title: temporal.txt e17.5 o-192006

description:
Individual ID; o-192006
Age; 17.5 dpc
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e17.5 Kidney


title: temporal.txt e15.5 o-192056

status: Public on Jul 20 2005

type: RNA

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

description:
Individual ID; o-192056
Age; 15.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

molecule: total RNA

organism: Mus musculus

source_name: Mouse Universal Reference RNA

source_name: e15.5 Kidney


title: temporal.txt e13.5 o-192080

description:
Individual ID; o-192080
Age; 13.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e13.5 Kidney


title: temporal.txt e10.5 o-192118

description:
Individual ID; 0-192118
Age; 10.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e10.5 Kidney


title: temporal.txt e11.5 o-192079

description:
Individual ID; o-192079
Age; 11.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e11.5 Kidney


title: temporal.txt e15.5 o-192082

description:
Individual ID; o-192082
Age; 15.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e13.5 o-192123

description:
Individual ID; o-192123
Age; 13.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e13.5 o-192081

description:
Individual ID; o-192081
Age; 13.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e11.5 0-192119

description:
Individual ID; o-192119
Age; 11.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e14.5 o-182502

description:
Individual ID; o-182502
Age; 14.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e14.5 Kidney


title: CGEN 10.5 Vs 13.5dpc.txt column 3

description:
Sample; 1
File Name; CGEN 10.5 Vs 13.5dpc.txt
Age; 10.5 V 13.5
Array Design; Mouse COmpugen 22K oligo
Author; Sean rimmond
Common Reference (Yes/No, ID); none
Concentration; 100
Data processing/normalization; R: Print tip Loess + between arrays (LIMAS+SMA)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green; green/red
Experiment Type; Pairwise comparison
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message AMp Ambion
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ
RNA type; aRNA
Sample Source; primary tissue
Sampling Method; microdissection
Sex; Pool of both
Strain/Cell-line; CD1
A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: 13.5 dpc Kidney

source_name: 10.5dpc Metanephric mesenchyme


title: S-T8_vs_R-T8_rep2 b

status: Public on Jul 21 2005

city: Urbana

first: min

last: li

state: IL

address: Rm230 1101 W peabody Dr

country: USA

institute: University of Illinois at Urbana-Champaign

description: Replicate 2

hyb_protocol: Hegde P et al Biotechniques 2000 29:548-56

scan_protocol: scanner: Perkin-Elmer ScanArray Express Software: ScanArray Express v2.1

data_processing:
Spot raw data from GenePix4.0
glowess normalization using R/MAANOVA

organism: Glycine max

source_name: Pooled unifoliate leaves from 3-4 plants

label_protocol: Indirect incorporation using aa-dUTP

growth_protocol:
Growth Chamber (22C)
Light 100-120 umol photons/m2/sec
16 hour daylength

extract_protocol: Trizol Phase Lock Gel RNA Extraction

treatment_protocol:
P. syringae avrB-
OD600:0.02 in 10mM MgCl2:vacuum infiltrated
8 hour post inoculation

tag: Cultivar

value: Williams 82

tag: Age

value: approximately 14 days

treatment_protocol:
P. syringae avrB+
OD600:0.02 in 10mM MgCl2:vacuum infiltrated
8 hour post inoculation


title: WM793_treated

city: Dublin

first: Edward

last: Fox

country: Ireland

institute: Conway Institute

description: Melanoma cell line WM793 treated with 2ug/ml DAC as per publication

organism: Homo sapiens


title: WM793-P2N1_2

description: Melanoma cell line.  Subline of WM793.  Highly tumourigenic in nude mice.  Biological replicate of WM793-P2N1_1.


title: WM793-P1N1-treated

description: Melanoma cell line WM793-P1N1 treated with 2ug/ml DAC as per publication


title: 1205-Lu-treated

description: Melanoma cell line 1205-Lu treated wit 2ug/ml of DAC as per publication


title: WM793

description: Melanoma cell line


title: S-T2_vs_S-T8 b

description: Replicate 1

treatment_protocol:
P. syringae avrB-
OD600:0.02 in 10mM MgCl2:vacuum infiltrated
2 hour post inoculation


title: WM793-P2N1_1

description: Melanoma cell line.  Subline of WM793.  Highly tumourigenic in nude mice.


title: WM793-P1N1_1


title: temporal.txt e13.5 o-192124

description:
Individual ID; o-192124
Age; 13.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e16.5 o-192120

description:
Individual ID; o-192120
Age; 16.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e16.5 Kidney


title: temporal.txt e17.5 o-182571

description:
Individual ID; o-182571
Age; 17.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: 1205-Lu

description: Melanoma cell line 1205-Lu


title: temporal.txt e19.5 o-182592

description:
Individual ID; o-182592
Age; 19.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e19.5 Kidney


title: temporal.txt e15.5 o-192125

description:
Individual ID; o-192125
Age; 15.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e14.5 o-182541

description:
Individual ID; o-182541
Age; 14.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e12.5 o-191934

description:
Individual ID; o-191934
Age; 12.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e12.5 Kidney


title: temporal.txt e19.5 o-182564

description:
Individual ID; o-182564
Age; 19.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: WM793_2

description: Melanoma cell line.  Poorly tumourigenic in nude mice.  Biological Replicate of WM793_1.


title: temporal.txt e11.5 0-192061

description:
Individual ID; 0-192061
Age; 11.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e18.5 o-182583

description:
Individual ID; o-182583
Age; 18.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e18.5 Kidney


title: temporal.txt e16.5 o-182615

description:
Individual ID; o-182615
Age; 16.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e18.5 o-192003

description:
Individual ID; o-192003
Age; 18.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e17.5 o-182630

description:
Individual ID; o-182630
Age; 17.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e19.5 o-191984

description:
Individual ID; o-191984
Age; 19.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e19.5 o-191988

description:
Individual ID; o-191988
Age; 19.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: WM793_1

description: Melanoma cell line.  Poorly tumourigenic in nude mice.


