title: PC12 Cells, GFP Transfected, NGF Untreated

status: Public on Mar 27 2007

type: RNA

city: Ann Arbor

first: Christin

last: Carter-Su

state: MI

address: 1301 Catherine St.

country: USA

institute: University of Michigan

description: PC12 Cells stably transfected with GFP, not treated with NGF

data_processing: MAS 5.0

label: Affymetrix standard labelling protocol

molecule: total RNA

organism: Rattus norvegicus

source_name: PC12 Cells


title: PC12 cells, GFP-SH2-Bb transfected, 6h NGF

description: PC12 Cells stably transfected with GFP-SH2-Bb, treated with 6h NGF

source_name: PC12 cells


title: Xenograft - shNOX1 - Rep 2

city: Duarte

first: Agnes

last: Juhasz

state: CA

address: 1500 E. Duarte Rd

department: Medical Oncology

institute: City of Hope Compr. Cancer Center

description: We have found that NOX1 over-expression in colon cancer cell lines as well as surgical samples suggests a role in colon cancer. We identified unique target sequences of siRNAs for post-transcriptional silencing of NOX1. Gene specific and scrambled (control) sequences carrying the U6 promoter/shRNA cassettes were cloned into a GFP expression vector. Stable clones were selected based on NOX1 expression after transient transfection of HT-29 cells.  HT-29 parental cells, clone SA (scrambled) and clone 6A (gene specific) were utilized to establish xenografts in athymic mice to investigate the effect of NOX1 silencing on tumor growth and gene expression in vivo. A significant decrease was measured in the volume of tumors formed.  The stable clones and corresponding xenografts were analyzed on microarray.  The microarray data was validated with real-time PCR and western-blot analysis demonstrating the inhibition of genes important in cell cycle regulation and angiogenesis.  The results of this study show silencing NOX1 levels of generated ROS decreased, the tumor formation attenuated in vivo suggesting NOX1 may be a therapeutic target for colon cancer.

data_processing: The following were applied using the affy library in the R-Project Bioconductor statistical tools package:  RMA background correction, pmonly probe-level correction, quantile normalization, median-polish summary method.

label: biotin

organism: Homo sapiens

source_name: Xenograft stable clone 6A14 (shNOX1)

tag: Xenograft - human colon cancer cells (transfected with shNOX1) injected into male athymic mice,

tag: tumors harvested on day 27,

tag: clone 6A14


title: Xenograft - shNOX1 - Rep 4

source_name: Xenograft stable clone 6A16 (shNOX1)

tag: clone 6A16


title: PC12 cells, GFP-SH2-Bb(R555E) transfected, 6h NGF

description: PC12 Cells stably transfected with GFP-SH2-Bb(R555E), treated with 6h NGF


title: Xenograft - Scrambled - Rep 3

source_name: Xenograft stable clone SA10 (scrambled)

tag: Xenograft - human colon cancer cells (transfected with scrambled sequence) injected into male athymic mice,

tag: clone SA10


title: PC12 cells, SH2-Bb(R555E) transfected, NGF untreated

description: PC12 Cells stably transfected with GFP-SH2-Bb(R555E), NGF untreated


title: Xenograft - Scrambled - Rep 1

source_name: Xenograft stable clone SA6 (scrambled)

tag: clone SA6


title: PC12 cells, SH2-Bb transfected, NGF untreated

description: PC12 Cells stably transfected with GFP-SH2-Bb, not treated with NGF


title: Xenograft - Control - Rep 1

source_name: Xenograft - Control (C18)

tag: Xenograft - human colon cancer cells (HT-29 parental cells) injected into male athymic mice

tag: Tumors harvested on day 27


title: Xenograft - Control - Rep 2

source_name: Xenograft - Control (C19)


title: Xenograft - shNOX1 - Rep 3

source_name: Xenograft stable clone 6A15 (shNOX1)

tag: clone 6A15


title: PC12 cells, GFP transfected, 6hrs NGF

tag: PC12 Cells stably transfected with GFP, treated with 6h NGF


title: Xenograft - Control - Rep 3

source_name: Xenograft - Control (C20)


title: Xenograft - Scrambled - Rep 2

source_name: Xenograft stable clone SA7 (scrambled)

tag: clone SA7


title: Xenograft - shNOX1 - Rep 1

source_name: Xenograft stable clone 6A12 (shNOX1)

tag: clone 6A12


title: HT-29 cell line - Scrambled - Rep 2

source_name: HT-29 stable clone SA2-1 (scrambled)

tag: HT-29 colon cancer cell line

tag: stably transfected with scrambled sequence (not present in human genome)

tag: clone SA2-1


title: HT-29 cell line - shNOX1 - Rep 4

source_name: HT-29 stable clone 6A4 (shNOX1)

tag: stably transfected with shNOX1

tag: clone 6A4


title: HT-29 cell line - Scrambled - Rep 3

source_name: HT-29 stable clone SA2-2 (scrambled)

tag: clone SA2-2


title: HT-29 cell line - control - Rep 3

description:
We have found that NOX1 over-expression in colon cancer cell lines as well as surgical samples suggests a role in colon cancer. We identified unique target sequences of siRNAs for post-transcriptional silencing of NOX1. Gene specific and scrambled (control) sequences carrying the U6 promoter/shRNA cassettes were cloned into a GFP expression vector. Stable clones were selected based on NOX1 expression after transient transfection of HT-29 cells.  HT-29 parental cells, clone SA (scrambled) and clone 6A (gene specific) were utilized to establish xenografts in athymic mice to investigate the effect of NOX1 silencing on tumor growth and gene expression in vivo. A significant decrease was measured in the volume of tumors formed.  The stable clones and corresponding xenografts were analyzed on microarray.  The microarray data was validated with real-time PCR and western-blot analysis demonstrating the inhibition of genes important in cell cycle regulation and angiogenesis.  The results of this study show silencing NOX1 levels of generated ROS decreased, the tumor formation attenuated in vivo suggesting NOX1 may be a therapeutic target for colon cancer.
We have found that NOX1 over-expression in colon cancer cell lines as well as surgical samples suggests a role in colon cancer. We identified unique target sequences of siRNAs for post-transcriptional silencing of NOX1. Gene specific and scrambled (control) sequences carrying the U6 promoter/shRNA cassettes were cloned into a GFP expression vector. Stable clones were selected based on NOX1 expression after transient transfection of HT-29 cells.  HT-29 parental cells, clone SA (scrambled) and clone 6A (gene specific) were utilized to establish xenografts in athymic mice to investigate the effect of NOX1 silencing on tumor growth and gene expression in vivo. A significant decrease was measured in the volume of tumors formed.  The stable clones and corresponding xenografts were analyzed on microarray.  The microarray data was validated with real-time PCR and western-blot analysis demonstrating the inhibition of genes important in cell cycle regulation and angiogenesis.  The results of this study show silencing NOX1 levels of generated ROS decreased, the tumor formation attenuated in vivo suggesting NOX1 may be a therapeutic target for colon cancer.

source_name: HT-29 parental cells (SM2)

tag: HT-29 parental cells

tag: colon cancer cell line


title: HT-29 cell line - shNOX1 - Rep 2

source_name: HT-29 stable clone 6A2 (shNOX1)

tag: clone 6A2


title: HT-29 cell line - control - Rep1

source_name: HT-29 parental cells L1


title: HT-29 cell line - shNOX1 - Rep 1

source_name: HT-29 stable clone 6A1 (shNOX1)

tag: clone 6A1


title: HT-29 cell line - Scrambled - Rep 1

source_name: HT-29 stable clone SA1 (scrambled)

tag: clone SA1


title: HT-29 cell line - control - Rep 2

source_name: HT-29 parental cells (L2)


title: treatmentAd5

status: Public on Mar 21 2007

city: Wilmington

first: Ann

last: Stapleton

state: NC

address: 601 S. College

department: Biological Sciences

institute: University of North Carolina Wilmington

description: Image analysis with TIGR Spotfinder.

data_processing: The data were arsinh standardized (Huber et al 2002) using vsn in Bioconductor (Gentleman et al 2004) in the R software package.  Missing intensities were imputed by replacing them with intensities of a replicate within the same time point and labeling scheme.

organism: Zea mays

source_name: seedling leaf treatment_IntA_Cy3 12 hr rep_d

tag: inbred B73


title: controlBc5

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntB_Cy5 12 hr rep_b


title: treatmentAc5

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntA_Cy3 12 hr rep_c


title: treatmentBb4

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntB_Cy5 8 hr rep_b


title: treatmentAc4

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntA_Cy3 8 hr rep_c


title: controlBd5

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntB_Cy5 12 hr rep_d


title: treatmentBb5

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntB_Cy5 12 hr rep_b


title: treatmentBa5

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntB_Cy5 12 hr rep_a


title: treatmentAd4

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntA_Cy3 8 hr rep_d


title: treatmentAd3

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntA_Cy3 4 hr rep_d


title: treatmentBa4

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntB_Cy5 8 hr rep_a


title: HT-29 cell line - shNOX1 - Rep 3

source_name: HT-29 stable clone 6A3 (shNOX1)

tag: clone 6A3


title: controlAa5

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntA_Cy3 12 hr rep_a


title: controlAa4

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntA_Cy3 8 hr rep_a


title: treatmentAc3

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntA_Cy3 4 hr rep_c


title: controlBc4

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntB_Cy5 8 hr rep_c


title: controlAb5

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntA_Cy3 12 hr rep_b


title: controlBd4

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntB_Cy5 8 hr rep_d


title: controlBc3

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntB_Cy5 4 hr rep_c


title: controlAb4

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntA_Cy3 8 hr rep_b


title: controlAb3

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntA_Cy3 4 hr rep_b


title: treatmentBb3

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntB_Cy5 4 hr rep_b


title: Tmc03m022

city: Indianapolis

first: Matthew

last: Grow

state: IN

department: Biochemistry and Molecular Biology

institute: Indiana University

description: Gene expression data from endothelial cells from wildtype newborn mice transfected with treated for four hours with soluble TNF-alpha for transient activation. The cells were cultured in DMEM supplemented with 10% FCS, 2mM glutamine and 1x penicillin/streptomycin. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Mus musculus

source_name: cultured endothelial cells from wildtype newborn mice

treatment_protocol: soluble sTNF 4 hour treatment

tag: endothelial cells from wildtype newborn mice that were cultured in DMEM supplemented with 10% FCS, 2mM glutamine and 1x penicillin/streptomycin


title: treatmentAc2

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntA_Cy3 2 hr rep_c

tag: inbred


title: treatmentBa3

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntB_Cy5 4 hr rep_a


title: controlBd3

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntB_Cy5 4 hr rep_d


title: Smc03m017

description: Gene expression data from endothelial cells from wildtype newborn mice transfected with transmembrane TNF-alpha for chronic activation. The cells were cultured in DMEM supplemented with 10% FCS, 2mM glutamine and 1x penicillin/streptomycin. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA.

treatment_protocol: transmembrane TNF-alpha (tmTNF) transfected - for constant activation


title: controlAa3

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntA_Cy3 4 hr rep_a


title: Tmc03m021


title: Tmc03m019


title: Tmc03m020


title: controlBc2

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntB_Cy5 2 hr rep_c


title: treatmentAd2

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntA_Cy3 2 hr rep_d


title: Cmc03m013

description: Gene expression data from control endothelial cells from wildtype newborn mice that were cultured in DMEM supplemented with 10% FCS, 2mM glutamine and 1x penicillin/streptomycin. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA.

