes are affected a low concentrations, but some genes are not affected at higher oxygen levels (for example, > 1 ppm). Anaerobic (~10 ppb O2, measured by using an oxygen monitor and confirmed by CHEMetrics oxygen kits) growth condition was created by using an anaerobic chamber (Coy Laboratory, Inc.) and by filling the chamber with a mixture of 5% H2 and 95% N2 in the presence of palladium catalyst. L51 yeast cells bearing the empty expression plasmid maintained under anaerobic conditions for 6 hours. The UAS1/CYC1-lacZ reporter plasmid was transformed into yeast cells to confirm the expression of Hap1 and the oxygen levels. Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.


title: HighDepression 2

description: Affymetrix U133A


title: LowDepression 1

description: Affymetrix U133A


title: HighDepression 4

description: Affymetrix U133A


title: YeastL51_[anaerobic_Hap1+]_6hrs_rep3

description: L51 yeast cells bearing the Hap1 expression plasmid maintained under anaerobic conditions for 6 hours. Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.

source_name: Saccharomyces cerevisiae L51 (HAP1) anaerobic conditions 6 hours, replicate 3

extract_protocol: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.]. RNA samples were prepared from L51 yeast cells bearing the Hap1 expression plasmid maintained under anaerobic conditions for 6 hours. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.

tag: Yeast strains used were L51 (MATa, ura3-52, leu2-3, 112, his4-519, ade1-100, trp1::HisG, hap1::LEU2). L51 was used for studies of oxygen regulation. To avoid variations from the differences accumulated after many generations of growth of strains, we transformed the L51 strain with the HAP1 gene deleted for studies of Hap1 function. Hap1 protein was expressed in L51 cells by transforming an ARS-CEN plasmid bearing the complete HAP1 genomic sequence. For comparison with cells without Hap1 expressed, an empty vector was transformed into L51 cells. The use of Hap1 expression plasmid generated much more reproducible results than the use of different strains. Yeast cells with or without Hap1 expressed grew at similar rates under both anaerobic and aerobic conditions. We chose to use a low oxygen level (~10 ppb) in this study, in order to identify all oxygen-regulated genes. Previous studies have shown that most, if not all, oxygen-regulated genes are affected a low concentrations, but some genes are not affected at higher oxygen levels (for example, > 1 ppm). Anaerobic (~10 ppb O2, measured by using an oxygen monitor and confirmed by CHEMetrics oxygen kits) growth condition was created by using an anaerobic chamber (Coy Laboratory, Inc.) and by filling the chamber with a mixture of 5% H2 and 95% N2 in the presence of palladium catalyst. L51 cells bearing the Hap1 expression were grown under anaerobic conditions for 6 hours. The UAS1/CYC1-lacZ reporter plasmid was transformed into yeast cells to confirm the expression of Hap1 and the oxygen levels. Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.


title: YeastL51_[air+Hap1-]_rep3

description: L51 yeast cells bearing the empty expression plasmid were maintained under aerobic conditions. Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.

source_name: Saccharomyces cerevisiae L51 (\delta HAP1) aerobic conditions, replicate 3

extract_protocol: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.]. RNA samples were prepared from L51 yeast cells bearing the empty expression plasmid maintained under aerobic conditions. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.


title: HighDepression 3

description: Affymetrix U133A


title: YeastL51_[anaerobic_Hap1-]_6hrs_rep2

source_name: Saccharomyces cerevisiae L51 (\delta HAP1) anaerobic conditions 6 hours, replicate 2


title: LowDepression 3

description: Affymetrix U133A


title: LowDepression 2

description: Affymetrix U133A


title: YeastL51_[anaerobic_Hap1+]_6hrs_rep2

data_processing: For each microarray, we converted the  .DAT image files into  .CEL files using the Affymetrix GCOS software.  These raw  .CEL files were further processed into expression values using the RMA express software by Bolstad.  This software uses the robust multiarray average method by Irrizary et al. which involves a background correction and a quantile-based normalization scheme.

source_name: Saccharomyces cerevisiae L51 (HAP1) anaerobic conditions 6 hours, replicate 2


title: YeastL51_[air+Hap1+Co+]_rep2

source_name: Saccharomyces cerevisiae L51 (HAP1), Cobalt induced, aerobic conditions, replicate 2


title: YeastL51_[anaerobic_Hap1+]_1.5hrs_rep3

description: L51 yeast cells bearing the Hap1 expression plasmid maintained under anaerobic conditions for 1.5 hours. Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.

source_name: Saccharomyces cerevisiae L51 (HAP1) anaerobic conditions 1.5 hours, replicate 3

extract_protocol: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.]. RNA samples were prepared from L51 yeast cells bearing the Hap1 expression plasmid maintained under anaerobic conditions for 1.5 hours. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.

tag: Yeast strains used were L51 (MATa, ura3-52, leu2-3, 112, his4-519, ade1-100, trp1::HisG, hap1::LEU2). L51 was used for studies of oxygen regulation. To avoid variations from the differences accumulated after many generations of growth of strains, we transformed the L51 strain with the HAP1 gene deleted for studies of Hap1 function. Hap1 protein was expressed in L51 cells by transforming an ARS-CEN plasmid bearing the complete HAP1 genomic sequence. For comparison with cells without Hap1 expressed, an empty vector was transformed into L51 cells. The use of Hap1 expression plasmid generated much more reproducible results than the use of different strains. Yeast cells with or without Hap1 expressed grew at similar rates under both anaerobic and aerobic conditions. We chose to use a low oxygen level (~10 ppb) in this study, in order to identify all oxygen-regulated genes. Previous studies have shown that most, if not all, oxygen-regulated genes are affected a low concentrations, but some genes are not affected at higher oxygen levels (for example, > 1 ppm). Anaerobic (~10 ppb O2, measured by using an oxygen monitor and confirmed by CHEMetrics oxygen kits) growth condition was created by using an anaerobic chamber (Coy Laboratory, Inc.) and by filling the chamber with a mixture of 5% H2 and 95% N2 in the presence of palladium catalyst. L51 cells bearing the Hap1 expression were grown under anaerobic conditions for 1.5 hours. The UAS1/CYC1-lacZ reporter plasmid was transformed into yeast cells to confirm the expression of Hap1 and the oxygen levels. Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.


title: YeastL51_[anaerobic_Hap1+]_6hrs_rep1

hyb_protocol: The yeast Saccharomyces cerevisiae genome 2.0 arrays were purchased from Affymetrix, Inc.  Probe hybridization and data collection were carried out by the Columbia University Affymetrix GeneChip processing center.  Specifically, the Affymetrix GeneChip Hybridization Oven 640 and the next generation GeneChip Fluidics Station 450 were used for hybridization and chip processing.  Chip scanning was performed by using the GeneChip scanner 3000.  Initial data acquisition, analysis was performed by using the Affymetrix Microarray suite.  By using GCOS1.2 with the advanced PLIER (probe logarithmic intensity error) algorithm, we calculated and examined the parameters reflecting the image quality of the arrays.  Arrays with a high background level in any region were discarded and replaced.  The average noise or background level was limited to less than 5%.  The average intensity for those genes judged to be present was at least 10-fold higher than those judged to be absent.  Also, arrays that deviated considerably in the percentage of present and absent genes from the majority of the arrays were replaced.  Arrays with a beta-actin 3’/5’ ratio greater than 2 were replaced.

source_name: Saccharomyces cerevisiae L51 (HAP1) anaerobic conditions 6 hours


title: YeastL51_[air+Hap1-]_rep2

source_name: Saccharomyces cerevisiae L51 (\delta HAP1) aerobic conditions replicate 2


title: YeastL51_[anaerobic_Hap1+]_1.5hrs_rep2

source_name: Saccharomyces cerevisiae L51 (HAP1) anaerobic conditions 1.5 hours replicate 2


title: YeastL51_[air+Hap1+]_rep2

source_name: Saccharomyces cerevisiae L51 (HAP1) aerobic conditions replicate 2


title: YeastL51_[anaerobic_Hap1-]_6hrs_rep1

scan_protocol: The yeast Saccharomyces cerevisiae genome 2.0 arrays were purchased from Affymetrix, Inc.  Probe hybridization and data collection were carried out by the Columbia University Affymetrix GeneChip processing center.  Specifically, the Affymetrix GeneChip Hybridization Oven 640 and the next generation GeneChip Fluidics Station 450 were used for hybridization and chip processing.  Chip scanning was performed by using the GeneChip scanner 3000.  Initial data acquisition, analysis was performed by using the Affymetrix Microarray suite.  By using GCOS1.2 with the advanced PLIER (probe logarithmic intensity error) algorithm, we calculated and examined the parameters reflecting the image quality of the arrays.  Arrays with a high background level in any region were discarded and replaced.  The average noise or background level was limited to less than 5%.  The average intensity for those genes judged to be present was at least 10-fold higher than those judged to be absent.  Also, arrays that deviated considerably in the percentage of present and absent genes from the majority of the arrays were replaced.  Arrays with a beta-actin 3’/5’ ratio greater than 2 were replaced.