title: WM793-P2N1-treated

description: Melanoma cell line WM793-P2N1 treated with 2ug/ml DAC as per publication


title: 4mo tg8

city: Madison

first: Tracy

last: Hagemann

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin, Madison

description: olfactory bulb from hGFAP transgenic FVB/N mouse at 4mos

source_name: olfactory bulb


title: MM V IM 10.5dpc_mean transf.txt column 18

description:
Sample; 4
File Name; MM V IM 10.5dpc_mean transf.txt
comparison; 1
Array Design; Mouse Compugen 22K Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); none
Concentration; 100
Developmental Stage; embryonic
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message Amp (Ambion)
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ, St Lucia, Australia
RNA type; aRNA
Sample Source; primary tissue
Sex; both
Age; 10.5
Sampling Method; dissection
Dye Swap; red/green; green/red
To account for dye swap, the signal channel and control channel measurements for sample(s) 3-4 were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: 10.5dpc Intermediate Mesenchyme

source_name: 10.5dpc Metanephric mesoderm


title: 4mo tg2


title: CGEN 15.5dpc GFP+Tree Vs Rest_Filtered column 13

description:
Sample; 3
File Name; CGEN 15.5dpc GFP+Tree Vs rest_Filtered GFP+Tree Vs
Array Design; 1
Age; 15.5
Array Design; Mouse Compugen 22K oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); none
Concentration; 100
Data processing/normalization; Lowess Normalisation
Developmental Stage; embryonic
Diseased/Normal; normal
Experiment Type; Pairwise comparison
Genetic Characteristic; HoxB7-GFP transgenic
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message AMp Amibon
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ
RNA type; aRNA
Sample Source; primary tissue
Sampling Method; FACS sorting of GFP +ve and -ve Cell populations
Sex; pool of both
Dye Swap; none
A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.
CGEN 15.5dpc GFP+Tree Vs rest_Filtered GFP+Tree Vs rest transf..base column 13

source_name: GFP+ cells from 15.5dpc HoxB7-GFP kidneys

source_name: GFP- cells from 15.5dpc HoxB7-GFP kidneys


title: 4mo wt10

description: olfactory bulb from wildtype FVB/N mouse at 4mos


title: temporal.txt e18.5 o-182591

description:
Individual ID; o-182591
Age; 18.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: Mouse Universal Reference RNA


title: temporal.txt e17.5 o-192005

description:
Individual ID; o-192005
Age; 17.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e17.5 Kidney


title: 23d tg7

description: olfactory bulb from hGFAP transgenic FVB/N mouse at P23


title: 4mo wt9


title: CGEN 15.5dpc GFP+Tree Vs Rest_Filtered column 3

description:
Sample; 1
File Name; CGEN 15.5dpc GFP+Tree Vs rest_Filtered GFP+Tree Vs
Array Design; 1
Age; 15.5
Array Design; Mouse Compugen 22K oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); none
Concentration; 100
Data processing/normalization; Lowess Normalisation
Developmental Stage; embryonic
Diseased/Normal; normal
Experiment Type; Pairwise comparison
Genetic Characteristic; HoxB7-GFP transgenic
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message AMp Amibon
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ
RNA type; aRNA
Sample Source; primary tissue
Sampling Method; FACS sorting of GFP +ve and -ve Cell populations
Sex; pool of both
Dye Swap; none
A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.
CGEN 15.5dpc GFP+Tree Vs rest_Filtered GFP+Tree Vs rest transf..base column 3


title: 4mo wt3


title: CGEN 15.5dpc GFP+Tree Vs Rest_Filtered column 8

description:
Sample; 2
File Name; CGEN 15.5dpc GFP+Tree Vs rest_Filtered GFP+Tree Vs
Array Design; 1
Age; 15.5
Array Design; Mouse Compugen 22K oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); none
Concentration; 100
Data processing/normalization; Lowess Normalisation
Developmental Stage; embryonic
Diseased/Normal; normal
Experiment Type; Pairwise comparison
Genetic Characteristic; HoxB7-GFP transgenic
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message AMp Amibon
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ
RNA type; aRNA
Sample Source; primary tissue
Sampling Method; FACS sorting of GFP +ve and -ve Cell populations
Sex; pool of both
Dye Swap; none
A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.
CGEN 15.5dpc GFP+Tree Vs rest_Filtered GFP+Tree Vs rest transf..base column 8


title: WM793-P1N1_2

description: Melanoma cell line.  Subline of WM793.  Highly tumourigenic in nude mice.  Biological replicate of WM793-P1N1_1.


title: 23d tg6


title: CGEN 11.5 Vs 13.5dpc.txt column 8

description:
Sample; 2
File Name; Copy of CGEN 11.5 Vs 13.5dpc.txt
Age; 11.5V13.5
Array Design; Mouse Compugen 22K oligo
Common Reference (Yes/No, ID); none
Concentration; 100
Data processing/normalization; R:Print-tip Loess +between arrays LIMAS+SMA)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; pairwise comparison
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message Amp Amibon
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ
RNA type; aRNA
Sample Source; primary tissue
Sampling Method; microdissection
Sex; Pool of both
Strain/Cell-line; CD1
Copy of CGEN 11.5 Vs 13.5dpc.txt column 8
Series_overall_design: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: 11.5dpc metanephroi

source_name: 13.5dpc fetal kidney


title: CGEN 11.5 Vs 13.5dpc.txt column 13

description:
Sample; 3
File Name; Copy of CGEN 11.5 Vs 13.5dpc.txt
Age; 11.5V13.5
Array Design; Mouse Compugen 22K oligo
Common Reference (Yes/No, ID); none
Concentration; 100
Data processing/normalization; R:Print-tip Loess +between arrays LIMAS+SMA)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; green/red
Experiment Type; pairwise comparison
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message Amp Amibon
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ
RNA type; aRNA
Sample Source; primary tissue
Sampling Method; microdissection
Sex; Pool of both
Strain/Cell-line; CD1
Copy of CGEN 11.5 Vs 13.5dpc.txt column 13
Series_overall_design: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.


title: CGEN 11.5 Vs 13.5dpc.txt column 3

description:
Sample; 1
File Name; Copy of CGEN 11.5 Vs 13.5dpc.txt
Age; 11.5V13.5
Array Design; Mouse Compugen 22K oligo
Common Reference (Yes/No, ID); none
Concentration; 100
Data processing/normalization; R:Print-tip Loess +between arrays LIMAS+SMA)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; pairwise comparison
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message Amp Amibon
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ
RNA type; aRNA
Sample Source; primary tissue
Sampling Method; microdissection
Sex; Pool of both
Strain/Cell-line; CD1
Copy of CGEN 11.5 Vs 13.5dpc.txt column 3
Series_overall_design: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.