treatment_protocol: Mock-transfected control


title: treatmentBa2

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntB_Cy5 2 hr rep_a


title: treatmentAd1

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntA_Cy3 1 hr rep_d


title: Smc03m018


title: Smc03m016


title: Cmc03m012


title: Smc03m015


title: Cmc03m014


title: controlBd2

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntB_Cy5 2 hr rep_d


title: controlAa2

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntA_Cy3 2 hr rep_a


title: Duodenum_control_2weeks

status: Public on Mar 09 2007

city: Tokushima

first: Tadatoshi

last: Sato

address: 3-18-15, Kuramoto-cho

country: Japan

institute: Department of Clinical Nutrition, Institute of Health Biosciences, The University of Tokushima Graduate School

description: The rat without immobilization was housed in a metabolic cage for 2 weeks in parallel with the test animal.

label: Biotin

source_name: duodenal epithelial cells

tag: Strain

value: Wistar

tag: Gendar

value: male

tag: Age

value: 15 weeks

tag: Tissue

value: duodenum


title: treatmentAc1

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntA_Cy3 1 hr rep_c


title: treatmentBa1

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntB_Cy5 1 hr rep_a


title: controlAb1

description: Image analysis with TIGR Spotfinder.

data_processing: The data were then arsinh standardized (Huber et al 2002) using vsn in Bioconductor (Gentleman et al 2004) in the R software package.  Missing intensities were imputed by replacing them with intensities of a replicate within the same time point and labeling scheme.

source_name: seedling leaf control_IntA_Cy3 1 hr rbp_a


title: controlBd1

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntB_Cy5 1 hr rep_d


title: treatmentBb1

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf treatment_IntB_Cy5 1 hr rep_b


title: Duodenum_immobilized_2weeks

description: The rat was housed in an immobilization cage for 2 weeks.


title: controlBc1

description: Image analysis with TIGR Spotfinder.

source_name: seedling leaf control_IntB_Cy5 1 hr rep_c


title: Soleus 1.0 mg/kg cerivastatin-treated exercised replicate 1

status: Public on Mar 05 2007

first: Jennifer

middle: L

last: Seachrist

address: 2800 Plymouth Road

department: Safety Sciences

institute: Pfizer Inc

description: Gene expression data from rat soleus muscle

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.1 (MAS5.1)

source_name: soleus muscle

label_protocol: Approximately 3 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

treatment_protocol: 1.0 mg/kg/day cerivastatin -treated for 14 days plus 20 min treadmill exercise 5 days/week

tag: Female Sprague-Dawley strain Crl:CD(SD)IGS BR, 10 weeks of age


title: Cmc03m011

source_name: cultured endothelial cells from wildtype newborn mice


title: Soleus 1.0 mg/kg cerivastatin-treated exercised replicate 4


title: Soleus 1.0 mg/kg/day cerivastatin-treated replicate 2

treatment_protocol: 1.0 mg/kg/day cerivastatin -treated for 14 days


title: Soleus vehicle-treated exercised replicate 4

treatment_protocol: vehicle (0.5% methylcellulose) -treated for 14 days plus 20 min treadmill exercise 5 days/week


title: Soleus 1.0 mg/kg/day cerivastatin-treated replicate 1


title: Soleus 1.0 mg/kg cerivastatin-treated exercised replicate 2


title: Soleus 1.0 mg/kg cerivastatin-treated exercised replicate 3


title: Soleus vehicle-treated exercised replicate 1


title: Soleus vehicle-treated exercised replicate 2


title: Soleus vehicle-treated exercised replicate 3


title: Soleus vehicle-treated replicate 1

treatment_protocol: vehicle (0.5% methylcellulose) -treated for 14 days


title: Soleus vehicle-treated replicate 4


title: Gastrocnemius 1.0 mg/kg cerivastatin-treated exercised replicate 3

description: Gene expression data from rat gastrocnemius muscle

source_name: gastrocnemius muscle

label_protocol: Approximately 4 µg of total RNA was processed to produce biotinylated cRNA targets.


title: Soleus vehicle-treated replicate 3


title: Gastrocnemius 1.0 mg/kg cerivastatin-treated exercised replicate 4


title: Soleus 1.0 mg/kg/day cerivastatin-treated replicate 3


title: Soleus vehicle-treated replicate 2


title: Gastrocnemius 0.5 mg/kg cerivastatin-treated exercised replicate 3

treatment_protocol: 0.5 mg/kg/day cerivastatin -treated for 14 days plus 20 min treadmill exercise 5 days/week


title: controlAa1

description: Scans were gridded with TIGR Spotfinder.

source_name: seedling leaf control_IntA_Cy3 1 hr rep_a

tag: Inbred


title: Gastrocnemius 0.5 mg/kg cerivastatin-treated exercised replicate 1


title: Gastrocnemius 0.1 mg/kg cerivastatin-treated exercised replicate 4

treatment_protocol: 0.1 mg/kg/day cerivastatin -treated for 14 days plus 20 min treadmill exercise 5 days/week


title: Gastrocnemius 0.5 mg/kg cerivastatin-treated exercised replicate 2


title: Gastrocnemius vehicle-treated exercised replicate 4

treatment_protocol: vehicle -treated for 14 days plus 20 min treadmill exercise 5 days/week


title: Gastrocnemius vehicle-treated exercised replicate 3


title: Gastrocnemius 0.1 mg/kg cerivastatin-treated exercised replicate 1


title: Gastrocnemius 1.0 mg/kg cerivastatin-treated exercised replicate 1


title: Gastrocnemius 0.1 mg/kg cerivastatin-treated exercised replicate 3


title: Gastrocnemius 1.0 mg/kg cerivastatin-treated exercised replicate 2


title: Gastrocnemius 0.1 mg/kg cerivastatin-treated exercised replicate 2


title: Gastrocnemius vehicle-treated exercised replicate 2


title: Gastrocnemius vehicle-treated exercised replicate 1


title: Gastrocnemius 1.0 mg/kg cerivastatin-treated no exercise replicate 3

treatment_protocol: 1 mg/kg/day Cerivastatin -treated for 14 days


title: Gastrocnemius 1.0 mg/kg cerivastatin-treated no exercise replicate 2


title: Gastrocnemius 0.5 mg/kg cerivastatin-treated no exercise replicate 4

treatment_protocol: 0.5 mg/kg/day Cerivastatin -treated for 14 days


title: Gastrocnemius 1.0 mg/kg cerivastatin-treated no exercise replicate 1


title: Gastrocnemius 0.5 mg/kg cerivastatin-treated no exercise replicate 2


title: Gastrocnemius 0.1 mg/kg cerivastatin-treated no exercise replicate 3

treatment_protocol: 0.1 mg/kg/day Cerivastatin -treated for 14 days


title: Gastrocnemius 0.5 mg/kg cerivastatin-treated no exercise replicate 1


title: Gastrocnemius 0.5 mg/kg cerivastatin-treated no exercise replicate 3


title: Gastrocnemius 0.1 mg/kg cerivastatin-treated no exercise replicate 4


title: 5SC-nbc

city: Columbus

first: Sashwati

last: Roy

state: OH

department: Surgery

institute: Ohio State University

description: male mice (8 wks) were treated (oral gavage) with niacin bound chromium (nbc; 10 mg/kg wt) in water for 10 weeks (5d per wk). At the end of study subcutaneous fat was harvested for microarray analysis.

source_name: subcutaneous fat

tag: db/db mice


title: Gastrocnemius 0.1 mg/kg cerivastatin-treated no exercise replicate 1


title: Gastrocnemius 0.1 mg/kg cerivastatin-treated no exercise replicate 2


title: Gastrocnemius vehicle-treated no exercise replicate 4

treatment_protocol: vehicle (0.5% methylcellulose) -treated once daily for 14 days


title: Gastrocnemius vehicle-treated no exercise replicate 1


title: Gastrocnemius vehicle-treated no exercise replicate 3


title: Gastrocnemius vehicle-treated no exercise replicate 2


title: 13SC-nbc


title: 11SC-nbc


title: 8SC-pbo

description: male mice (8 wks) were treated with placebo (water only) for 10 weeks (5d per wk). At the end of study subcutaneous fat was harvested for microarray analysis.


title: Caco_Lp_10h_100_rep2

status: Public on Mar 02 2007

city: Zeist

first: Sonia

last: Pavan

address: Utrechtseweg 48

department: Physiological Sciences

country: Netherlands

institute: TNO Quality of Life

description: Cells incubated for 10h with Lp dose 100; sample replicate 2

data_processing: Spots with a signal/background ratio less than 1.5 or spots that were flagged by Imagene were not included in the analysis. For each spot local background intensity was subtracted from mean signal intensity and the expression ratio was calculated by dividing background-corrected signal intensity of the sample by the background-corrected signal intensity of the reference. Expression ratios were then log (base 2)-transformed and normalized per slide using an intensity-dependent method (Yang et al. Nucleic Acids Res 2002, 30:e15)

source_name: undifferentiated Caco-2 (common reference)

treatment_protocol: no treatment

tag: ATCC HTB-37 Caco-2

source_name: differentiated Caco-2_Lp100

treatment_protocol: cells differentiated for 18 days on filters and exposed for 10h to Lactobacillus plantarum dose 100


title: Caco_Lp_10h_1000_rep2

description: Cells incubated for 10h with Lp dose 1000; sample replicate 2

source_name: differentiated Caco-2_Lp1000

treatment_protocol: cells differentiated for 18 days on filters and exposed for 10h to Lactobacillus plantarum dose 1000


title: 9SC- nbc


title: 14SC-pbo


title: Caco_Lp_10h_1000_rep1

description: Cells incubated for 10h with Lp dose 1000; sample replicate 1


title: 10SC-pbo


title: Caco_Lp_10h_100_rep3

description: Cells incubated for 10h with Lp dose 100; sample replicate 3


title: Caco_Lp_10h_10_rep4

description: Cells incubated for 10h with Lp dose 10; sample replicate 4

source_name: differentiated Caco-2_Lp10

treatment_protocol: cells differentiated for 18 days on filters and exposed for 10h to Lactobacillus plantarum dose 10


title: Caco_Lp_10h_100_rep4

description: Cells incubated for 10h with Lp dose 100; sample replicate 4


title: Caco_Lp_10h_100_rep1

description: Cells incubated for 10h with Lp dose 100; sample replicate 1


title: Caco_Lp_10h_10_rep1

description: Cells incubated for 10h with Lp dose 10; sample replicate 1


title: Caco_Lp_10h_10_rep3

description: Cells incubated for 10h with Lp dose 10; sample replicate 3


title: 0%sugar_LS_1

status: Public on Feb 23 2007

city: Tsukuba

first: Jun

last: Shima

state: Ibaraki

address: 1-2-12 Kannondai

department: Applied Microbiology

institute: National Food Research Institute

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

hyb_protocol: DNA microarray hybridization was done according to the Affymetrix GeneChip® Expression Analysis Technical Manual. In brief, hybridization was at 45C in a hybridization oven (model 640, Affymetrix) at 60 rpm for 16 h. The EukGE-WS2v4 fluidics protocol of the Affymetrix GeneChip Operating Software 1.2 (GCOS) was used to perform staining and washing procedures.