source_name: Saccharomyces cerevisiae L51 (\delta HAP1) anaerobic conditions 6 hours


title: 13371173_532nm_720PMT_635nm_800PMT_45ka.gpr

status: Public on Sep 07 2008

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

description: IR24 rice seedling grown in dark for 2 weeks.

hyb_protocol: HS4800 Automated Slide Hybridization Station.  Geneframes Hybridization solution, incubated in boiling water for 3 minutes, centrifuged, then hybridized.  Hybridized for 16 hours at 50C, washed 2x SSC/0.2%, SDS, 1x SSC and 0.5x SSC and dried with N2

scan_protocol: GenePix 4000B scanner at 5um resolution. 100% laser power for 532nm and 635nm.  Scanned twice using high PMT and low PMT settings.

data_processing:
Average normalized spot intensities for each oligo in the light and dark conditions were calculated using the lowess method of the lmgene package of R.

Log ratio data not available; normalized signal intensity data linked as supplementary file.

organism: Oryza sativa

label_protocol: SuperScript Labeling System

growth_protocol: TP309 rice seedling grown in light for 2 weeks

extract_protocol: TRIZOL treatment, followed by DNaseI treatment and purified with RNeasy Midi Kit

tag: Oryza sativa, light, dark

growth_protocol: TP309 rice seedling grown in dark for 2 weeks


title: 13371169_532nm_660PMT_635nm_840PMT_45Ka.gpr

growth_protocol: IR24 rice seedling grown in dark for 2 weeks

growth_protocol: IR24 rice seedling grown in light for 2 weeks


title: 13371168_532nm_660PMT_635nm_840PMT_45Ka.gpr

treatment_protocol: IR24 rice seedling grown in light for 2 weeks

treatment_protocol: IR24 rice seedling grown in dark for 2 weeks


title: 13371171_532nm_660PMT_635nm_840PMT_45Ka.gpr

growth_protocol: Nipponbare rice seedling grown in light for 2 weeks

growth_protocol: Nipponbare rice seedling grown in dark for 2 weeks


title: 13371002_532nm_660PMT_635nm_840PMT_45Kb.gpr

growth_protocol: Kitaake rice seedling grown in dark for 2 weeks

growth_protocol: Kitaake rice seedling grown in light for 2 weeks


title: 13371170_532nm_650PMT_635nm_840PMT_45Ka.gpr

treatment_protocol: Kitaake rice seedling grown in light for 2 weeks

treatment_protocol: Kitaake rice seedling grown in dark for 2 weeks


title: 13360999_532nm_720PMT_635nm_800PMT_0045b.gpr

treatment_protocol: TP309 rice seedling grown in dark for 2 weeks

treatment_protocol: TP309 rice seedling grown in light for 2 weeks


title: 13371166_532nm_660PMT_635nm_840PMT_45Ka.gpr

treatment_protocol: Nipponbare rice seedling grown in dark for 2 weeks

treatment_protocol: Nipponbare rice seedling grown in light for 2 weeks


title: 13371006_532nm_660PMT_635nm_840PMT_45Kb.gpr


title: 13371000_532nm_720PMT_635nm_800PMT_45kb.gpr


title: 13371004_532nm_660PMT_635nm_840PMT_45Kb.gpr


title: 13371003_532nm_660PMT_635nm_840PMT_45Kb.gpr


title: YeastL51_[air+Hap1-]_rep1

source_name: Saccharomyces cerevisiae L51 (\delta HAP1) aerobic conditions

extract_protocol: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.].  RNA samples were prepared from L51 yeast cells bearing the empty expression plasmid maintained under aerobic conditions. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.


title: YeastL51_[air+Hap1+]_rep1

description: L51 cells bearing the Hap1 expression were grown under normoxic conditions.  The UAS1/CYC1-lacZ reporter plasmid was transformed into yeast cells to confirm the expression of Hap1 and the oxygen levels.  Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.

source_name: Saccharomyces cerevisiae L51 (HAP1) aerobic conditions

extract_protocol: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.].  RNA samples were prepared from L51 yeast cells bearing the Hap1 expression plasmid maintained under aerobic conditions. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.

tag: Yeast strains used were L51 (MATa, ura3-52, leu2-3, 112, his4-519, ade1-100, trp1::HisG, hap1::LEU2).  L51 was used for studies of oxygen regulation.  To avoid variations from the differences accumulated after many generations of growth of strains, we transformed the L51 strain with the HAP1 gene deleted for studies of Hap1 function.  Hap1 protein was expressed in L51 cells by transforming an ARS-CEN plasmid bearing the complete HAP1 genomic sequence.  For comparison with cells without Hap1 expressed, an empty vector was transformed into L51 cells.  The use of Hap1 expression plasmid generated much more reproducible results than the use of different strains.  Yeast cells with or without Hap1 expressed grew at similar rates under both anaerobic and aerobic conditions.


title: YeastL51_[anaerobic_Hap1+]_1.5hrs_rep1

source_name: Saccharomyces cerevisiae L51 (HAP1) anaerobic conditions 1.5 hours

extract_protocol: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.].  RNA samples were prepared from L51 yeast cells bearing the Hap1 expression plasmid maintained under anaerobic conditions for 1.5 hours. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.

tag: Yeast strains used were L51 (MATa, ura3-52, leu2-3, 112, his4-519, ade1-100, trp1::HisG, hap1::LEU2). L51 was used for studies of oxygen regulation.  To avoid variations from the differences accumulated after many generations of growth of strains, we transformed the L51 strain with the HAP1 gene deleted for studies of Hap1 function.  Hap1 protein was expressed in L51 cells by transforming an ARS-CEN plasmid bearing the complete HAP1 genomic sequence. For comparison with cells without Hap1 expressed, an empty vector was transformed into L51 cells.  The use of Hap1 expression plasmid generated much more reproducible results than the use of different strains.  Yeast cells with or without Hap1 expressed grew at similar rates under both anaerobic and aerobic conditions.

tag: We chose to use a low oxygen level (~10 ppb) in this study, in order to identify all oxygen-regulated genes.  Previous studies have shown that most, if not all, oxygen-regulated genes are affected a low concentrations, but some genes are not affected at higher oxygen levels (for example, > 1 ppm).  Anaerobic (~10 ppb O2, measured by using an oxygen monitor and confirmed by CHEMetrics oxygen kits) growth condition was created by using an anaerobic chamber (Coy Laboratory, Inc.) and by filling the chamber with a mixture of 5% H2 and 95% N2 in the presence of palladium catalyst.  L51 cells bearing the Hap1 expression were grown under anaerobic conditions for 1.5 hours.  The UAS1/CYC1-lacZ reporter plasmid was transformed into yeast cells to confirm the expression of Hap1 and the oxygen levels.  Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.


title: YeastL51_[air+Hap1+Co+]_rep1

source_name: Saccharomyces cerevisiae L51 (HAP1), Cobalt induced, aerobic conditions

extract_protocol: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.].  RNA samples were prepared from L51 yeast cells bearing the empty expression plasmid in the presence of 400 microM cobalt chloride for 6 hours. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.

tag: The UAS1/CYC1-lacZ reporter plasmid was transformed into yeast cells to confirm the expression of Hap1 and the oxygen levels.  Cells were grown in yeast synthetic complete media.  Co2+-induced cells were grown in the presence of 400 microM cobalt chloride for 6 hours.


title: 13371005_532nm_640PMT_635nm_840PMT_45Kb.gpr


title: 13371172_532nm_660PMT_635nm_840PMT_45Ka.gpr


title: 13371177_532nm_720PMT_635nm_800PMT_45ka.gpr


title: msn2/4 mutant 3 hours exposure to zymolyase 1

status: Public on Sep 06 2008

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

country: Spain

institute: Facultad de Farmacia (UCM)

description: For each condition tested, comparison of treated and non-treated samples, the total RNA from two different cultures was analyzed, and, in addition, for each sample two different hybridizations were performed, including fluorochrome swapping in order to minimize transcriptional changes due to technical variability. This therefore corresponded to four DNA microarrays analyzed for each condition.