title: Wild type Mice-M128

city: Valhalla

first: Caroline

last: Ojaimi

state: NY

institute: New York Medical College

description:
There is cardiac dysfunction in male eNOS (-/-) with age and 50% mortality at 21M. It was of interest to investigate the gene expression profile of aged eNOS (-/-) male in comparison to (+/+) in order to explore the genetic markers and molecular mechanisms leading to heart failure. RNA was extracted from the left ventricle from male (-/-) (n=3) and (+/+) (n=4) at the age of 21M.
Keywords = eNOS knockout
Keywords = microarray
Keywords = exercise

source_name: Heart tissues


title: Wild type Mice-M158


title: CGEN 10.5 Vs 11.5.txt column 13

description:
Sample; 3
File Name; CGEN 10.5 Vs 11.5.txt
Age; 10.5 V 11.5
Array Design; Mouse Compugen 22K oligo
Common Reference (Yes/No, ID); none
Concentration; 100
Data processing/normalization; R: Print tip Lowes+ between arrays (LIMAS+SMA)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; green/red
Experiment Type; pairwise comparison
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message Amp Ambion
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ
RNA type; aRNA
Sample Source; primary tissue
Sampling Method; microdissection
Sex; pool of both
Strain/Cell-line; CD1
A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.
CGEN 10.5 Vs 11.5.txt column 13

source_name: 10.5dpc metanephric mesenchyme


title: Wild type Mice-M23


title: eNOS Knockout Mice-M140


title: CGEN 10.5 Vs 11.5.txt column 8

description:
Sample; 2
File Name; CGEN 10.5 Vs 11.5.txt
Age; 10.5 V 11.5
Array Design; Mouse Compugen 22K oligo
Common Reference (Yes/No, ID); none
Concentration; 100
Data processing/normalization; R: Print tip Lowes+ between arrays (LIMAS+SMA)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; pairwise comparison
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message Amp Ambion
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ
RNA type; aRNA
Sample Source; primary tissue
Sampling Method; microdissection
Sex; pool of both
Strain/Cell-line; CD1
A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.
CGEN 10.5 Vs 11.5.txt column 8


title: 23d wt12

description: olfactory bulb from wildtype FVB/N mouse at P23


title: hGSTA4 transfected HLE B-3 cells

city: Galveston

first: Brad

middle: Allen

last: Patrick

state: TX

address: 14th and Strand streets

department: Human Biological Chem & Genetics

institute: University of Texas, Medical Branch

description: HLE B-3 cells were transfected with recombinant hGSTA4-4 expressing construct within pTarget vector and transformed cells were harvested for microarray

source_name: hGSTA4 transfected HLE B-3 cells


title: 23d tg5


title: pTarget transfected HLE B-3 cells

description: HLE B-3 cells were transfected with empty pTarget vector and cells were harvested for microarray

source_name: pTarget transfected HLE B-3 cells


title: CGEN 10.5 Vs 11.5.txt column 3

description:
Sample; 1
File Name; CGEN 10.5 Vs 11.5.txt
Age; 10.5 V 11.5
Array Design; Mouse Compugen 22K oligo
Common Reference (Yes/No, ID); none
Concentration; 100
Data processing/normalization; R: Print tip Lowes+ between arrays (LIMAS+SMA)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; pairwise comparison
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message Amp Ambion
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ
RNA type; aRNA
Sample Source; primary tissue
Sampling Method; microdissection
Sex; pool of both
Strain/Cell-line; CD1
A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.
CGEN 10.5 Vs 11.5.txt column 3


title: 23d wt11


title: eNOS Knockout Mice-M4


title: eNOS Knockout Mice-M10


title: 4mo tg1

description: olfactory bulb from hGFAP transgenic FVB/N mouse at 4mos


title: 23d wt4


title: temporal.txt e14.5 o-192115

description:
Individual ID; o-192115
Age; 14.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e14.5 Kidney


title: F1 lean male A

status: Public on Jul 18 2005

first: Alan

middle: D

last: Attie

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

description: Sam's file name: 1208sn4

data_processing: dChip

label: F1 lean male A

source_name: Adipose tissue

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  (C57BL/6J X BTBR)F1, 14 weeks old, male, 4-hr fast.


title: F1 lean female A

description: Sam's file name: 1208sn3

label: F1 lean female A

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  (C57BL/6J X BTBR)F1, 14 weeks old, female, 4-hr fast.


title: F2 ob low glucose A

description: Sam's file name: 1208sn11

label: F2 ob low glucose

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  (C57BL/6J X BTBR) F2, 14-wk old, gender unknown, 4-hr fast, low plasma glucose group.


title: F2 ob high glucose B

description: Sam's file name: 1206sn9

label: F2 ob high glucose B

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  (C57BL/6J X BTBR) F2-ob/ob, 14-wk old, gender unknown, 4-hr fast, high plasma glucose group.


title: F2 ob high glucose A

description: Sam's file name: 1208sn9

label: F2 ob high glucose A

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  (C57BL/6J X BTBR) F2, 14-wk old, gender unknown, 4-hr fast, high plasma glucose group.


title: F2 ob med glucose A

description: Sam's file name: 1208sn8

label: F2 ob med glucose

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  (C57BL/6J X BTBR) F2, 14-wk old, gender unknown, 4-hr fast, medium plasma glucose group.


title: BTBR ob A

description: Sam's file name: 011800sn20scan2

label: BTBR ob A

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  BTBR-ob/ob, 14 weeks old, gender unknown, 4-hr fast.


title: BTBR lean male A

description: Sam's file name: 1208sn6

label: BTBR lean male A

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  BTBR, 14 weeks old, male, 4-hr fast.


title: human gd PBS

city: Bozeman

first: Jodi

middle: Fern

last: Hedges

state: MT

address: 960 Technology Blvd.

department: Veterinary Molecular Biology

institute: Montana State University

description: Human gd T cells were expanded in culture, sorted and stimulated with PBS for 4 hours.  RNA was extracted and amplified.  RNA pooled from 4 different individuals.

source_name: cultured gamma delta T cells


title: F2 ob med glucose B

description: Sam's file name: 1206sn8

label: F2 ob med glucose B

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  (C57BL/6J X BTBR) F2-ob/ob, 14-wk old, gender unknown, 4-hr fast, medium plasma glucose group.


title: BTBR lean female A

description: Sam's file name: sn-1-12-5-scan2

label: BTBR lean female A

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  BTBR, 14 weeks old, female, 4-hr fast.


