title: wild type 12.5 day murine embryo fibroblasts

city: Baltimore

first: Anne

last: Hamburger

address: 655 W. Baltimore St

department: Cancer Center

institute: University of Maryland Baltimore

description: Effect of depletion of EBp1 in knock out murine embryo fibroblasts.

hyb_protocol: The cRNA pellet was resuspended and fragmented by heat and ion-mediated hydrolysis at 95oC for 35 mins in 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc. The fragmented cRNA was hybridized for 16hr at 45oC to U133A oligonucleotide arrays (Affymetrix) containing ~39,000 full length annotated genes together with additional probe sets designed to represent EST sequences. Arrays were washed at 25oC with 6 X SSPE (0.9M NaCl, 60 mMNaH2PO4, 6 mM EDTA + 0.01% Tween 20) followed by a stringent wash at 50oC with 100 mM MES, 0.1M [Na+], 0.01% Tween 20. The arrays were then stained with phycoerythrein conjugated streptavidin (Molecular Probes) and the fluorescence intensities were determined using a laser confocal scanner (Hewlett-Packard).

scan_protocol: The scanned images were analyzed using Microarray software (Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to constant target intensity (2500) for all arrays used

data_processing: Data Analysis was conducted using Microarray Suite 5.0 (Affymetrix) following user guidelines. The signal intensity for each gene was calculated as (PM - MM)/(number of probe“the average intensity difference, represented by [ pairs)], where PM and MM denote perfect-match and mismatch probes

source_name: wild type murine embryo fibroblasts

label_protocol:
cRNA synthesis and labeling. First and second strand cDNA were synthesized g of total RNA using the SuperScript Double-Stranded cDNA Synthesisfrom 5-15  Kit (Gibco Life Technologies) and oligo-dT24-T7 (5â€™-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3â€™) primer according to the manufacturerâ€™s instructions.
cRNA was synthesized labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter coupled double stranded cDNA as template and the T7 RNA Transcript Labeling Kit (ENZO Diagnostics Inc.). Briefly, double stranded cDNA synthesized from the previous steps were washed twice with 70% l Rnase-free H2O. The cDNA was incubated with 4ethanol and resuspended in 22  l of 10X each Reaction Buffer, Biotin Labeled Ribonucleotides, DTT, Rnase l 20X T7 RNA Polymerase for 5 hr at 37oC. The labeled cRNAInhibitor Mix and 2  was separated from unincorporated ribonucleotides by passing through a CHROMA SPIN-100 column (Clontech) and precipitated at â€“20oC for 1 hr to overnight

growth_protocol: Cells propagated in complete medium and 10% FBS. Passage 2.

extract_protocol: RNA was extracted with Trizol

treatment_protocol: Embryos (12.5 days) were minced and incubated in 0.25% trypsin and 5 U of DNAse I for 37º C for 30 min. Dulbeccos MEM supplemented with 10% fetal bovine serum and penicillin and streptomycin were added to the cell suspension and cells centrifuged at 1000 rpm for 10 min.

tag: Murine embryos from wild type littermates were minced at 12.5 day and fibroblast cell lines established.


title: Gene expression in Ebp1 knock out murine embryo fibroblasts

status: Public on Mar 31 2009

type: RNA

state: MD

country: USA

description: Expression of RNA in 12.5 day murine embryo fibroblasts from Ebp1 knock out mice.

scan_protocol: The scanned images were analyzed using Microarray software (Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to constant target intensity (2500) for all arrays used.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Ebp1 knock out murine embryo (12.5 day) fibroblasts

growth_protocol: Fibroblasts were propagated in complete media with 10% FBS. RNA harvested at passage 2.

extract_protocol: RNA was extracted with Trizol.

tag: Murine embryos 12.5 day (Ebp1 knock out) were harvested and minced in trypsin. Fibroblasts were propagated as described.


title: stage 3-normoblasts A

city: Raanana

first: Yuval

last: Tabach

address: Hativat Givaty 30

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: gene expression data from late erythroid cells