scan_protocol: The scanning of arrays were carried out using the GeneChip® scanner (Affymetrix, Santa Clara, CA, USA)

data_processing: Affymetrix GeneChip Operating Software Version 1.2

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: mRNA

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

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

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


title: Caco_Lp_10h_10_rep2

description: Cells incubated for 10h with Lp dose 10; sample replicate 2


title: Control_10h_rep1

description: Control hybridization sample (untreated cells)- replicate 1

tag: ATCC HTB-37 Caco-2 cell line

value: colon, colorectal adenocarcinoma

tag: Morphology

value: epithelial

source_name: differentiated Caco-2

treatment_protocol: cells differentiated for 18 days on filters. No treatment


title: Control_10h_rep4

description: Control hybridization sample (untreated cells)- replicate 4


title: Control_10h_rep3

description: Control hybridization sample (untreated cells)- replicate 3


title: H20_S_B2

status: Public on Jan 01 2007

city: Zurich

first: Michael

last: Zaugg

address: Raemistrasse 100

department: Anesthesiology

country: Switzerland

institute: Anesthesiology, University Hospital Zurich

description: coronary artery bypass surgery patient

data_processing: RMA

label: SAPE

source_name: heart, atrial tissue, after CABG surgery

tag: male

tag: CABG patient, atrial tissue, sevoflurane anesthesia, after CABG surgery


title: Control_10h_rep2

description: Control hybridization sample (untreated cells)- replicate 2


title: H20_S_B1

description: coronary artery bypass surgery patient

source_name: heart, atrial tissue, baseline

tag: CABG patient, atrial tissue,

tag: baseline before CABG surgery


title: H19_P_B2

description: coronary artery bypass surgery patient

tag: CABG patient, atrial tissue, propofol anesthesia, after CABG surgery


title: 6SC-PBO

source_name: subcuteneous fat

tag: db/db mice (stock 000642 Jackson lab)


title: H18_P_B2

description: coronary artery bypass surgery patient


title: H17_S_B2

description: coronary artery bypass surgery patient


title: H16_P_B2

description: coronary artery bypass surgery patient


title: H19_P_B1

description: coronary artery bypass surgery patient


title: H15_S_B2

description: coronary artery bypass surgery patient


title: H18_P_B1

description: coronary artery bypass surgery patient


title: H15_S_B1

description: coronary artery bypass surgery patient


title: H17_S_B1

description: coronary artery bypass surgery patient


title: H16_P_B1

description: coronary artery bypass surgery patient


title: H14_P_B1

description: coronary artery bypass surgery patient


title: H13_S_B2

description: coronary artery bypass surgery patient


title: H14_P_B2

description: coronary artery bypass surgery patient


title: H12_P_B2

description: coronary artery bypass surgery patient


title: H12_P_B1

description: coronary artery bypass surgery patient


title: H08_P_B1

description: coronary artery bypass surgery patient


title: H08_P_B2

description: coronary artery bypass surgery patient


title: H11_S_B2

description: coronary artery bypass surgery patient


title: H11_S_B1

description: coronary artery bypass surgery patient


title: H07_S_B1

description: coronary artery bypass surgery patient


title: H09_S_B2

description: coronary artery bypass surgery patient


title: H04_P_B1

description: coronary artery bypass surgery patient


title: H10_P_B1

description: coronary artery bypass surgery patient


title: H06_S_B1

description: coronary artery bypass surgery patient


title: H10_P_B2

description: coronary artery bypass surgery patient


title: H03_P_B1

description: coronary artery bypass surgery patient

tag: CABG patient, atrial tissue


title: H06_S_B2

description: coronary artery bypass surgery patient


title: H01_S_B2

description: coronary artery bypass surgery patient

tag: sevoflurane anesthesia, after CABG surgery


title: H01_S_B1

description:
coronary artery bypass surgery patient
baseline atrial biopsy

tag: CABG patient atrial tissue


title: H07_S_B2

description: coronary artery bypass surgery patient


title: H04_P_B2

description: coronary artery bypass surgery patient


title: Rice_Shoot_No N_rep1

status: Public on Dec 07 2006

city: Nanjing

first: Guohua

last: Xu

state: Jiangsu

address: Tongwei Road #1

department: Plant Nutrition

country: China

institute: Nanjing Agricultural University

description:
Plant material and growth condition:
The cultivar of rice used in the experiments was a Japonica sub-species of Oryza sativa "Wuyunjing #7". Seeds were surface sterilized, placed individually in the hole of a nylon-net which was submerged into water for germination in a growth chamber for 10 days. The plantlets were then transplanted onto a hydroponics system in a temperature and light controlled glasshouse. During the growing period, the temperature ranged between 22 to 24 0C at night and 30 to 32 0C at day-time, and photo-period was maintained 14h/10h (light/dark).

Nutritional treatments and plant sampling:
The transplanted plantlets were first supplied with full nutrition solution containing 1.25 mM ammonium nitrate as N source for 12 days, followed by a solution with N completely removed for one week. After that, the plants were re-supplied with four different treatments: ammonium nitrate (1:1 ratio), only ammonium, only nitrate and continued N starvation for further 96 h with twelve replicates for each of the treatments. The full nutrition concentration formula of the major elements is described in Table 1. In addition, the solution contained 2-mM Na2SiO4 and integrated mixture of micro-nutrients (in µM): 20.0 FeSO4, 36.7 H3BO4, 9.1 MnCl2, 0.77 ZnSO4, 0.32 CuSO4, and 0.39 H2MoO4. pH of the solution was adjusted to 5.8. The solution was replaced completely once every two days before the treatments and everyday during the treatments.
	After weighting, both the fresh roots and leaves of each treatment were sampled at 96-h after the treatment initiation.

RNA preparation, array hybridization and data analysis:
We used an RNeasy Plant Mini Kit (Qiagen, Shanghai, China) to extract total RNA. RNA concentration and quality were analyzed by NanoDrop (NanoDrop Technologies) and 2100 Bioanalyzer (Agilent Technologies).
We used Agilent low RNA input fluorescent linear amplification kit for fluorescent cDNA synthesis, fluorescent cRNA amplification and synthesis. The hybridization and washing were followed Agilent 60-mer oligo microarray processing protocol. The data scanning, quantification, and processing were done as described by Yazaki et al. (2004).

Yazaki, J., Shimatani, Z., Hashimoto, A., Nagata, Y., Fujii, F., Kojima, K., Suzuki, K., Taya, T., Tonouchi, M., Nelson, C., Nakagawa, A., Otomo, Y., Murakami, K., Matsubara, K., Kawai, J., Carninci, P., Hayashizaki, Y., and Kikuchi, S. (2004). Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. Physiol. Genomics 17, 87-100.

data_processing: Agilent Technologies Feature extraction ver6.1.1

organism: Oryza sativa

source_name: NH4NO3 treated shoot sample labeled by green

tag: variety

value: a Japonica sub-species of Oryza sativa "Wuyunjing #7". growth stage:23 days after planting. tissue:roots

source_name: NH4NO3 treated shoot sample labeled by red


title: H03_P_B2

description: coronary artery bypass surgery patient

tag: propofol anesthesia, after CABG surgery


title: H13_S_B1

description: coronary artery bypass surgery patient


title: Rice_Shoot_NO3_rep1

description:
Plant material and growth condition: The cultivar of rice used in the experiments was a Japonica sub-species of Oryza sativa "Wuyunjing #7". Seeds were surface sterilized, placed individually in the hole of a nylon-net which was submerged into water for germination in a growth chamber for 10 days. The plantlets were then transplanted onto a hydroponics system in a temperature and light controlled glasshouse. During the growing period, the temperature ranged between 22 to 24 0C at night and 30 to 32 0C at day-time, and photo-period was maintained 14h/10h (light/dark).

Nutritional treatments and plant sampling:
The transplanted plantlets were first supplied with full nutrition solution containing 1.25 mM ammonium nitrate as N source for 12 days, followed by a solution with N completely removed for one week. After that, the plants were re-supplied with four different treatments: ammonium nitrate (1:1 ratio), only ammonium, only nitrate and continued N starvation for further 96 h with twelve replicates for each of the treatments. The full nutrition concentration formula of the major elements is described in Table 1. In addition, the solution contained 2-mM Na2SiO4 and integrated mixture of micro-nutrients (in µM): 20.0 FeSO4, 36.7 H3BO4, 9.1 MnCl2, 0.77 ZnSO4, 0.32 CuSO4, and 0.39 H2MoO4. pH of the solution was adjusted to 5.8. The solution was replaced completely once every two days before the treatments and everyday during the treatments.
	After weighting, both the fresh roots and leaves of each treatment were sampled at 96-h after the treatment initiation.

RNA preparation, array hybridization and data analysis:
We used an RNeasy Plant Mini Kit (Qiagen, Shanghai, China) to extract total RNA. RNA concentration and quality were analyzed by NanoDrop (NanoDrop Technologies) and 2100 Bioanalyzer (Agilent Technologies).
We used Agilent low RNA input fluorescent linear amplification kit for fluorescent cDNA synthesis, fluorescent cRNA amplification and synthesis. The hybridization and washing were followed Agilent 60-mer oligo microarray processing protocol. The data scanning, quantification, and processing were done as described by Yazaki et al. (2004).

Yazaki, J., Shimatani, Z., Hashimoto, A., Nagata, Y., Fujii, F., Kojima, K., Suzuki, K., Taya, T., Tonouchi, M., Nelson, C., Nakagawa, A., Otomo, Y., Murakami, K., Matsubara, K., Kawai, J., Carninci, P., Hayashizaki, Y., and Kikuchi, S. (2004). Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. Physiol. Genomics 17, 87-100.

tag: varirty

source_name: NO3-only treated shoot sample labeled by red


title: Rice_Root_NH4_rep2

source_name: NH4 only treated root sample labeled by green

source_name: NH4NO3 treated root sample labeled by red


title: Rice_Shoot_NH4_rep1

source_name: NH4-only treated shoot sample labeled by red


title: Rice_Root_NH4_rep1

source_name: NH4NO3 treated root sample labeled by green

source_name: NH4-only treated root sample labeled by red


title: H05_S_B1

description: coronary artery bypass surgery patient


title: H09_S_B1

description: coronary artery bypass surgery patient


title: 4 hour CpG ODN - repeat 1 - mAdbID:75119

status: Public on Oct 30 2006

city: Frederick

first: Dennis

middle: M

last: Klinman

state: MD

department: CIP

institute: NCI Frederick

description: mAdb experiment ID: 75119

hyb_protocol: Hybridization Protocol Other: Cy-labeled reference and sample cDNAs (7.5 microliter each) were combined, de-naturated by heating for 2' at 98 C and mixed with 36 microliter of hybridization solution at 42 C (Ambion, Austin, TX). A low volume active mixing chamber was applied to the microarray via an adhesive gasket (MAUI mixer FL, BioMicro Systems, Salt Lake City, Utah), the hybridization solution containing the sample was added to the array, and was placed for 18 h at 42 C in the base unit of the actively mixing MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah). Post hybridization, the arrays were washed in 1X SSC/0.05X SDS and 0.1X SSC, centrifuged to remove remaining liquid with unbound cDNA, and dried.

data_processing: Data were background corrected, flagged values were removed, spots with both signals less than 190 were filtered out, ratios were log base 2 transformed and lowess intensity dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes. Only genes present on >70% of the arrays were included in the subsequent analysis

source_name: CpG ODN treated - 4 h

label_protocol:
Cy5 Labeling Protocol
Other: 20 microgram of total RNA was reverse-transcribed using 3 microliter 10X first strand buffer (Stratagene, La Jolla, CA), 2 microliter (1 microgram) Oligo(dT) (Invitrogen, Carlsbad, CA), 3 microliter (150 U) reverse transcriptase (StrataScript HC RT, Stratagene, La Jolla, CA), 2 microliter 20X aminoallyl-dUTP/dNTP mix, and 3 microliter 0.1 M DTT in a final volume of 30 microliter at 42 C for 1 h. cDNA was purified using a MinElute PCR Purification Kit (Qiagen, Valencia, CA). 10 microliter of cDNA was labeled with Cy5 reactive dye (Amersham Biosciences, UK) diluted in 5 microliter of DMSO plus 1.7 microliter of 1M NaHCO3 for 90' in the dark.

extract_protocol:
RNA Extraction Protocol
Other: Total RNA was extracted from spleen cell cultures using TRIzol reagent (Invitrogen, Carlsbad, CA) as specified by the manufacturer.

