title: 14N108

city: Kiel

first: Timothy

middle: TeHua

last: Lu

institute: Christian-Albrechts-University Kiel

description:
Sex: Male; Age: 44yrs; 15ug total RNA

Target Labeling and Hybridization procedure:

100-250 ng mRNA was isolated from total RNA for each patient using the Oligotex kit (Qiagen) according to the manufacturers instructions.  Prior to hybridization, 20ng of Arabidopsis thaliana DNA template was labeled with a-33P dCTP (10 microCi/microL; Amersham) during a random priming labeling reaction (pd(N)6, Amersham) (Feinberg and Vogelstein, 1983).  Reversed transcribed cDNA from patient targets were prepared in a final volume of 30microL as described in detail previously, with the exception that the labeling reaction was carried out at 42°C for 50 min (Eickhoff et al. 2000).  RNA was hydrolyzed under alkaline conditions by the addition of 3.5 microL of 3M NaOH and incubation for 20 min at 68°C. The samples were neutralized with the addition of 10 microL of 1M Tris-HCl (pH 7.4) and 10.5 microL of 1M HCl.  Unincorporated radioactive nucleotides were removed from both control and patient targets by filtration through Microspin G-50 columns according to the product manual (Amersham).

Prior to each hybridization reaction, unused filters were initially washed in 1 X SSC; 0.1% SDS at room temperature for 10 min (X 2) followed by three washes in 0.1 X SSC; 0.1% SDS for 20 min at 80°C.  These washes eliminated the potential problem for unbound or loosely bound probe cDNA from interfering with the hybridization reaction.  Each cDNA filter was pre-wetted with deionized water and placed in a hybridization bottle (3.5 X 25 cm).  The water was completely poured off and the filter was pre-hybridized for 2 hrs at 50°C in a 10 mL of hybridization solution containing 7% SDS, 50% formamide, 5 X SCC, 2% blocking reagent (Roche Diagnostics), 50mM sodium phosphate (pH 7.0) and denatured herring sperm DNA (50microg/microL).  The labeled target was added to the filters in 5 mL of the same preheated solution and hybridization of the filters was performed overnight (24 hrs) at 42°C.  Following overnight hybridization, membranes were removed from the bottles and washed in 1 X SSC/0.1% SDS buffer for 10 min at room temperature followed by two washes for 30 min in 0.2 X SSC/0.1% SDS at 65°C.  Excess moisture was removed by briefly placing the membranes on filter paper (Whatman) and the damp filters were wrapped in commercial grade plastic wrap.  Filters were exposed ~24 hrs to imaging plates (BAS-MS 2325, Fujifilm, Japan) and scanning was carried out at a resolution of 50microns on a FLA-3000G imaging system (Fujifilm, Japan). After hybridization, filters were individually stripped in a boiling solution of 0.5% SDS for 5 min, taken off the heat and agitated for an additional 3 hrs at room temperature and stored damp wrapped in plastic wrap at 20ºC for 7-8 weeks (half-life of 33P is 25.4 days). Prior to re-use, filters were re-scanned as above to ensure that residual radioactivity was negligible. For the purposes of the microarray comparison study, all filters were chosen from the same spotting production run and all filters were used for the first time.

Spot quantitation:
An exposure time of ~24 h was sufficient to yield signals from cDNA clones, yet keeping the data overflow to a mimimum.  Images were quantified using VisualGrid® software V3.4 (http://www.gpc-biotech.com). Each grid was manually adjusted to the image such that the linear correlation coefficient between duplicate spots was greater than 0.984. The following output values from VisualGrid were used for subsequent data analysis: SIGNAL_RAW1 (the weighted mean pixel intensity within the node mask for the first duplicate), SIGNAL_RAW2 (the weighted mean pixel intensity within the node mask for the second duplicate), BKD_MEAN (the mean of the weighted means of all background spots in a 6 X 6 block).  For this dataset, the weight of each pixel was set to one.

source_name: sigmoid colon biopsy : normal tissue : normal, healthy individual


title: App11-20C

status: Public on Jul 03 2004

type: RNA

city: Laramie

first: Mark

last: Gomelsky

state: WY

department: Molecular Biology

country: USA

institute: University of Wyoming

description:
App11 (AppA-null) strain derived from R.sphaeroides 2.4.1. Growth at 20% O2, 1% CO2, 79% N2 in the dark. Cells are collected at OD 0.18. RNA was isolated with bead beater + RNeasy kits
Sample_series_id: GSE1515

molecule: total RNA

organism: Cereibacter sphaeroides

source_name: Rhodobacter sphaeroides App11


title: 15N116

country: Germany

description:
Sex: Male; Age: 46yrs; 15ug total RNA

Target Labeling and Hybridization procedure:

100-250 ng mRNA was isolated from total RNA for each patient using the Oligotex kit (Qiagen) according to the manufacturers instructions.  Prior to hybridization, 20ng of Arabidopsis thaliana DNA template was labeled with a-33P dCTP (10 microCi/microL; Amersham) during a random priming labeling reaction (pd(N)6, Amersham) (Feinberg and Vogelstein, 1983).  Reversed transcribed cDNA from patient targets were prepared in a final volume of 30microL as described in detail previously, with the exception that the labeling reaction was carried out at 42°C for 50 min (Eickhoff et al. 2000).  RNA was hydrolyzed under alkaline conditions by the addition of 3.5 microL of 3M NaOH and incubation for 20 min at 68°C. The samples were neutralized with the addition of 10 microL of 1M Tris-HCl (pH 7.4) and 10.5 microL of 1M HCl.  Unincorporated radioactive nucleotides were removed from both control and patient targets by filtration through Microspin G-50 columns according to the product manual (Amersham).

Prior to each hybridization reaction, unused filters were initially washed in 1 X SSC; 0.1% SDS at room temperature for 10 min (X 2) followed by three washes in 0.1 X SSC; 0.1% SDS for 20 min at 80°C.  These washes eliminated the potential problem for unbound or loosely bound probe cDNA from interfering with the hybridization reaction.  Each cDNA filter was pre-wetted with deionized water and placed in a hybridization bottle (3.5 X 25 cm).  The water was completely poured off and the filter was pre-hybridized for 2 hrs at 50°C in a 10 mL of hybridization solution containing 7% SDS, 50% formamide, 5 X SCC, 2% blocking reagent (Roche Diagnostics), 50mM sodium phosphate (pH 7.0) and denatured herring sperm DNA (50microg/microL).  The labeled target was added to the filters in 5 mL of the same preheated solution and hybridization of the filters was performed overnight (24 hrs) at 42°C.  Following overnight hybridization, membranes were removed from the bottles and washed in 1 X SSC/0.1% SDS buffer for 10 min at room temperature followed by two washes for 30 min in 0.2 X SSC/0.1% SDS at 65°C.  Excess moisture was removed by briefly placing the membranes on filter paper (Whatman) and the damp filters were wrapped in commercial grade plastic wrap.  Filters were exposed ~24 hrs to imaging plates (BAS-MS 2325, Fujifilm, Japan) and scanning was carried out at a resolution of 50microns on a FLA-3000G imaging system (Fujifilm, Japan). After hybridization, filters were individually stripped in a boiling solution of 0.5% SDS for 5 min, taken off the heat and agitated for an additional 3 hrs at room temperature and stored damp wrapped in plastic wrap at 20ºC for 7-8 weeks (half-life of 33P is 25.4 days). Prior to re-use, filters were re-scanned as above to ensure that residual radioactivity was negligible. For the purposes of the microarray comparison study, all filters were chosen from the same spotting production run and all filters were used for the first time.

Spot quantitation:
An exposure time of ~24 h was sufficient to yield signals from cDNA clones, yet keeping the data overflow to a mimimum.  Images were quantified using VisualGrid® software V3.4 (http://www.gpc-biotech.com). Each grid was manually adjusted to the image such that the linear correlation coefficient between duplicate spots was greater than 0.984. The following output values from VisualGrid were used for subsequent data analysis: SIGNAL_RAW1 (the weighted mean pixel intensity within the node mask for the first duplicate), SIGNAL_RAW2 (the weighted mean pixel intensity within the node mask for the second duplicate), BKD_MEAN (the mean of the weighted means of all background spots in a 6 X 6 block).  For this dataset, the weight of each pixel was set to one.

organism: Homo sapiens


title: 25N115

description:
Sex:  Female;  Age: 56yrs; 15ug total RNA

Target Labeling and Hybridization procedure:

100-250 ng mRNA was isolated from total RNA for each patient using the Oligotex kit (Qiagen) according to the manufacturers instructions.  Prior to hybridization, 20ng of Arabidopsis thaliana DNA template was labeled with a-33P dCTP (10 microCi/microL; Amersham) during a random priming labeling reaction (pd(N)6, Amersham) (Feinberg and Vogelstein, 1983).  Reversed transcribed cDNA from patient targets were prepared in a final volume of 30microL as described in detail previously, with the exception that the labeling reaction was carried out at 42°C for 50 min (Eickhoff et al. 2000).  RNA was hydrolyzed under alkaline conditions by the addition of 3.5 microL of 3M NaOH and incubation for 20 min at 68°C. The samples were neutralized with the addition of 10 microL of 1M Tris-HCl (pH 7.4) and 10.5 microL of 1M HCl.  Unincorporated radioactive nucleotides were removed from both control and patient targets by filtration through Microspin G-50 columns according to the product manual (Amersham).

Prior to each hybridization reaction, unused filters were initially washed in 1 X SSC; 0.1% SDS at room temperature for 10 min (X 2) followed by three washes in 0.1 X SSC; 0.1% SDS for 20 min at 80°C.  These washes eliminated the potential problem for unbound or loosely bound probe cDNA from interfering with the hybridization reaction.  Each cDNA filter was pre-wetted with deionized water and placed in a hybridization bottle (3.5 X 25 cm).  The water was completely poured off and the filter was pre-hybridized for 2 hrs at 50°C in a 10 mL of hybridization solution containing 7% SDS, 50% formamide, 5 X SCC, 2% blocking reagent (Roche Diagnostics), 50mM sodium phosphate (pH 7.0) and denatured herring sperm DNA (50microg/microL).  The labeled target was added to the filters in 5 mL of the same preheated solution and hybridization of the filters was performed overnight (24 hrs) at 42°C.  Following overnight hybridization, membranes were removed from the bottles and washed in 1 X SSC/0.1% SDS buffer for 10 min at room temperature followed by two washes for 30 min in 0.2 X SSC/0.1% SDS at 65°C.  Excess moisture was removed by briefly placing the membranes on filter paper (Whatman) and the damp filters were wrapped in commercial grade plastic wrap.  Filters were exposed ~24 hrs to imaging plates (BAS-MS 2325, Fujifilm, Japan) and scanning was carried out at a resolution of 50microns on a FLA-3000G imaging system (Fujifilm, Japan). After hybridization, filters were individually stripped in a boiling solution of 0.5% SDS for 5 min, taken off the heat and agitated for an additional 3 hrs at room temperature and stored damp wrapped in plastic wrap at 20ºC for 7-8 weeks (half-life of 33P is 25.4 days). Prior to re-use, filters were re-scanned as above to ensure that residual radioactivity was negligible. For the purposes of the microarray comparison study, all filters were chosen from the same spotting production run and all filters were used for the first time.