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

organism: Homo sapiens

source_name: normoblasts

label_protocol: Affymetrix protocol

growth_protocol: cells were cultured in 2 phases. 6 days in phase I in medium with cyclosporin A and than in phase II with SCF, dexamethason and erythropoietin

extract_protocol: RNA was extracted with Tri-reagent according to the manufacturer's instruction.

treatment_protocol: cells were collected on days 6, 10 and 12 of differentiation.

tag: day 12 of culture


title: stage 2-intermediate A

description: gene expression data from intermediate erythroblasts.

source_name: intermediate erythroid cells

tag: day 10 of culture


title: stage 1-early erythroblast A

description: gene expression data from early erythroblasts.

source_name: early erythroid cells

tag: day 6 of culture


title: 161b; Patient 1, pre-Gleevec treatment

city: South San Francisco

first: Adam

middle: S

last: Adler

state: CA

address: 1 DNA Way

institute: Genentech

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78029.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 280, 5000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.66; Parameter Scan Time = 12:33:01; Parameter PMT Volts = 640; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 47972; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.66; Parameter Scan Time = 12:33:01; Parameter PMT Volts = 780; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 292812; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler

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

source_name: Total human reference

label_protocol: not provided

extract_protocol: not provided

tag: Total human reference

extract_protocol: Total RNA was extracted from skin biopsies before and after imatinib (Gleevec) treatment using Qiagen RNeasy fibrous tissue kit. RNA was amplified using the Ambion Amino Allyl MessageAmp II aRNA kit.


title: stage 3-normoblasts B


title: stage 2-intermediate B


title: Abomasum control 27 days

city: College Station

first: Kathryn

middle: M

last: MacKinnon

state: TX

address: 2881 F&B Road

institute: USDA-ARS-SPARC

description: Spot alignment was performed using MolecularWare DigitalGENOME Pro 2.5 (MolecularWare, Cambridge, MA), and spots were visualized for abnormalities.  Spots that were abnormal in shape, intensity saturation, or array imperfections were removed from subsequent analyses.  Total intensity values were obtained for each dye channel and normalized as described below to determine differences in gene expression.

hyb_protocol: Abomasal samples were hybridized to Michigan State University’s National Bovine Functional Genome Consortium (NBFGC) cDNA microarray according to procedures outlined by Suchyta et al., 2003-physiological Genomics. Hybridized arrays were washed at room temperature in 0.2X SSC, rinsed in double-distilled water, and dried by centrifugation.

scan_protocol: Images were scanned using the GeneTAC LS IV (Genomics Solutions) scanner and accompanying software (version 3.01).

data_processing:
Scanned florescent intensities for each individual array were log2 transformed to correct for right-tailed skewness.  Transformed data were inspected for Cy3 versus Cy5 dye bias using M vs A scatter plots for each array, where log intensity ratios M = log2(Cy3/Cy5) were plotted against mean log intensities A = [log2 (Cy3) + log2 (Cy5)]/2 for each spot on the array (Yang et al., 2002).    Adjustments were made for differential dye binding using locally weighted regression procedures (PROC LOESS) of SAS (SAS Institute, Cary, NC) (Madsen et al., 2004)).  Boxplots of normalized data from each array were compared, and median intensity and variance were found to differ.  To directly compare arrays, median intensity value was subtracted from all values for each array to obtain a median intensity of zero.  Deviations from the geometric mean of each array were calculated, and the mean of the absolute value of the deviation was used to adjust the variance of each array.  This adjustment equalized variance across arrays within day and infection status.  Raw images and LOESS-transformed normalized spot intensities are available at http://www.ebi.ac.uk/microarray-as/ae/.
A two-step mixed model analysis using the mixed-model procedure of SAS (SAS Institute, Cary, NC) was then performed (Wolfinger et al., 2001).  The first step adjusted for array-specific variation using the following model:
yijk = µ + αi + βj + εijk
where yijk is the normalized intensity value, µ is the overall mean, αi is the random effect for array i, βj is the fixed effect for dye j, and εijk is the residual.  Residuals were then carried over to the second step, which tested for gene-specific effects of breed composites using the model:
εijkl = µl + αil + βjl + γkl + βγjkl + φijkl
where all effects have the same definition as before except effects are now gene-specific (indicated by subscript l), γkl is the fixed effect for breed type k, and φijkl is the residual.  Differences in gene expression of hair and wool sheep were assessed using two-tailed t-tests of least square means for each experimental group.