hyb_protocol: Slides were prehybridized in prehybridization solution (6 x SSC, 0.5% SDS, 1% bovine serum albumin (A-7906, Sigma) for 1 h and were then hybridized overnight in a LucideaTM SlidePro Automated Hybridization Station (Amersham Biosciences). Before scanning, the chips were washed and dried in a same  LucideaTM SlidePro Automated Hybridization

scan_protocol: Microarrays were scanned with aGenePix 4000B scanner (Axon Instruments, Union City, CA) at a resolution of 5 μm (PMT values ranging from 550 to 700 and laser power 100%). GenePix Pro 4.0 analysis software (Axon Instruments, Union City, CA) was used to locate spots in the microarray with the appropriate grid and to obtain the two Cy3/Cy5 image TIFF files. All images were further processed using GenePix 4.0 software according to the manufacturer’s instructions.

data_processing: Flagged spots and spots with an average intensity minus background below the mean of the background (considering this as the median of the local background for each spot) for all the non-flagged spots in any of the channels (Cy3 or Cy5) were not retained for further analysis. Within this group, the spots showing in one channel a value of intensity minus background higher than 5 times the mean of the background for all spots in the microarray for that channel were recovered. The reproducibility of replicates in each microarray (two spots per ORF) was analyzed by creating a normal distribution log2 (RA _ 1/RB), where RA and RB are the ratios of replicated spots after background subtraction and normalization. Replicates that exceeded the average by more than _3 S.D. were discarded. Data analysis was accomplished using the GeneSight 4.0 software package (BioDiscovery Inc, El Segundo, CA). Locally weighed linear regression (lowess) analysis was performed as a normalization method to remove the intensity-dependent deviation in the log2(ratio) values. Significance analysis of the results was conducted using a Student’s t test (GeneSight). Genes with p values of less than 0.05 were considered to be significantly differentially expressed with respect to the treatment condition.

source_name: total RNA Saccharomyces cereviase msn2/4 mutant, without zymolyase

label_protocol: cDNA was synthesized from 25–30 μg of total RNA by reverse transcription, using the CyScribeTM First-Strand cDNA Labeling Kit, incorporating Cy5- dUTP (Amersham Biosciences) into the cDNA corresponding to each sample to be compared. Labeled cDNA was dried in a vacuum trap and used as a hybridization probe after resuspension in 45 μl of hybridization solution (50% Formamide, 6 x SSC, 0.5% SDS, 5 x Denhardt’s, 20 μg of poly(A) (P-9403, Sigma) and salmon sperm (Invitrogen, 100 μg/ml)

extract_protocol: Total RNA was isolated from exponentially growing cells (5 x 108) by the “mechanical disruption protocol” using the RNeasy MIDI kit (Qiagen, Hilden, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

tag: S. cerevisiae (msn2/4 mutant strain BY4741) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Zymolyase to a final concentration of 0,8U/ml. Cells were collected at 3 hours of growth, frozen at -80 °C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase msn2/4 mutant, 3 hours exposure to zymolyase

label_protocol: cDNA was synthesized from 25–30 μg of total RNA by reverse transcription, using the CyScribeTM First-Strand cDNA Labeling Kit, incorporating Cy3-dUTP (Amersham Biosciences) into the cDNA corresponding to each sample to be compared. Labeled cDNA was dried in a vacuum trap and used as a hybridization probe after resuspension in 45 μl of hybridization solution (50% Formamide, 6 x SSC, 0.5% SDS, 5 x Denhardt’s, 20 μg of poly(A) (P-9403, Sigma) and salmon sperm (Invitrogen, 100 μg/ml)


title: rlm1 mutant 3 hours exposure to zymolyase 4

source_name: total RNA Saccharomyces cereviase rlm1 mutant, 3 hours exposure to zymolyase

tag: S. cerevisiae (rlm1 mutant strain BY4741) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Zymolyase to a final concentration of 0,8U/ml. Cells were collected at 3 hours of growth, frozen at -80 °C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase rlm1 mutant, without zymolyase


title: msn2/4 mutant 3 hours exposure to zymolyase 2


title: rlm1 mutant 3 hours exposure to zymolyase 3


title: slt2 mutant 3 hours exposure to zymolyase 3

source_name: total RNA Saccharomyces cereviase slt2 mutant, without zymolyase

tag: S. cerevisiae (slt2 mutant strain BY4741) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Zymolyase to a final concentration of 0,8U/ml. Cells were collected at 3 hours of growth, frozen at -80 °C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase wild type, 3 hours exposure to zymolyase


title: slt2 mutant 3 hours exposure to zymolyase 2

source_name: total RNA Saccharomyces cereviase slt2 mutant, 3 hours exposure to zymolyase


title: rlm1 mutant 3 hours exposure to zymolyase 1


title: slt2 mutant 3 hours exposure to zymolyase 4


title: GGS4_BR1_3F_12424172annot_MDS_MDS.tav.refIsIB.out

status: Public on Sep 05 2008

first: Chun-Hua

last: Wan

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

description: No additional info.

hyb_protocol: HYBRIDIZATION PROTOCOL:  Prehybridization of the array which was printed on UltraGaps aminosilane coated slides (Corning Life Sciences) consisted of their immersion in a solution of 5X SSC, 0.1% SDS and 1% bovine-serum albumin for 45 minutes at 42ºC after which slides were washed and dried. Labeled cDNA was resuspended in a solution of 50% formamide, 5X SSC, 0.1% SDS and allowed to hybridize for 18-20 hours at 42ºC under glass coverslips. Post hybridization, slides were washed two times for four minutes each in the following series of solutions: 1X SSC, 0.2% SDS; 0.1X SSC, 0.1% SDS; 0.1X SSC. A final wash for 30 seconds at 0.05X SSC was completed prior to drying by centrifugation.

scan_protocol: SCAN PROTOCOL:  After hybridization and post-processing, slides were promptly scanned at a 10 µm resolution using an Axon 4000B scanner with GenePix 4.0 software. PMT values were optimized during scanning to balance channel intensities.

data_processing: Processing of 16-bit TIFF images from hybridized arrays were produced using the TIGR TM4 package (www.tigr.org/software). Intensity values for Cy3 and Cy5 channels were obtained using TIGR-Spotfinder software. Normalization was performed using the LOWESS algorithm available in TIGR-MIDAS using block mode and a smooth parameter of 0.33. All intensity values less than two times greater than background were removed from subsequent analysis and replicate reporter intensities on one slide (one technical replicate) were reduced to a single value by computing the geometric mean.

organism: Geobacter sulfurreducens

source_name: Geobacter sulfurreducens strain DL1 cell culture in chemostats

label_protocol: LABEL PROTOCOL:  Approximately 5µg of total RNA was reverse transcribed using SuperScript II RNase H– reverse transcriptase (Invitrogen) to create cDNA into which amino allyl dUTP (Ambion) was incorporated for the purposes of indirect labeling with either Cyanine 3 or Cyanine 5 (Cy3/Cy5) fluorescent dyes. Labeled cDNA was purified using a modification of the Qiaquick PCR purification kit (QIAGEN).

growth_protocol: GROWTH PROTOCOL: All cells were cultured anaerobically in NBAF (acetate/fumarate) or FWFC [acetate/Fe(III) citrate] medium at 30°C as previously described (Coppi, M. V. et al. 2001). Steady-state growth occurred in chemostats under strict anaerobic conditions (N2-CO2 [80:20, vol/vol]) in a freshwater medium containing Fe(III) citrate (56 mM) as the electron acceptor and limited acetate (5.5 mM) as the electron donor using a dilution rate of 0.05 h–1.

extract_protocol: EXTRACT PROTOCOL:  In order to extract total RNA, cells were mechanically disrupted using a FastPrep instrument (Qbiogene) with Lysing Matrix B (Qbiogene) and nucleic acids were extracted with TRIzol Reagent (Invitrogen) (a mono-phasic solution of phenol and guanidine isothiocyanate). Any residual DNA was removed using RNase free DNase according to manufacturer’s instructions (Ambion). The treated RNA was subsequently cleaned and concentrated with RNeasy minicolumns (Qiagen Inc.). Quality of total RNA was assessed by agarose/formaldehyde gel electrophoresis and the concentration determined using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies).

treatment_protocol: No treatment

tag: Geobacter sulfurreducens strain DL1 (Coppi, M. V. et al. 2001. Development of a genetic system for Geobacter sulfurreducens. Appl. Environ. Microbiol. 67:3180-3187) was cultured anaerobically in NBAF (acetate/fumarate) or FWFC [acetate/Fe(III) citrate] medium at 30°C as previously described (Coppi, M. V. et al. 2001). Steady-state growth occurred in chemostats under strict anaerobic conditions (N2-CO2 [80:20, vol/vol]) in a freshwater medium containing Fe(III) citrate (56 mM) as the electron acceptor and limited acetate (5.5 mM) as the electron donor using a dilution rate of 0.05 h–1.