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 1 uM
Treatment time: 4 hours
Treatment temperature: 37 C
In-vivo treatment: Single spleen cell suspensions were sterilely prepared in complete RPMI 1640 supplemented with 10% FBS, 50 mg/ml penicillin/streptomycin, 2 mM L-glutamine, 10 mM Hepes buffer, 0.11 mg/ml sodium pyruvate, and 0.5 mM beta-mercaptoethanol. Cells were cultured at 37C in a 5% CO2 incubator + 1 uM ODN for 4 h

tag: Strain

value: BALB/c

tag: Gender

value: female

tag: Age

value: 2 months

tag: Cell type

value: spleen cells

source_name: Universal Mouse Reference RNA

label_protocol:
Cy3 Labeling Protocol
Other: 20 microgram of total RNA (universal reference mouse RNA, Stratagene, La Jolla, CA) was reverse-transcribed using 3 microliter 10X first strand buffer (Stratagene, La Jolla, CA), 2 microliter (1 microgram) Oligo(dT) (Invitrogen, Carlsbad, CA), 3 microliter (150 U) reverse transcriptase (StrataScript HC RT, Stratagene, La Jolla, CA), 2 microliter 20X aminoallyl-dUTP/dNTP mix, and 3 microliter 0.1 M DTT in a final volume of 30 microliter at 42 C for 1 h. cDNA was purified using a MinElute PCR Purification Kit (Qiagen, Valencia, CA). 10 microliter of cDNA was labeled with Cy3 reactive dye (Amersham Biosciences, UK) diluted in 5 microliter of DMSO plus 1.7 microliter of 1M NaHCO3 for 90' in the dark

value: mixture of B-lymphocyte, embryo, kidney, liver, macrophages, mammary gland, muscle, skin, testis, T-lymphocyte


title: H02_P_B2

description: coronary artery bypass surgery patient


title: H02_P_B1

description: coronary artery bypass surgery patient


title: 4 hour control ODN - repeat 3 - mAdbID:75118

description: mAdb experiment ID: 75118

source_name: Control ODN treated - 4 h

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture of ODN 1612, 1471
Treatment dose: 1 uM
Treatment time: 4 hours
Treatment temperature: 37 C
In-vivo treatment: Single spleen cell suspensions were sterilely prepared in complete RPMI 1640 supplemented with 10% FBS, 50 mg/ml penicillin/streptomycin, 2 mM L-glutamine, 10 mM Hepes buffer, 0.11 mg/ml sodium pyruvate, and 0.5 mM beta-mercaptoethanol. Cells were cultured at 37C in a 5% CO2 incubator + 1 uM ODN for 4 h


title: 4 hour control ODN - repeat 1 - mAdbID:75116

description: mAdb experiment ID: 75116


title: S.cerevisiae Sok2::13myc chIP chip replicate 1 (Slide 40345)

status: Public on Dec 13 2006

type: genomic

city: Urrbrae

first: Anthony

middle: R

last: Borneman

state: South Australia

address: Paratoo Rd

country: Australia

institute: The Australian Wine Research Institute

hyb_protocol: Nimblegen

scan_protocol: Nimblegen

data_processing: Samples were scanned and with each channel (635 (ch1) and 532 (ch2)) normalized separately according to Nimblegen protocols. log(2) ratios were calculated from these normalized 635 and 532 signals, with Random control spots removed during processing.

molecule: genomic DNA

label_protocol: Klenow random priming (Borneman et al Genes Dev 2006)

growth_protocol: Grown at 30¡C to OD600 = 0.3 in SD media. Transferred to liquid SLAD for 4 hrs at 30¡C.

extract_protocol: Chromatin immunoprecipitation (Borneman et al Genes Dev 2006)

tag: Sigma1278b diploid strain (825/6 L1) containing Sok2 with C-terminal 13myc tag

tag: Sigma1278b diploid control strain


title: 4 hour control ODN - repeat 2 - mAdbID:75115

description: mAdb experiment ID: 75115


title: Rice_Shoot_No N_rep2

source_name: No N treated shoot sample labeled by green


title: Rice_Root_No N_rep2

source_name: No N treated root sample labeled by green


title: 2 hour medium alone - repeat 4 - mAdbID:75108

description: mAdb experiment ID: 75108

source_name: Incubated in medium alone - 2 h

treatment_protocol:
Treatment type: compound
Agent: medium alone
Treatment time: 2 hours
Treatment temperature: 37 C
In-vivo treatment: Single spleen cell suspensions were sterilely prepared in complete RPMI 1640 supplemented with 10% FBS, 50 mg/ml penicillin/streptomycin, 2 mM L-glutamine, 10 mM Hepes buffer, 0.11 mg/ml sodium pyruvate, and 0.5 mM beta-mercaptoethanol. Cells were cultured at 37C in a 5% CO2 incubator for 2 h


title: 2 hour CpG ODN - repeat 2 - mAdbID:75105

description: mAdb experiment ID: 75105

source_name: CpG ODN treated - 2 h

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 1 uM
Treatment time: 2 hours
Treatment temperature: 37 C
In-vivo treatment: Single spleen cell suspensions were sterilely prepared in complete RPMI 1640 supplemented with 10% FBS, 50 mg/ml penicillin/streptomycin, 2 mM L-glutamine, 10 mM Hepes buffer, 0.11 mg/ml sodium pyruvate, and 0.5 mM beta-mercaptoethanol. Cells were cultured at 37C in a 5% CO2 incubator + 1 uM ODN for 2 h


title: Rice_Root_No N_rep1

source_name: No N treated root sample labeled by red


title: 2 hour medium alone - repeat 3 - mAdbID:75114

description: mAdb experiment ID: 75114


title: 8 hour medium alone - repeat 1 - mAdbID:75111

description: mAdb experiment ID: 75111

source_name: Incubated in medium alone - 8 h

treatment_protocol:
Treatment type: compound
Agent: medium alone
Treatment time: 8 hours
Treatment temperature: 37 C
In-vivo treatment: Single spleen cell suspensions were sterilely prepared in complete RPMI 1640 supplemented with 10% FBS, 50 mg/ml penicillin/streptomycin, 2 mM L-glutamine, 10 mM Hepes buffer, 0.11 mg/ml sodium pyruvate, and 0.5 mM beta-mercaptoethanol. Cells were cultured at 37C in a 5% CO2 incubator for 8 h


title: 8 hour CpG ODN - repeat 1 - mAdbID:75086

description: mAdb experiment ID: 75086

source_name: CpG ODN treated - 8 h

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 1 uM
Treatment time: 8 hours
Treatment temperature: 37 C
In-vivo treatment: Single spleen cell suspensions were sterilely prepared in complete RPMI 1640 supplemented with 10% FBS, 50 mg/ml penicillin/streptomycin, 2 mM L-glutamine, 10 mM Hepes buffer, 0.11 mg/ml sodium pyruvate, and 0.5 mM beta-mercaptoethanol. Cells were cultured at 37C in a 5% CO2 incubator + 1 uM ODN for 8 h


title: 8 hour CpG ODN - repeat 3 - mAdbID:75104

description: mAdb experiment ID: 75104


title: 8 hour medium alone - repeat 3 - mAdbID:75110

description: mAdb experiment ID: 75110


title: 2 hour CpG ODN - repeat 4 - mAdbID:75107

description: mAdb experiment ID: 75107


title: Rice_Shoot_NH4_rep2

source_name: NH4 only treated shoot sample labeled by green

source_name: NH4NO3 treated shoot sample labeled by red


title: Rice_Shoot_NO3_rep2

source_name: NO3 only treated shoot sample labeled by green


title: Rice_Root_NO3_rep2

source_name: NO3-only treated root sample labeled by green

source_name: NH4NO3 treated root sample labeled by red


title: H05_S_B2

description: coronary artery bypass surgery patient

source_name: heart, atrial tissue, after CABG surgery

tag: male

tag: CABG patient, atrial tissue, sevoflurane anesthesia, after CABG surgery


title: 4 hour medium alone - repeat 3 - mAdbID:75126

description: mAdb experiment ID: 75126

source_name: Incubated in medium alone - 4 h

treatment_protocol:
Treatment type: compound
Agent: medium alone
Treatment time: 4 hours
Treatment temperature: 37 C
In-vivo treatment: Single spleen cell suspensions were sterilely prepared in complete RPMI 1640 supplemented with 10% FBS, 50 mg/ml penicillin/streptomycin, 2 mM L-glutamine, 10 mM Hepes buffer, 0.11 mg/ml sodium pyruvate, and 0.5 mM beta-mercaptoethanol. Cells were cultured at 37C in a 5% CO2 incubator for 4 h


title: S.cerevisiae Sok2::13myc chIP chip replicate 2 (slide 40348)


title: 8 hour CpG ODN - repeat 2 - mAdbID:75084

description: mAdb experiment ID: 75084


title: 4 hour medium alone - repeat 4 - mAdbID:75125

description: mAdb experiment ID: 75125


title: Rice_Root_NO3-rep1

description:
Plant material and growth condition:
The cultivar of rice used in the experiments was a Japonica sub-species of Oryza sativa "Wuyunjing #7". Seeds were surface sterilized, placed individually in the hole of a nylon-net which was submerged into water for germination in a growth chamber for 10 days. The plantlets were then transplanted onto a hydroponics system in a temperature and light controlled glasshouse. During the growing period, the temperature ranged between 22 to 24 0C at night and 30 to 32 0C at day-time, and photo-period was maintained 14h/10h (light/dark).

Nutritional treatments and plant sampling:
The transplanted plantlets were first supplied with full nutrition solution containing 1.25 mM ammonium nitrate as N source for 12 days, followed by a solution with N completely removed for one week. After that, the plants were re-supplied with four different treatments: ammonium nitrate (1:1 ratio), only ammonium, only nitrate and continued N starvation for further 96 h with twelve replicates for each of the treatments. The full nutrition concentration formula of the major elements is described in Table 1. In addition, the solution contained 2-mM Na2SiO4 and integrated mixture of micro-nutrients (in µM): 20.0 FeSO4, 36.7 H3BO4, 9.1 MnCl2, 0.77 ZnSO4, 0.32 CuSO4, and 0.39 H2MoO4. pH of the solution was adjusted to 5.8. The solution was replaced completely once every two days before the treatments and everyday during the treatments.
After weighting, both the fresh roots and leaves of each treatment were sampled at 96-h after the treatment initiation.

RNA preparation, array hybridization and data analysis:
We used an RNeasy Plant Mini Kit (Qiagen, Shanghai, China) to extract total RNA. RNA concentration and quality were analyzed by NanoDrop (NanoDrop Technologies) and 2100 Bioanalyzer (Agilent Technologies).
We used Agilent low RNA input fluorescent linear amplification kit for fluorescent cDNA synthesis, fluorescent cRNA amplification and synthesis. The hybridization and washing were followed Agilent 60-mer oligo microarray processing protocol. The data scanning, quantification, and processing were done as described by Yazaki et al. (2004).