label: Cy3, Cy5

organism: Ovis aries

label_protocol: Total RNA from abomasum  (12 µg) was used as a template for reverse transcription (Superscript III, Invitrogen).  Resulting amino-allyl modified cDNA was then labeled with either Cy3 or Cy5 dye (Amersham Pharmacia Biotech, Piscataway, NJ).   Unincorporated dye was removed, and labeled cDNA was concentrated to a volume of less than 10 µL using Microcon 30 spin columns (Millipore Corp.).  Concentrated cDNAs were mixed with 100 µL of SlideHyb #3 (Ambion, Inc., Austin, TX) and incubated at 70°C for 5 minutes before hybridization to glass microarrays.

extract_protocol: Total RNA was extracted from abomasal tissue using TRIzol reagent (Invitrogen Inc., Carlsbad, CA) according to manufacturer’s protocols.  Quantity of RNA was assessed using a UV spectrophotometer, and gel electrophoresis was used to ensure that RNA was of high quality with minimal degradation.

tag: tissue

value: abomasum

tag: strain

value: St. Croix hair sheep

value: 50% Dorset, 25% Finnsheep, 25% Ramboillet wool sheep composite


title: stage 1-early erythroblast B


title: 232a; Patient 2, post-Gleevec treatment

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78034.gif
Compound Based Treatment: 200 mg

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 4880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 13:18:50; Parameter PMT Volts = 650; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 48017; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 13:18:50; Parameter PMT Volts = 790; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 292858; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler

treatment_protocol: Treated with 200 mg Gleevec daily for 6 months


title: ABomasum infected 3 days


title: 161a; Patient 1, pre-Gleevec treatment

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78028.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 4840; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.66; Parameter Scan Time = 12:21:16; Parameter PMT Volts = 640; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 47959; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.66; Parameter Scan Time = 12:21:16; Parameter PMT Volts = 770; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 292800; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: 232b; Patient 2, post-Gleevec treatment

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78035.gif
Compound Based Treatment: 200 mg

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 4960; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.85; Parameter Scan Time = 13:27:15; Parameter PMT Volts = 650; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 48025; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.85; Parameter Scan Time = 13:27:15; Parameter PMT Volts = 780; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 292865; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: 215b; Patient 2, pre-Gleevec treatment

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78033.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 240, 4880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 13:09:35; Parameter PMT Volts = 650; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 48007; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 13:09:35; Parameter PMT Volts = 770; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 292848; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: N3, Normal blood neutrophils

city: Bern

first: Shida

last: Yousefi

state: Bern

address: Inselspital, INO-F

department: Pharmacology

country: Switzerland

institute: University of Bern

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: After scanning of the probe arrays, digitalized image data were processed using Affymetrix Microarray Suite 5.0 software. In addition to determining the expression level for each gene (so called "signal"), this software assigns a "detection" call, absent (A) (not expressed), present (P) (expressed) and marginal (M) (marginally expressed) for each gene measured. The overall fluorescence intensity was scaled to a global intensity of 500 to enable the comparison between chips. The expression data for all genes were exported to GeneSpring 5.0 (Silicon Genetics, Redwood City, CA). The following criteria were used to select differentially expressed genes in GM-CSF-treated versus freshly isolated neutrophils: 1) Student's t test with a multiple testing correction (Benjamini-Hochberg) significance level p < 0.05; 2) fold-change cut-off of 2 in both directions; 3) the P calls had to coincide with the regulation in question, e.g. if a candidate gene were to be called "up-regulated" in GM-CSF treated cells, triplicate samples in the "treated" group had to be called P, and vice versa, if a gene were to be called "down-regulated", triplicate samples in the untreated group had to have a P call. The selected differentially expressed genes were normalized to a mean of 0 and a S.D. of 1, log2-transformed, and subjected to average-linkage hierarchical clustering using the uncentered Pearson similarity matrix.