source_name: Geobacter sulfurreducens strain DL6 cell culture in chemostats

tag: Geobacter sulfurreducens strain DL6 (omcB::cam) (Leang, C. et al. 2003. OmcB, a c-type polyheme cytochrome, involved in Fe(III) reduction in Geobacter sulfurreducens. J. Bacteriol. 185:2096-2103.) was cultured anaerobically in NBAF (acetate/fumarate) or FWFC [acetate/Fe(III) citrate] medium at 30°C as previously described (Coppi, M. V. et al. 2001). Steady-state growth occurred in chemostats under strict anaerobic conditions (N2-CO2 [80:20, vol/vol]) in a freshwater medium containing Fe(III) citrate (56 mM) as the electron acceptor and limited acetate (5.5 mM) as the electron donor using a dilution rate of 0.05 h–1.


title: GGS4_BR2_2S_12420013annot_MDS_MDS.tav.refIsIA.out

description: No additional info.


title: slt2 mutant 3 hours exposure to zymolyase 1


title: GGS4_BR1_3S_12419857annot_MDS_MDS.tav.refIsIA.out

description: No additional info.


title: GGS4_BR2_1S_12419856annot_MDS_MDS.tav.refIsIA.out

description: No additional info.


title: rlm1 mutant 3 hours exposure to zymolyase 2


title: hog1 mutant 3 hours exposure to zymolyase 2

source_name: total RNA Saccharomyces cereviase hog1 mutant, 3 hours exposure to zymolyase

tag: S. cerevisiae (hog1 mutant strain BY4741) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Zymolyase to a final concentration of 0,8U/ml. Cells were collected at 3 hours of growth, frozen at -80 °C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase hog1 mutant, without zymolyase


title: GGS4_BR2_2F_12414580annot_MDS_MDS.tav.refIsIB.out

description: No additional info.


title: GGS4_BR2_1Fa_12414664annot_MDS_MDS.tav.refIsIB.out

description: No additional info.


title: GGS4_BR2_3F_12414663annot_MDS_MDS.tav.refIsIB.out

description: No additional info.


title: hog1 mutant 3 hours exposure to zymolyase 3


title: hog1 mutant 3 hours exposure to zymolyase 4


title: Wild type 3 hours exposure to zymolyase 4

label_protocol:
cDNA was synthesized from 25–30 μg of total RNA by reverse transcription, using the CyScribeTM First-Strand cDNA Labeling Kit, incorporating Cy5-dUTP (Amersham Biosciences) into the cDNA corresponding to each sample to be compared. Labeled cDNA was dried in a vacuum trap and used as a hybridization probe after resuspension in 45 μl of hybridization solution (50% Formamide, 6 x SSC, 0.5% SDS, 5 x Denhardt’s, 20
μg of poly(A) (P-9403, Sigma) and salmon sperm (Invitrogen, 100 μg/ml)

tag: S. cerevisiae (strain BY4741) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Zymolyase to a final concentration of 0,8U/ml. Cells were collected at 3 hours of growth, frozen at -80 °C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase wild type, without zymolyase

label_protocol:
cDNA was synthesized from 25–30 μg of total RNA by reverse transcription, using the CyScribeTM First-Strand cDNA Labeling Kit, incorporating Cy3-dUTP (Amersham Biosciences) into the cDNA corresponding to each sample to be compared. Labeled cDNA was dried in a vacuum trap and used as a hybridization probe after resuspension in 45 μl of hybridization solution (50% Formamide, 6 x SSC, 0.5% SDS, 5 x Denhardt’s, 20
μg of poly(A) (P-9403, Sigma) and salmon sperm (Invitrogen, 100 μg/ml)


title: GGS4_BR1_2F_12424171annot_MDS_MDS.tav.refIsIB.out

description: No additional info.


title: hog1 mutant 3 hours exposure to zymolyase 1


title: Wild type 3 hours exposure to zymolyase 2

source_name: : total RNA Saccharomyces cereviase wild type, 3 hours exposure to zymolyase


title: GGS4_BR1_1S_12420014annot_MDS_MDS.tav.refIsIA.out

description: No additional info.

data_processing: SCAN PROTOCOL:  After hybridization and post-processing, slides were promptly scanned at a 10 µm resolution using an Axon 4000B scanner with GenePix 4.0 software. PMT values were optimized during scanning to balance channel intensities.


title: Wild type 3 hours exposure to zymolyase 1

source_name: RNA Saccharomyces cereviase wild type, 3 hours exposure to zymolyase


title: Wild type 3 hours exposure to zymolyase 3


title: AGY0249 NaCl 60 min H2O2 30 min rep 1 (v1.0)

city: Madison

first: David

middle: B

last: Berry

state: WI

address: 3456 Genetics Biotech. Building

department: Laboratory of Genetics

institute: University of Wisconsin: Madison

hyb_protocol: As in Gasch, Methods in Enzymology, 2002

scan_protocol: Arrays were scanned using GenePix (4000B from Axon Instruments)

data_processing: Bahler normalized, background subtracted VALUE determined by a moving window local to the spot normalized

label: Oyster 556

source_name: AGY0249 grown 2 doublings in YPD and collected

label_protocol: Cyanine dyes (Flownamics, Madison, WI) were used; otherwise, as in Gasch, Methods in Enzymology, 2002

growth_protocol: Grown two or more doublings in YPD to an OD600 of 0.3, and exposed to stress in YPD.

extract_protocol: Hot phenol extraction as in Gasch, Methods in Enzymology, 2002

treatment_protocol: Stressors were added to the final concentrations of 0.7M NaCl or 0.5mM H2O2, for 60 and 40 minutes respectively

tag: Strain AGY0249 (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 msn2::KanMX msn4::URA3)

label: Oyster 645

source_name: AGY0249 grown 2 doublings and exposed to 0.7M NaCl 60 min, then removed from stress and exposed to 0.5mM H2O2 30 min


title: AGY0249 NaCl 60 min H2O2 40 min rep 1 (v1.0)

source_name: AGY0249 grown 2 doublings and exposed to 0.7M NaCl 60 min, then removed from stress and exposed to 0.5mM H2O2 40 min


title: GGS4_BR1_2S_12571988annot_MDS_MDS.tav.refIsIA.out

description: No additional info.


title: GGS4_BR1_1F_12424169annot_MDS_MDS.tav.refIsIB.out

description: No additional info.


title: AGY0249 NaCl 60 min H2O2 20 min rep 1 (v1.0)

source_name: AGY0249 grown 2 doublings and exposed to 0.7M NaCl 60 min, then removed from stress and exposed to 0.5mM H2O2 20 min


title: AGY0249 NaCl 60 min H2O2 10 min rep 1 (v1.0)

source_name: AGY0249 grown 2 doublings and exposed to 0.7M NaCl 60 min, then removed from stress and exposed to 0.5mM H2O2 10 min


title: AGY0249 NaCl 15 min rep 1 (v1.0)

source_name: AGY0249 grown 2 doublings and exposed to 0.7M NaCl 15 min


title: AGY0249 H2O2 10 min rep 1 (v1.0)

source_name: AGY0249 grown 2 doublings and exposed to 0.5mM H2O2 for 10 min


title: BY4741 NaCl 60 min H2O2 40 min rep 2 (v1.0)

source_name: BY4741 grown 2 doublings in YPD and collected

tag: Strain BY4741 (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0)

source_name: BY4741 grown 2 doublings and exposed to 0.7M NaCl 60 min, then removed from stress and exposed to 0.5mM H2O2 40 min


title: AGY0249 NaCl 60 min rep 1 (v1.0)

source_name: AGY0249 grown 2 doublings and exposed to 0.7M NaCl 60 min


title: AGY0249 H2O2 40 min rep 1 (v1.0)

source_name: AGY0249 grown 2 doublings and exposed to 0.5mM H2O2 for 40 min


title: AGY0249 NaCl 45 min rep 1 (v1.0)

source_name: AGY0249 grown 2 doublings and exposed to 0.7M NaCl 45 min


title: AGY0249 H2O2 30 min rep 1 (v1.0)

source_name: AGY0249 grown 2 doublings and exposed to 0.5mM H2O2 for 30 min


title: AGY0249 H2O2 20 min rep 1 (v1.0)

source_name: AGY0249 grown 2 doublings and exposed to 0.5mM H2O2 for 20 min


title: BY4741 NaCl 60 min H2O2 40 min rep 1 (v1.0)