Yazaki, J., Shimatani, Z., Hashimoto, A., Nagata, Y., Fujii, F., Kojima, K., Suzuki, K., Taya, T., Tonouchi, M., Nelson, C., Nakagawa, A., Otomo, Y., Murakami, K., Matsubara, K., Kawai, J., Carninci, P., Hayashizaki, Y., and Kikuchi, S. (2004). Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. Physiol. Genomics 17, 87-100.

source_name: NH4NO3 treated root sample labeled by green

tag: growth stage

value: 23 days after planting

tag: tissue

value: roots

source_name: NO3-only treated root sample labeled by red


title: 4 hour medium alone - repeat 2 - mAdbID:75124

description: mAdb experiment ID: 75124

source_name: Universal Mouse Reference RNA


title: TCHW P24_ir29 salt stress, biological rep3

status: Public on Sep 15 2006

city: Riverside

first: HARKAMAL

last: WALIA

address: Department of Botany & Plant Sciecnes

institute: University of California

description: Gene expression data from unstressed crown and growing point tissue of rice

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with GCOS 1.2 using Affymetrix default analysis settings and global scaling as normalization method

organism: Oryza sativa Indica Group

source_name: rice crown and growing point tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA

extract_protocol: Trizol extraction of total RNA

treatment_protocol: salt stressed growth condition

tag: salt tolerant


title: 8 hour control ODN - repeat 2 - mAdbID:75081

description: mAdb experiment ID: 75081

source_name: Control ODN treated - 8 h

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture of ODN 1612, 1471
Treatment dose: 1 uM
Treatment time: 8 hours
Treatment temperature: 37 C
In-vivo treatment: Single spleen cell suspensions were sterilely prepared in complete RPMI 1640 supplemented with 10% FBS, 50 mg/ml penicillin/streptomycin, 2 mM L-glutamine, 10 mM Hepes buffer, 0.11 mg/ml sodium pyruvate, and 0.5 mM beta-mercaptoethanol. Cells were cultured at 37C in a 5% CO2 incubator + 1 uM ODN for 8 h


title: 2 hour control ODN - repeat 4 - mAdbID:75076

description: mAdb experiment ID: 75076

source_name: Control ODN treated - 2 h

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture of ODN 1612, 1471
Treatment dose: 1 uM
Treatment time: 2 hours
Treatment temperature: 37 C
In-vivo treatment: Single spleen cell suspensions were sterilely prepared in complete RPMI 1640 supplemented with 10% FBS, 50 mg/ml penicillin/streptomycin, 2 mM L-glutamine, 10 mM Hepes buffer, 0.11 mg/ml sodium pyruvate, and 0.5 mM beta-mercaptoethanol. Cells were cultured at 37C in a 5% CO2 incubator + 1 uM ODN for 2 h


title: 4 hour medium alone - repeat 1 - mAdbID:66134

description: mAdb experiment ID: 66134


title: TCHW P22_ir29 salt stress, biological rep1


title: 4 hour CpG ODN - repeat 2 - mAdbID:75123

description: mAdb experiment ID: 75123

source_name: CpG ODN treated - 4 h


title: TCHW P23_ir29 salt stress, biological rep2


title: 4 hour CpG ODN - repeat 4 - mAdbID:75121

description: mAdb experiment ID: 75121


title: S.cerevisiae Sok2::13myc chIP chip replicate 1 (Slide 39907)


title: 2 hour medium alone - repeat 1 - mAdbID:75113

description: mAdb experiment ID: 75113

source_name: Incubated in medium alone - 2 h


title: 4 hour control ODN - repeat 4 - mAdbID:75117

description: mAdb experiment ID: 75117

source_name: Control ODN treated - 4 h


title: 2 hour medium alone - repeat 2 - mAdbID:75112

description: mAdb experiment ID: 75112


title: 4 hour CpG ODN - repeat 3 - mAdbID:75122

description: mAdb experiment ID: 75122


title: TCHW P13_agami control, biological rep1

organism: Oryza sativa Japonica Group

treatment_protocol: unstressed growth condition


title: 8 hour medium alone - repeat 2 - mAdbID:75109

description: mAdb experiment ID: 75109

source_name: Incubated in medium alone - 8 h


title: TCHW P12_ir29 salt stress, biological rep3

tag: salt sensitive


title: 2 hour control ODN - repeat 1 - mAdbID:61412

description: mAdb experiment ID: 61412


title: TCHW P17_agami salt stress, biological rep2


title: TCHW P7_ir29 control, biological rep1


title: 8 hour control ODN - repeat 1 - mAdbID:75082

description: mAdb experiment ID: 75082


title: TCHW P19_ir29 control, biological rep1


title: 2 hour CpG ODN - repeat 1 - mAdbID:61411

description: mAdb experiment ID: 61411

source_name: CpG ODN treated - 2 h


title: TCHW P14_agami control, biological rep2


title: 2 hour control ODN - repeat 2 - mAdbID:61737

description: mAdb experiment ID: 61737


title: TCHW P11_ir29 salt stress, biological rep2


title: TCHW P16_agami salt stress, biological rep1


title: TCHW P20_ir29 control, biological rep2


title: TCHW P4_m103 salt stress, biological rep1


title: 2 hour CpG ODN - repeat 3 - mAdbID:75106

description: mAdb experiment ID: 75106


title: TCHW P21_ir29 control, biological rep3


title: TCHW P10_ir29 salt stress, biological rep1


title: TCHW P18_agami salt stress, biological rep3


title: 2 hour control ODN - repeat 3 - mAdbID:75077

description: mAdb experiment ID: 75077


title: 8 hour control ODN - repeat 3 - mAdbID:75083

description: mAdb experiment ID: 75083


title: TCHW P5_m103 salt stress, biological rep2


title: TCHW P8_ir29 control, biological rep2


title: rat#57

status: Public on Sep 01 2006

city: Lille

first: Jamal

last: Khalife

address: 1 rue du Prof. Calmette

country: France

institute: Inserm U547

description: integrity and purity of RNA were assessed by use of the Agilent Bioanalyser (Agilent Technologies). Ten micrograms of purified total RNA was then utilized for linear amplification following the CodeLink Gene Expression System Protocol (GE Healthcare). Ten micrograms of the resulting cRNA was hybridized to each CodeLink Rat UniSet I Bioarray following the CodeLink Gene Expression System Protocol without any modification. Each bioarray contains 9911 rat sequences and 300 negative bacterial control probes. The bioarrays were scanned using an Axon GenePix 4000B scanner at 635nm, 10µm resolution and a PMT value of 600.

hyb_protocol: CodeLink standard protocol

scan_protocol: CodeLink standard protocol

data_processing: Intensity is defined as the sum of the pixel signals in the area of interest minus the scaled 2-pixel median background. The intensities are then median-normalized by calculating the median of all spots except for the control probes and blanks and dividing each spot intensity by the median value

label_protocol: CodeLink standard protocol

extract_protocol: spleen was minced in 2ml/100mg tissue of RNA+ solution (Qbiogen) and crude RNA was isolated following the manufacturer's protocol

treatment_protocol: rats were infected with Plasmodium berghei ANKA at age of 8 weeks. After parasite clearance (~4 weeks later) spleens were recovered

tag: strain

tag: gender

tag: age

value: 12 weeks

value: spleen


title: rat#39

data_processing: Intensity is defined as the sum ofthe pixel signals in the area of interest minus the scaled 2-pixel median background. The intensities are then median-normalized by calculating the median of all spots except for the control probes and blanks and dividing each spot intensity by the median value


title: TCHW P9_ir29 control, biological rep3


title: rat#53

source_name: spleen #53

treatment_protocol: healthy control rat


title: rat#38


title: rat#54


title: rat#56


title: TCHW P15_agami control, biological rep3


title: rat#52

source_name: spleen #52

treatment_protocol:
healthy control rat
spleen recovered at 12 weeks of age

tag: sratin


title: HCC827 U133A run at UTSW

status: Public on Aug 31 2006

city: Aurora

first: Christopher

middle: D

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

description: Baseline (unstimulated) cell line

scan_protocol: standard Affymetrix procedures, using the Affy GCS3000

source_name: NSCLC cell line

label_protocol: Approximately 5 micrograms of total RNA was processed to produce biotinylated cRNA targets using the older (ENZO) Affymetrix protocol

extract_protocol: Qiagen RNEasy, following standard protocol for cultured cells

tag: Test set


title: HCC515 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: HCC95 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: TCHW P6_m103 salt stress, biological rep3


title: HCC193 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: TCHW P2_m103 control, biological rep2


title: HCC78 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H460 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: TFII-I knock-out vs wild type embryo

city: New Havem

first: Nyam-Osor

last: Chimgee

state: CT

address: 266 Whitney Ave

department: MCDB

institute: Yale University

data_processing: log base 2 ratio of cy5 to cy3

source_name: wild type embryos

tag: wild type embryo

source_name: TFII-I knock-out mouse embryos

tag: mutant embryo


title: TCHW P3_m103 control, biological rep3


title: HCC461 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: HCC44 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: Gtf2iRd1 knock-out vs wild type embryo (rep1)

source_name: Gtf2iRd1 knock-out mouse embryos


title: TCHW P1_m103 control, biological rep1


title: TFII-I knock-out vs wild type embryo (rep1)


title: HCC15 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: HCC366 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: Gtf2iRd1 knock-out vs wild type embryo (rep2)


title: H358 U133B run at UCHSC

description: Baseline (unstimulated) cell line

tag: Training set


title: H358 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H2882 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: HCC1171 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: HCC1359 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: HCC827 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H1703 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H2347 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: HCC1195 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H460 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H2887 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H1648 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H322 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H2279 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H520 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H820 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H2087 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: HCC4006 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H1648 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H2126 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: Calu3 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H157 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H2122 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H1975 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H3255 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H1993 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H1770 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H322 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H358 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H1650 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H1395 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H3255 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H1299 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H1437 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H2009 U133A run at UTSW

description: Baseline (unstimulated) cell line


title: H1703 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H157 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: HCC4006 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H125 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H460 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H1334 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H520 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H125 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H2279 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H820 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H157 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: Calu3 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H1650 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H1648 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: H1975 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: A549 U133B run at UCHSC

description: Baseline (unstimulated) cell line


title: H1334 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: NT1 Vs TBV_9

status: Public on Aug 02 2006

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: NT1 vs TBV, different passages

hyb_protocol: Total RNA from individual samples was obtained according to manufacturer's protocols using RNeasy Midi kits (Qiagen). 15 µg total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 50µl hybridisation buffer and mixed with 50µl of reference cDNA solution labelled with the second dye. The hybridisation mix is placed on a pre-hybridised microarray and incubated at 42°C for 16h in a hybstation.

scan_protocol: Slides were scanned for both CY3 and Cy5 signal with a GenePix 4000A.

data_processing: images were processed by GenePixPro 6.0. Mean intensities with subtracted background were normalised so that the median of there rations has become 1.


title: NT1 Vs TBV_1

description: NT1 vs TBV, different passages


title: NT1 Vs TBV_12

description: NT1 vs TBV, different passages


title: A549 U133A run at UCHSC

description: Baseline (unstimulated) cell line


title: NT1 Vs TBV_6

description: NT1 vs TBV, different passages


title: NT1 Vs TBV_5

description: NT1 vs TBV, different passages


title: NT1 Vs TBV_11

description: NT1 vs TBV, different passages


title: NT1 Vs TBV_4

description: NT1 vs TBV, different passages


title: NT1 Vs TBV_2

description: NT1 vs TBV, different passages

source_name: NT1 1

tag: NT1 1


title: NT1 Vs TBV_3

description: NT1 vs TBV, different passages


title: NT1 Vs TBV_10

description: NT1 vs TBV, different passages


title: NT1 Vs TBV_8

description: NT1 vs TBV, different passages


title: WT 3.5dpf zebrafish muscle 1

status: Public on Jul 30 2006

city: Boston

first: Leta

middle: S

last: Steffen

state: MA

address: 320 Longwood Ave

department: Program in Genomics

institute: Harvard Medical School, Children's Hospital

description: Arrays were scanned in an Affymetrix/GeneChip Scanner 3000 and the resulting signals quantified and stored using default parameters of the Affymetrix GeneChip Operating Software Version 1.2.  All data  were in accordance with set limits provided by Affymetrix.