source_name: GMCSF treated neutrophils

label_protocol: Affymetrix

growth_protocol: Mature human blood neutrophils were isolated from peripheral blood of healthy donors by Ficoll-Hypaque centrifugation. Briefly, peripheral blood mononuclear cells (PBMC) were separated by centrifugation on Ficoll-Hypaque (Seromed-Fakola AG, Basel, Switzerland). The lower phase, mainly granulocytes and  erythrocytes, was treated with erythrocyte lysis solution (155 mmol/l NH4Cl, 10 mmol/l KHCO3, and 0.1 mmol/l EDTA, pH 7.3). The resulting cell populations contained greater than 95% mature neutrophils as assessed by staining with Diff-Quik (Medion GmbH, Düdingen, Switzerland) and light microscopy analysis. Human neutrophils were cultured at 1million cells per ml in complete culture medium (RPMI 1640 containing 10% fetal calf serum) and treated with GM-CSF (50 ng/ml).

extract_protocol: RNA was extracted using TRIZOL (Invitrogen) exactly as recommeded.

treatment_protocol: Cells were centrifuged at 1400 rpm for 7 min at 4°C, washed once with cold PBS and the pellet was resuspended in TRIZOL reagent (Invitrogen).

tag: cell type

value: GM-CSF treated neutrophils


title: 215a; Patient 2, pre-Gleevec treatment

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78032.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 4960; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 13:00:49; Parameter PMT Volts = 650; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 47999; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 13:00:49; Parameter PMT Volts = 770; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 292840; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: 170a; Patient 1, post-Gleevec treatment

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78030.gif
Compound Based Treatment: 100 mg

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 5000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.87; Parameter Scan Time = 12:41:37; Parameter PMT Volts = 640; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 47979; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.87; Parameter Scan Time = 12:41:37; Parameter PMT Volts = 760; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 292820; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler

treatment_protocol: Treated with 100 mg Gleevec twice daily for 3 months


title: Abomasum control 17 days


title: N2, Normal blood neutrophils


title: N1, Normal blood neutrophils


title: Lymph node control 17 days

hyb_protocol: Lymph node samples were hybridized to Michigan State University’s Bovine total leukocyte version 3 (BOTL3) cDNA microarray according to procedures outlined by Suchyta et al., 2003-physiological Genomics. Hybridized arrays were washed at room temperature in 0.2X SSC, rinsed in double-distilled water, and dried by centrifugation.

label_protocol: Total RNA from lymph node (10 µg) was used as a template for reverse transcription (Superscript III, Invitrogen).  Resulting amino-allyl modified cDNA was then labeled with either Cy3 or Cy5 dye (Amersham Pharmacia Biotech, Piscataway, NJ).   Unincorporated dye was removed, and labeled cDNA was concentrated to a volume of less than 10 µL using Microcon 30 spin columns (Millipore Corp.).  Concentrated cDNAs were mixed with 100 µL of SlideHyb #3 (Ambion, Inc., Austin, TX) and incubated at 70°C for 5 minutes before hybridization to glass microarrays.

extract_protocol: Total RNA was extracted from abomasal lymph node tissue using RNeasy miniprep kit (qiagen)  according to manufacturer’s protocols.  Quantity of RNA was assessed using a UV spectrophotometer, and gel electrophoresis was used to ensure that RNA was of high quality with minimal degradation.

value: lymph node


title: Lymph node control 27 days


title: Lymph node control 38 days


title: Mtb strain TB294 overexpressing sigma factor A (experiment 2 dye-flip)

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

description: File name for original .gpr "09-21-05_Comparison1-2", VM(cy5) vs SM(cy3)