title: F1 lean male B

description: Sam's file name: 1206sn4

label: F1 lean male B

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  (C57BL/6J X BTBR) F1, 14-wk old, male, 4-hr fast.


title: F2 ob low glucose B

description: Sam's file name: 1207sn11

label: F2 ob low glucose B

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  (C57BL/6J X BTBR) F2-ob/ob, 14-wk old, gender unknown, 4-hr fast, low plasma glucose group.


title: human gd LPS

description: Human gd T cells were expanded in culture, sorted and stimulated with LPS for 4 hours.  RNA was extracted and amplified.  RNA pooled from 4 different individuals.


title: BTBR lean male B

description: Sam's file name: 1206sn6

label: BTBR lean male B

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  BTBR, 14-wk old, male, 4-hr fast.


title: BTBR ob B

description: Sam's file name: HEB-20scan2

label: BTBR ob B

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  BTBR-ob/ob, 14-wk old, gender unknown, 4-hr fast.


title: B6 lean male A

description: Sam's file name: 1208sn2

label: B6 lean male A

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  C57BL/6J, 14 weeks old, male, 4-hr fast.


title: F1 lean female B

description: Sam's file name: 1206sn3

label: F1 lean female B

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  (C57BL/6J X BTBR) F1, 14-wk old, female, 4-hr fast.


title: B6 ob A

description: Sam's file name: sn-1-12-19-scan2

label: B6 ob A

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  C57BL/6J-ob/ob, 14 weeks old, gender unknown, 4-hr fast.


title: Liver-Cpr-null_pool 3

city: Albany

first: Xinxin

last: Ding

institute: Wadsworth Center, NYSDOH

description:
Liver was obtained from 8 or 9 male, two-month-old, mice for each transgenic model. Three different models were compared, including liver-Cpr-null, Cpr-low, and Cpr-lox (control model), all on mixed C57BL/6 and 129/Sv genetic background. Total RNA was prepared from individual liver samples. Three independent pools of RNA samples were prepared and analyzed for each model. Five micrograms of total RNA were used for the synthesis of biotin-labeled antisense RNA using Ambion's MESSAGEAMP(TM) aRNA Kit.
Keywords = Cytochrome P450
Keywords = NADPH-cytochrome P450 reductase
Keywords = transgenic mice
Keywords = liver
Keywords = nuclear recetpor

source_name: Murine liver


title: B6 lean female A

description: Sam's file name: 1208sn1

label: B6 lean female A

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese and diabetic mice, C57BL/6J, 14-wk old, female, 4-hr fast


title: BTBR lean female B

description: Sam's file name: HEB-5-2scan2

label: BTBR lean female B

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice. BTBR, 14-wk old, female, 4-hr fast.


title: Liver-Cpr-null_pool 2


title: B6 ob B

description: Sam's file name: HEB-19scan2

label: B6 ob B

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  C57BL/6J-ob/ob, 14-wk old, gender unknown, 4-hr fast.


title: Cpr-low_pool 3


title: temporal.txt e18.5 o-192004

description:
Individual ID; o-192004
Age; 18.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e18.5 Kidney


title: B6 lean female B

description: Sam's file name: 1206sn1

label: B6 lean female B

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  C57BL/6J, 14-wk old, female, 4-hr fast.


title: Cpr-low_pool 1


title: B6 lean male B

description: Sam's file name: 1207sn2

label: B6 lean male B

tag: Adipose tissue gene expression profiles of lean, insulin resistant, obese, and diabetic mice.  C57BL/6J, 14-wk old, male, 4-hr fast.


title: Gene expression profile of the keloid tissue

status: Public on Jul 16 2005

city: Kyoto

first: Motoko

last: Naitoh

state: Kyoto

address: Shyogoin-Kawahara cho 53

department: Molecular and Cellular Biology

country: Japan

institute: Institute for Frontier Medical Science, Kyoto University

description:
RNA preparation and cDNA microarray analysis : Keloids and surrounding unaffected skin tissue specimens were surgically obtained from the patients with informed consent.
Total RNAs were isolated from tissue specimens using the single-step method (Chomczynski, P. & Sacchi, N. (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162, 156-159). For microarray analysis, mRNA was purified from total RNA using an Oligotex-dT30 mRNA Purification kit (TAKARA, Kyoto, Japan). 200ng of each mRNA derived from keloid and unaffected skin tissue were used to generate Cy5-labeled and Cy3-labeled cDNA, respectively.
The cDNA microchip array experiment was performed using the public domain HUMAN Uni GEM version 2.0 array that contains 9128 cDNA fragments and was analyzed with GemTools software (Incyte Genomics, Palo Alto, CA).  Labeled cDNAs were hybridized simultaneously to the microarray. Fluorescent ratios were calculated for all elements and normalized using controls for sensitivity, differential expression, reverse transcription quality, and signal-to-background ratio.

data_processing: Value represent log ratio of balanced diffrential expression.

source_name: unaffected skin tissue

tag: Cy3-lbeled cDNA derived from unaffected skin tissue.

source_name: keloid tissue

tag: Cy5-labeled cDNA derived from keloid tissue


title: Cpr-lox_pool 3


title: Aldosterone-responsive genes in kidney cortical collecting duct cell mpkCCDc14 (6 hr treatment)-3

status: Public on Jul 15 2005

city: Belmont

first: Ting Ting

last: Zhang

state: MA

address: 115 Millman st

department: Mclean Hospital

institute: Harvard University

description: Array data were collected with Genepix 4.0 scanner.  The quality of array was examined with RBioconductor.   First, the uniformity of spot and labeling, and the intensity of labeling were checked with MA-plot (M=log2(Cy5/Cy3), A=log2((Cy5*Cy3)/2).  Quantitative assessment such as signal to noise ratio and the median signal intensity were also performed.  Only these arrays which have the reasonable qualities would be used for further analysis.  The significantly different expressed genes are selected with SAM using the one class response with data (log2 Cy5/Cy3) normalized in RBioconductor.  Hierarchical clustering is performed with Acuity 4.0 (Axon Instruments).

hyb_protocol: After cleanup Cy3 or Cy5-labeled cDNA with CyScribe GFX purification kit (Amersham Biosciences), the labeled cDNA was hybridized with microarray slide at 50oC for >40 hours.