title: BY4741 NaCl 60 min H2O2 30 min rep 1 (v1.0)

source_name: BY4741 grown 2 doublings and exposed to 0.7M NaCl 60 min, then removed from stress and exposed to 0.5mM H2O2 30 min


title: BY4741 NaCl 60 min H2O2 30 min rep 2 (v1.0)


title: BY4741 NaCl 60 min H2O2 20 min rep 2 (v1.0)

source_name: BY4741 grown 2 doublings and exposed to 0.7M NaCl 60 min, then removed from stress and exposed to 0.5mM H2O2 20 min


title: BY4741 NaCl 60 min H2O2 20 min rep 1 (v1.0)


title: BY4741 NaCl 60 min H2O2 10 min rep 2 (v1.0)

source_name: BY4741 grown 2 doublings and exposed to 0.7M NaCl 60 min, then removed from stress and exposed to 0.5mM H2O2 10 min


title: BY4741 NaCl 60 min H2O2 10 min rep 1 (v1.0)


title: BY4741 H2O2 30 min rep 2 (v1.0)

source_name: BY4741 grown 2 doublings and exposed to 0.5mM H2O2 for 30 min


title: AGY0249 NaCl 30 min rep 1 (v1.0)

source_name: AGY0249 grown 2 doublings in YPD and collected

source_name: AGY0249 grown 2 doublings and exposed to 0.7M NaCl 30 min


title: BY4741 H2O2 20 min rep 2 (v1.0)

source_name: BY4741 grown 2 doublings and exposed to 0.5mM H2O2 for 20 min


title: BY4741 H2O2 40 min rep 2 (v1.0)

source_name: BY4741 grown 2 doublings and exposed to 0.5mM H2O2 for 40 min


title: BY4741 H2O2 40 min rep 1 (v1.0)


title: BY4741 H2O2 10 min rep 2 (v1.0)

source_name: BY4741 grown 2 doublings and exposed to 0.5mM H2O2 for 10 min


title: BY4741 H2O2 20 min rep 1 (v1.0)


title: BY4741 H2O2 10 min rep 1 (v1.0)


title: BY4741 NaCl 60 min rep 2 (v1.0)

source_name: BY4741 grown 2 doublings and exposed to 0.7M NaCl 60 min


title: BY4741 H2O2 30 min rep 1 (v1.0)

source_name: BY4741 grown 2 doublings in YPD and collected


title: BY4741 NaCl 45 min rep 1 (v1.0)

source_name: BY4741 grown 2 doublings and exposed to 0.7M NaCl 45 min


title: 13371001_532nm_650PMT_635nm_840PMT_45Kb.gpr


title: BY4741 NaCl 60 min rep 1 (v1.0)


title: BY4741 NaCl 30 min rep 2 (v1.0)

source_name: BY4741 grown 2 doublings and exposed to 0.7M NaCl 30 min


title: BY4741 NaCl 15 min rep 2 (v1.0)

source_name: BY4741 grown 2 doublings and exposed to 0.7M NaCl 15 min


title: BY4741 NaCl 30 min rep 1 (v1.0)


title: BY4741 NaCl 45 min rep 2 (v1.0)


title: Microbeam 25c 6 h B

status: Public on Sep 02 2008

city: Chiba

first: Kaori

last: Imadome

state: Chiba

address: Anagawa 4-9-1

department: Research Center of Charged Particle Therapy

country: Japan

institute: National institute of radiological sciences

description: cells with 25 microbeam irradiated cell, harvested at 6 h postirradiatin

hyb_protocol: according to standard Agilent protocol

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Signals were calculated by the Agilent Feature Extraction software and automatically underwent Lowess normalization.

source_name: Normal human fibroblast cells

label_protocol: Agilent Low RNA Input Linear Amplification Kit

extract_protocol: RNeasy Mini Kit (QIAGEN)

tag: AG01522D primary normal human diploid fibroblasts were obtained and routinely passaged as previously described (N. Hamada et al. LET-dependent survival of irradiated normal human fibroblasts and their descendents, Radiat. Res. 166 (2006) 24-30).


title: Microbeam 25c 2 h A

description: cells with 25 microbeam irradiated cell, harvested at 2 h postirradiatin


title: Microbeam sham 6 h A

description: no irradiated cells with sham microbeam irradiation, harvested at 6 h postirradiatin


title: Microbeam 5c 6 h B

description: cells with 5 microbeam irradiated cell, harvested at 6 h postirradiatin


title: Microbeam 1c 6 h A

description: cells with 1 microbeam irradiated cell, harvested at 6 h postirradiatin


title: Microbeam 5c 6 h A


title: Microbeam 25c 6 h A


title: Microbeam Control B

description: no treatment control cells cultured samely as microbeam irradiated cells


title: Microbeam 5c 2 h B

description: cells with 5 microbeam irradiated cell, harvested at 2 h postirradiatin


title: Microbeam 1c 2 h B

description: cells with 1 microbeam irradiated cell, harvested at 2 h postirradiatin


title: Microbeam 1c 2 h A


title: Broadbeam 0.1D 2 h B

description: irradiated cells with broadbeam at 0.1D dose, harvested at 2 h postirradiatin


title: Broadbeam 0.01D 6 h B

description: irradiated cells with broadbeam at 0.01D dose, harvested at 6 h postirradiatin


title: Microbeam sham 2 h A

description: no irradiated cells with sham microbeam irradiation, harvested at 2 h postirradiatin


title: Microbeam 1c 6 h B


title: Broadbeam 0.01D 2 h A

description: irradiated cells with broadbeam at 0.01D dose, harvested at 2 h postirradiatin


title: Microbeam 5c 2 h A


title: Microbeam Control A


title: Broadbeam 0.1D 2 h A


title: Microbeam sham 6 h B


title: Microbeam sham 2 h B


title: Broadbeam D 2 h B

description: irradiated cells with broadbeam at D dose, harvested at 2 h postirradiatin


title: Broadbeam D 6 h B

description: irradiated cells with broadbeam at D dose, harvested at 6 h postirradiatin


title: Broadbeam D 2 h A


title: Microbeam 25c 2 h B


title: Broadbeam 0.01D 2 h B


title: Broadbeam 0.1D 6 h A

description: irradiated cells with broadbeam at 0.1D dose, harvested at 6 h postirradiatin


title: Broadbeam 0.01D 6 h A


title: Broadbeam 0.1D 6 h B


title: D3 ES Cells in Attached Culture Rep2 (251411710065)

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: D3 ES Cells in Attached Culture

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um.  A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format.  Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3).

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See NIA Array Analysis website for details.

organism: Mus musculus

source_name: D3 ES Cells in Attached Culture

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: Total RNA was prepared from cultured cells using Isogen (Wako) according to manufacture???s protocol.  First-strand cDNA was prepared using Super Script reverse transcriptase(Invitrogen) primed with random hexamer in a 20-?? l reaction mixture containing 3?? g of total RNA.

tag: ES cells

tag: Strain

tag: Gender

value: male

tag: Genetic modification

value: transgenic

tag: Individual Identifier

source_name: Universal Mouse Reference Cell Line Pool

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: D3 ES Cells in Suspension Culture Rep2 (251411710067)

description: D3 ES Cells in Suspension Culture

source_name: D3 ES Cells in Suspension Culture


title: D3 ES Cells in Suspension Culture Rep1 (251411710066)

description: D3 ES Cells in Suspension Culture


title: D3 ES Cells in Attached Culture Rep1 (251411710064)

description: D3 ES Cells in Attached Culture


title: Broadbeam sham 6 h B

description: no irradiated cells with sham broadbeam irradiation, harvested at 2 h postirradiatin


title: Broadbeam D 6 h A


title: B6.CAST_control_biological rep2

status: Public on Sep 01 2008

city: Davis

first: Ana

middle: Elena

last: Vazquez

address: 1515 Newton Court

department: Otolaryngology-Head and Neck Surgery

institute: University of California, Davis

description: The knowledge that some inbred mice exhibit very high resistance to noise overexposure is intriguing.  The primary aim of this study was to further our understanding of the endogenous molecular mechanisms that confer such protection.  The results of a microarray analysis of gene expression in microdissected membranous labyrinth from different mouse strains representing unique susceptibilities to noise damage are compiled here. To our knowledge, no previous comprehensive gene-expression study has been reported in different stains of mice specifically aimed at understanding the molecular basis of the remarkable resistance to noise damage that is characteristic of 129 mice.

hyb_protocol: A hybridization cocktail was prepared, as recommended by Affymetrix, including the fragmented target, probe array controls, BSA, and herring sperm DNA. This cocktail was then hybridized to the probe array for an overnight incubation. The hybridization process was performed at the Microarray Core Facility of the University of California, Davis School of Medicine using a Hybridization Oven 640, as described in the Affymetrix manual for the MU74V2 gene chip.