Spot quantitation:
An exposure time of ~24 h was sufficient to yield signals from cDNA clones, yet keeping the data overflow to a mimimum.  Images were quantified using VisualGrid® software V3.4 (http://www.gpc-biotech.com). Each grid was manually adjusted to the image such that the linear correlation coefficient between duplicate spots was greater than 0.984. The following output values from VisualGrid were used for subsequent data analysis: SIGNAL_RAW1 (the weighted mean pixel intensity within the node mask for the first duplicate), SIGNAL_RAW2 (the weighted mean pixel intensity within the node mask for the second duplicate), BKD_MEAN (the mean of the weighted means of all background spots in a 6 X 6 block).  For this dataset, the weight of each pixel was set to one.


title: LFY22h4

status: Public on Jul 02 2004

city: Pasadena

first: Frank

last: Wellmer

state: CA

address: 1200 E. California Blvd.

department: Biology 156-29

institute: California Institute of Technology

description: Dye-labeled RNA samples derived from dexamethasone- or mock-treated 35S:LFY-GR root explants were co-hybridized to a cDNA array enriched for flower-specific transcripts. The data were analyzed with Rosetta Resolver as described in Wagner et al. (2004).

organism: Arabidopsis thaliana

source_name: Callus of 35S:LFY-GR plants treated for 22 hours with a dexamethasone-containing solution

source_name: Callus of 35S:LFY-GR plants treated for 22 hours with a control solution


title: App11-20B


title: 26N155

description:
Sex:  Female; Age:  76yrs; 15ug of total RNA

Target Labeling and Hybridization procedure:

100-250 ng mRNA was isolated from total RNA for each patient using the Oligotex kit (Qiagen) according to the manufacturers instructions.  Prior to hybridization, 20ng of Arabidopsis thaliana DNA template was labeled with a-33P dCTP (10 microCi/microL; Amersham) during a random priming labeling reaction (pd(N)6, Amersham) (Feinberg and Vogelstein, 1983).  Reversed transcribed cDNA from patient targets were prepared in a final volume of 30microL as described in detail previously, with the exception that the labeling reaction was carried out at 42°C for 50 min (Eickhoff et al. 2000).  RNA was hydrolyzed under alkaline conditions by the addition of 3.5 microL of 3M NaOH and incubation for 20 min at 68°C. The samples were neutralized with the addition of 10 microL of 1M Tris-HCl (pH 7.4) and 10.5 microL of 1M HCl.  Unincorporated radioactive nucleotides were removed from both control and patient targets by filtration through Microspin G-50 columns according to the product manual (Amersham).

Prior to each hybridization reaction, unused filters were initially washed in 1 X SSC; 0.1% SDS at room temperature for 10 min (X 2) followed by three washes in 0.1 X SSC; 0.1% SDS for 20 min at 80°C.  These washes eliminated the potential problem for unbound or loosely bound probe cDNA from interfering with the hybridization reaction.  Each cDNA filter was pre-wetted with deionized water and placed in a hybridization bottle (3.5 X 25 cm).  The water was completely poured off and the filter was pre-hybridized for 2 hrs at 50°C in a 10 mL of hybridization solution containing 7% SDS, 50% formamide, 5 X SCC, 2% blocking reagent (Roche Diagnostics), 50mM sodium phosphate (pH 7.0) and denatured herring sperm DNA (50microg/microL).  The labeled target was added to the filters in 5 mL of the same preheated solution and hybridization of the filters was performed overnight (24 hrs) at 42°C.  Following overnight hybridization, membranes were removed from the bottles and washed in 1 X SSC/0.1% SDS buffer for 10 min at room temperature followed by two washes for 30 min in 0.2 X SSC/0.1% SDS at 65°C.  Excess moisture was removed by briefly placing the membranes on filter paper (Whatman) and the damp filters were wrapped in commercial grade plastic wrap.  Filters were exposed ~24 hrs to imaging plates (BAS-MS 2325, Fujifilm, Japan) and scanning was carried out at a resolution of 50microns on a FLA-3000G imaging system (Fujifilm, Japan). After hybridization, filters were individually stripped in a boiling solution of 0.5% SDS for 5 min, taken off the heat and agitated for an additional 3 hrs at room temperature and stored damp wrapped in plastic wrap at 20ºC for 7-8 weeks (half-life of 33P is 25.4 days). Prior to re-use, filters were re-scanned as above to ensure that residual radioactivity was negligible. For the purposes of the microarray comparison study, all filters were chosen from the same spotting production run and all filters were used for the first time.

Spot quantitation:
An exposure time of ~24 h was sufficient to yield signals from cDNA clones, yet keeping the data overflow to a mimimum.  Images were quantified using VisualGrid® software V3.4 (http://www.gpc-biotech.com). Each grid was manually adjusted to the image such that the linear correlation coefficient between duplicate spots was greater than 0.984. The following output values from VisualGrid were used for subsequent data analysis: SIGNAL_RAW1 (the weighted mean pixel intensity within the node mask for the first duplicate), SIGNAL_RAW2 (the weighted mean pixel intensity within the node mask for the second duplicate), BKD_MEAN (the mean of the weighted means of all background spots in a 6 X 6 block).  For this dataset, the weight of each pixel was set to one.


title: Cha EC Neg a

status: Public on Jul 04 2004

city: Duarte

first: Paul

middle: M.

last: Salvaterra

address: 1500 E. Duarte Rd.

department: Stem Cell and Developmental Biology

institute: Beckman Research Institute of the City of Hope

description: 3-5 day Drosophila Embryo Culture labeled with GFP expression in Cholinergic neurons.  Negative fraction from FACS sorting

organism: Drosophila melanogaster

source_name: Drosophila Embryo Cell Culture


title: LFY22h2


title: 23N104

description:
Target Labeling and Hybridization procedure:

100-250 ng mRNA was isolated from total RNA for each patient using the Oligotex kit (Qiagen) according to the manufacturers instructions.  Prior to hybridization, 20ng of Arabidopsis thaliana DNA template was labeled with a-33P dCTP (10 microCi/microL; Amersham) during a random priming labeling reaction (pd(N)6, Amersham) (Feinberg and Vogelstein, 1983).  Reversed transcribed cDNA from patient targets were prepared in a final volume of 30microL as described in detail previously, with the exception that the labeling reaction was carried out at 42°C for 50 min (Eickhoff et al. 2000).  RNA was hydrolyzed under alkaline conditions by the addition of 3.5 microL of 3M NaOH and incubation for 20 min at 68°C. The samples were neutralized with the addition of 10 microL of 1M Tris-HCl (pH 7.4) and 10.5 microL of 1M HCl.  Unincorporated radioactive nucleotides were removed from both control and patient targets by filtration through Microspin G-50 columns according to the product manual (Amersham).

Prior to each hybridization reaction, unused filters were initially washed in 1 X SSC; 0.1% SDS at room temperature for 10 min (X 2) followed by three washes in 0.1 X SSC; 0.1% SDS for 20 min at 80°C.  These washes eliminated the potential problem for unbound or loosely bound probe cDNA from interfering with the hybridization reaction.  Each cDNA filter was pre-wetted with deionized water and placed in a hybridization bottle (3.5 X 25 cm).  The water was completely poured off and the filter was pre-hybridized for 2 hrs at 50°C in a 10 mL of hybridization solution containing 7% SDS, 50% formamide, 5 X SCC, 2% blocking reagent (Roche Diagnostics), 50mM sodium phosphate (pH 7.0) and denatured herring sperm DNA (50microg/microL).  The labeled target was added to the filters in 5 mL of the same preheated solution and hybridization of the filters was performed overnight (24 hrs) at 42°C.  Following overnight hybridization, membranes were removed from the bottles and washed in 1 X SSC/0.1% SDS buffer for 10 min at room temperature followed by two washes for 30 min in 0.2 X SSC/0.1% SDS at 65°C.  Excess moisture was removed by briefly placing the membranes on filter paper (Whatman) and the damp filters were wrapped in commercial grade plastic wrap.  Filters were exposed ~24 hrs to imaging plates (BAS-MS 2325, Fujifilm, Japan) and scanning was carried out at a resolution of 50microns on a FLA-3000G imaging system (Fujifilm, Japan). After hybridization, filters were individually stripped in a boiling solution of 0.5% SDS for 5 min, taken off the heat and agitated for an additional 3 hrs at room temperature and stored damp wrapped in plastic wrap at 20ºC for 7-8 weeks (half-life of 33P is 25.4 days). Prior to re-use, filters were re-scanned as above to ensure that residual radioactivity was negligible. For the purposes of the microarray comparison study, all filters were chosen from the same spotting production run and all filters were used for the first time.

Spot quantitation:
An exposure time of ~24 h was sufficient to yield signals from cDNA clones, yet keeping the data overflow to a mimimum.  Images were quantified using VisualGrid® software V3.4 (http://www.gpc-biotech.com). Each grid was manually adjusted to the image such that the linear correlation coefficient between duplicate spots was greater than 0.984. The following output values from VisualGrid were used for subsequent data analysis: SIGNAL_RAW1 (the weighted mean pixel intensity within the node mask for the first duplicate), SIGNAL_RAW2 (the weighted mean pixel intensity within the node mask for the second duplicate), BKD_MEAN (the mean of the weighted means of all background spots in a 6 X 6 block).  For this dataset, the weight of each pixel was set to one.


title: LFY12h3

source_name: Callus of 35S:LFY-GR plants treated for 12 hours with a control solution

source_name: Callus of 35S:LFY-GR plants treated for 12 hours with a dexamethasone-containing solution


title: LFY22h3


title: LFY10h1

source_name: Callus of 35S:LFY-GR plants treated for 10 hours with a control solution

source_name: Callus of 35S:LFY-GR plants treated for 10 hours with a dexamethasone-containing solution


title: LFY10h3


title: LFY8h4

source_name: Callus of 35S:LFY-GR plants treated for 8 hours with a dexamethasone-containing solution

source_name: Callus of 35S:LFY-GR plants treated for 8 hours with a control solution


title: LFY12h2


title: LFY6h4

source_name: Callus of 35S:LFY-GR plants treated for 6 hours with a dexamethasone-containing solution

source_name: Callus of 35S:LFY-GR plants treated for 6 hours with a control solution


title: LFY22h1


title: LFY10h2


title: LFY6h3


title: Exp1-2-2

city: Nantes

first: Nolwenn

last: Le Meur

address: 1 rue Gaston Veil

country: France

institute: INSERM

description: patient affected by  idiopathic dilated cardiomyopathy compare to common reference.

source_name: idiopathic dilated cardiomyopathy

source_name: common reference of pooled RNAs extracted from the left and right ventricles of explanted hearts from 47 end-stage heart failure patients


title: LFY6h2


title: LFY6h1


title: LFY4h4

source_name: Callus of 35S:LFY-GR plants treated for 4 hours with a dexamethasone-containing solution

source_name: Callus of 35S:LFY-GR plants treated for 4 hours with a control solution


title: LFY8h1


title: LFY4h2


title: LFY8h2


title: LFY4h3


title: Exp2-2-2

description: patient affected by  valvular heart disease and coronary artery disease compare to common reference.


title: Exp2-1-2

source_name: valvular heart disease and coronary artery disease


title: LFY2h3

source_name: Callus of 35S:LFY-GR plants treated for 2 hours with a control solution

source_name: Callus of 35S:LFY-GR plants treated for 2 hours with a dexamethasone-containing solution


title: LFY2h4


title: LFY2h2


title: Exp1-1-2

description: patien affected by  idiopathic dilated cardiomyopathy compare to common reference.


title: Exp1-1-1


title: Exp2-1-1

description: patien affected by valvular heart disease and coronary artery diseasecompare to common reference.


title: LFY2h1


title: LFY4h1


title: LFY0h4

source_name: Callus of 35S:LFY-GR plants treated for 0 hours with a dexamethasone-containing solution

source_name: Callus of 35S:LFY-GR plants treated for 0 hours with a control solution


title: LFY0h3


title: Exp1-2-1

description: patient affected by idiopathic dilated cardiomyopathy compare to common reference.


title: LFY0h1


title: YPR019W TET_mutant

status: Public on Jul 01 2004

city: Toronto

middle: Richard

last: Hughes

state: ON

address: 112 College St.

department: Banting and Best Department of Medical Research

country: Canada

institute: University of Toronto

description: RNA extracted from YPR019W TET_mutant

organism: Saccharomyces cerevisiae

source_name: Wild-Type (WT)

source_name: YPR019W TET_mutant


title: YAL038W TET_mutant

description: RNA extracted from YAL038W TET_mutant

source_name: YAL038W TET_mutant


title: Exp2-2-1

description: patient affected by valvular heart disease and coronary artery disease compare to common reference.