data_processing: data (log2 Cy5/Cy3)  is normalized in RBioconductor

source_name: Kidney cortical collecting duct cell line (mpkCCDc14)

label_protocol: Microarray analysis was performed following the protocol from UCSF genomics core laboratories (original document can be found at www.arrays.ucsf.edu).  Briefly, the first strand cDNA was synthesized with 20 µg total RNA, 1.0 µg oligo dT, 830 µM each dATP, dCTP, dGTP, 166 µM dTTP, 666 µM 5-(3-aminoallyl)- dUTP (Ambion),0.1 m DTT, 1 µl RNase inhibitor ( Fisher), 600 U RT, 10x RT buffer and H2O to final 30 ul for 2 hours at 42oC.  After hydrolysis with 10 µl 1N NaOH and 10 µl 0.5 M EDTA, cDNA was purified and recovered with Microcon 30. The Cy5 (Amersham Biosciences) was then coupled with cDNA in 0.05 M NaBiocarbonate (pH 9.0) in the dark at the room temperature for more than 1.5 hours.

growth_protocol: mpkCCD cells were cultured on 30 mm collagen-coated 6-transwell plates at a density of 1.5-2.0 x 106 cells/well in a modified medium described previously with 1% Pen-strep.  Fresh medium was changed every other day. 2-3 days later, while transepithelial cell  resistance reach ~2 KΩ, cell medium was replaced with dexamethasone-free and charcoal-treated steroid-free FBS for another 2-3 days.  Fresh medium was changed everyday.

extract_protocol: Total RNAs were isolated with RNA STAT-60 (Tel-Test, Inc).   The contaminated genomic DNA in the total RNA was removed with DNase treatment & removal reagents (Ambion).

treatment_protocol: Cells were treated with 10-6M aldosteron for 6 hr.

label_protocol: Microarray analysis was performed following the protocol from UCSF genomics core laboratories (original document can be found at www.arrays.ucsf.edu).  Briefly, the first strand cDNA was synthesized with 20 µg total RNA, 1.0 µg oligo dT, 830 µM each dATP, dCTP, dGTP, 166 µM dTTP, 666 µM 5-(3-aminoallyl)- dUTP (Ambion),0.1 m DTT, 1 µl RNase inhibitor ( Fisher), 600 U RT, 10x RT buffer and H2O to final 30 ul for 2 hours at 42oC.  After hydrolysis with 10 µl 1N NaOH and 10 µl 0.5 M EDTA, cDNA was purified and recovered with Microcon 30. The Cy3 (Amersham Biosciences) was then coupled with cDNA in 0.05 M NaBiocarbonate (pH 9.0) in the dark at the room temperature for more than 1.5 hours.

treatment_protocol: Cells were treated with vehicle (ethanol)for 6 hr.


title: Aldosterone-responsive genes in kidney cortical collecting duct cell mpkCCDc14 (1 hr treatment)

scan_protocol: Array data were collected with Genepix 4.0 scanner.  The quality of array was examined with RBioconductor.

treatment_protocol: Cells were treated with 10-6M aldosteron for 1 hr.

tag: Kidney cortical collecting duct cell line (mpkCCDc14)

treatment_protocol: Cells were treated with vehicle (ethanol)for 1 hr.


title: Cpr-lox_pool 1

description:
Liver was obtained from 8 or 9 male, two-month-old, mice for each transgenic model. Three different models were compared, including liver-Cpr-null, Cpr-low, and Cpr-lox (control model), all on mixed C57BL/6 and 129/Sv genetic background. Total RNA was prepared from individual liver samples. Three independent pools of RNA samples were prepared and analyzed for each model. Five micrograms of total RNA were used for the synthesis of biotin-labeled antisense RNA using Ambion's MESSAGEAMP(TM) aRNA Kit.
Keywords = Cytochrome P450
Keywords = NADPH-cytochrome P450 reductase
Keywords = transgenic mice
Keywords = liver
Keywords = nuclear receptor


title: Aldosterone-responsive genes in kidney cortical collecting duct cell mpkCCDc14 (6 hour treatment)


title: BTBR_Islet_rep1

status: Public on Jul 12 2005

description: Total RNA pooled from 4 mice: BTBR-ob/ob 215, BTBR-ob/ob 301, BTBR-ob/ob 347, BTBR-ob/ob 348

source_name: Pancreatic islets

tag: BTBR-ob/ob

tag: Pancreatic islets

tag: Age

value: 14 weeks

tag: Gender

value: Male


title: BTBR_Muscle_rep2

description: Total RNA pooled from 2 mice: BTBR-ob/ob 347 and BTBR-ob/ob 348

source_name: Soleus muscle

tag: Soleus muscle


title: Aldosterone-responsive genes in kidney cortical collecting duct cell mpkCCDc14 (1 hour treatment)


title: BTBR_Islet_rep2

description: Total RNA pooled from 4 mice: BTBR-ob/ob 229, BTBR-ob/ob 309, BTBR-ob/ob 318, BTBR-ob/ob 346


title: na_5_31

status: Public on Jul 14 2005

type: genomic

city: Worcester

first: Oliver

last: Rando

address: 364 Plantation St.

institute: UMass Medical School

description:
Nucleosomal DNA was isolated and labeled with Cy3 fluorescent dye (green), and mixed with Cy5-labeled total genomic DNA (red). This mixture was hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.
Keywords = nucleosome
Keywords = yeast
Keywords = tiling microrray

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: MNase digested DNA

source_name: genomic DNA


title: C57BL/6J_Islet_rep1

description: Total RNA pooled from 2 mice: B6-ob/ob 278 and B6-ob/ob 281


title: Aldosterone-responsive genes in kidney cortical collecting duct mpkCCDc14 (1 hour treatment)


title: BTBR_Muscle_rep1

description: Total RNA pooled from 2 mice: BTBR-ob/ob 318 and BTBR-ob/ob 346


title: C57BL/6J_Islet_rep2

description: Total RNA pooled from 2 mice: B6-ob/ob 296 and B6-ob/ob 297


title: Liver-Cpr-null_pool 1


title: Aldosterone-responsive genes in kidney cortical collecting duct cell mpkCCDc14 (6 hr treatment)


title: na_5_44


title: C57BL/6J_Muscle_rep1


title: Aldosterone-responsive genes in kidney cortical collecting duct cell mpkCCDc14 (6 hr treatment)-4


title: na_4_45

description: Nucleosomal DNA was isolated and labeled with Cy3 fluorescent dye (green), and mixed with Cy5-labeled total genomic DNA (red). This mixture was hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.