scan_protocol: A 3000 GeneChip Scanner (Affymetrix, Santa Clara CA) available in the Microarray Core Facility of the University of California, Davis School of Medicine was used for scanning the gene chips.  The scanner is controlled by software installed in the microarray facility Affymetrix GeneChip Analysis Software (GCOS) for generating cell and tissue specific gene expression profiles.

data_processing: The data were analyzed using dChip software (http://biosun1.harvard.edu/complab/dchip/). Using dChip the data was normalized at PM and MM probe level to an array of  median intensity of the set of arrays then model-based expression levels were computed.

source_name: cochlea; B6.CAST; control

label_protocol: An in vitro transcription reaction was performed to synthetized biotin labeled cRNA using purified double-stranded cDNA as template.  The in vitro transcription reaction was carried out using the Message AmpTM kit (Ambion, Austin TX) following the Ambion's protocols including a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip test arrays for evaluation of the quality.

extract_protocol: Total RNA was extracted using the Rneasy Protect Mini Kit, following QIAGEN protocols (QIAGEN Inc, Valencia CA)

tag: Microdissected membranous labyrinth from eight 10-wk-old control, no exposed to noise B6.CAST mice


title: 129XI/SvJ_noise_biological rep3

data_processing: The data were analyzed using dChip software (http://biosun1.harvard.edu/complab/dchip/). Using dChip the data was normalized at PM and MM probe level to an array of median intensity of the set of arrays then model-based expression levels were computed.

source_name: cochlea; 129XI/SvJ; noise

tag: Microdissected membranous labyrinth from eight 10-wk-old 129X1/SvJ mice sacrificed 6h after a 1h 105 dB octave band of noise exposure centered at 10 kHz


title: 129XI/SvJ_control_biological rep3

source_name: cochlea; 129XI/SvJ; control

tag: Microdissected membranous labyrinth from eight 10-wk-old 129X1/SvJ control mice no exposed to noise


title: Broadbeam sham 2 h B


title: B6.CAST_noise_biological rep2

source_name: cochlea; B6.CAST; noise

tag: Microdissected membranous labyrinth from eight 10-wk-old B6.CAST mice sacrificed 6h after a 1h 105 dB OBN exposure


title: B6.CAST_control_biological rep1


title: 129X1/SvJ_control_biological rep1

source_name: cochlea; 129X1/SvJ; control

tag: Microdissected membranous labyrinth from eight 10-wk-old control, no exposed to noise 129X1/SvJ mice


title: 129X1/SvJ_control_biological rep2

tag: 10-wk-old control, no exposed to noise, 129X1/SvJ mice microdissected membranous labyrinth from 8 mice


title: 129X1/SvJ_noise_biological rep1

source_name: cochlea; 129X1/SvJ; noise

tag: Membranous labyrinth from 10-wk-old noise-exposed 129X1/SvJ mice sacrificed 6h after a 1h 105 dB octave band of noise exposure centered at 10 kHz


title: 129X1/SvJ_noise_biological rep2


title: B6.CAST_noise_biological rep1

tag: Microdissected membranous labyrinth from eight 10-wk-old B6.CAST mice sacrificed 6h after 1h 105 dB octave band of noise exposure centered at 10 kHz


title: Broadbeam sham 6 h A

description: no irradiated cells with sham broadbeam irradiation, harvested at 6 h postirradiatin


title: Broadbeam control B

description: no treatment control cells cultured samely as broadbeam irradiated cells


title: Broadbeam control A


title: Activated B cells 3hr - mAdbID:18797

city: Bethesda

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 18797

hyb_protocol: Lymphochip Hybridization Protocol Wash procedure: 1-2xssc 0.1%SDS 2-1xssc 1-0.5xssc 1-0.25xssc spin dry Qty. of labeled target: 50ug total RNA Time: 16-20 hrs Volume: 40 ul Temperature: 65C Other: see Nature. 2000 Feb 3;403(6769):503-11. AND Immunity. 2000 Aug;13(2):199-212.

scan_protocol: Creator: GenePix Pro 3.0.1.22 Scanner: GenePix 4000A PMTVolts: 730;; 600 LaserPower: 1.48;; 1.66 Temperature: 1.55

data_processing:
mAdb Data Processing Protocol (v. 1)
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

molecule: polyA RNA

source_name: Primary B cells anti-Ig 3hr

label_protocol:
Lymphochip Labeling-cy5
Label amount: 4 ul
Label method: reverse transcription
Other: see Immunity. 2000 Aug;13(2):199-212.

extract_protocol:
Fast Track PolyA+ protocol
Extraction method: Oligo dT capture of polyA+ RNA
Other: Followed manufacturer's (Invitrogen) protocol.

treatment_protocol:
Treatment type: compound
Agent: anti-Ig
Treatment dose: 25 mg/ml
Treatment time: 3 hour
Treatment temperature: 37C

tag: Developmental stage

value: adult

tag: Cell type

value: primary human B cell

source_name: Lymphochip Cell Line Pool

label_protocol:
Lymphochip Labeling-cy3
Label amount: 4 ul
Label method: reverse transcription
Other: see Immunity. 2000 Aug;13(2):199-212.

value: cell line pool


title: Broadbeam sham 2 h A

tag: AG01522D primary normal human diploid fibroblasts were obtained and routinely passaged as previously described (N. Hamada et al. LET-dependent survival of irradiated normal human fibroblasts and their descendents, Radiat. Res. 166 (2006) 24-30).


title: Activated B cells 1hr - mAdbID:18781

description: mAdb experiment ID: 18781

scan_protocol: Creator: GenePix Pro 3.0.1.22 Scanner: GenePix 4000A PMTVolts: 640;; 610 LaserPower: 1.48;; 1.59 Temperature: 1.54

source_name: Primary B cells anti-Ig 1hr

treatment_protocol:
Treatment type: compound
Agent: anti-Ig
Treatment dose: 25 mg/ml
Treatment time: 1 hour
Treatment temperature: 37C


title: E4A2- AI to BI

city: College Station

first: Huaijun

last: Zhou

state: TX

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

description: Four arrays are included in one slide

hyb_protocol: A 825 ng of labeled cRNA with specificity over 8 were used for the hybridization reaction using the in situ hybridization kit plus (Agilent Technologies). A 100 ul hybridization solution was loaded on each of array in Agilent 4x44K microarrays. Arrays were incubated at 65 ℃ for 17h in Agilent’s microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol.

scan_protocol: Slides were scanned at 5-μm resolution using GenePix Personal 4100A (Molecular Devices Corporation, Sunnyvale, CA) and were saved as TIFF images. Auto Photomultiplier tube (PMT) were selected and adjusted to get the ratio of the overall intensities between the two channels (Cy3 and Cy5) was 0.9~1.1. The intensities of the spots on each image were quantified by Genepix pro 6.0 software (Molecular Devices Corporation, Downingtown, PA), and data were saved as .txt files for further analyses.

data_processing: The signal intensity of each gene was globally normalized using LOWESS by R program (Yang et al, 2002).

organism: Gallus gallus

source_name: Salmonella enteritidis resistant line AI treated with infection

label_protocol: A 500 ng of aliquot of total RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The synthesized cDNA was transcribed into cRNA labeled with one of two cyanine-labeled nucleotides (Perkin Elmer, Wellesley, MA). Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity measured with ND-100 spectrophotometer (NanoDrop Technologies).

extract_protocol: Treated heterophils were pelleted, washed with RPMI (485×g for 15 min at 4°C), the supernatant discarded, the cells re-suspended in lysis buffer (Qiagen RNeasy mini RNA extraction kit, Qiagen Inc., Valencia, CA), and frozen. The lysed cells were transferred to QIAshredder homogenizer columns and centrifuged for 2 min at _ 8000 × g. Total RNA was extracted from the homogenized lysate according to the manufacturer’s instructions, eluted with 50 µl RNase-free water and stored at -80°C.

treatment_protocol: Heterophils (1×10^7) were treated with 300 µl SE (#97-11771) for 30 min at 39°C on a rotary shaker.

tag: Heterophils from 1 wk chicken

source_name: Salmonella enteritidis susceptible line BI treated with infection


title: E4A4- AC to BC

description: Four arrays are included in one slide

source_name: Salmonella enteritidis resistant line AC not infected

treatment_protocol: Heterophils (1×10^7) were treated with 300 µl RPMI for 30 min at 39°C on a rotary shaker.

source_name: Salmonella enteritidis susceptible line BC not infected


title: Resting B cells - repeat 2 - mAdbID:18779

description: mAdb experiment ID: 18779

scan_protocol: Creator: GenePix Pro 3.0.1.22 Scanner: GenePix 4000A PMTVolts: 610;; 620 LaserPower: 1.49;; 1.73 Temperature: 1.52

source_name: Primary B cells, resting - repeat 2


title: E3A1- AI to AC

description: Four arrays are included in one slide

treatment_protocol: Heterophils (1×10^7) were treated with 300 µl SE (#97-11771) for 30 min at 39°C on a rotary shaker..


title: E3A3- BI to BC

description: Four arrays are included in one slide


title: Plasma cell-repeat 1 - mAdbID:36175

description: mAdb experiment ID: 36175

hyb_protocol: Lymphochip Hybridization Protocol Wash procedure: 1-2xssc 0.1%SDS 2-1xssc 1-0.5xssc 1-0.25xssc spin dry Qty. of labeled target: 50ug total RNA Time: 16-20hrs Volume: 40ul final volume Temperature: 65C Other: see Nature. 2000 Feb 3;403(6769):503-11. AND Immunity. 2000 Aug;13(2):199-212.