hyb_protocol: cRNA was produced by the Microarray Core Facility (Children's Hospital, Boston) and hybridized to Affymetrix Zebrafish Genome Arrays as previously described (Shepard et al., 2005).

data_processing: Affymetrix default parameters

organism: Danio rerio

source_name: trunk and tail muscle, wildtype sibling 3.5 dpf

extract_protocol: At 3-3.5 dpf (at the onset of the visible phenotype), runzel mutants (ruz) and wildtype siblings (WT) were quickly dissected to remove head, heart and gut from skeletal muscle of the trunk and tail.  Pooled muscle was homogenized by douncing in Buffer RLT (Qiagen) and centrifuging through a QiaShredder column (Qiagen).  RNA was extracted from homogenate using either the Qiagen RNeasy or RNeasy Micro kit with an on-column DNase step according to manufacturer instructions.

tag: Wildtype siblings of runzel homozygotes on a TU/TL background (mix of heterozygotes and homozygous WT)

tag: 3.5 dpf


title: NT1 Vs TBV

description: NT1 vs TBV, different passages

tag: NT1, passage 14

tag: TBV, passage 13


title: WT 3.5dpf zebrafish muscle 2

source_name: trunk and tail muscle, wildtype siblings 3.5dpf

label_protocol: cRNA was produced by the Microarray Core Facility (Children's Hospital, Boston) and hybridized to Affymetrix Zebrafish Genome Arrays as previously described (Shepard et al., 2005).

tag: Wildtype siblings of Runzel homozygotes on a TU/TL background (mix of heterozygous and homozygous WT)


title: Gtf2iRD1 transfected vs mock transfected (rep2)

status: Public on Aug 01 2006

source_name: mock transfected MEF cell line

tag: mock transfected

source_name: Gtf2iRD1 transfected MEF cell line

tag: Gtf2iRD1 transfected


title: WT 3.5dpf zebrafish muscle 3

tag: Wildtype siblings of runzel homozygous mutants on a TU/TL background (mix of homozygous and heterozygous WT)


title: Ruz 3.5dpf zebrafish muscle 1

source_name: Trunk and tail muscle, runzel mutant, 3.5dpf

tag: Danio rerio Ruz homozygous mutant on a TL/TU background


title: AKH033

status: Public on Jul 01 2006

city: tours

first: pierre

last: charbord

address: 10 bd tonnellé

institute: Laboratoire d'hématologie de tours

description: AFT024 Versus BMC10

hyb_protocol: For each target preparation, 20 µg total RNA was reverse-transcribed using SuperscriptTM II reverse transcriptase (Life Technologies) in the presence of oligo(dT) primers and an amino-modified nucleotide (amino allyl dUTP). Amino-modified cDNAs were purified through a Microcon Centricon 30 microconcentrator (Amicon) and ethanol-precipitated. In a second step, monofunctional forms of Cy3 and Cy5 dyes (Amersham Biosciences) were coupled with the purified amino-modified cDNAs. Unincorporated fluorescent molecules and salts were removed using the Microcon Centricon 30. Labeled cDNA was mixed with 10 µg poly(A) RNA (Boehringer), 10 µg tRNA (Life Technologies), and 10 µg mouse Cot1 DNA (Life Technologies). Each slide was rehydrated over boiling water and quickly heated on a hot plate, and the probes were ultraviolet light-cross-linked in a Stratalinker at 254 nm/250 mJ. The slides were prehybridized in 5x SSC-0.1% SDS-1% BSA for 30 min at 50°C. Purified labeled targets were resuspended in 40 µl of hybridization solution (70% formamide-3.6x Dehnardt-0.7% SDS-8.6x saline-sodium phosphate-EDTA) and heated at 95°C for denaturation. The labeled targets were applied to prehybridized slides and covered with a 60 x 22-mm polyethylene coverslip (Sigma). The hybridization was performed at 42°C overnight. Washings were performed at room temperature for 15 min in 0.1x SSC-0.1% SDS and for 2 x 15 min in 0.1x SCC. The cell lines 2018, BFC012, BMC9 and BMC10 were each compared to AFT024. Each comparison was performed 4 times in both labeling orientations (8 hybridizations per comparison, 4 DyeSwap).

scan_protocol: Microarray Data Processing: fluorescence intensities of Cy3 and Cy5 were measured separately at 532 and 635 nm with a laser scanner (Axon Genepix4000A). The resulting 16-bit data files were imported into GenePix Pro 4.0 software (Axon) for image analysis. Spots with obvious blemishes were flagged. Genes with null intensity values and low mean intensity were also annotated with a specific flag.

data_processing: Ratio of Raw Data

tag: Obtained from Kateri Moore after infection of the stromal layer by the antigen T-Sv40. AFT024 appears to be a model of mesenchymal stem cells with the capacity of hematopoietic support and of differentiation into vascular smooth muscle

tag: Obtained from James E Dennis. Bone marrow lines had been obtained from transgenic immorta-mice generated by ES cells transfected with tsT. BMC10 had showed a low result in studied for their osteoclastic support  and positiv differentiation in osteoblastic, adipocytic (low) and chondrocytic.


title: AKH039

description: AFT024 Versus BMC10


title: TFII-I transfected vs mock transfected (rep1)

source_name: TFII-I transfected MEF cell line

tag: TFII-I transfected


title: Ruz 3.5dpf zebrafish muscle 2

source_name: Trunk and tail muscle, runzel mutant 3.5 dpf

tag: Runzel homozygous mutant on a TL/TU background


title: Ajx017

description: AFT024 versus BFC012

data_processing: ratio of raw data

source_name: BFC012 Fetal liver cell line

extract_protocol: After thawing, the cell lines were cultivated at 33°C (because of thermosensitive SV-40 T antigen) to obtain a sufficient cell number for the experiment (approximately 3.107 cells). Before confluence, cells were placed at 37°C, to slow growth in order to obtain the transcriptome at basal level. Total RNA was isolated directly from the cell layer, using the Trizol reagent (Invitrogen) following the manufacturer's instructions. Isopropanol was added with High Salt Solution (HSS) solution to accentuate the precipitation (HSS:  Sodium Citrate 0,8 M, NaCl 1,2 M). After precipitation and rinsing, RNA was solubilized in TE solution (Tris-HCl 10mM, EDTA 1mM) and preserved at -80°C. RNA was quantified by measuring the absorbance at 260 nm, the purity and integrity were checked by measuring the 260nm/280nm absorbance ratio and the ratio 28S/18S using an Agilent 2100 Bioanalyzer. All RNA presented optimal conditions to be used in the experiments.

tag: Obtained from Kateri Moore after infection of the stromal layer by the antigen T-Sv40. BFC012 show good capacity of vascular smooth muscle differentiation, but at the level of hematopoietic support,  BFC012 induces the rapid differentiation of hematopoietic stem cells

source_name: AFT024 fetal liver cell line


title: Ajx018

description: AFT024 versus BFC012

data_processing: Ratio of raw data

source_name: AFT024 Fetal liver cell line

source_name: BFC012 Fetal Liver cell line


title: TFII-I transfected vs mock transfected (rep2)

description: real MOGN_OMM16K-635_9-22-05


title: Gtf2iRD1 transfected vs mock transfected (rep1)


title: Ruz 3.5dpf zebrafish muscle 3

tag: Runzel homozygous mutant on a TU/TL background


title: NT1 Vs TBV_7

description: NT1 vs TBV, different passages


title: AKH040

description: AFT024 Versus BMC10


title: Akh030

description: AFT024 Versus BMC9

tag: Obtained from James E Dennis. Bone marrow lines had been obtained from transgenic immorta-mice generated by ES cells transfected with tsT. BMC9 had showed a positiv result in studied for their osteoclastic support  and positiv differentiation in osteoblastic, adipocytic and chondrocytic.


title: AKH006

description: AFT024 Versus BMC10


title: AKH004

description: AFT024 Versus BMC10


title: Akh029

description: AFT024 Versus BMC9


title: Akh035

description: AFT024 Versus BMC9


title: AKH005

description: AFT024 Versus BMC10


title: Alr016

description: AFT024 Versus BMC9


title: Alr017

description: AFT024 Versus BMC9


title: Akh014

description: AFT024 Versus BMC9


title: Alr010

description: AFT024 Versus 2018

tag: Obtained from Kateri Moore after infection of the stromal layer by the antigen T-Sv40. 2018 show good capacity of vascular smooth muscle differentiation, but at the level of hematopoietic support, 2018 is only B-lymphopoiesis-supportive


title: Alr008

description: AFT024 Versus 2018


title: Alr007

description: AFT024 versus 2018


title: Alr011

description: AFT024 Versus 2018


title: Akh003

description: AFT024 Versus BMC10


title: Alr012

description: AFT024 Versus 2018


title: Akh001

description: AFT024 versus BFC012

source_name: BFC012 fetal liver cell line


title: Alr013

description: AFT024 Versus 2018


title: Akh012

description: AFT024 Versus BMC9


title: Alr006

description: AFT024 versus 2018


title: Akh036

description: AFT024 Versus BMC9


title: Alr005

description: AFT024 versus BFC012

source_name: BFC012 Fetal Liver Cell Line

source_name: AFT024 Fetal Liver Cell Line


title: Akh032

description: AFT024 Versus BFC012

data_processing: Ratio of Raw data

source_name: AFT024 Fetal liver Cell Line


title: Treatment 1

status: Public on Jun 13 2006

city: LUBBOCK

last: San Francisco

state: TX

address: Flint and Main St

institute: Texas Tech University

description: Data for specific genes confirmed by Q-RT-PCR.

hyb_protocol: Equivalent amounts of cDNA (control and sample) labeled with Cy3 or Cy5 were mixed with 25 µl control target, 105 µl of 2 x hybridization buffer (Agilent Technologies, Inc. CA., USA) and then assembled in a chamber for hybridization.  Hybridization was carried out for 17 hours at 60°C in an Agilent oven. After hybridization, the slides were washed at room temperature, and then dried by spin.

scan_protocol: Arrays were scanned using an ArrayWoRx Auto scanner (Applied Precision Inc) with various exposure settings for Cy3 (595 nm) and Cy5 (685 nm) at 9.756 µm resolution, generating separate TIFF images.  Intensity data were acquired from images using SoftWoRx Tracker software.

data_processing: Images were imported and aligned with probe position (Agilent GAL file) using analyzerDG software automated and manual grid alignment features (MolecularWare Inc).  Median signal spot and individual median background intensity values were extracted for each wavelength and imported into GeneSpring (v. 7.2; Agilent), whereby replicate spots in each array were averaged.  Background-subtracted signals were corrected for unequal dye incorporation or unequal load of labeled product.  The algorithm consisted of a rank consistency filter and normalization using the LOWESS (locally weighted linear regression) method.  Saturated spots and the spots shown a reference signal lower than background were excluded from subsequent analyses.  Based on standard deviation calculations, probes (genes) having ≥ 1.5 or ≤ 0.66 final sample/control (S/C) ratios were selected as statistically significant sample up-regulated or sample down-regulated.  An increase or decrease of average signal log ratio from three biological replicates were evaluated by the GeneSpring software as significantly changed (t-test, P-value ≤ 0.05).

organism: Dickeya chrysanthemi

source_name: E. chrysanthemi exposed to phenolic acids

label_protocol: cDNA with aminoally-dUTP (Ambion) was labeled with Cy3 or Cy5 and purified on Qiagen MiniElute colums.

growth_protocol: Bacteria were grown at 30C in Luria Bertani medium shaken at 150 rpm for the duration of the experiment (90 min).

extract_protocol: Total RNA was extracted using manufacturer's instructions (Qiagen). RNA was quantified using NanoDrop and cDNA synthesized using Superscript (Invitrogen).

treatment_protocol: Exponentially growing bacteria were treated for 90 min with 0.078 mM each, Salicylic acid, Benzoic acid, t-cinnamic acid for the Treatment.

tag: Gram negative bacterium

tag: Enterobacteriaceae

tag: Plant pathogen

tag: Strain 3937

source_name: control

treatment_protocol: Exponentially growing bacteria were treated for 90 min with 0.078 mM Solvent dimethylsulfoxide (DMSO) as a control.


title: Alr004

description: AFT024 versus BFC012


title: Alr009

description: AFT024 Versus 2018


title: Akh011

description: AFT024 Versus BMC9


title: CD4+ splenocytes at 6h, biological replicate 1 sham-3

status: Public on Jun 01 2006

city: Saint Louis

first: Jonathan

middle: E

last: McDunn

state: MO

address: 660 South Euclid Avenue

institute: Washington University School of Medicine

description: Gene expression data from CD4+ splenocytes from a sham-manipulated mouse 6h after the induction of sham laparotomy.