title: C57BL/6J_Muscle_rep2


title: na_5_45


title: Cpr-low_pool 2


title: na_4_49


title: na_4_38

description:
Nucleosomal DNA was isolated and labeled with Cy3 fluorescent dye (green), and mixed with Cy5-labeled total genomic DNA (red). This mixture was hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.
Keywords = nucleosome
Keywords = yeast
Keywords = tiling microarray


title: na_4_39


title: na_5_54


title: C57BL/6J_Liver_rep2

source_name: Liver

tag: Liver


title: BTBR_Liver_rep2


title: BTBR_Adipose_rep2

tag: Adipose tissue


title: BTBR_Liver_rep1


title: C57BL/6J_Liver_rep1


title: Cpr-lox_pool 2


title: BTBR_Adipose_rep1


title: Day3 Genistein treatment replicate 1

status: Public on Jul 08 2005

first: Lei

last: Liu

address: 1201 W. Gregory

department: W. M. Keck Center

description: 21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. Animals were fed with a diet containing 1500 ppm genistein (Indofine Chemicals, Somerville, NJ) ad libitum by adding genistein to the AIN-93G diet.. RNA were extracted at day 3 after experiment started. Total 6 animals were treated. RNA samples were pooled from 3 animals, resulting two independent biological replicates.

data_processing: Affymetrix Microarray Suite Version 5.0

label: biotin

source_name: Thymuse

tag: Femal C57BL/6, ovariectomized


title: Day6 Genistein treatment replicate 2

description: 21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. Animals were fed with a diet containing 1500 ppm genistein (Indofine Chemicals, Somerville, NJ) ad libitum by adding genistein to the AIN-93G diet. RNA were extracted at day 6 after experiment started. Total 6 animals were treated. RNA samples were pooled from 3 animals, resulting two independent biological replicates.


title: Day2 Genistein treatment replicate 1

description: 21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. Animals were fed with a diet containing 1500 ppm genistein (Indofine Chemicals, Somerville, NJ) ad libitum by adding genistein to the AIN-93G diet.. RNA were extracted at day 2 after experiment started. Total 6 animals were treated. RNA samples were pooled from 3 animals, resulting two independent biological replicates.


title: Day3 Estrogen treatment replicate 1

description: 21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. Animals received daily subcutaneous injections of 125 ng of E2 (Signma-Aldrich, St. Louis, MO) in 0.02 ml corn oil. RNA were extracted at day 3 after experiment started. Total 6 animals were treated. RNA samples were pooled from 3 animals, resulting two independent biological replicates.


title: Day2 Genistein treatment replicate 2


title: Day3 Estrogen treatment replicate 2


title: C57BL/6J_Adipose_rep1


title: Day2 Estrogen treatment replicate 2

description: 21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. Animals received daily subcutaneous injections of 125 ng of E2 (Signma-Aldrich, St. Louis, MO) in 0.02 ml corn oil. RNA were extracted at day 2 after experiment started. Total 6 animals were treated. RNA samples were pooled from 3 animals, resulting two independent biological replicates.


title: Day6 Estrogen treatment replicate 1

description: 21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. Animals received daily subcutaneous injections of 125 ng of E2 (Signma-Aldrich, St. Louis, MO) in 0.02 ml corn oil. RNA were extracted at day 6 after experiment started. Total 6 animals were treated. RNA samples were pooled from 3 animals, resulting two independent biological replicates.


title: Day3 Genistein treatment replicate 2


title: C57BL/6J_Adipose_rep2

description: Total RNA pooled from 2 mice: B6-ob/ob 297 and B6-ob/ob 297


title: Day6 Estrogen treatment replicate 2


title: Sham DRG 50 days replicate 1 Chip C

status: Public on Jul 07 2005

city: London

first: Jakir

last: Ullah

country: United Kingdom

institute: Novartis

description: L4 and L5 DRG collected from sham operated rats 50 days post surgery. Samples were pooled from 30 rats and hybridised to two replicate affymetrix rat arrays (Rg_u34C)

data_processing: Affymetrix MAS 5

organism: Rattus norvegicus

source_name: Dorsal root ganglia

tag: sprague dawley male rats, L4 and L5 DRG


title: Sham DRG 28 days replicate 2 Chip C

description: L4 and L5 DRG collected from sham operated rats 28 days post surgery. Samples were pooled from 30 rats and hybridised to two replicate affymetrix rat arrays (Rg_u34C)


title: Day6 Genistein treatment replicate 1


title: control (day 0) replicate 2

description: 21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. RNA samples were extracted at day0 without any treatment. Total 6 animals were used. RNA from 3 animals were pooled together as one sample, resulting in two independent biological replicates.


title: Sham DRG 28 days replicate 1 Chip C

tag: Sprague dawley male rats, L4 and L5 DRG


title: control (day 0) replicate 1


title: L5 DRG 28 days technical replicate 2 Chip C

description: L5 DRG collected from SNL rats 28 days post injury. Samples were pooled from 30 rats and hybridised to two replicate affymetrix rat arrays (Rg_u34C)

tag: sprague dawley male rats, L5 DRG


title: Day2 Estrogen treatment replicate 1


title: L5 DRG 50 days technical replicate 1 Chip C

description: L5 DRG collected from SNL rats 50 days post injury. Samples were pooled from 30 rats and hybridised to two replicate affymetrix rat arrays (Rg_u34C)


title: L4 DRG 50 days technical replicate 2 chip C

description: L4 DRG collected from SNL rats 50 days post injury. Samples were pooled from 30 rats and hybridised to two replicate affymetrix rat arrays (Rg_u34C)

tag: sprague dawley male rats, L4 DRG


title: L5 DRG 28 days technical replicate 1 Chip C


title: L5 DRG 50 days technical replicate 2 Chip C


title: L4 DRG 50 days technical replicate 1 chip C

description: L4 DRG collected from SNL rats after 50 days post injury.  Samples were pooled and hybridised to two replicate rat affymetrix arrays (Rg_u34C)

tag: Sprague dawley male rats, L4 DRG


title: L4 DRG 28 days technical replicate 2 chip C

description: L4 DRG collected from SNL rats after 28 days post injury.  Samples were pooled and hybridised to two replicate rat affymetrix arrays (Rg_u34C)