hyb_protocol: II. Prehybridization 1. Prepare Prehybridization Solution (Fresh Each Time) **this volume is based on a glass dish with a base measurement of 11x8cm. This dish allows for a pre-hyb of 1-4 slides. Adjust volume accordingly based on size of dish and/or number of slides. 106.0ml dH2O 3.0g BSA 1.2ml 10%SDS 2. Add Prehybridization solution to a glass slide-staining dish and place post-processed slides array side up into solution. Make sure there are no bubbles on the surfaces of the slides. 3. Place the staining jar containing the Prehybridization solution and slides into a waterbath and hybridize for 1 hour at 42oC. 4. Take the prehybridized slides out of the Prehybridization solution and place into a slide holder submerged in a slide-washing tray containing nuclease-free water. Wash slides for 2 minutes with constant shaking up and down. 5. Transfer slide rack to a slide washing tray containing isopropanol and wash for 2 minutes with constant shaking up and down. 6. Take the slides in the isopropanol bath to the centrifuge to keep the slides wet until you can dry them rapidly. Spin at 600 RPM in a 50ml conical for 3 minutes to dry. **Complete this step within one hour of hybridization III. Hybridization 1. Add the following to the 5µl labeled sample. 0.5µl 10 mg/ml tRNA 1.0µl 20X SSC 2.5ul Formamide 1.0µl 1% SDS 2. Heat to 98 oC for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg. Let cool for 5 min. 3. Pipette cooled 10µl hybridization solution on microarray. Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate). 4. OPTIONAL: Apply thin wall of rubber cement around the 4 corners of the coverslip to avoid movement. This step is recommended if your waterbath is not perfectly level. 5. Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50oC water bath **Bubbles (esp. large ones) can be troublesome for your arrays since they can cause areas of non-hybridization. To avoid bubbles, do not use the blowout feature of the pipette when adding the probe to the slide. Also, clean your coverslips with alcohol and lint-free wipes before placing over probe. IV. Post Hyb washes (next day) 1. Remove cover slip while array is submerged in first wash solution (2XSSC + 0.1% SDS), transfer to submerged microscope slide staining racks and rinse for 1 min in 1X SSC+0.05% SDS with agitation/shaking. 2. Rinse in 0.06X SSC with shaking. Transfer to another submerged staining rack and wash 2 min in fresh 0.06X SSC with shaking. 3. Centrifuge 3 min at 1000 rpm in a 50ml conical (array edge up) to dry. Scan immediately.

scan_protocol: After washing, the arrays were scanned with a GenePix4000B scanner (Molecular Devices, Sunnyvale, CA). The images were processed using GenePix 5.1 and the resulting text files were exported to Microsoft Excel.

data_processing: The data were filtered by removing all spots that were below the background noise or flagged as ‘bad’. Spots were considered to be below the background noise if the sum of the median intensities of the two channels was less than twice the highest average background of the chip. The chips were normalized by the print-tip Lowess method {Dudoit, 2000 #200}.

organism: Mycobacterium tuberculosis

source_name: strain TB294-pCV

label_protocol:
I. Synthesis and Labeling of cDNA
1. Bring 1.5µg of RNA to a volume of 11µl (in a PCR tube) with nucleotide-free water and add 2.2µl (2mg/ml) random primers (pulse spin to collect contents).
2. Heat 2 min at 98oC, snap cool on ice.
3. (Keep on ice) and add 11.1µl of the following reaction mix:
5.0µl 5X First-Strand buffer
2.5µl 100 mM DTT
2.3µl low dTdNTP mix (5mM A,G,C and 0.2mM T stock)
1.5ul Cy3 or Cy5
Then add 1.2ul Superscript, vortex to mix and spin to collect contents
4. Incubate 10 min at 25oC followed by 90 min at 42oC in PCR machine.
**Can freeze or leave at 4oC overnight if necessary
5. Prime a microcon10 column (YM10 from Millipore) with 400µl TE and spin for 10 min at 10,000 Xg. Empty flow-through in collection tube and return primed column. Add both reactions (cy3 and cy5) to column and centrifuge at 10,000 Xg until ~25µl remaining (~20-30 min). Wash with 200µl TE and spin until almost dry (<5µl).
6. Recover cDNA by inverting microcon into new collection 1.5 ml tube and centrifuge at half max speed 1 min.
7. Bring sample to 5µl with TE.
The detailed labeling and hybridization protocol can be obtained at http://www.cag.icph.org/downloads_page.htm#LabelingProtocols.