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Mouse Transcriptome 430 2.0 (Affymetrix) according to the manufacturer's instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner G3000.

data_processing: The data were analyzed with dChip.

source_name: negatively selected CD4+ splenocytes from an individual mouse treated with sham laparotomy

label_protocol: Biotinylated cRNA was prepared using a two round amplification strategy for small (<1 microgram) samples  according to the manufacturer's instructions (Affymetrix)

extract_protocol: Total RNA was extracted according to the manufacturer's instructions (RNeasy, Qiagen)

treatment_protocol: Each mouse was anesthetized under halothane, its cecum exteriorized by laparotomy and manipulated (sham).  The cecum was then replaced and the belly closed in two layers.  Six hours later the spleen was harvested and the mouse euthanized.  The spleen was disaggregated over nylon mesh and CD4+ splenocytes were enriched by immunomagnetic selection (Miltenyi) according to manufacturer's instructions, lysed and RNA isolated.

tag: Genotype

value: C57Bl/6 mice

tag: Age

value: 8-12 weeks old


title: CD4+ splenocytes at 6h, biological replicate 1 sham-2


title: septic CD4+ splenocytes at 6h, biological replicate 5

description: Gene expression data from CD4+ splenocytes from a septic mouse.

source_name: negatively selected CD4+ splenocytes from an individual mouse treated with cecal ligation and puncture

treatment_protocol: Each mouse was anesthetized under halothane, its cecum exteriorized by laparotomy and ligated and punctured (septic).  The cecum was then replaced and the belly closed in two layers.  Six hours later the spleen was harvested and the mouse euthanized.  The spleen was disaggregated over nylon mesh and CD4+ splenocytes were enriched by immunomagnetic selection (Miltenyi) according to manufacturer's instructions, lysed and RNA isolated.


title: Akh013

description: AFT024 Versus BMC9


title: septic CD4+ splenocytes at 6h, biological replicate 2


title: DLD1

first: Damian

middle: Darren

last: Medici

address: 188 Longwood Ave. REB 413

department: Cell Biology

institute: Harvard Medical School

description: Control Sample

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

source_name: Colon Carcinoma

label_protocol: Affymetrix

extract_protocol: RNeasy mini (Qaigen)

treatment_protocol: Untreated

tag: See description from American Tissue Culture Collection (ATCC)


title: CD4+ splenocytes at 6h, biological replicate 1 sham-5


title: septic CD4+ splenocytes at 6h, biological replicate 3


title: septic CD4+ splenocytes at 6h, biological replicate 1

description: Gene expression data from CD4+ splenocytes from a septic mouse 6h after the induction of septic peritonitis.


title: CD4+ splenocytes at 6h, biological replicate 1 sham-4


title: septic CD4+ splenocytes at 6h, biological replicate 4


title: intactmale_day3_P.chabaudi_infected_rep03

city: Baltimore

first: Sabra

middle: Lynn

last: Klein

address: 615 North Wolfe Street

department: Molecular Microbiology and Immunology

description: Intensity of hybridization for each probe pair was computed by GCOS 1.2 software (Affymetrix). (For more detailed methods, please refer to the website of the Malaria Research Institute Gene Array Core Facility (MRI-GACF) at the Johns Hopkins Bloomberg School of Public Health http://jhmmi.jhsph.edu)

scan_protocol: standard Affymetrix procedures using affy GCS3000

data_processing: Affymetrix Microarray Suite version 5.0

source_name: WBCs from spleen

label_protocol: standard Affymetrix procedures

extract_protocol: trizol extraction followed by qiagen RNeasy total RNA cleanup protocol

tag: 'strain:C57BL/6', 'sex:male', 'treatment:intact', 'age:8-10wks', 'tissue

value: WBC from spleen', 'condition:infected 3 days'


title: CD4+ splenocytes at 6h, biological replicate 1 sham-1


title: gdxmale_day7_P.chabaudi_infected_rep03

institute: Johns Hopkins Bloomberg School of Public Health

tag: 'strain:C57BL/6', 'sex:male', 'treatment:gdx', 'age:8-10wks', 'tissue

value: WBC from spleen', 'condition:infected 7 days'


title: gdxmale_day3_P.chabaudi_infected_rep03


title: intactmale_day7_P.chabaudi_infected_rep03


title: intactmale_day14_P.chabaudi_infected_rep03

value: WBC from spleen', 'condition:infected 14 days'


title: gdxmale_day14_P.chabaudi_infected_rep03


title: gdxmale_day0_control_rep03

tag: 'strain:C57BL/6', 'sex:male', 'treatment:gonadectomized', 'age:8-10wks', 'tissue

value: WBC from spleen', 'condition:uninfected control'


title: gdxfemale_day0_control_rep03

tag: 'strain:C57BL/6', 'sex:female', 'treatment:gonadectomized', 'age:8-10wks', 'tissue


title: gdxfemale_day14_P.chabaudi_infected_rep03

tag: 'strain:C57BL/6', 'sex:female', 'treatment:gdx', 'age:8-10wks', 'tissue


title: gdxfemale_day3_P.chabaudi_infected_rep03


title: Akh002

description: AFT024 versus BFC012

tag: Obtained from Kateri Moore after infection of the stromal layer by the antigen T-Sv40. AFT024 appears to be a model of mesenchymal stem cells with the capacity of hematopoietic support and of differentiation into vascular smooth muscle


title: intactmale_day0_control_rep03


title: intactfemale_day7_P.chabaudi_infected_rep03

tag: 'strain:C57BL/6', 'sex:female', 'treatment:intact', 'age:8-10wks', 'tissue


title: intactfemale_day14_P.chabaudi_infected_rep03


title: Akh038

description: AFT024 versus BFC012

tag: After thawing, the cell lines were cultivated at 33°C (because of thermosensitive SV-40 T antigen) to obtain a sufficient cell number for the experiment (approximately 3.107 cells). Before confluence, cells were placed at 37°C, to slow growth in order to obtain the transcriptome at basal level. Total RNA was isolated directly from the cell layer, using the Trizol reagent (Invitrogen) following the manufacturer's instructions. Isopropanol was added with High Salt Solution (HSS) solution to accentuate the precipitation (HSS

value: Sodium Citrate 0,8 M, NaCl 1,2 M). After precipitation and rinsing, RNA was solubilized in TE solution (Tris-HCl 10mM, EDTA 1mM) and preserved at -80°C. RNA was quantified by measuring the absorbance at 260 nm, the purity and integrity were checked by measuring the 260nm/280nm absorbance ratio and the ratio 28S/18S using an Agilent 2100 Bioanalyzer. All RNA presented optimal conditions to be used in the experiments.


title: gdxmale_day0_control_rep02


title: intactmale_day14_P.chabaudi_infected_rep02


title: gdxmale_day7_P.chabaudi_infected_rep02


title: gdxmale_day14_P.chabaudi_infected_rep02


title: AKH034

description: AFT024 Versus BMC10

tag: Obtained from James E Dennis. Bone marrow lines had been obtained from transgenic immorta-mice generated by ES cells transfected with tsT. BMC10 had showed a low result in studied for their osteoclastic support  and positiv differentiation in osteoblastic, adipocytic (low) and chondrocytic.


title: gdxfemale_day7_P.chabaudi_infected_rep03


title: intactfemale_day3_P.chabaudi_infected_rep03


title: intactmale_day7_P.chabaudi_infected_rep02


title: intactmale_day0_control_rep02


title: intactfemale_day14_P.chabaudi_infected_rep02


title: intactfemale_day7_P.chabaudi_infected_rep02


title: gdxfemale_day0_control_rep02


title: intactfemale_day0_control_rep03


title: intactfemale_day0_control_rep02


title: gdxfemale_day14_P.chabaudi_infected_rep02


title: gdxfemale_day3_P.chabaudi_infected_rep02


title: gdxmale_day7_P.chabaudi_infected_rep01


title: gdxmale_day3_P.chabaudi_infected_rep02


title: gdxmale_day14_P.chabaudi_infected_rep01


title: intactmale_day3_P.chabaudi_infected_rep02


title: gdxmale_day3_P.chabaudi_infected_rep01


title: intactmale_day14_P.chabaudi_infected_rep01


title: gdxmale_day0_control_rep01


title: intactmale_day7_P.chabaudi_infected_rep01


title: intactfemale_day3_P.chabaudi_infected_rep02


title: gdxfemale_day14_P.chabaudi_infected_rep01


title: gdxfemale_day7_P.chabaudi_infected_rep02


title: intactmale_day3_P.chabaudi_infected_rep01


title: intactmale_day0_control_rep01


title: Anidulans_ethanol_3

status: Public on May 30 2006

city: Kgs. Lyngby

first: Ana Paula

last: Oliveira

address: Building 223

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

hyb_protocol: The biotin-labeled cRNA was then fragmented and approximately 13 micro-g of fragmented cRNA were hybridized to the custom-made NimbleExpressTM array (CBS01CMBA530008N), as described in the Affymetrix GeneChip® Expression Analysis Technical Manual (2004).

scan_protocol: The array was scanned by an Agilent GeneArray® Scanner. The scanned probe array images (.DAT files) were converted into .CEL-files using the GeneChip® Operating Software (GCOS) (Affymetrix).

data_processing: Raw probe intensities were pre-processed by applying the RMA (Robust Multiarray Average) method for background correction (based on PM probe information) (Irizarry et al, 2003), and were subsequently normalized using the qspline method (Workman et al, 2002). Gene expression index values were calculated using the method developed by Li & Wong (2001), using the PM-only model.

organism: Aspergillus nidulans

source_name: Aspergillus nidulans, growth in ethanol

label_protocol: Biotin-labeled cRNA was prepared from approximately 10 micro-g of total RNA, according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual (2004). An additional cleanup step was performed before fragmentation, using the Qiagen RNeasy Mini Kit (protocol for RNA Cleanup), in order to guarantee good-quality cRNA samples for subsequent processing. The cRNA was quantified in a spectrophotometer (Pharmacia Biotech) and its quality was assessed by gel electrophoresis and using a bioanalyzer (Agilent).