tag: Sprague dawley rats, L4 DRG


title: L4 DRG 28 days technical replicate 1 chip C


title: Sham DRG 50 days replicate 2

description: L4 and L5  DRG collected from sham operated rats after 50 days post surgery.  Samples were pooled from 30 rats and hybridised to two replicate rat affymetrix arrays (Rg_u34A)

tag: L4 and L5 DRG from sham animals


title: Sham DRG 50 days replicate 1 Chip B

description: L4 and L5 DRG collected from sham operated rats after 50 days post injury.  samples were pooled and hybridised to two replicate rat affymetrix arrays (Rg_u34)


title: Sham DRG 50 days replicate 2 Chip B


title: Sham DRG 50 days replicate 1


title: Sham DRG 28 days replicate 2

description: L4 and L5  DRG collected from sham operated rats after 28 days post surgery.  Samples were pooled from 30 rats and hybridised to two replicate rat affymetrix arrays (Rg_u34A)


title: Sham DRG 28 days replicate 1 Chip B

description: L4 and L5 DRG collected from sham operated rats after 50 days post surgery.  Samples were pooled from 30 rats and hybridised to two replicate rat affymetrix arrays (Rg_u34B)


title: L5 DRG 28 days technical replicate 2 Chip B

description: L5 DRG collected from SNL rats after 28 days post injury.  Samples were pooled from 30 rats and hybridised to two replicate rat affymetrix arrays (Rg_u34B)

tag: Sprague dawley male rats, L5 DRG


title: L5 DRG 50 days technical replicate 1

description: L5 DRG collected from L5 SNL rats after 50 days post injury.  Samples were pooled from 30 rats and hybridised to two replicate rat affymetrix arrays (Rg_u34A)

tag: Lumbar L5


title: Sham DRG 28 days replicate 1


title: L5 DRG 28 days technical replicate 1 Chip B


title: L5 DRG 28 days technical replicate 2

description: L5 DRG collected from L5 SNL rats after 28 days post injury.  Samples were pooled from 30 rats and hybridised to two replicate rat affymetrix arrays (Rg_u34A)

tag: Lumbar L5 DRG


title: L5 DRG 50 days technical replicate 2 Chip B

description: L5 DRG collected from SNL rats after 50 days post injury.  Samples were pooled from 30 rats and hybridised to two replicate rat affymetrix arrays (Rg_u34B)


title: Sham DRG 28 days replicate 2 Chip B

description: L4 and L5 DRG collected from sham operated rats after 28 days post injury.  samples were pooled and hybridised to two replicate rat affymetrix arrays (Rg_u34)


title: L5 DRG 50 days technical replicate 2


title: L5 DRG 50 days technical replicate 1 Chip B


title: L4 DRG 28 days technical replicate 2

description: L4 DRG collected from L5 SNL rats after 28 days post injury.  Samples were pooled from 30 rats and hybridised to two replicate rat affymetrix arrays (Rg_u34A)

tag: Lumbar L4 DRG


title: L4 DRG 50 days technical replicate 2

description: L4 DRG collected from L5 SNL rats after 50 days post injury.  Samples were pooled from 30 rats and hybridised to two replicate rat affymetrix arrays (Rg_u34A)


title: L4 DRG 28 days technical replicate 2 chip B

description: L4 and DRG collected from SNL rats after 28 days post injury.  Samples were pooled from 30 rats and hybridised to two replicate rat affymetrix arrays (Rg_u34B)


title: L4 DRG 50 days technical replicate 1


title: L4 DRG 28 days technical replicate 1

tag: Lumbar 4 DRG


title: L4 DRG 50 days technical replicate 2 chip B

description: L4 DRG collected from SNL rats after 50 days post injury.  Samples were pooled from 30 rats and hybridised to two replicate rat affymetrix arrays (Rg_u34B)


title: L4 DRG 50 days technical replicate 1 chip B

tag: Sprague Dawley male rats, L4 DRG


title: Wild type Mice-M125

description:
There is cardiac dysfunction in male eNOS (-/-) with age and 50% mortality at 21M. It was of interest to investigate the gene expression profile of aged eNOS (-/-) male in comparison to (+/+) in order to explore the genetic markers and molecular mechanisms leading to heart failure. RNA was extracted from the left ventricle from male (-/-) (n=3) and (+/+) (n=4) at the age of 21M.
Keywords = eNOS knockout
Keywords = microarray
Keywords = exercise

source_name: Heart tissues


title: L4 DRG 28 days technical replicate 1 chip B

tag: Sprauge Dawley male rats. L4 DRG


title: L5 DRG 28 days technical replicate 1

tag: L5 lumbar DRG


title: M244 E- TN swap dye

status: Public on Jan 28 2005

city: Columbia

first: Sachin

middle: S

last: Bhusari

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: Univ of Missouri

description:
M244 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is 2nd technical replicate of this sample done in swap dye design.
Keywords = Endophyte
Keywords = fescue

data_processing: log2(ch2/ch1) normalized using plant control genes.

source_name: M244 mouse fed E- diet at TN condition

source_name: universal mouse reference RNA


title: F223 E- TN 1st rep

description:
F223 belongs to group of mice fed endophyte-free fescue diet (E-). This is the 1st technical replicate of this sample.
Keywords = Endophyte
Keywords = Fescue

source_name: RNA from F223 mouse fed E- diet at TN.

source_name: RNA from universal mouse reference RNA


title: F223 E- TN swap dye

description:
F223 belongs to group of mice fed endophyte-free fescue diet (E-). This is the 2nd technical replicate of this sample done in swap dye design.
Keywords = Endophyte
Keywords = Fescue

data_processing: log2(ch2/ch1) normalized using control plant genes.


title: M244 E- TN 1st rep

description:
M244 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is 1st technical replicate of this sample.
Keywords = Endophyte
Keywords = fescue

data_processing: log2(ch1/ch2) normalized using plant control spikes.


title: F235 E-TN 1st rep

description:
F235 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is 1st technical replicate of this sample.
Keywords = Endophyte
Keywords = fescue

data_processing: normalized using plant control genes.

source_name: RNA from F235 mouse fed E- diet


title: Young vs. Old Calvariae

status: Public on Jul 09 2005

city: Stanford

last: Aalami

state: CA

address: 257 Campus Dr.