title: YLR229C TET_mutant

description: RNA extracted from YLR229C TET_mutant

source_name: YLR229C TET_mutant


title: YBL084C TET_mutant

description: RNA extracted from YBL084C TET_mutant

source_name: YBL084C TET_mutant


title: YDR054C TET_mutant replicate 1

description: RNA extracted from YDR054C TET_mutant

source_name: YDR054C TET_mutant


title: YGL155W TET_mutant

description: RNA extracted from YGL155W TET_mutant

source_name: YGL155W TET_mutant


title: YJR076C TET_mutant

description: RNA extracted from YJR076C TET_mutant

source_name: YJR076C TET_mutant


title: YGL155W TET_mutant  replicate 1

description: RNA extracted from YGL155W TET_mutant


title: YLR229C TET_mutant replicate 1

description: RNA extracted from YLR229C TET_mutant


title: YDR054C TET_mutant

description: RNA extracted from YDR054C TET_mutant


title: LFY0h2


title: YOL077C TET_mutant

description: RNA extracted from YOL077C TET_mutant

source_name: YOL077C TET_mutant


title: YER172C TET_mutant

description: RNA extracted from YER172C TET_mutant

source_name: YER172C TET_mutant


title: YHR040W TET_mutant

description: RNA extracted from YHR040W TET_mutant

source_name: YHR040W TET_mutant


title: LFY12h4

source_name: Callus of 35S:LFY-GR plants treated for 12 hours with a dexamethasone-containing solution

source_name: Callus of 35S:LFY-GR plants treated for 12 hours with a control solution


title: LFY8h3

source_name: Callus of 35S:LFY-GR plants treated for 8 hours with a control solution

source_name: Callus of 35S:LFY-GR plants treated for 8 hours with a dexamethasone-containing solution


title: YER172C TET_mutant replicate 1

description: RNA extracted from YER172C TET_mutant


title: YNR035C TET_mutant

description: RNA extracted from YNR035C TET_mutant

source_name: YNR035C TET_mutant


title: YGL116W TET_mutant

description: RNA extracted from YGL116W TET_mutant

source_name: YGL116W TET_mutant


title: YOR335C TET_mutant

description: RNA extracted from YOR335C TET_mutant

source_name: Wild-Type (WT)

source_name: YOR335C TET_mutant


title: YPR180W TET_mutant

description: RNA extracted from YPR180W TET_mutant

source_name: YPR180W TET_mutant


title: YDL132W TET_mutant

description: RNA extracted from YDL132W TET_mutant

source_name: YDL132W TET_mutant


title: YBR234C TET_mutant

description: RNA extracted from YBR234C TET_mutant

source_name: YBR234C TET_mutant


title: YER006W TET_mutant replicate 2

description: RNA extracted from YER006W TET_mutant

source_name: YER006W TET_mutant


title: YJL081C TET_mutant

description: RNA extracted from YJL081C TET_mutant

source_name: YJL081C TET_mutant


title: YGR198W TET_mutant replicate 4

description: RNA extracted from YGR198W TET_mutant

source_name: YGR198W TET_mutant


title: YFR037C TET_mutant replicate 2

description: RNA extracted from YFR037C TET_mutant

source_name: YFR037C TET_mutant


title: YBR243C TET_mutant

description: RNA extracted from YBR243C TET_mutant

source_name: YBR243C TET_mutant


title: YBL020W TET_mutant

description: RNA extracted from YBL020W TET_mutant

source_name: YBL020W TET_mutant


title: YGR198W TET_mutant

description: RNA extracted from YGR198W TET_mutant


title: YGR103W TET_mutant replicate 1

description: RNA extracted from YGR103W TET_mutant

source_name: YGR103W TET_mutant


title: YOR262W TET_mutant

description: RNA extracted from YOR262W TET_mutant

source_name: YOR262W TET_mutant


title: YML046W TET_mutant

description: RNA extracted from YML046W TET_mutant

source_name: YML046W TET_mutant


title: YOR146W TET_mutant

description: RNA extracted from YOR146W TET_mutant

source_name: YOR146W TET_mutant


title: YOR169C TET_mutant

description: RNA extracted from YOR169C TET_mutant

source_name: YOR169C TET_mutant


title: YOR060C TET_mutant

description: RNA extracted from YOR060C TET_mutant

source_name: YOR060C TET_mutant


title: YOR259C TET_mutant

description: RNA extracted from YOR259C TET_mutant

source_name: Wild-Type (WT)

source_name: YOR259C TET_mutant


title: YOR145C TET_mutant

description: RNA extracted from YOR145C TET_mutant

source_name: YOR145C TET_mutant


title: YOR004W TET_mutant replicate 1

description: RNA extracted from YOR004W TET_mutant

source_name: YOR004W TET_mutant


title: YPR169W TET_mutant

description: RNA extracted from YPR169W TET_mutant

source_name: YPR169W TET_mutant


title: YMR001C TET_mutant

description: RNA extracted from YMR001C TET_mutant

source_name: YMR001C TET_mutant


title: YGL048C TET_mutant

description: RNA extracted from YGL048C TET_mutant

source_name: YGL048C TET_mutant


title: YOR206W TET_mutant

description: RNA extracted from YOR206W TET_mutant

source_name: YOR206W TET_mutant


title: YOL022C TET_mutant

description: RNA extracted from YOL022C TET_mutant

source_name: YOL022C TET_mutant


title: YNR054C TET_mutant

description: RNA extracted from YNR054C TET_mutant

source_name: YNR054C TET_mutant


title: YNL313C TET_mutant replicate 3

description: RNA extracted from YNL313C TET_mutant

source_name: YNL313C TET_mutant


title: YOL026C TET_mutant

description: RNA extracted from YOL026C TET_mutant

source_name: YOL026C TET_mutant


title: YNL313C TET_mutant replicate 1

description: RNA extracted from YNL313C TET_mutant


title: YOR004W TET_mutant

description: RNA extracted from YOR004W TET_mutant


title: YOL026C TET_mutant replicate 1

description: RNA extracted from YOL026C TET_mutant


title: YNL313C TET_mutant replicate 2

description: RNA extracted from YNL313C TET_mutant


title: YNL313C TET_mutant

description: RNA extracted from YNL313C TET_mutant


title: YNL247W TET_mutant

description: RNA extracted from YNL247W TET_mutant

source_name: YNL247W TET_mutant


title: YNL158W TET_mutant

description: RNA extracted from YNL158W TET_mutant

source_name: YNL158W TET_mutant


title: YNL150W TET_mutant

description: RNA extracted from YNL150W TET_mutant

source_name: YNL150W TET_mutant


title: YNL149C TET_mutant relicate 1

description: RNA extracted from YNL149C TET_mutant

source_name: YNL149C TET_mutant


title: YNL182C TET_mutant

description: RNA extracted from YNL182C TET_mutant

source_name: YNL182C TET_mutant


title: YNR054C TET_mutant replicate 1

description: RNA extracted from YNR054C TET_mutant

source_name: Wild-Type (WT)


title: YNL310C TET_mutant

description: RNA extracted from YNL310C TET_mutant

source_name: YNL310C TET_mutant


title: YLR359W TET_mutant

description: RNA extracted from YLR359W TET_mutant

source_name: YLR359W TET_mutant


title: YNL158W TET_mutant replicate 1

description: RNA extracted from YNL158W TET_mutant


title: YLR424W TET_mutant

description: RNA extracted from YLR424W TET_mutant

source_name: YLR424W TET_mutant


title: YLR440C TET_mutant replicate 1

description: RNA extracted from YLR440C TET_mutant

source_name: YLR440C TET_mutant


title: LFY12h1

source_name: Callus of 35S:LFY-GR plants treated for 12 hours with a control solution

source_name: Callus of 35S:LFY-GR plants treated for 12 hours with a dexamethasone-containing solution


title: YHR090C TET_mutant

description: RNA extracted from YHR090C TET_mutant

source_name: YHR090C TET_mutant


title: YLR243W TET_mutant

description: RNA extracted from YLR243W TET_mutant

source_name: YLR243W TET_mutant


title: YLR310C TET_mutant

description: RNA extracted from YLR310C TET_mutant

source_name: YLR310C TET_mutant


title: YNL149C TET_mutant

description: RNA extracted from YNL149C TET_mutant


title: YLR101C TET_mutant

description: RNA extracted from YLR101C TET_mutant

source_name: YLR101C TET_mutant


title: YLR008c TET_mutant replicate 1

description: RNA extracted from YLR008c TET_mutant

source_name: YLR008c TET_mutant


title: YLR440C TET_mutant

description: RNA extracted from YLR440C TET_mutant


title: YLR145W TET_mutant

description: RNA extracted from YLR145W TET_mutant

source_name: YLR145W TET_mutant


title: YLL034C TET_mutant replicate 1

description: RNA extracted from YLL034C TET_mutant

source_name: YLL034C TET_mutant


title: YLR008C TET_mutant

description: RNA extracted from YLR008C TET_mutant

source_name: YLR008C TET_mutant


title: YLJ097W TET_mutant

description: RNA extracted from YLJ097W TET_mutant

source_name: YLJ097W TET_mutant


title: YJL091C TET_mutant

description: RNA extracted from YJL091C TET_mutant

source_name: YJL091C TET_mutant


title: YKL033W TET_mutant replicate 1

description: RNA extracted from YKL033W TET_mutant

source_name: Wild-Type (WT)

source_name: YKL033W TET_mutant


title: LFY10h4

source_name: Callus of 35S:LFY-GR plants treated for 10 hours with a dexamethasone-containing solution

source_name: Callus of 35S:LFY-GR plants treated for 10 hours with a control solution


title: YLL034C TET_mutant

description: RNA extracted from YLL034C TET_mutant


title: YLR076C TET_mutant

description: RNA extracted from YLR076C TET_mutant

source_name: YLR076C TET_mutant


title: YKL033W TET_mutant

description: RNA extracted from YKL033W TET_mutant


title: YJL097W TET_mutant

description: RNA extracted from YJL097W TET_mutant

source_name: YJL097W TET_mutant


title: YKR079C TET_mutant

description: RNA extracted from YKR079C TET_mutant

source_name: YKR079C TET_mutant


title: YKL180W TET_mutant

description: RNA extracted from YKL180W TET_mutant

source_name: YKL180W TET_mutant


title: YKL052C TET_mutant

description: RNA extracted from YKL052C TET_mutant

source_name: YKL052C TET_mutant


title: YJR041C TET_mutant

description: RNA extracted from YJR041C TET_mutant

source_name: YJR041C TET_mutant


title: YHR122W TET_mutant replicate 1

description: RNA extracted from YHR122W TET_mutant

source_name: YHR122W TET_mutant


title: YJR041C TET_mutant replicate 1

description: RNA extracted from YJR041C TET_mutant


title: YHR122W TET_mutant replicate 2

description: RNA extracted from YHR122W TET_mutant


title: YGR172C TET_mutant

description: RNA extracted from YGR172C TET_mutant

source_name: YGR172C TET_mutant


title: YJL009W TET_mutant

description: RNA extracted from YJL009W TET_mutant

source_name: YJL009W TET_mutant


title: YGR251W TET_mutant replicate 1

description: RNA extracted from YGR251W TET_mutant

source_name: YGR251W TET_mutant


title: YGR280C TET_mutant

description: RNA extracted from YGR280C TET_mutant

source_name: YGR280C TET_mutant


title: YGR251W TET_mutant

description: RNA extracted from YGR251W TET_mutant


title: YHR122W TET_mutant

description: RNA extracted from YHR122W TET_mutant


title: YGR198W TET_mutant replicate 3

description: RNA extracted from YGR198W TET_mutant

source_name: YGR198W TET_mutant


title: YGR198W TET_mutant replicate 1

description: RNA extracted from YGR198W TET_mutant


title: YGR198W TET_mutant replicate 2

description: RNA extracted from YGR198W TET_mutant


title: YDR412W TET_mutant

description: RNA extracted from YDR412W TET_mutant

source_name: YDR412W TET_mutant


title: YGL047W TET_mutant replicate 1

description: RNA extracted from YGL047W TET_mutant

source_name: Wild-Type (WT)