growth_protocol: Bacteria were grown in monocytes as follows. Prior to infection, the human monocytic cell line MonoMac6 was cultured in RPMI medium containing 10% heat-inactivated fetal bovine serum, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate and 9 ug/ml of bovine insulin. The cells were then infected with single-cell suspensions of M. tuberculosis in RPMI containing 10% heat-inactivated human serum at a multiplicity of infection of 1:1. Infected monocytes were incubated at 37 ˚C in 5% CO2.

extract_protocol: At 6 days after infection, the supernatant was aspirated from the infected monocytes, and the monocytes were lysed with 1 ml of extraction buffer (2 M guanidine isothiocyanate, 200 mM Tris-HCl, pH 8.3, 300 mM LiCl, 10 mM EDTA) per 106 cells. After sonication for 10 seconds with an ultrasonic cell disrupter, the suspension was centrifuged at 7000 g for 10 min to pellet the bacilli. The pellet was washed with the extraction buffer. To disrupt the bacteria and extract the RNA, samples were transferred to Lysing Matrix B tubes (BIO 101) containing RNAzol B (TEL-TEST) and were agitated using a FastPrep FP120 shaker (BIO 101). Chloroform extraction was performed to remove proteins and DNA and then the RNA was precipitated using isopropanol. Pellets were washed with 70% ethanol, dried, resuspended in DEPC-water and then any remaining chromosomal DNA was removed with “DNA-free” treatment and removal reagents (Ambion). The bacterial RNA was further purified with the MICROBEnrich kit (Ambion) which removes eukaryotic RNA. RNA integrity was confirmed by electrophoresis on an agarose gel.

tag: recombinant strain TB294-pCV, the vector control strain for TB294-pSigA. Strain contains the same extrachromosomal plasmid as TB294-pSigA without the sigma factor A gene

source_name: recombinant strain TB294-pSigA

tag: recombinant strain TB294-pSigA, contains an extrachromosomal plasmid that overexpresses the sigma factor A gene from the hsp60 promoter. Strain is derived from TB294, which is a clinical isolate of strain 210, and a member of the W-Beijing family of M. tuberculosis strains


title: Lymph node infected 27 days

source_name: Lymph node, infected, 27 days_hair

label_protocol: Total RNA from abomasum  (10 µg) was used as a template for reverse transcription (Superscript III, Invitrogen).  Resulting amino-allyl modified cDNA was then labeled with either Cy3 or Cy5 dye (Amersham Pharmacia Biotech, Piscataway, NJ).   Unincorporated dye was removed, and labeled cDNA was concentrated to a volume of less than 10 µL using Microcon 30 spin columns (Millipore Corp.).  Concentrated cDNAs were mixed with 100 µL of SlideHyb #3 (Ambion, Inc., Austin, TX) and incubated at 70°C for 5 minutes before hybridization to glass microarrays.

source_name: Lymph node, infected, 27 days_Wool


title: Neu2, GMCSF treated neutrophils

source_name: Normal blood neutrophils

value: Normal blood neutrophils


title: Neu1, GMCSF treated neutrophils


title: Neu3, GMCSF treated neutrophils


title: Lymph node infected 3 days


title: 170b; Patient 1, post-Gleevec treatment

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78031.gif
Compound Based Treatment: 100 mg

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.12; Parameter Scan Time = 12:50:13; Parameter PMT Volts = 650; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 47988; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.12; Parameter Scan Time = 12:50:13; Parameter PMT Volts = 770; Parameter Scan Date = 2008-01-03; Parameter Pixel Size = 10; Parameter Laser on time = 292829; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Mtb strain TB294 overexpressing sigma factor A (experiment 1)

description: File name for original .gpr "04-07-05_Comparison1-1", VHU(cy3) vs SHU(cy5)