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 650;; 660 ScanPower: 100;; 100 LaserPower: 1.19;; 2.05 Temperature: 36.55

source_name: Lymphopool

label_protocol:
Lymphochip Labeling-cy3
Label amount: 4ul
Label method: reverse transcription
Other: see Immunity. 2000 Aug;13(2):199-212.

tag: Other

value: Mixture of multiple human cell line polyA+ RNA. Weller, et al. Blood. 2004 Dec 1;104(12):3647-54.

source_name: Bone Marrow Plasma Cells

label_protocol:
Lymphochip Labeling-cy5
Label amount: 4ul
Label method: reverse transcription
Other: see Immunity. 2000 Aug;13(2):199-212.

tag: Tissue

value: bone marrow

value: human bone marrow plasma cells


title: E4A1- BI to AI

description: Four arrays are included in one slide


title: Naive B cell-repeat 2 - mAdbID:36185

description: mAdb experiment ID: 36185

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 620;; 680 ScanPower: 100;; 100 LaserPower: 1.25;; 1.85 Temperature: 38.45

source_name: Naive Blood B cells

value: blood

value: human peripheral blood B cell


title: E1A3- BI to BC

description: Four arrays are included in one slide


title: E3A4- BC to BI

description: Four arrays are included in one slide


title: E2A1- BI to AI

description: Four arrays are included in one slide


title: Naive B cell-repeat 1 - mAdbID:36184

description: mAdb experiment ID: 36184

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 610;; 680 ScanPower: 100;; 100 LaserPower: 1.21;; 2.31 Temperature: 37.1


title: Resting B cells - repeat 1 - mAdbID:18780

description: mAdb experiment ID: 18780

scan_protocol: Creator: GenePix Pro 3.0.1.22 Scanner: GenePix 4000A PMTVolts: 610;; 610 LaserPower: 1.48;; 1.58 Temperature: 1.53

source_name: Primary B cells, resting - repeat 1


title: Mature B cell-repeat 2 - mAdbID:36167

description: mAdb experiment ID: 36167

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 600;; 710 ScanPower: 100;; 100 LaserPower: 1.26;; 2.48 Temperature: 38.62

source_name: Mature Bone Marrow B cells

value: human mature bone marrow B cell


title: E2A3- BC to AC

description: Four arrays are included in one slide


title: E2A2- AI to BI

description: Four arrays are included in one slide


title: E3A2- AC to AI

description: Four arrays are included in one slide

treatment_protocol: Heterophils (1×10^7) were treated with 300 µl RPMI for 30 min at 39°C on a rotary shaker..


title: E2A4- AC to BC

description: Four arrays are included in one slide


title: E4A3- BC to AC

description: Four arrays are included in one slide


title: ATF2 KO-3

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

description: Technical replicate #3 of ATF2 knockout. These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.

hyb_protocol: Hybridization was per Illumina standard protocol

scan_protocol: Images were scanned on an Illumina BeadStation scanner

data_processing: Data were extracted using BeadStudio version 3 without any normalization and were then processed after log2 transformation using quantile normalization.

source_name: RNA was prepared from papilomas of 2-3 mice (2 for WT and 3 for Knockout) and this was pooled to perform the array. Each pooled sample was run in triplicates.   The mice were treated once with DMBA, followed by TPA application for 30 wks.

label_protocol: Labeling was per Illumina standard protocol.

tag: ATF2 Genotype

value: KO


title: Mature B cell-repeat 1 - mAdbID:36166

description: mAdb experiment ID: 36166

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 620;; 660 ScanPower: 100;; 100 LaserPower: 1.23;; 2.58 Temperature: 37.65


title: Plasma cell-repeat 2 - mAdbID:36176

description: mAdb experiment ID: 36176

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 680;; 650 ScanPower: 100;; 100 LaserPower: 1.25;; 2.36 Temperature: 38.25


title: ATF2 KO-1

description: Technical replicate #1 of ATF2 knockout. These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.

extract_protocol: RNA was prepared from papilomas of 2-3 mice (2 for WT and 3 for Knockout) and this was pooled to perform the array.

treatment_protocol: The mice were treated once with DMBA, followed by TPA application for 30 wks.


title: ATF2 KO-2

description: Technical replicate #2 of ATF2 knockout. These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.


title: E1A4- BC to BI

description: Four arrays are included in one slide


title: E1A2- AC to AI

description: Four arrays are included in one slide


title: E1A1- AI to AC

description: Four arrays are included in one slide

extract_protocol: Treated heterophils were pelleted, washed with RPMI (485×g for 15 min at 4°C), the supernatant discarded, the cells re-suspended in lysis buffer (Qiagen RNeasy mini RNA extraction kit, Qiagen Inc., Valencia, CA), and frozen. The lysed cells were transferred to QIAshredder homogenizer columns and centrifuged for 2 min at 8000 × g. Total RNA was extracted from the homogenized lysate according to the manufacturer’s instructions, eluted with 50 µl RNase-free water and stored at -80°C.


title: T4-2_NCOR2_TRAIL_rep4

city: San Francisco

first: Kelvin

middle: Kun-Chih

last: Tsai

address: 513 Parnassus Avenue, Rm S1364

department: Surgery

institute: University of California, San Francisco

description: Please refer to Affymetrix Expression Analysis Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) for detailed experimental procedures.

hyb_protocol: Heat the following mixture at 99 degrees for 5 min: Control Oligonucleotide B2 (3nM) 5 ul, 20X Eukaryotic Hybridization controls 15 ul, Herring Sperm DNA (10mg/mL) 3 ul, BSA (50mg/ml) 3 ul, 2X Hybridization Buffer 150 ul, DMSO 30 ul, H2O to final volume of 300 ul.  Moisten array with 200 ul 1X hybridization buffer and then place tough spots on and incubate in rotating oven for 10 minutes at 45 degrees. Transfer the cRNA hyb mix to the 45 degree oven to cool down for 5 minutes. Spin down tube at max speed in a microcentrifuge for 5 minutes. Remove the  1X hyb buffer from chips carefully and carefully load the spun-down samples (250 ul) onto chip. Reapply new tough spots. Place chips in rotating oven O/N.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The hybridization intensity data was processed using the GeneChip Operating software (Affymetrix). Affymetrix .cel files (probe intensity files) were processed with ArrayAssist Lite (v3.4, Stratagene). The files were imported and processed with the GC-RMA algorithm to yield probe set intensities and additionally, Affymetrix Preset, Absent, Marginal flags were computed. These values were exported in .chp files, which were subsequently imported into the Partek Genomics Suite software (v6.2, Partek).

source_name: T4-2 breast epithelial cells stably expressing NCOR2, TRAIL treated

label_protocol: Twenty microgram of total RNA from each sample was processed to produce biotinylated cRNA targets.

growth_protocol: Cells were propagated in chemically defined H14 medium (V. M. Weaver et al., J. Cell Biol. 137, 231 (1997)) for 7 days, after which they were cultured on top of reconstituted basement membrane (Matrigel, BD Biosciences) for 6 days (G. Y. Lee et al., Nat Method 4, 359 (2007)).

extract_protocol: Total RNA was extracted from monolayer culture or 3D culture by a modified TRI reagent procedure (P. Chomczynski et al., Biotechniques 19, 942 (1995)) and purified using an RNeasy Mini Kit (Qiagen).

treatment_protocol: T4-2 cells carrying pMFG-tet-GFP-NCOR2 and stably express GFP tagged NCOR2 by retrovirus-mediated gene transduction; treated with TRAIL (1 ug/ml) in three-dimensional reconstituted basement membrane culture for 4 hours.