source_name: YGL047W TET_mutant


title: YGR173W TET_mutant

description: RNA extracted from YGR173W TET_mutant

source_name: YGR173W TET_mutant


title: YGL245W TET_mutant

description: RNA extracted from YGL245W TET_mutant

source_name: YGL245W TET_mutant


title: YGR094W TET_mutant

description: RNA extracted from YGR094W TET_mutant

source_name: YGR094W TET_mutant


title: YDR412W TET_mutant replicate 1

description: RNA extracted from YDR412W TET_mutant


title: YDR527W TET_mutant

description: RNA extracted from YDR527W TET_mutant

source_name: YDR527W TET_mutant


title: YGL047W TET_mutant

description: RNA extracted from YGL047W TET_mutant


title: YDR527W TET_mutant replicate 1

description: RNA extracted from YDR527W TET_mutant


title: YGR090W TET_mutant replicate 2

description: RNA extracted from YGR090W TET_mutant

source_name: YGR090W TET_mutant


title: YDR327W TET_mutant

description: RNA extracted from YDR327W TET_mutant

source_name: YDR327W TET_mutant


title: YDL196W TET_mutant

description: RNA extracted from YDL196W TET_mutant

source_name: YDL196W TET_mutant


title: YCR013C TET_mutant

description: RNA extracted from YCR013C TET_mutant

source_name: YCR013C TET_mutant


title: YBR190W TET_mutant

description: RNA extracted from YBR190W TET_mutant

source_name: YBR190W TET_mutant


title: YDR365C TET_mutant replicate 1

description: RNA extracted from YDR365C TET_mutant

source_name: YDR365C TET_mutant


title: YBR190W TET_mutant replicate 1

description: RNA extracted from YBR190W TET_mutant


title: YDR365C TET_mutant

description: RNA extracted from YDR365C TET_mutant


title: YGR090W TET_mutant replicate 1

description: RNA extracted from YGR090W TET_mutant


title: YGR090W TET_mutant

description: RNA extracted from YGR090W TET_mutant


title: YBL004W TET_mutant

description: RNA extracted from YBL004W TET_mutant

source_name: YBL004W TET_mutant


title: YDR168W TET_mutant

description: RNA extracted from YDR168W TET_mutant

source_name: YDR168W TET_mutant


title: YKL210W TET_mutant replicate 1

description: RNA extracted from YKL210W TET_mutant

source_name: YKL210W TET_mutant


title: YKL210W TET_mutant replicate 2

description: RNA extracted from YKL210W TET_mutant


title: YGR048W TET_mutant

description: RNA extracted from YGR048W TET_mutant

source_name: YGR048W TET_mutant


title: YDL064W TET_mutant

description: RNA extracted from YDL064W TET_mutant

source_name: YDL064W TET_mutant


title: YKL210W TET_mutant

description: RNA extracted from YKL210W TET_mutant

source_name: Wild-Type (WT)


title: YDL060W TET_mutant

description: RNA extracted from YDL060W TET_mutant

source_name: YDL060W TET_mutant


title: YBR143C TET_mutant

description: RNA extracted from YBR143C TET_mutant

source_name: YBR143C TET_mutant


title: YJR007W TET_mutant

description: RNA extracted from YJR007W TET_mutant

source_name: YJR007W TET_mutant


title: YOR110W TET_mutant

description: RNA extracted from YOR110W TET_mutant

source_name: YOR110W TET_mutant


title: YPL063W TET_mutant

description: RNA extracted from YPL063W TET_mutant

source_name: YPL063W TET_mutant


title: YNL222W TET_mutant replicate 1

description: RNA extracted from YNL222W TET_mutant

source_name: YNL222W TET_mutant


title: YCR042C TET_mutant

description: RNA extracted from YCR042C TET_mutant

source_name: YCR042C TET_mutant


title: YKL018W TET_mutant

description: RNA extracted from YKL018W TET_mutant

source_name: YKL018W TET_mutant


title: YLR005W TET_mutant

description: RNA extracted from YLR005W TET_mutant

source_name: YLR005W TET_mutant


title: YHR070W TET_mutant

description: RNA extracted from YHR070W TET_mutant

source_name: YHR070W TET_mutant


title: YNL131W TET_mutant

description: RNA extracted from YNL131W TET_mutant

source_name: YNL131W TET_mutant


title: YPL243W TET_mutant

description: RNA extracted from YPL243W TET_mutant

source_name: YPL243W TET_mutant


title: YIR012W TET_mutant

description: RNA extracted from YIR012W TET_mutant

source_name: YIR012W TET_mutant


title: YDR464W TET_mutant

description: RNA extracted from YDR464W TET_mutant

source_name: YDR464W TET_mutant


title: YKR037C TET_mutant

description: RNA extracted from YKR037C TET_mutant

source_name: YKR037C TET_mutant


title: YLR005W TET_mutant replicate 1

description: RNA extracted from YLR005W TET_mutant


title: YNL222W TET_mutant

description: RNA extracted from YNL222W TET_mutant


title: YDR201W TET_mutant replicate 1

description: RNA extracted from YDR201W TET_mutant

source_name: YDR201W TET_mutant


title: YDR201W TET_mutant

description: RNA extracted from YDR201W TET_mutant

source_name: Wild-Type (WT)


title: YLR086W TET_mutant

description: RNA extracted from YLR086W TET_mutant

source_name: YLR086W TET_mutant


title: YLR147C TET_mutant

description: RNA extracted from YLR147C TET_mutant

source_name: YLR147C TET_mutant


title: YIL147C TET_mutant

description: RNA extracted from YIL147C TET_mutant

source_name: YIL147C TET_mutant


title: YLR275W TET_mutant

description: RNA extracted from YLR275W TET_mutant

source_name: YLR275W TET_mutant


title: YDR489W TET_mutant

description: RNA extracted from YDR489W TET_mutant

source_name: YDR489W TET_mutant


title: YLR147C TET_mutant replicate 1

description: RNA extracted from YLR147C TET_mutant


title: YLR336C TET_mutant

description: RNA extracted from YLR336C TET_mutant

source_name: YLR336C TET_mutant


title: YDL047W TET_mutant

description: RNA extracted from YDL047W TET_mutant

source_name: YDL047W TET_mutant


title: YLL003W TET_mutant

description: RNA extracted from YLL003W TET_mutant

source_name: YLL003W TET_mutant


title: YKL108W TET_mutant

description: RNA extracted from YKL108W TET_mutant

source_name: YKL108W TET_mutant


title: YNL272C TET_mutant

description: RNA extracted from YNL272C TET_mutant

source_name: YNL272C TET_mutant


title: YFL005W TET_mutant

description: RNA extracted from YFL005W TET_mutant

source_name: YFL005W TET_mutant


title: YLR378C TET_mutant

description: RNA extracted from YLR378C TET_mutant

source_name: YLR378C TET_mutant


title: YMR079W TET_mutant

description: RNA extracted from YMR079W TET_mutant

source_name: YMR079W TET_mutant


title: YIR022W TET_mutant

description: RNA extracted from YIR022W TET_mutant

source_name: YIR022W TET_mutant


title: YGR245C TET_mutant

description: RNA extracted from YGR245C TET_mutant

source_name: YGR245C TET_mutant


title: YHR205W TET_mutant replicate 1

description: RNA extracted from YHR205W TET_mutant

source_name: YHR205W TET_mutant


title: YHR205W TET_mutant replicate 2

description: RNA extracted from YHR205W TET_mutant

source_name: Wild-Type (WT)


title: YOR077W TET_mutant replicate 3

description: RNA extracted from YOR077W TET_mutant

source_name: YOR077W TET_mutant


title: YOR077W TET_mutant replicate 2

description: RNA extracted from YOR077W TET_mutant


title: YOR077W TET_mutant replicate 4

description: RNA extracted from YOR077W TET_mutant


title: YHR205W TET_mutant

description: RNA extracted from YHR205W TET_mutant


title: YKL125W TET_mutant

description: RNA extracted from YKL125W TET_mutant

source_name: YKL125W TET_mutant


title: YGR245C TET_mutant replicate 1

description: RNA extracted from YGR245C TET_mutant


title: YKL082C TET_mutant

description: RNA extracted from YKL082C TET_mutant

source_name: YKL082C TET_mutant


title: YOR077W TET_mutant

description: RNA extracted from YOR077W TET_mutant


title: YOR294W TET_mutant

description: RNA extracted from YOR294W TET_mutant

source_name: YOR294W TET_mutant


title: YGR095C TET_mutant

description: RNA extracted from YGR095C TET_mutant

source_name: YGR095C TET_mutant


title: YFR037C TET_mutant replicate 1

description: RNA extracted from YFR037C TET_mutant

source_name: YFR037C TET_mutant


title: YDL007W TET_mutant

description: RNA extracted from YDL007W TET_mutant

source_name: YDL007W TET_mutant


title: YBL020W TET_mutant replicate 1

description: RNA extracted from YBL020W TET_mutant

source_name: YBL020W TET_mutant


title: YOL005C TET_mutant replicate 1

description: RNA extracted from YOL005C TET_mutant

source_name: YOL005C TET_mutant


title: YFR037C TET_mutant

description: RNA extracted from YFR037C TET_mutant


title: YKL082C TET_mutant replicate 1

description: RNA extracted from YKL082C TET_mutant


title: YJL011C TET_mutant

description: RNA extracted from YJL011C TET_mutant

source_name: YJL011C TET_mutant


title: YOL005C TET_mutant

description: RNA extracted from YOL005C TET_mutant


title: YOR077W TET_mutant replicate 1

description: RNA extracted from YOR077W TET_mutant


title: YMR200W TET_mutant

description: RNA extracted from YMR200W TET_mutant

source_name: YMR200W TET_mutant


title: YMR235C TET_mutant replicate 1

description: RNA extracted from YMR235C TET_mutant

source_name: YMR235C TET_mutant


title: YOR261C TET_mutant

description: RNA extracted from YOR261C TET_mutant

source_name: YOR261C TET_mutant


title: YMR239C TET_mutant replicate 1

description: RNA extracted from YMR239C TET_mutant

source_name: YMR239C TET_mutant


title: YMR239C TET_mutant

description: RNA extracted from YMR239C TET_mutant


title: YMR239C TET_mutant replicate 2

description: RNA extracted from YMR239C TET_mutant


title: YOL038W TET_mutant

description: RNA extracted from YOL038W TET_mutant

source_name: YOL038W TET_mutant


title: YMR235C TET_mutant

description: RNA extracted from YMR235C TET_mutant


title: YBR192W TET_mutant

description: RNA extracted from YBR192W TET_mutant

source_name: YBR192W TET_mutant


title: YDR091C TET_mutant

description: RNA extracted from YDR091C TET_mutant

source_name: Wild-Type (WT)

source_name: YDR091C TET_mutant


title: YOR095C TET_mutant

description: RNA extracted from YOR095C TET_mutant

source_name: YOR095C TET_mutant


title: YJL072C TET_mutant

description: RNA extracted from YJL072C TET_mutant

source_name: YJL072C TET_mutant


title: YBR049C TET_mutant

description: RNA extracted from YBR049C TET_mutant

source_name: YBR049C TET_mutant


title: YBR002C TET_mutant

description: RNA extracted from YBR002C TET_mutant

source_name: YBR002C TET_mutant


title: YPR186C TET_mutant

description: RNA extracted from YPR186C TET_mutant

source_name: YPR186C TET_mutant


title: YAL043C TET_mutant

description: RNA extracted from YAL043C TET_mutant

source_name: YAL043C TET_mutant


title: YPR178W TET_mutant

description: RNA extracted from YPR178W TET_mutant

source_name: YPR178W TET_mutant


title: YPL010W TET_mutant

description: RNA extracted from YPL010W TET_mutant

source_name: YPL010W TET_mutant


title: YOR119C TET_mutant

description: RNA extracted from YOR119C TET_mutant

source_name: YOR119C TET_mutant


title: YKR086W TET_mutant

description: RNA extracted from YKR086W TET_mutant

source_name: YKR086W TET_mutant


title: YDL055C TET_mutant

description: RNA extracted from YDL055C TET_mutant

source_name: YDL055C TET_mutant


title: YAL033W TET_mutant

description: RNA extracted from YAL033W TET_mutant

source_name: YAL033W TET_mutant


title: YER023W TET_mutant

description: RNA extracted from YER023W TET_mutant

source_name: YER023W TET_mutant


title: YNL221C TET_mutant

description: RNA extracted from YNL221C TET_mutant

source_name: YNL221C TET_mutant


title: YLR196W TET_mutant

description: RNA extracted from YLR196W TET_mutant

source_name: YLR196W TET_mutant


title: YBR088C TET_mutant

description: RNA extracted from YBR088C TET_mutant

source_name: Wild-Type (WT)