hyb_protocol: II.  Prehybridization 1.  Prepare Prehybridization Solution (Fresh Each Time) **this volume is based on a glass dish with a base measurement of 11x8cm.  This dish allows for a pre-hyb of 1-4 slides.  Adjust volume accordingly based on size of dish and/or number of slides. 	106.0ml dH2O 	3.0g BSA 	1.2ml 10%SDS 2.	Add Prehybridization solution to a glass slide-staining dish and place post-processed slides array side up into solution.  Make sure there are no bubbles on the surfaces of the slides. 3.	Place the staining jar containing the Prehybridization solution and slides into a waterbath and hybridize for 1 hour at 42oC. 4.	Take the prehybridized slides out of the Prehybridization solution and place into a slide holder submerged in a slide-washing tray containing nuclease-free water.   Wash slides for 2 minutes with constant shaking up and down. 5.	Transfer slide rack to a slide washing tray containing isopropanol and wash for 2 minutes with constant shaking up and down. 6.	Take the slides in the isopropanol bath to the centrifuge to keep the slides wet until you can dry them rapidly.  Spin at 600 RPM in a 50ml conical for 3 minutes to dry. **Complete this step within one hour of hybridization  III.  Hybridization 1.	Add the following to the 5µl labeled sample. 0.5µl 10 mg/ml tRNA 1.0µl 20X SSC 2.5ul Formamide 1.0µl 1% SDS 2.	Heat to 98 oC for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg.  Let cool for 5 min. 3.	Pipette cooled 10µl hybridization solution on microarray.  Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate). 4.	OPTIONAL:  Apply thin wall of rubber cement around the 4 corners of the coverslip to avoid movement.  This step is recommended if your waterbath is not perfectly level. 5.	Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50oC water bath **Bubbles (esp. large ones) can be troublesome for your arrays since they can cause areas of non-hybridization.  To avoid bubbles, do not use the blowout feature of the pipette when adding the probe to the slide.  Also, clean your coverslips with alcohol and lint-free wipes before placing over probe. IV. Post Hyb washes (next day) 1.	Remove cover slip while array is submerged in first wash solution (2XSSC + 0.1% SDS), transfer to submerged microscope slide staining racks and rinse for 1 min in 1X SSC+0.05% SDS with agitation/shaking. 2.	Rinse in 0.06X SSC with shaking. Transfer to another submerged staining rack and wash 2 min in fresh 0.06X SSC with shaking. 3.	Centrifuge 3 min at 1000 rpm in a 50ml conical (array edge up) to dry.  Scan immediately.

scan_protocol: After washing, the arrays were scanned with a GenePix4000B scanner (Molecular Devices, Sunnyvale, CA).  The images were processed using GenePix 5.1 and the resulting text files were exported to Microsoft Excel.

data_processing: The data were filtered by removing all spots that were below the background noise or flagged as ‘bad’.  Spots were considered to be below the background noise if the sum of the median intensities of the two channels was less than twice the highest average background of the chip.  The chips were normalized by the print-tip Lowess method {Dudoit, 2000 #200}.

label_protocol:
I.  Synthesis and Labeling of cDNA
1.	Bring 1.5µg of RNA to a volume of 11µl (in a PCR tube) with nucleotide-free water and add 2.2µl (2mg/ml) random primers (pulse spin to collect contents).
2.	Heat 2 min at 98oC, snap cool on ice.
3.	(Keep on ice) and add 11.1µl of the following reaction mix:
	5.0µl 5X First-Strand buffer
2.5µl 100 mM DTT
2.3µl low dTdNTP mix (5mM A,G,C and 0.2mM T stock)
1.5ul Cy3 or Cy5
	Then add 1.2ul Superscript, vortex to mix and spin to collect contents
4.	Incubate 10 min at 25oC followed by 90 min at 42oC in PCR machine.
**Can freeze or leave at 4oC overnight if necessary
5.	Prime a microcon10 column (YM10 from Millipore) with 400µl TE and spin for 10 min at 10,000 Xg.  Empty flow-through in collection tube and return primed column.  Add both reactions (cy3 and cy5) to column and centrifuge at 10,000 Xg until ~25µl remaining (~20-30 min).  Wash with 200µl TE and spin until almost dry (<5µl).
6.	Recover cDNA by inverting microcon into new collection 1.5 ml tube and centrifuge at half max speed 1 min.
7.	Bring sample to 5µl with TE.
The detailed labeling and hybridization protocol can be obtained at http://www.cag.icph.org/downloads_page.htm#LabelingProtocols.