tag: HMT3522 T4-2 neoplastic breast epithelial cells derived from epidermal growth factor withdrawal (P. Briand et al., Cancer Res 56, 2039 (1996)).


title: T4-2_NCOR2_TRAIL_rep1


title: ATF2 WT-3

description: Technical replicate #3 of ATF2 wildtype. These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.

value: WT


title: T4-2_vector_TRAIL_rep3

source_name: T4-2 breast epithelial cells stably expressing an empty retroviral vector, TRAIL treated

treatment_protocol: T4-2 cells carrying pMFG-tet-GFP and stably express GFP by retrovirus-mediated gene transduction; treated with TRAIL (1 ug/ml) in three-dimensional reconstituted basement membrane culture for 4 hours.


title: T4-2_NCOR2_TRAIL_rep2


title: T4-2_NCOR2_TRAIL_rep3


title: Microarray-Bioinformatics analysis of altered genomic expression profiles in the human fetal and infant myocardium

city: Beijing

first: bo

last: kong

address: 167 Beilishi Road

country: China

institute: Cardiovascular Institute and Fuwai Hospital,CAMS&PUMC

description: For individual channel data extract, faint spots were removed for which intensities were below 400 unit after background subtracted in both channels (Cy3 and Cy5).

hyb_protocol: Labeled fetus and infant samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized at 42℃ overnight in a rotating oven and washed with two consecutive solutions (0.2% SDS, 23 SSC at 42℃ for 5 min, and 0.23 SSC for 5 min) at room temperature.

scan_protocol: Arrays were scanned with a confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal(Cy5)/processed Green signal(Cy3).

source_name: myocardium of fetus1 from an elective abortions fetus.

label_protocol:
　Double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 5μg total RNA using the cDNA synthesis system according to the manufacturer’s protocol (Promega, USA). A T7-oligo(dT) primer (5’-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT- 3’) was used instead of the poly-T primer provided in the kit.
　After completion of double-stranded cDNA synthesis, cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and eluted with 30 μL elution buffer. The eluted double-stranded cDNA products were vacuum evaporated to 8 μL and subjected to 20-uL in vitro transcription reactions at 37℃ for 3 hr using the T7 RiboMAX Express large scale RNA production system (Promega). The amplified RNA was purified using the RNA Clean-up Kit (MN).
　Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 4 μL of first-strand buffer, 2 μL of 0.1M DTT, 1μL 10 mM dNTP, and 1.5μL M-MLV (Promega) were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14μL. The cDNA was mixed with 4μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 2.5μL Klenow buffer, dNTP, and Cy5-dCTP (Amersham Pharmacia Biotech) were added to final concentrations of 240 μM dATP, 240μM dGTP, 240μM dTTP, 120μM dCTP, and 40μM Cy-dCTP. 1μL Klenow enzyme (TaKaRa) was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

extract_protocol: Total RNA was isolated from tissue samples by using Trizol reagent according to the protocol outlined by the manufacturer (Invitrogen). RNA concentrations were determined spectrophotometrically at 260 nm, and quality was confirmed by running a 50- to 250-ng aliquot on the Agilent 2100 Bioanalyzer (Palo Alto, Calif).

tag: myocardium of fetus1, Gender :female; Age of gestation:28 weeks;Bodyweight :1.6kg

source_name: myocardium of infant1 from a heart valve donors who died as a result of noncardiac complications

label_protocol:
Double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 5μg total RNA using the cDNA synthesis system according to the manufacturer’s protocol (Promega, USA). A T7-oligo(dT) primer (5’-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT- 3’) was used instead of the poly-T primer provided in the kit.
　After completion of double-stranded cDNA synthesis, cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and eluted with 30 μL elution buffer. The eluted double-stranded cDNA products were vacuum evaporated to 8 μL and subjected to 20-uL in vitro transcription reactions at 37℃ for 3 hr using the T7 RiboMAX Express large scale RNA production system (Promega). The amplified RNA was purified using the RNA Clean-up Kit (MN).
　Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 4 μL of first-strand buffer, 2 μL of 0.1M DTT, 1μL 10 mM dNTP, and 1.5μL M-MLV (Promega) were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14μL. The cDNA was mixed with 4μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 2.5μL Klenow buffer, dNTP, and Cy3-dCTP (Amersham Pharmacia Biotech) were added to final concentrations of 240 μM dATP, 240μM dGTP, 240μM dTTP, 120μM dCTP, and 40μM Cy-dCTP. 1μL Klenow enzyme (TaKaRa) was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

tag: myocardium of infant1, Gender :female; Age :18 months  ;Bodyweight :10kg


title: T4-2_NCOR2_rep4

source_name: T4-2 breast epithelial cells stably expressing NCOR2

treatment_protocol: T4-2 cells carrying pMFG-tet-GFP-NCOR2 and stably express GFP tagged NCOR2 by retrovirus-mediated gene transduction.


title: T4-2_NCOR2_rep1


title: T4-2_NCOR2_rep2


title: T4-2_vector_TRAIL_rep2


title: T4-2_vector_TRAIL_rep4


title: T4-2_vector_TRAIL_rep1


title: Microarray-Bioinformatics analysis of altered genomic expression profiles in the human fetal and infant myocardium(2)

source_name: myocardium of fetus2 from an elective abortions fetus

label_protocol:
Double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 5μg total RNA using the cDNA synthesis system according to the manufacturer’s protocol (Promega, USA). A T7-oligo(dT) primer (5’-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT- 3’) was used instead of the poly-T primer provided in the kit.
　After completion of double-stranded cDNA synthesis, cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and eluted with 30 μL elution buffer. The eluted double-stranded cDNA products were vacuum evaporated to 8 μL and subjected to 20-uL in vitro transcription reactions at 37℃ for 3 hr using the T7 RiboMAX Express large scale RNA production system (Promega). The amplified RNA was purified using the RNA Clean-up Kit (MN).
　Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 4 μL of first-strand buffer, 2 μL of 0.1M DTT, 1μL 10 mM dNTP, and 1.5μL M-MLV (Promega) were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14μL. The cDNA was mixed with 4μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 2.5μL Klenow buffer, dNTP, and Cy5-dCTP (Amersham Pharmacia Biotech) were added to final concentrations of 240 μM dATP, 240μM dGTP, 240μM dTTP, 120μM dCTP, and 40μM Cy-dCTP. 1μL Klenow enzyme (TaKaRa) was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

tag: myocardium of fetus2, Gender :female; Age of gestation:25 weeks;Bodyweight :0.8kg

source_name: myocardium of infant2 from a heart valve donors who died as a result of noncardiac complications

tag: myocardium of infant1, Gender :female; Age :10 months  ;Bodyweight :9.2kg


title: Microarray-Bioinformatics analysis of altered genomic expression profiles in the human fetal and infant myocardium(5)

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Green signal(Cy3)/processed Red signal(Cy5).

source_name: myocardium of infant5 from a mild type of tetralogy of Fallot infant

tag: myocardium of infant1, Gender :female; Age :9 months  ;Bodyweight :9kg

source_name: myocardium of fetus5 from an elective abortions fetus.

tag: myocardium of fetus1, Gender :female; Age of gestation:25 weeks;Bodyweight :0.9kg


title: T4-2_vector_rep4

source_name: T4-2 breast epithelial cells expressing an empty retrovial vector

treatment_protocol: T4-2 cells carrying pMFG-tet-GFP and stably express GFP by retrovirus-mediated gene transduction.


title: Microarray-Bioinformatics analysis of altered genomic expression profiles in the human fetal and infant myocardium(3)

source_name: myocardium of fetus3 from an elective abortions fetus

tag: myocardium of fetus1, Gender :male; Age of gestation:28 weeks;Bodyweight :1.7kg

source_name: myocardium of infant3 from a mild type of tetralogy of Fallot infant

tag: myocardium of infant3, Gender :male; Age :15 months  ;Bodyweight :15kg


title: Microarray-Bioinformatics analysis of altered genomic expression profiles in the human fetal and infant myocardium(4)

source_name: myocardium of fetus4 from an elective abortions fetus

tag: myocardium of fetus1, Gender :female; Age of gestation:25 weeks;Bodyweight :1.0kg

source_name: myocardium of infant4 from a mild type of tetralogy of Fallot infant

tag: myocardium of infant4, Gender :female; Age :15 months  ;Bodyweight :10kg


title: T4-2_NCOR2_rep3


title: ATF2 WT-2

description: Technical replicate #2 of ATF2 wildtype. These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.