source_name: YBR088C TET_mutant


title: YBR196C TET_mutant

description: RNA extracted from YBR196C TET_mutant

source_name: YBR196C TET_mutant


title: YOR281C TET_mutant

description: RNA extracted from YOR281C TET_mutant

source_name: YOR281C TET_mutant


title: YEL055C TET_mutant

description: RNA extracted from YEL055C TET_mutant

source_name: YEL055C TET_mutant


title: YER006W TET_mutant replicate 1

description: RNA extracted from YER006W TET_mutant

source_name: YER006W TET_mutant


title: YHR118C TET_mutant

description: RNA extracted from YHR118C TET_mutant

source_name: YHR118C TET_mutant


title: YJL061W TET_mutant

description: RNA extracted from YJL061W TET_mutant

source_name: YJL061W TET_mutant


title: YER006W TET_mutant

description: RNA extracted from YER006W TET_mutant


title: YMR076C TET_mutant

description: RNA extracted from YMR076C TET_mutant

source_name: YMR076C TET_mutant


title: YJL039C TET_mutant

description: RNA extracted from YJL039C TET_mutant

source_name: YJL039C TET_mutant


title: YPR144C TET_mutant

description: RNA extracted from YPR144C TET_mutant

source_name: YPR144C TET_mutant


title: YPL093W TET_mutant

description: RNA extracted from YPL093W TET_mutant

source_name: YPL093W TET_mutant


title: YOR372C TET_mutant

description: RNA extracted from YOR372C TET_mutant

source_name: YOR372C TET_mutant


title: YLR007W TET_mutant

description: RNA extracted from YLR007W TET_mutant

source_name: YLR007W TET_mutant


title: YLR457C TET_mutant

description: RNA extracted from YLR457C TET_mutant

source_name: YLR457C TET_mutant


title: YCL017C TET_mutant

description: RNA extracted from YCL017C TET_mutant

source_name: YCL017C TET_mutant


title: YNL124W TET_mutant

description: RNA extracted from YNL124W TET_mutant

source_name: YNL124W TET_mutant


title: YPL190C TET_mutant

description: RNA extracted from YPL190C TET_mutant

source_name: Wild-Type (WT)

source_name: YPL190C TET_mutant


title: YGR103W TET_mutant

description: RNA extracted from YGR103W TET_mutant

source_name: YGR103W TET_mutant


title: YPL126W TET_mutant

description: RNA extracted from YPL126W TET_mutant

source_name: YPL126W TET_mutant


title: YNR043W TET_mutant

description: RNA extracted from YNR043W TET_mutant

source_name: YNR043W TET_mutant


title: YGL122C TET_mutant

description: RNA extracted from YGL122C TET_mutant

source_name: YGL122C TET_mutant


title: YGL122C TET_mutant replicate 1

description: RNA extracted from YGL122C TET_mutant


title: YAL034W-A TET_mutant

description: RNA extracted from YAL034W-A TET_mutant

source_name: YAL034W-A TET_mutant


title: YJR002W TET_mutant

description: RNA extracted from YJR002W TET_mutant

source_name: YJR002W TET_mutant


title: YML031W TET_mutant

description: RNA extracted from YML031W TET_mutant

source_name: YML031W TET_mutant


title: YBR193C TET_mutant

description: RNA extracted from YBR193C TET_mutant

source_name: YBR193C TET_mutant


title: YOR232W TET_mutant

description: RNA extracted from YOR232W TET_mutant

source_name: YOR232W TET_mutant


title: YLR106C TET_mutant replicate 1

description: RNA extracted from YLR106C TET_mutant

source_name: YLR106C TET_mutant


title: YHR023W TET_mutant

description: RNA extracted from YHR023W TET_mutant

source_name: YHR023W TET_mutant


title: YNR053C TET_mutant

description: RNA extracted from YNR053C TET_mutant

source_name: YNR053C TET_mutant


title: YIL106W TET_mutant

description: RNA extracted from YIL106W TET_mutant

source_name: YIL106W TET_mutant


title: YGL122C TET_mutant replicate 2

description: RNA extracted from YGL122C TET_mutant


title: YMR043W TET_mutant

description: RNA extracted from YMR043W TET_mutant

source_name: YMR043W TET_mutant


title: YLR106C TET_mutant

description: RNA extracted from YLR106C TET_mutant


title: YDR062W TET_mutant

description: RNA extracted from YDR062W TET_mutant

source_name: YDR062W TET_mutant


title: YLR163C TET_mutant

description: RNA extracted from YLR163C TET_mutant

source_name: Wild-Type (WT)

source_name: YLR163C TET_mutant


title: YGL073W TET_mutant replicate 1

description: RNA extracted from YGL073W TET_mutant

source_name: YGL073W TET_mutant


title: YHR197W TET_mutant

description: RNA extracted from YHR197W TET_mutant

source_name: YHR197W TET_mutant


title: YHR085W TET_mutant

description: RNA extracted from YHR085W TET_mutant

source_name: YHR085W TET_mutant


title: YHR085W TET_mutant replicate 1

description: RNA extracted from YHR085W TET_mutant


title: YER112W TET_mutant

description: RNA extracted from YER112W TET_mutant

source_name: YER112W TET_mutant


title: YER112W TET_mutant replicate 1

description: RNA extracted from YER112W TET_mutant


title: YGL073W TET_mutant replicate 2

description: RNA extracted from YGL073W TET_mutant


title: YBR142W TET_mutant

description: RNA extracted from YBR142W TET_mutant

source_name: YBR142W TET_mutant


title: YDL087C TET_mutant

description: RNA extracted from YDL087C TET_mutant

source_name: YDL087C TET_mutant


title: YOL133W TET_mutant

description: RNA extracted from YOL133W TET_mutant

source_name: YOL133W TET_mutant


title: YLL035W TET_mutant

description: RNA extracted from YLL035W TET_mutant

source_name: YLL035W TET_mutant


title: YPR033C TET_mutant

description: RNA extracted from YPR033C TET_mutant

source_name: YPR033C TET_mutant


title: YGL073W TET_mutant

description: RNA extracted from YGL073W TET_mutant


title: YHR188C TET_mutant

description: RNA extracted from YHR188C TET_mutant

source_name: YHR188C TET_mutant


title: YDR047W TET_mutant

description: RNA extracted from YDR047W TET_mutant

source_name: YDR047W TET_mutant


title: YOR168W TET_mutant

description: RNA extracted from YOR168W TET_mutant

source_name: YOR168W TET_mutant


title: YDR373W TET_mutant

description: RNA extracted from YDR373W TET_mutant

source_name: YDR373W TET_mutant


title: YDL207W TET_mutant

description: RNA extracted from YDL207W TET_mutant

source_name: YDL207W TET_mutant


title: YLR291C TET_mutant

description: RNA extracted from YLR291C TET_mutant

source_name: YLR291C TET_mutant


title: YMR290C TET_mutant

description: RNA extracted from YMR290C TET_mutant

source_name: Wild-Type (WT)

source_name: YMR290C TET_mutant


title: YPL075W TET_mutant replicate 1

description: RNA extracted from YPL075W TET_mutant

source_name: YPL075W TET_mutant


title: YDR373W TET_mutant replicate 1

description: RNA extracted from YDR373W TET_mutant


title: YPL076W TET_mutant

description: RNA extracted from YPL076W TET_mutant

source_name: YPL076W TET_mutant


title: YLR060W TET_mutant

description: RNA extracted from YLR060W TET_mutant

source_name: YLR060W TET_mutant


title: YPL075W TET_mutant

description: RNA extracted from YPL075W TET_mutant


title: YFL024C TET_mutant

description: RNA extracted from YFL024C TET_mutant

source_name: YFL024C TET_mutant


title: YML130C TET_mutant

description: RNA extracted from YML130C TET_mutant

source_name: YML130C TET_mutant


title: YPL231W TET_mutant

description: RNA extracted from YPL231W TET_mutant

source_name: YPL231W TET_mutant


title: YGR060W TET_mutant

description: RNA extracted from YGR060W TET_mutant

source_name: YGR060W TET_mutant


title: YAL003W TET_mutant

description: RNA extracted from YAL003W TET_mutant

source_name: YAL003W TET_mutant


title: YGR060W TET_mutant replicate 1

description: RNA extracted from YGR060W TET_mutant


title: YGR175C TET_mutant

description: RNA extracted from YGR175C TET_mutant

source_name: YGR175C TET_mutant


title: YBL040C TET_mutant

description: RNA extracted from YBL040C TET_mutant

source_name: YBL040C TET_mutant


title: YNL258C TET_mutant replicate 1

description: RNA extracted from YNL258C TET_mutant

source_name: YNL258C TET_mutant


title: YIL003W TET_mutant

description: RNA extracted from YIL003W TET_mutant

source_name: YIL003W TET_mutant


title: YNL258C TET_mutant

description: RNA extracted from YNL258C TET_mutant


title: YMR128W TET_mutant

description: RNA extracted from YMR128W TET_mutant

source_name: YMR128W TET_mutant


title: YOR204W TET_mutant

description: RNA extracted from YOR204W TET_mutant

source_name: YOR204W TET_mutant


title: YNL245C TET_mutant

description: RNA extracted from YNL245C TET_mutant

source_name: YNL245C TET_mutant


title: YDR141C TET_mutant replicate 1

description: RNA extracted from YDR141C TET_mutant

source_name: Wild-Type (WT)

source_name: YDR141C TET_mutant


title: YNL245C TET_mutant replicate 1

description: RNA extracted from YNL245C TET_mutant


title: YDL031W TET_mutant replicate 1

description: RNA extracted from YDL031W TET_mutant

source_name: YDL031W TET_mutant


title: YDL031W TET_mutant

description: RNA extracted from YDL031W TET_mutant


title: YLR459W TET_mutant

description: RNA extracted from YLR459W TET_mutant

source_name: YLR459W TET_mutant


title: YPL228W TET_mutant

description: RNA extracted from YPL228W TET_mutant

source_name: YPL228W TET_mutant


title: YMR213W TET_mutant

description: RNA extracted from YMR213W TET_mutant

source_name: YMR213W TET_mutant


title: YGR278W TET_mutant

description: RNA extracted from YGR278W TET_mutant

source_name: YGR278W TET_mutant


title: YPR105C TET_mutant

description: RNA extracted from YPR105C TET_mutant

source_name: YPR105C TET_mutant


title: YDR141C TET_mutant

description: RNA extracted from YDR141C TET_mutant


title: YBR029C TET_mutant replicate 1

description: RNA extracted from YBR029C TET_mutant

source_name: YBR029C TET_mutant


title: YBR029C TET_mutant

description: RNA extracted from YBR029C TET_mutant


title: YJL194W TET_mutant

description: RNA extracted from YJL194W TET_mutant

source_name: YJL194W TET_mutant


title: YOR236W TET_mutant

description: RNA extracted from YOR236W TET_mutant

source_name: YOR236W TET_mutant


title: YPR019W TET_mutant  replicate 1

description: RNA extracted from YPR019W TET_mutant

source_name: YPR019W TET_mutant


title: Dex2

status: Public on Jun 30 2004

city: Cambridge

first: Akhilesh

middle: Basi

last: Reddy

address: Hills Road

department: Institute of Metabolic Science

country: United Kingdom

institute: University of Cambridge

description: Mouse liver RNA was extracted using Trizol (Invitrogen) and Qiagen RNeasy kits. RNA was checked with an Agilent Bioanalyzer for evidence of sub-genomic DNA and degradation. Targets were produced using standard Affymetrix protocols. This represents data from a single mouse liver.

organism: Mus musculus

source_name: Liver


title: Dex8


title: Dex3


title: Dex6


title: Dex5


title: Dex7


title: Dex9


title: Dex4


title: Veh3


title: Veh2


title: Con9


title: TAP-YGL245W

description: RNA extracted from TAP-YGL245W


title: Veh7


title: Veh6


title: Veh5


title: Veh1


title: Veh9


title: Dex1


title: Veh4


title: Veh8


title: Con8


title: Con5


title: Con4


title: Con3


title: Con7


title: Con2


title: Con6


title: Sup/WCE fraction (8)

status: Public on Jun 29 2004

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description: Sup/WCE fraction used for Comparison/Normalization of GSM24767


title: Sup/WCE fraction (9)

description: Sup/WCE fraction used for Comparison/Normalization of GSM24768


title: Scc2 distribution in S phase, arrested by HU

description: Scc2 binding profile on chromosome VI. Cells arrested by HU (Hydoroxy Urea) were used.


title: Scc4 distribution in S phase, arrested by HU

description: Scc4 binding profile on chromosome VI. Cells arrested by HU (Hydoroxy Urea) were used.

source_name: S. cerevisiae


title: Sup/WCE fraction (6)

description: Sup/WCE fraction used for Comparison/Normalization of GSM24759, GSM24760 and GSM24877.