institute: Stanford University

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33195.gif; format: GIF

data_processing: VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: adult calvaria

tag: adult calvaria

source_name: young calvaria

tag: young calvaria


title: F235 E-TN swap dye

description:
F235 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is 3rd technical replicate of this sample done in swap dye fashion.
Keywords = Endophyte
Keywords = fescue

source_name: F235 mouse fed E- diet at TN condition


title: M243 E-TN 3rd rep swap dye

description:
M243 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is 3rd technical replicate of this sample done in swap dye design.
Keywords = Endophyte
Keywords = fescue

data_processing: log2(ch2/ch1) normalized using plant control spikes.

source_name: M243 mouse fed E- diet at TN condition

tag: ICR mice, male, 27d age, liver tissue.

tag: RNA is mix of 11 different mouse cell lines.


title: M243 E- TN 2nd rep

description:
M243 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is 2nd technical replicate of this sample.
Keywords = Endophyte
Keywords = fescue

data_processing: log2(ch1/ch2) normalized using plant control genes.

source_name: RNA from M243 mouse fed E- diet at TN

tag: ICR mice, Female, 27d old, liver

tag: RNA from 11 different mice cell lines.


title: M243 E- TN 1st rep

description:
M243 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is 1st technical replicate of this sample.
Keywords = Endophyte
Keywords = fecsue

data_processing: log2(ch1/ch2) normalized using plant control genes

source_name: M243 mouse fed E- diet at TN

tag: ICR strain mice, Female, 27d old, liver.

tag: Mix of RNA from 11 different mice cell lines.


title: F235 E- TN 2nd rep

description:
F235 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is 2nd technical replicate of this sample.
Keywords = Endophyte
Keywords = fescue

data_processing: log2(ch1/ch2) normalized using plant spikes

source_name: RNA from F235 fed E- diet at TN


title: M251 E- TN 1st rep

description:
M251 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is first technical replicate of this sample .
Keywords = Endophyte
Keywords = fescue
Keywords = Thermo neutral.

source_name: M251 fed E- diet at TN

extract_protocol: RNAquious-Midi kit, Ambion inc, Austin, Tx

treatment_protocol: Mice fed control E- diet at thermoneutral (TN) condition.

tag: ICR strain mice, Male, 27d old, liver tissue.

tag: RNA extracted from 11 different mice cell lines.


title: Sham DRG 50 days replicate 2 Chip C

description: L4 and L5 DRG collected from sham operated rats 50 days post surgery. Samples were pooled from 30 rats and hybridised to two replicate affymetrix rat arrays (Rg_u34C)

tag: sprague dawley male rats, L4 and L5 DRG


title: M211 E- TN swap dye

description:
M211 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is third technical replicate of this sample done in swap dye design.
Keywords = Endophyte
Keywords = fescue
Keywords = Thermoneutral

scan_protocol: using Axon genepix scanner and software.

source_name: M211 mouse fed E- diet at TN

label_protocol: indirect amino-allyl labeling.

treatment_protocol: mice fed control diet at thermoneutral (TN) conditions.

tag: ICR strain, Male, 27d old, liver.

tag: RNA extracted from 11 different mouse cell lines.


title: M251 E- TN 2nd rep

description:
M251 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is third hybridization of this sample out of 4 total replicates done.
Keywords = Endophyte
Keywords = fescue
Keywords = Thermoneutral

treatment_protocol: Mice fed E- diet at TN condition.

tag: ICR mice, Male, 27d old, liver tissue

tag: RNA mix from 11 different mice cell lines.


title: M251 E- TN swap dye

description:
M251 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is fourth hybridization of this sample out of 4 total replicates done. This was done in swap dye design.
Keywords = Endophyte
Keywords = fescue
Keywords = Thermoneutral

source_name: M251 mouse fed E-diet at TN.

treatment_protocol: mice fed E- diet at thermoneutral (TN ) conditions.

tag: ICR mice, Male, 27d old, Liver

tag: Mix of 11 different mice cell lines.


title: M251 E- TN 1st rep B

description:
M251 mouse belongs to mice group fed endophyte-free fescue diet (E-). This is second technical replicate of this sample out of 4 total replicates done.
Keywords = Endophyte
Keywords = Fescue

source_name: M251 mouse fed E- diet at TN

tag: ICR strain mice, Male, 27d age, liver tissue.

tag: mix of RNA from 11 different cell lines.


title: M211 E- TN 1st rep

description:
M211 mouse belongs to group fed endophyte-free fescue diet. This is the first technical replicate of this sample.
Keywords = Endophyte
Keywords = fescue
Keywords = Thermoneutrality (TN)

scan_protocol: scanned using Axon scanner and image analysed using genepix software.

data_processing: log2(ch1/ch2) normalized using plant controls spikes.

source_name: M211 fed E- diet at TN

extract_protocol: RNAquious-Midi kit, Ambion inc, Austin, tx

treatment_protocol: Mice fed E- control diet at Thermoneutral (TN) conditions

tag: ICR strain of mice, Male, 27d old, liver tissue.


title: F236 E-TN 2nd Rep

description: F236 mouse belongs to group fed endophyte-free fescue diet. This is the second technical replicate of this sample.

data_processing: log2(ch1/ch2) normalized using plant control spikes

source_name: RNA from F236 fed E- control diet


title: F236 E- TN swap dye

description:
F236 mouse belongs to group fed endophyte-free fescue diet. This is the third technical replicate of this sample done in swap dye fashion.
Keywords = Endophyte
Keywords = fescue
Keywords = Thermoneutrality

data_processing: normalized log2(ch2/ch1) using plant control spikes.

source_name: F236 mouse fed E- diet at TN conditions

extract_protocol: RNAquious-Midi kit, Ambion inc, Austin, Tx.

treatment_protocol: These are control mice fed E- control diet at Thermo neutral conditions (TN).

tag: ICR strain mice, Female, 27d old, liver tissue.

source_name: Universal mouse reference RNA


title: HMEC X BT474 (sva117_sf)

status: Public on Jun 27 2002

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Category: Cell-line
Subcategory: HMEC
Scanning Software: unknown
Software version: unknown
Lot batch = sva117_sf

source_name: HMEC


title: F236 E-TN 1st rep

description:
F236 belongs to group of mice fed endophyte-free fescue diet (E-) at thermoneutral conditions. This is the first technical replicate done in reference design.
Keywords = Endophyte
Keywords = Fescue

source_name: RNA from F236 mouse fed endophyte-free fescue diet

source_name: universal mouse reference RNA