growth_protocol: Batch cultivation in a chemically defined medium as described by Agger et al (2002), with the following modifications: NH4Cl was used as the nitrogen source, in a concentration of 12.2 g/L, and three different carbon sources were tested, namely glucose, glycerol, and ethanol (10 g/L). Yeast extract was added to the fermenter in a concentration of 3 mg/L in order to encourage the germination of spores. Furthermore, the nutritional supplement p-aminobenzoic acid (PABA) was added to the medium in a concentration of 1 mg/L, as well as the antifoam agent 204 (Sigma), in a concentration of 0.05 mL/L.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini Kit, according to the protocol for isolation of total RNA from animal tissues. For the purpose, approximately 20-30 mg of frozen mycelium were placed in a 2 mL Eppendorf tube, pre-cooled in liquid nitrogen, containing three RNase-treated steel-balls (two balls with a diameter of 2 mm and one ball with a diameter of 5 mm). The tubes were then shaken in a Retsch Mixer Mill, at 3 degrees C, during 6-8 minutes, until the mycelia were ground to powder, and thus ready for extraction of total RNA. The quality and quantity of the total RNA extracted were determined by spectrophotometric analysis and by gel electrophoresis. The total RNA was stored at -80 degree C until further processing.

tag: Strain

value: Aspergillus nidulans A187 (pabaA1 ya1)

tag: Maximum specific growth rate

tag: Temperature

value: 30 degrees C

tag: pH


title: gdxfemale_day0_control_rep01


title: intactfemale_day14_P.chabaudi_infected_rep01


title: gdxfemale_day3_P.chabaudi_infected_rep01


title: Anidulans_glycerol_3

source_name: Aspergillus nidulans, growth in glycerol


title: intactfemale_day3_P.chabaudi_infected_rep01


title: intactfemale_day7_P.chabaudi_infected_rep01


title: gdxfemale_day7_P.chabaudi_infected_rep01


title: Anidulans_glycerol_2


title: Anidulans_glycerol_1


title: Anidulans_ethanol_2


title: Anidulans_ethanol_1


title: intactfemale_day0_control_rep01


title: Anidulans_glucose_2

source_name: Aspergillus nidulans, growth in glucose

growth_protocol: Batch cultivation was in a chemically defined medium as described by Agger et al (2002), with the following modifications: NH4Cl was used as the nitrogen source, in a concentration of 12.2 g/L, and three different carbon sources were tested, namely glucose, glycerol, and ethanol (10 g/L). Yeast extract was added to the fermenter in a concentration of 3 mg/L in order to encourage the germination of spores. Furthermore, the nutritional supplement p-aminobenzoic acid (PABA) was added to the medium in a concentration of 1 mg/L, as well as the antifoam agent 204 (Sigma), in a concentration of 0.05 mL/L.


title: Anidulans_glucose_3


title: Glucose uptake_PrfA interaction_3_1

status: Public on May 01 2006

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

description: scanning software: ScanArray express software version: 3.0

data_processing: value: log2 transformed ratio of normalized channel 2 median to channel 1 median; normalization method: LOWESS algorithm

organism: Listeria monocytogenes

source_name: prfA wild type

tag: Delta prfA containing plasmid pERL3 wild type prfA grown to OD 1.0 in minimal medium

source_name: prfA Star

tag: Delta prfA containing plasmid pERL3 pPrfAStar harvested at the same time when the other strain reached an OD 600 nm 1.0


title: Glucose uptake_PrfA interaction_3_6


title: Glucose uptake_PrfA interaction_3_3


title: inv/inv, inv-deltaC::GFP

city: Kyoto

first: Noriyuki

last: Sugiyama

state: Kyoto

department: Anatomy and Developmental Biology

institute: Kyoto Prefectural University of Medicine

description: The inv mutant is Nephronophthisis (NPHP) type 2 model mouse. The inv/inv,inv-deltaC::GFP mouse that was created by introduction of inv gene lacking the C-terminus into inv/inv mice develops multiple renal cysts without situs abnormality. The RNA used this array was inv/inv,inv-deltaC::GFP mice as cystic sample.

data_processing: MAS5.0, scaled to 500

source_name: kidney

tag: Gender

value: female

tag: Age

value: 28 days

tag: Tissue

value: kidney


title: Glucose uptake_PrfA interaction_3_4


title: Glucose uptake_PrfA interaction_3_5


title: +/+,inv-deltaC::GFP

description: The inv mutant is Nephronophthisis (NPHP) type 2 model mouse. The inv/inv,inv-deltaC::GFP mouse that was created by introduction of inv gene lacking the C-terminus into inv/inv mice develops multiple renal cysts without situs abnormality. The RNA used this array was +/+,inv-deltaC::GFP mice as control.

tag: Age:28 days

tag: tissue


title: Glucose uptake_PrfA interaction_2_2

source_name: Delta prfA

tag: Delta prfA containing plasmid pERL3 grown to OD 1.0 in minimal medium

tag: Delta prfA containing plasmid pERL3 pPrfAStar grown to OD 1.0 in minimal medium


title: Glucose uptake_PrfA interaction_2_6


title: Glucose uptake_PrfA interaction_2_1


title: Glucose uptake_PrfA interaction_1_2

tag: Delta prfA containing plasmid pERL3 pPrfAStar grown to OD 0.3 in minimal medium


title: Glucose uptake_PrfA interaction_1_3


title: Glucose uptake_PrfA interaction_3_2


title: Glucose uptake_PrfA interaction_1_1


title: Glucose uptake_PrfA interaction_2_3


title: Dark rearing, biological rep2 CHB DR-2

status: Public on Apr 30 2006

city: Cambridge

first: gabriel

last: kreiman

address: 77 Massachusetts Avenue MIT 46-5155

department: BCS

institute: MIT

description: Gene expression data from mouse primary visual cortex

hyb_protocol: Affymetrix hybridization protocol

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

source_name: Mouse primary visual cortex (V1)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 to 45 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals came from different litters and the tissue was derived from primary visual cortex (V1) of at least two different animals. In both groups of animals, monocular and binocular portions were included for analysis. Mice were anesthetized with Nembutal before tissue extraction.

extract_protocol: Followed the “Eukaryotic Target Preparation”  Affymetrix manual.

treatment_protocol: We followed the Eukaryotic Target Preparation” protocol as described in the Affymetrix manual.

tag: 129/SvEv male and female mice P27 primary visual cortex

tag: monocular deprivation was started at P11-12 before eye opening


title: Control, biological rep1 CHB Con-1


title: Glucose uptake_PrfA interaction_1_5

tag: Characteristics Delta prfA containing plasmid pERL3 grown to OD 1.0 in minimal medium


title: Control, biological rep2 CHB Con-2


title: Control, biological rep3 CHB Con-3


title: Dark rearing, biological rep3 CHB DR-3


title: Dark rearing, biological rep1 CHB DR-1


title: Glucose uptake_PrfA interaction_1_4


title: Monocular deprivation left cortex, biological rep3 CHB MD-6


title: Monocular deprivation left cortex, biological rep2 CHB MD-5


title: Monocular deprivation right cortex, biological rep2, CHB MD-2


title: Monocular deprivation right cortex, biological rep1 CHB MD-1


title: Glucose uptake_PrfA interaction_2_4


title: Monocular deprivation left cortex, biological rep1 CHB MD-4


title: Control, biological rep3


title: Control, biological rep2


title: Dark rearing, biological rep3

tag: animals reared in darkness until P27


title: Dark rearing, biological rep2


title: Monocular deprivation left cortex, biological rep1

treatment_protocol: We followed the "Eukaryotic Target Preparation” protocol as described in the Affymetrix manual."


title: Monocular deprivation right cortex, biological rep2


title: NEWBORN2_LIVER_sample2

first: Elizabeth

last: George

address: 715 Albany St

department: Bioinformatics

institute: Boston University

description: whole liver taken at 2 hours after birth.  RNA extracted for hybridization to MGU74Av2 chip.

label: affy kit

source_name: mouse liver at 2 hours after birth

tag: Strain

value: 2 hours

value: Liver


title: NEWBORN2_LIVER_sample1


title: NEWBORN6_LIVER_sample1

description: whole liver taken at 6 hours after birth.  RNA extracted for hybridization to MGU74Av2 chip.

source_name: mouse liver at 6 hours after birth

value: 6 hours


title: Monocular deprivation right cortex, biological rep1


title: FETAL_DAY21_LIVER_sample3

description: whole liver taken at gestation day 21.  RNA extracted for hybridization to MGU74Av2 chip.

source_name: mouse liver at gestation day 21

value: gestation day 21


title: Dark rearing, biological rep1


title: NEWBORN6_LIVER_sample2


title: Monocular deprivation left cortex, biological rep3


title: Monocular deprivation left cortex, biological rep2


title: Control, biological rep1


title: NEWBORN6_10%_OXYGEN_sample2

description: whole lung taken from mouse 6 hours after birth into 10% oxygen.

source_name: mouse lung 6 hours after birth into 10% oxygen

value: Lung

tag: Oxygen


title: NEWBORN6_10%_OXYGEN_sample1


title: FETAL_DAY21_LIVER_sample2


title: Glucose uptake_PrfA interaction_1_6


title: Glucose uptake_PrfA interaction_2_5


title: NEWBORN2_10%_OXYGEN_sample2

description: whole lung taken from mouse 2 hours after birth into 10% oxygen.

source_name: mouse lung at 2 hours after birth into 10% oxygen

value: 2 hours after birth


title: NEWBORN2_LIVER_sample3


title: NEWBORN6_10%_OXYGEN_sample3


title: NEWBORN2_10%_OXYGEN_sample1


title: NEWBORN2_10%_OXYGEN_sample3

source_name: mouse lung 2 hours after birth into 10% oxygen


title: NEWBORN6_LIVER_sample3


title: FETAL_DAY21_LIVER_sample1


title: Anidulans_glucose_1

tag: Maximum specific growth rate

tag: Temperature

tag: pH


title: Monocular deprivation right cortex, biological rep3, CHB MD-3


title: FETAL_DAY21_10%_OXYGEN_sample1

description: whole lung taken from mouse at day 21 of gestation, after mother was in 10% oxygen for 12 hours.

source_name: mouse lung at day 21 of gestation, 12 hours after mother placed in 10% oxygen

value: fetal day 21

value: lung


title: FETAL_DAY21_10%_OXYGEN_sample3

source_name: mouse lung at gestation day 21 in 10% oxygen


title: FETAL_DAY21_10%_OXYGEN_sample2

source_name: mouse lung at fetal day 21 in 10% oxygen


title: DLD1+LEF-1

description: Experimental Sample

source_name: Colon Carcinoma

treatment_protocol: Treatment with adenoviral LEF-1 expression construct (1:100) for 48 hours

tag: See description from American Tissue Culture Collection (ATCC)


title: Monocular deprivation right cortex, biological rep3


title: NEWBORN12_21%_OXYGEN_sample2

description: whole lung taken from mouse 12 hours after birth.  RNA extracted for hybridization.

source_name: mouse lung 12 hours after birth

tag: strain

tag: age

value: 12 hours after birth

value: whole lung


title: NEWBORN12_21%_OXYGEN_sample3


title: NEWBORN24_21%_OXYGEN_sample2

description: whole lung taken from mouse 24 hours after birth.  RNA extracted for hybridization.

source_name: mouse lung 24 hours after birth

value: 24 hours after birth


title: NEWBORN12_21%_OXYGEN_sample1


title: NEWBORN2_21%_OXYGEN_sample1

description: whole lung taken from mouse 2 hours after birth.  RNA extracted for hybridization.

source_name: mouse lung 2 hours after birth


title: NEWBORN6_21%_OXYGEN_sample1

description: whole lung taken from mouse 6 hours after birth.  RNA extracted for hybridization.

source_name: mouse lung 6 hours after birth

value: 6 hours after birth


title: FETAL_DAY21_21%_OXYGEN_sample3

description: whole fetal lung taken at day 21 of gestation.  RNA extracted for hybridization.

source_name: mouse lung fetal day 21

tag: Age

value: Fetal day 21

tag: Tissue