title: Sup/WCE fraction (7)

description: Sup/WCE fraction used for Comparison/Normalization of GSM24638


title: Scc3 distribution in G2

description: Distribution of Scc3 on chromosome VI in G2. Cells arrested in G2 phase by benomyl were used.


title: Sup/WCE fraction (3)

description: Sup(WCE) fraction used for Comparison/Normalization of GSM24756, GSM24758, GSM24762, GSM24763, and GSM24878


title: Sup/WCE fraction (1)

description: Sup(WCE) fraction used for Comparison/Normalization of GSM24754 & GSM24764


title: PDS5 distribution in G2, arrested by benomyl

description: PDS5 distribution in G2. Cells arrested by benomyl were used.


title: Scc4 distribution in G2

description: Distribution of Scc4 on chromosome VI in G2. Cells arrested in G2 phase by benomyl were used.


title: Sup/WCE fraction (2)

description: Sup(WCE) fraction used for Comparison/Normalization of GSM24755


title: Sup/WCE fraction (4)

description: Sup/WCE fraction used for Comparison/Normalization of GSM24757


title: Scc4 distribution in G1

description: Distribution of Scc4 on chromosome VI in G1. Cells arrested in G1 phase by alpha-factor were used.


title: Scc1 distribution G2/ste2 promoter deletion

description: Distribution of Scc1 on chromosome VI which is deleted for ste2 promoter region. Cells arrested at G2 phase with benomyl were used.


title: PDS5 distribution in S phase, arrested by HU

description: PDS5 distribution in S phase. Cells released from alpha-factor arrest into HU for 60min. were used.


title: Scc1 distribution in S phase, arrested by HU

description: Distribution of Scc1 on chromosome VI in S-phase. Cells released from alpha-factor arrest in the presence of 200mM HU were used.


title: Scc1 distribution in S phase (10min.)

description: Distribution of Scc1 on chromosome VI in S-phase. Cells release from alpha-factor arrest for 10 min. at 16C were used.


title: Scc1 distribution in G2

description: Scc1 distribution on chromosome VI. Cells arrested with benomyl were used.


title: Scc1 distribution in scc2-4 mutant

description: Distribution of Scc1 on chromosome VI in scc2-4 mutant background. scc2-4 mutant cells arrested at S phase with HU at 37C were used.


title: Smc3 distribution in G2

description: Smc3 distribution on chromosome VI. Cells arrested with benomyl were used.


title: Sup/WCE fraction (Sk1 in meiotic cell-cycle)

description: Normalization/Comparison file used for GSM24720.


title: Scc1 distribution in G2 (W303 background)

description: Distribution of Scc1 on chromosome VI. W303 cells arrested at G2 phase with nocodazole were used.


title: Con1

description: Mouse liver RNA was extracted using Trizol (Invitrogen) and Qiagen RNeasy kits. RNA was checked with an Agilent Bioanalyzer for evidence of sub-genomic DNA and degradation. Targets were produced using standard Affymetrix protocols. This represents data from a single mouse liver.


title: logarithmically growing BY4741 cells

description:
Gene expression profile of logarithmically growing Yeast cells.
BY4741 cell was used.


title: Sup/WCE fraction (5)

description: Sup/WCE fraction used for the normalization/comparison of GSM24765 and GSM24766


title: Scc1 distribution in S phase (30min.)

description: Distribution of Scc1 on chromosome VI in S-phase. Cells release from alpha-factor arrest for 30min. at 16C were used.


title: Sup/WCE fraction (Sk1 in mitotic cell-cycle)

description: Normalization/Comparison data used for GSM24718.


title: Scc1 distribution in G2 (SK1 cells)

description: Distribution of Scc1 in SK1 cells in G2.


title: Rec8 distribution in meiosis (SK1 cells)

description: Rec8 binding profile of meiotic SK1 cells. Cells after 4hrs induction of meiosis were used.


title: Scc1 distribution on chr.3 4 and 5 in G2

description: Scc1 distribution on chr.3, 4, and 5 of S.cerevisiae. Cells arrested by benomyl in G2 phase were used.


title: Sup/WCE fraction (S.pombe)

description: Normalization/Comparison data for pombe RAD21 binding profile (GSM24638). Genomic DNA retrieved from whole cell extract. Asynchronus culture was used.

organism: Schizosaccharomyces pombe


title: Pombe RAD21 Binding Profile

description:
Pombe RAD21 (cohesin subunit tagged by HA) distribution on chr2 and 3. Asynchronus culture was used.
Keywords = cohesin


title: Scc1 distribution in G2 after heatshock at 37C

description: Scc1 distribution on chr.3, 4, and 5 of S.cerevisiae at 37. Cells arrested by benomyl in G2 phase were used.


title: CGEN12588980

status: Public on Jun 27 2004

city: Bar Harbor

first: Janet

last: Pereira

state: ME

address: 600 Main St.

department: Gene Expression Service

institute: The Jackson Laboratory

description: Epithelial to mesenchymal transition in mice transgenic for Myc


title: CGEN12588858


title: CGEN12588595

description: Tumor progression in mice transgenic for c-Myc


title: ISB Yeast ORF Oligo Array 04868

status: Public on Jun 28 2004

city: Seattle

first: Bruz

last: Marzolf

state: WA

institute: Institute for Systems Biology

description: polyA+ RNA isolated from a tfb5 deletion strain grown at 30C in YPD at time 0 vs.   	polyA+ RNA isolated from a wild type strain grown at 30C in YPD at time 0

source_name: wt


title: CGEN12585694


title: CGEN12588596


title: CGEN12588597


title: ISB Yeast ORF Oligo Array 04877

description: polyA+ RNA isolated from a wild type strain grown at 30C in YPD time 0 vs. polyA+ RNA isolated from a tfb5 deletion strain grown at 30C in YPD time 0


title: CGEN12588979


title: CGEN12588898


title: CGEN12588821


title: CGEN12588823


title: CGEN12588822


title: CGEN12588982


title: CGEN12588813


title: CGEN12588978


title: ISB Yeast ORF Oligo Array 04894

description: RNA isolated from wild type strain grown at 37oC for 1 hour vs. RNA isolated from wild type strain grown at 37oC for 1 hour


title: CGEN12588820


title: CGEN12585693


title: CGEN12588854


title: CGEN12588855


title: CGEN12588810


title: CGEN12588812


title: CGEN12588599


title: CGEN12588811


title: CGEN12588598


title: CGEN12588981


title: CGEN12588814


title: CGEN12585697


title: PDGF_24h_d

status: Public on Jun 23 2004

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description:
Subconfluent AG01518 fibroblasts were starved for 16 hours in the presence of 0.1% BSA, and then stimulated for 1, 4, 10 or 24 hours with PDGF-BB (10 ng/ml in starvation medium), or left untreated for the same periods of time. Total RNA was isolated using the RNeasy kit (Qiagen). The RNA quality was checked by formaldehyde agarose gel electrophoresis (RNeasy protocol, Qiagen). Total RNA (40 mg) from cells treated for a given period of time with PDGF or starvation medium alone were labelled in reverse transcription reactions (Superscript II kit, Invitrogen) with dCTP-Cy5 and dCTP-Cy3, respectively (Amersham). In every second replicate experiment the fluorescent deoxynucleotides were swapped. Purified cDNA probes labelled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (hver1.2.1) from the Sanger Institute/LICR/CRUK Consortium (see http://www.sanger.ac.uk/Projects/Microarrays/
for details and hybridization protocols). For each time point, we performed at least four independent hybridizations, and used at least two different batches of RNA. Chips were scanned in a Perkin Elmer/GSI Lumonics ScanArray 4000 scanner and spot intensities were measured using the QuantArray software (histogram method with background subtraction). Normalization and statistical analysis of the quadruplicate data sets were performed using GeneSpring 5.0 analysis software (Silicon Genetics). A Lowess non-linear normalization was applied and the median of the ratio distribution for each array was set to 1. Regulated spots were selected based on the average ratio values above 1.750 for up-regulated genes and below 0.571 for down-regulated genes. In addition, we considered only genes that were significantly regulated (t-test, p<0.05) based on replicate hybridizations (global error model, GeneSpring). For all features selected using this protocol, the signal was significantly above the background, indicating that the expression of these genes was detectable. Finally, Hver1.2.1 microarrays contain replicate spots (1 to 6) corresponding to the same gene. Genes represented by spots that were not regulated in a similar manner were discarded. We show the average ratio of one representative spot for each regulated gene, with standard error calculated from multiple hybridizations and with the annotation provided by the microarray facility (Hver1.2.1_NCBI33).
Lot batch = 31

source_name: starved fibroblasts (control 24h)

source_name: PDGF-treated fibroblasts (24h)


title: PDGF_10h_e

description:
Subconfluent AG01518 fibroblasts were starved for 16 hours in the presence of 0.1% BSA, and then stimulated for 1, 4, 10 or 24 hours with PDGF-BB (10 ng/ml in starvation medium), or left untreated for the same periods of time. Total RNA was isolated using the RNeasy kit (Qiagen). The RNA quality was checked by formaldehyde agarose gel electrophoresis (RNeasy protocol, Qiagen). Total RNA (40 mg) from cells treated for a given period of time with PDGF or starvation medium alone were labelled in reverse transcription reactions (Superscript II kit, Invitrogen) with dCTP-Cy5 and dCTP-Cy3, respectively (Amersham). In every second replicate experiment the fluorescent deoxynucleotides were swapped. Purified cDNA probes labelled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (hver1.2.1) from the Sanger Institute/LICR/CRUK Consortium (see http://www.sanger.ac.uk/Projects/Microarrays/
for details and hybridization protocols). For each time point, we performed at least four independent hybridizations, and used at least two different batches of RNA. Chips were scanned in a Perkin Elmer/GSI Lumonics ScanArray 4000 scanner and spot intensities were measured using the QuantArray software (histogram method with background subtraction). Normalization and statistical analysis of the quadruplicate data sets were performed using GeneSpring 5.0 analysis software (Silicon Genetics). A Lowess non-linear normalization was applied and the median of the ratio distribution for each array was set to 1. Regulated spots were selected based on the average ratio values above 1.750 for up-regulated genes and below 0.571 for down-regulated genes. In addition, we considered only genes that were significantly regulated (t-test, p<0.05) based on replicate hybridizations (global error model, GeneSpring). For all features selected using this protocol, the signal was significantly above the background, indicating that the expression of these genes was detectable. Finally, Hver1.2.1 microarrays contain replicate spots (1 to 6) corresponding to the same gene. Genes represented by spots that were not regulated in a similar manner were discarded. We show the average ratio of one representative spot for each regulated gene, with standard error calculated from multiple hybridizations and with the annotation provided by the microarray facility (Hver1.2.1_NCBI33).
Lot batch = 28

source_name: starved fibroblasts (control 10h)

source_name: PDGF-treated fibroblasts (10h)


title: CGEN12585696


title: CGEN12588824


title: CGEN12585695


title: PDGF_24h_e

description:
Subconfluent AG01518 fibroblasts were starved for 16 hours in the presence of 0.1% BSA, and then stimulated for 1, 4, 10 or 24 hours with PDGF-BB (10 ng/ml in starvation medium), or left untreated for the same periods of time. Total RNA was isolated using the RNeasy kit (Qiagen). The RNA quality was checked by formaldehyde agarose gel electrophoresis (RNeasy protocol, Qiagen). Total RNA (40 mg) from cells treated for a given period of time with PDGF or starvation medium alone were labelled in reverse transcription reactions (Superscript II kit, Invitrogen) with dCTP-Cy5 and dCTP-Cy3, respectively (Amersham). In every second replicate experiment the fluorescent deoxynucleotides were swapped. Purified cDNA probes labelled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (hver1.2.1) from the Sanger Institute/LICR/CRUK Consortium (see http://www.sanger.ac.uk/Projects/Microarrays/
for details and hybridization protocols). For each time point, we performed at least four independent hybridizations, and used at least two different batches of RNA. Chips were scanned in a Perkin Elmer/GSI Lumonics ScanArray 4000 scanner and spot intensities were measured using the QuantArray software (histogram method with background subtraction). Normalization and statistical analysis of the quadruplicate data sets were performed using GeneSpring 5.0 analysis software (Silicon Genetics). A Lowess non-linear normalization was applied and the median of the ratio distribution for each array was set to 1. Regulated spots were selected based on the average ratio values above 1.750 for up-regulated genes and below 0.571 for down-regulated genes. In addition, we considered only genes that were significantly regulated (t-test, p<0.05) based on replicate hybridizations (global error model, GeneSpring). For all features selected using this protocol, the signal was significantly above the background, indicating that the expression of these genes was detectable. Finally, Hver1.2.1 microarrays contain replicate spots (1 to 6) corresponding to the same gene. Genes represented by spots that were not regulated in a similar manner were discarded. We show the average ratio of one representative spot for each regulated gene, with standard error calculated from multiple hybridizations and with the annotation provided by the microarray facility (Hver1.2.1_NCBI33).
Lot batch = 41


title: PDGF_1h_d

description:
Subconfluent AG01518 fibroblasts were starved for 16 hours in the presence of 0.1% BSA, and then stimulated for 1, 4, 10 or 24 hours with PDGF-BB (10 ng/ml in starvation medium), or left untreated for the same periods of time. Total RNA was isolated using the RNeasy kit (Qiagen). The RNA quality was checked by formaldehyde agarose gel electrophoresis (RNeasy protocol, Qiagen). Total RNA (40 mg) from cells treated for a given period of time with PDGF or starvation medium alone were labelled in reverse transcription reactions (Superscript II kit, Invitrogen) with dCTP-Cy5 and dCTP-Cy3, respectively (Amersham). In every second replicate experiment the fluorescent deoxynucleotides were swapped. Purified cDNA probes labelled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (hver1.2.1) from the Sanger Institute/LICR/CRUK Consortium (see http://www.sanger.ac.uk/Projects/Microarrays/
for details and hybridization protocols). For each time point, we performed at least four independent hybridizations, and used at least two different batches of RNA. Chips were scanned in a Perkin Elmer/GSI Lumonics ScanArray 4000 scanner and spot intensities were measured using the QuantArray software (histogram method with background subtraction). Normalization and statistical analysis of the quadruplicate data sets were performed using GeneSpring 5.0 analysis software (Silicon Genetics). A Lowess non-linear normalization was applied and the median of the ratio distribution for each array was set to 1. Regulated spots were selected based on the average ratio values above 1.750 for up-regulated genes and below 0.571 for down-regulated genes. In addition, we considered only genes that were significantly regulated (t-test, p<0.05) based on replicate hybridizations (global error model, GeneSpring). For all features selected using this protocol, the signal was significantly above the background, indicating that the expression of these genes was detectable. Finally, Hver1.2.1 microarrays contain replicate spots (1 to 6) corresponding to the same gene. Genes represented by spots that were not regulated in a similar manner were discarded. We show the average ratio of one representative spot for each regulated gene, with standard error calculated from multiple hybridizations and with the annotation provided by the microarray facility (Hver1.2.1_NCBI33).
Lot batch = 29

source_name: starved fibroblasts (control 1h)

source_name: PDGF-treated fibroblasts (1h)


title: PDGF_24h_a

description:
Subconfluent AG01518 fibroblasts were starved for 16 hours in the presence of 0.1% BSA, and then stimulated for 1, 4, 10 or 24 hours with PDGF-BB (10 ng/ml in starvation medium), or left untreated for the same periods of time. Total RNA was isolated using the RNeasy kit (Qiagen). The RNA quality was checked by formaldehyde agarose gel electrophoresis (RNeasy protocol, Qiagen). Total RNA (40 mg) from cells treated for a given period of time with PDGF or starvation medium alone were labelled in reverse transcription reactions (Superscript II kit, Invitrogen) with dCTP-Cy5 and dCTP-Cy3, respectively (Amersham). In every second replicate experiment the fluorescent deoxynucleotides were swapped. Purified cDNA probes labelled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (hver1.2.1) from the Sanger Institute/LICR/CRUK Consortium (see http://www.sanger.ac.uk/Projects/Microarrays/
for details and hybridization protocols). For each time point, we performed at least four independent hybridizations, and used at least two different batches of RNA. Chips were scanned in a Perkin Elmer/GSI Lumonics ScanArray 4000 scanner and spot intensities were measured using the QuantArray software (histogram method with background subtraction). Normalization and statistical analysis of the quadruplicate data sets were performed using GeneSpring 5.0 analysis software (Silicon Genetics). A Lowess non-linear normalization was applied and the median of the ratio distribution for each array was set to 1. Regulated spots were selected based on the average ratio values above 1.750 for up-regulated genes and below 0.571 for down-regulated genes. In addition, we considered only genes that were significantly regulated (t-test, p<0.05) based on replicate hybridizations (global error model, GeneSpring). For all features selected using this protocol, the signal was significantly above the background, indicating that the expression of these genes was detectable. Finally, Hver1.2.1 microarrays contain replicate spots (1 to 6) corresponding to the same gene. Genes represented by spots that were not regulated in a similar manner were discarded. We show the average ratio of one representative spot for each regulated gene, with standard error calculated from multiple hybridizations and with the annotation provided by the microarray facility (Hver1.2.1_NCBI33).
Lot batch = 35


title: PDGF_4h_e

source_name: starved fibroblasts (control 4h)

source_name: PDGF-treated fibroblasts (4h)


title: PDGF_4h_c


title: PDGF_10h_c


title: PDGF_24h_c


title: PDGF_4h_d


title: PDGF_24h_b


title: PDGF_4h_b


title: PDGF_10h_b


title: abf1-1 microarray#4

city: Charlottesville

first: Tsuyoshi

last: Miyake

state: VA

address: 1300 Jefferson Park Ave.

department: Biochemistry & Molecular Genetics

institute: Univ. Virginia

description:
The abf1-1 mutant and wild type cells were grown at 30 degrees C in YPAD until OD600 reached 1.0-1.2.  The same volume of 42 degrees C preheated YPAD was added for each flask.  After 45min incubation at 36 degrees C, cells were harvested and RNA was isolated.
Keywords = ABF1

source_name: abf1-1 shift from 30 to 36 degree (45min)

source_name: wild type shift from 30 to 36 degree (45min)


title: PDGF_4h_a


title: abf1-1 microarray#3


title: PDGF_1h_a


title: PDGF_1h_b


title: abf1-1 microarray#2


title: TBI dose 2 FS

status: Public on Jun 17 2004

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

description: RNA from human peripheral blood lymphocytes was labeled with Cy3 (control) and Cy5 (treated), and hybridized to a spotted cDNA microarray.

source_name: PBL after 3 Gy TBI

source_name: Pre-treatment PBL


title: abf1-1 microarray#1


title: TBI dose 1 FS

description: RNA from human peripheral blood lymphocytes was labeled with Cy5 (control) and Cy3 (treated), and hybridized to a spotted cDNA microarray.

source_name: PBL 6h post 1.5 Gy TBI

source_name: PBL pre-treatment control


title: CGEN12588853


title: TBI dose2

source_name: PBL after 3 Gy total TBI


title: 10A

description: Growth at 10% O2, 1% CO2, 89% N2 in the dark. Cells are collected at OD 0.18. RNA was isolated with bead beater + RNeasy kits

source_name: Rhodobacter sphaeroides 2.4.1


title: BL-45B

description: Growth at 10% O2, 1% CO2, 89% N2 in the dark, illumination with blue light (10 mkmols m(-2) s(-1)) during 45 min before harvesting of cells at OD(600)=0.18. RNA was isolated with bead beater + RNeasy kits with DNase treatment. Expression values were generated using MAS5.0 (scaled to target=500). Probe intensity (.CEL) files are available upon request


title: BL-135A

description: Growth at 10% O2, 1% CO2, 89% N2 in the dark, illumination with blue light (10 mkmols m(-2) s(-1)) during 135 min before harvesting of cells at OD(600)=0.18. RNA was isolated with bead beater + RNeasy kits with DNase treatment. Expression values were generated using MAS5.0 (scaled to target=500). Probe intensity (.CEL) files are available upon request


title: BL-5B

description: Growth at 10% O2, 1% CO2, 89% N2 in the dark, illumination with blue light (10 mkmols m(-2) s(-1)) during 5 min before harvesting of cells at OD(600)=0.18. RNA was isolated with bead beater + RNeasy kits with DNase treatment. Expression values were generated using MAS5.0 (scaled to target=500). Probe intensity (.CEL) files are available upon request


title: TBI dose1

source_name: Human PBL 6h after 1.5Gy TBI

source_name: Human PBL pre-treatment control


title: BL-45A


title: 10BL-dark

description: Growth at 10% O2, 1% CO2, 89% N2 in the dark. (This particular sample was grown in parallel with samples exposed to blue light). Cells were collected at OD(600)=0.18. RNA was isolated with bead beater + RNeasy kits with DNase treatment. Expression values were generated using MAS5.0 (scaled to target=500). Probe intensity (.CEL) files are available upon request


title: 10B

description: Growth at 10% O2, 1% CO2, 89% N2 in the dark. Cells were collected at OD(600)=0.18. RNA was isolated with bead beater + RNeasy kits with DNase treatment. Expression values were generated using MAS5.0 (scaled to target=500). Probe intensity (.CEL) files are available upon request


title: Endothelial expression profile comparison

city: Antwerp

first: Jan

last: Hendrickx

address: Groenenborgerlaan 171

department: Pharmacology

institute: University of Antwerp

description: Endocardial (EE) and Aortic (AE) endothelial cells were isolated from the same two rats, pooled (EE and AE kept separately) and cultured for 2 passages. Culture conditions and confluence of EE and AE cell cultures were kept as identical as possible. RNA was isolated and the expression profile of both endothelial cell types was compared using the Affymetrix rat genome U34A array.

organism: Rattus norvegicus

source_name: Aortic endothelial cells


title: PDGF_10h_a

source_name: starved fibroblasts (control 10h)


title: Endothelial expression profile comparison (EE)

source_name: Endocardial endothelial cells


title: BL-135B

description:
Growth at 10% O2, 1% CO2, 89% N2 in the dark, illumination with blue light (10 mkmols m(-2) s(-1)) during 135 min before harvesting of cells at OD(600)=0.18. RNA was isolated with bead beater + RNeasy kits with DNase treatment. Expression values were generated using MAS5.0 (scaled to target=500). Probe intensity (.CEL) files are available upon request
Keywords = blue light
Keywords = oxidative stress


title: T84, LTb 1

status: Public on Jun 16 2004

city: Epalinges

first: Pascale

last: Anderle

country: Switzerland

institute: ISREC

description: T84 cells were seeded on Transwell filters, cultured for 14 days and then treated for 4 h with lymphotoxin beta.

source_name: 14 day old T84 cells


title: T84, TNFa 3

description: T84 cells were seeded on Transwell filters, cultured for 14 days and then treated for 4 h with TNF alpha.


title: T84, Flagellin 2

description: T84 cells were seeded on Transwell filters, cultured for 14 days and then treated for 4 h with flagellin.


title: T84, TNFa 1


title: T84, LTb 2


title: T84, TNFa 2


title: T84, Control 2

description: T84 cells were seeded on Transwell filters, cultured for 14 days.


title: BL-5A


title: T84, LTb 3


title: PDGF_1h_c

description:
Subconfluent AG01518 fibroblasts were starved for 16 hours in the presence of 0.1% BSA, and then stimulated for 1, 4, 10 or 24 hours with PDGF-BB (10 ng/ml in starvation medium), or left untreated for the same periods of time. Total RNA was isolated using the RNeasy kit (Qiagen). The RNA quality was checked by formaldehyde agarose gel electrophoresis (RNeasy protocol, Qiagen). Total RNA (40 mg) from cells treated for a given period of time with PDGF or starvation medium alone were labelled in reverse transcription reactions (Superscript II kit, Invitrogen) with dCTP-Cy5 and dCTP-Cy3, respectively (Amersham). In every second replicate experiment the fluorescent deoxynucleotides were swapped. Purified cDNA probes labelled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (hver1.2.1) from the Sanger Institute/LICR/CRUK Consortium (see http://www.sanger.ac.uk/Projects/Microarrays/
for details and hybridization protocols). For each time point, we performed at least four independent hybridizations, and used at least two different batches of RNA. Chips were scanned in a Perkin Elmer/GSI Lumonics ScanArray 4000 scanner and spot intensities were measured using the QuantArray software (histogram method with background subtraction). Normalization and statistical analysis of the quadruplicate data sets were performed using GeneSpring 5.0 analysis software (Silicon Genetics). A Lowess non-linear normalization was applied and the median of the ratio distribution for each array was set to 1. Regulated spots were selected based on the average ratio values above 1.750 for up-regulated genes and below 0.571 for down-regulated genes. In addition, we considered only genes that were significantly regulated (t-test, p<0.05) based on replicate hybridizations (global error model, GeneSpring). For all features selected using this protocol, the signal was significantly above the background, indicating that the expression of these genes was detectable. Finally, Hver1.2.1 microarrays contain replicate spots (1 to 6) corresponding to the same gene. Genes represented by spots that were not regulated in a similar manner were discarded. We show the average ratio of one representative spot for each regulated gene, with standard error calculated from multiple hybridizations and with the annotation provided by the microarray facility (Hver1.2.1_NCBI33).
Lot batch = 41

source_name: starved fibroblasts (control 1h)

source_name: PDGF-treated fibroblasts (1h)


title: T84, Control 3


title: Caco-2, TNFa 2

description: Caco-2 cells were seeded on Transwell filters, cultured for 14 days, and then treated for 4 h with TNF alpha.

source_name: 14 day old Caco-2 cells


title: T84, Control 1


title: Caco-2, TNFa 3


title: Caco-2, LTb 1

description: Caco-2 cells were seeded on Transwell filters, cultured for 14 days, and then treated for 4 h with Lymphotoxin beta.


title: Caco-2, LTb 3


title: T84, Flagellin 3


title: Caco-2, LTb 2


title: Caco-2, Flagellin 1

description: Caco-2 cells were seeded on Transwell filters, cultured for 14 days, and then treated for 4 h with flagellin


title: T84, Flagellin 1


title: Caco-2, Control 3

description: Caco-2 cells were seeded on Transwell filters, cultured for 14 days.


title: Caco-2, TNFa 1


title: Caco-2, Flagellin 2


title: Caco-2, Control 2


title: 8 week old EOM MDX rep 2

status: Public on Jun 15 2004

city: Cleveland

first: Henry

middle: J.

last: Kaminski

state: OH

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

description: Standard Affymetrix Protocol

source_name: 8 week old mouse extraocular muscle


title: Caco-2, Control 1


title: 8 week old EOM MDX rep 4

description: Standard Affymetrix Protocol


title: 8 week old leg MDX rep 3

description: Standard Affymetrix Protocol

source_name: 8 week old mouse leg muscle


title: 8 week old leg MDX rep 4

description: Standard Affymetrix Protocol


title: 8 week old EOM MDX rep 5

description: Standard Affymetrix Protocol


title: 8 week old EOM MDX rep 1

description: Standard Affymetrix Protocol


title: 8 week old leg MDX rep 2

description: Standard Affymetrix Protocol


title: 8 week old leg MDX rep 5

description: Standard Affymetrix Protocol


title: 8 week old EOM MDX rep 3

description: Standard Affymetrix Protocol


title: 8 week old leg MDX rep 1

description: Standard Affymetrix Protocol


title: EV111, ddm1 seedlings H3mK9

status: Public on Jun 12 2004

type: genomic

city: Austin

first: Matthew

middle: Wayne

last: Vaughn

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

description:
Wild-type seedlings, 9 days
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) (Upstate Biotechnology) was performed as previously described in Gendrel et al. (2002) on material from nine-day-old seedlings, except that the immunoprecipitated (IP) DNA was resuspended in 15ul H20. Seven l from each sample (H3mK9, no antibody control, and input DNA) was used for random amplification. The DNA amplification was performed as described at <http://www.microarrays.org>, except that after Round A (Sequenase step), we carried out only a single Round B of 35 cycles. The DNA obtained was quantified and resolved on a 1.5% agarose gel to check that the range of sizes was between 500bp and ~1.5kb.
1.5ug from each sample was labeled with Cy3 (H3mK9) and Cy5 (Total) using the Megaprime DNA labeling kit (Amersham Pharmacia). Labeled DNA samples were then mixed, purified, and concentrated using Microcon YM-30 columns. The volume was brought to 25ul in a final concentration of 4X SSC, 0.2% SDS.
Hybridizations were carried out at 65C for approximately 15 hrs. Slides were washed in 1X SSC, 0.2% SDS once and 0.2X SSC twice.
Slides were scanned with a GenePix 4000A scanner (Axon Instruments). We quantified the fluorescence with the GenePix Pro software.
Sample_series_id: EV110+111

molecule: genomic DNA

source_name: Total ChIP ddm1 DNA

source_name: H3mK9 ChIP ddm1 DNA


title: EV108, Wild-type seedlings H3mK9

description:
Wild-type seedlings, 9 days
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) (Upstate Biotechnology) was performed as previously described in Gendrel et al. (2002) on material from nine-day-old seedlings, except that the immunoprecipitated (IP) DNA was resuspended in 15ul H20. Seven l from each sample (H3mK9, no antibody control, and input DNA) was used for random amplification. The DNA amplification was performed as described at <http://www.microarrays.org>, except that after Round A (Sequenase step), we carried out only a single Round B of 35 cycles. The DNA obtained was quantified and resolved on a 1.5% agarose gel to check that the range of sizes was between 500bp and ~1.5kb.
1.5ug from each sample was labeled with Cy5 (H3mK9) and Cy3 (Total) using the Megaprime DNA labeling kit (Amersham Pharmacia). Labeled DNA samples were then mixed, purified, and concentrated using Microcon YM-30 columns. The volume was brought to 25ul in a final concentration of 4X SSC, 0.2% SDS.
Hybridizations were carried out at 65C for approximately 15 hrs. Slides were washed in 1X SSC, 0.2% SDS once and 0.2X SSC twice.
Slides were scanned with a GenePix 4000A scanner (Axon Instruments). We quantified the fluorescence with the GenePix Pro software.
Sample_series_id: EV108+109

source_name: H3mK9 ChIP wild-type DNA

source_name: Total ChIP wild-type DNA


title: EV51, Wild-type seedlings H3mK9

description:
Wild-type seedlings, 9 days
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) (Upstate Biotechnology) was performed as previously described in Gendrel et al. (2002) on material from nine-day-old seedlings, except that the immunoprecipitated (IP) DNA was resuspended in 15ul H20. Seven l from each sample (H3mK9, no antibody control, and input DNA) was used for random amplification. The DNA amplification was performed as described at <http://www.microarrays.org>, except that after Round A (Sequenase step), we carried out only a single Round B of 35 cycles. The DNA obtained was quantified and resolved on a 1.5% agarose gel to check that the range of sizes was between 500bp and ~1.5kb.
1.5ug from each sample was labeled with Cy5 (H3mK9) and Cy3 (Total) using the Megaprime DNA labeling kit (Amersham Pharmacia). Labeled DNA samples were then mixed, purified, and concentrated using Microcon YM-30 columns. The volume was brought to 25ul in a final concentration of 4X SSC, 0.2% SDS.
Hybridizations were carried out at 65C for approximately 15 hrs. Slides were washed in 1X SSC, 0.2% SDS once and 0.2X SSC twice.
Slides were scanned with a GenePix 4000A scanner (Axon Instruments). We quantified the fluorescence with the GenePix Pro software.
Sample_series_id: EV51+52


title: EV60, ddm1 seedlings H3mK9

description:
ddm1 seedlings, 9 days
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) (Upstate Biotechnology) was performed as previously described in Gendrel et al. (2002) on material from nine-day-old seedlings, except that the immunoprecipitated (IP) DNA was resuspended in 15ul H20. Seven l from each sample (H3mK9, no antibody control, and input DNA) was used for random amplification. The DNA amplification was performed as described at <http://www.microarrays.org>, except that after Round A (Sequenase step), we carried out only a single Round B of 35 cycles. The DNA obtained was quantified and resolved on a 1.5% agarose gel to check that the range of sizes was between 500bp and ~1.5kb.
1.5ug from each sample was labeled with Cy5 (H3mK9) and Cy3 (Total) using the Megaprime DNA labeling kit (Amersham Pharmacia). Labeled DNA samples were then mixed, purified, and concentrated using Microcon YM-30 columns. The volume was brought to 25ul in a final concentration of 4X SSC, 0.2% SDS.
Hybridizations were carried out at 65C for approximately 15 hrs. Slides were washed in 1X SSC, 0.2% SDS once and 0.2X SSC twice.
Slides were scanned with a GenePix 4000A scanner (Axon Instruments). We quantified the fluorescence with the GenePix Pro software.
Sample_series_id: EV59+60


title: EV52, Wild-type seedlings H3mK9

description:
Wild-type seedlings, 9 days
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) (Upstate Biotechnology) was performed as previously described in Gendrel et al. (2002) on material from nine-day-old seedlings, except that the immunoprecipitated (IP) DNA was resuspended in 15ul H20. Seven l from each sample (H3mK9, no antibody control, and input DNA) was used for random amplification. The DNA amplification was performed as described at <http://www.microarrays.org>, except that after Round A (Sequenase step), we carried out only a single Round B of 35 cycles. The DNA obtained was quantified and resolved on a 1.5% agarose gel to check that the range of sizes was between 500bp and ~1.5kb.
1.5ug from each sample was labeled with Cy3 (H3mK9) and Cy5 (Total) using the Megaprime DNA labeling kit (Amersham Pharmacia). Labeled DNA samples were then mixed, purified, and concentrated using Microcon YM-30 columns. The volume was brought to 25ul in a final concentration of 4X SSC, 0.2% SDS.
Hybridizations were carried out at 65C for approximately 15 hrs. Slides were washed in 1X SSC, 0.2% SDS once and 0.2X SSC twice.
Slides were scanned with a GenePix 4000A scanner (Axon Instruments). We quantified the fluorescence with the GenePix Pro software.
Sample_series_id: EV51+52


title: EV106, WT seedlings H3mK4

description:
WT seedlings, 9 days
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-4 (H3mK4) (Upstate Biotechnology) was performed as previously described in Gendrel et al. (2002) on material from nine-day-old seedlings, except that the immunoprecipitated (IP) DNA was resuspended in 15ul H20. Seven l from each sample (H3mK4, no antibody control, and input DNA) was used for random amplification. The DNA amplification was performed as described at <http://www.microarrays.org>, except that after Round A (Sequenase step), we carried out only a single Round B of 35 cycles. The DNA obtained was quantified and resolved on a 1.5% agarose gel to check that the range of sizes was between 500bp and ~1.5kb.
1.5ug from each sample was labeled with Cy5 (H3mK4) and Cy3 (Total) using the Megaprime DNA labeling kit (Amersham Pharmacia). Labeled DNA samples were then mixed, purified, and concentrated using Microcon YM-30 columns. The volume was brought to 25ul in a final concentration of 4X SSC, 0.2% SDS.
Hybridizations were carried out at 65C for approximately 15 hrs. Slides were washed in 1X SSC, 0.2% SDS once and 0.2X SSC twice.
Slides were scanned with a GenePix 4000A scanner (Axon Instruments). We quantified the fluorescence with the GenePix Pro software.
Sample_series_id: EV106+107

source_name: H3mK4 ChIP WT DNA

source_name: Total ChIP WT DNA


title: EV56, ddm1 seedlings H3mK4

description:
ddm1 seedlings, 9 days
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-4 (H3mK4) (Upstate Biotechnology) was performed as previously described in Gendrel et al. (2002) on material from nine-day-old seedlings, except that the immunoprecipitated (IP) DNA was resuspended in 15ul H20. Seven l from each sample (H3mK9, no antibody control, and input DNA) was used for random amplification. The DNA amplification was performed as described at <http://www.microarrays.org>, except that after Round A (Sequenase step), we carried out only a single Round B of 35 cycles. The DNA obtained was quantified and resolved on a 1.5% agarose gel to check that the range of sizes was between 500bp and ~1.5kb.
1.5ug from each sample was labeled with Cy3 (H3mK4) and Cy5 (Total) using the Megaprime DNA labeling kit (Amersham Pharmacia). Labeled DNA samples were then mixed, purified, and concentrated using Microcon YM-30 columns. The volume was brought to 25ul in a final concentration of 4X SSC, 0.2% SDS.
Hybridizations were carried out at 65C for approximately 15 hrs. Slides were washed in 1X SSC, 0.2% SDS once and 0.2X SSC twice.
Slides were scanned with a GenePix 4000A scanner (Axon Instruments). We quantified the fluorescence with the GenePix Pro software.
Sample_series_id: EV55+56

source_name: H3mK4 ChIP ddm1 DNA