extract_protocol: At 6 days after infection, the supernatant was aspirated from the infected monocytes, and the monocytes were lysed with 1 ml of extraction buffer (2 M guanidine isothiocyanate, 200 mM Tris-HCl, pH 8.3, 300 mM LiCl, 10 mM EDTA) per 106 cells. After sonication for 10 seconds with an ultrasonic cell disrupter, the suspension was centrifuged at 7000 g for 10 min to pellet the bacilli. The pellet was washed with the extraction buffer.  To disrupt the bacteria and extract the RNA, samples were transferred to Lysing Matrix B tubes (BIO 101)  containing RNAzol B (TEL-TEST) and were agitated using a FastPrep FP120 shaker (BIO 101).  Chloroform extraction was performed to remove proteins and DNA and then the RNA was precipitated using isopropanol. Pellets were washed with 70% ethanol, dried, resuspended in DEPC-water and then any remaining chromosomal DNA was removed with “DNA-free” treatment and removal reagents (Ambion). The bacterial RNA was further purified with the MICROBEnrich kit (Ambion) which removes eukaryotic RNA.  RNA integrity was confirmed by electrophoresis on an agarose gel.

tag: recombinant strain TB294-pSigA, contains an extrachromosomal plasmid that overexpresses the sigma factor A gene from the hsp60 promoter. Strain is derived from TB294, which is a clinical isolate of strain 210, and a member of the W-Beijing family of M. tuberculosis strains.

source_name: recombinant strain TB294-pCV


title: Mtb strain TB294 overexpressing sigma factor A (experiment 1 dye-flip)

description: File name for original .gpr "04-07-05_Comparison1-2", VHU(cy5) vs SHU(cy3)


title: Mtb strain TB294 overexpressing sigma factor A (experiment 2)

description: File name for original .gpr "09-21-05_Comparison1-1", VM(cy3) vs SM(cy5)


title: Rat lung-1 vs mix1

status: Public on Mar 30 2009

city: Shanghai

first: Jing

last: Liao

address: 320 Yue Yang Road

country: China

institute: Institute of Biochemistry and Cell Biology  Shanghai Institutes for Biological Sciences  Chinese Academy of Science

description: Please see manufacturer's web site at http://www.agilent.com/

data_processing: The microarray was scanned by Agilent G2565BA scanner,raw data were extracted by Feature Extraction Software. Signal intensity were normalized using Lowess method ,GeneSpring 10.0 . VALUE:Cy3/Cy5 signal intensity, ratio:Log2 transformed

organism: Rattus norvegicus

source_name: Rat lung-1

growth_protocol: without cell culture

extract_protocol: Total RNA are isolated from cell pellets using TriZol reagent(Invitrogen) followed by Rneasy mini kit (Qiagen) clean-up.

treatment_protocol: untreated

tag: Rat lung-1 was extracted directed from the rat heart tissue skived with liquid nitrogen and then solved in Trizol.

growth_protocol: Rat bone marrow cells (BMC) were cultured in αDMEM culture medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum. Rat primary ear fibroblasts (PEF) were cultured in DMEM culture medium (Invitrogen) supplemented with 10% fetal bovine serum.

tag: mix1 was the mixture of Rat bone marrow cells (BMC) and Rat primary ear fibroblasts (PEF).


title: Rat lung-2 vs mix1

department: Institute of Biochemistry and Cell Biology

hyb_protocol: Please see manufacturer's web site at http://www.agilent.com/

source_name: Rat lung-2

tag: Rat lung-2 was extracted directed from the rat heart tissue skived with liquid nitrogen and then solved in Trizol.


title: Rat heart-1 vs mix1

scan_protocol: Please see manufacturer's web site at http://www.agilent.com/

source_name: Rat heart-1

tag: Rat heart-1 was extracted directed from the rat heart tissue skived with liquid nitrogen and then solved in Trizol.


title: Rat heart-2 vs mix1

source_name: Rat heart-2

label_protocol: Please see manufacturer's web site at http://www.agilent.com/


title: Rat iPS M13-3 vs mix1

description: This is one of the three repeated sample data.

data_processing: The microarray was scanned by Agilent G2565BA scanner,raw data  were extracted by Feature Extraction Software. Signal intensity  were normalized using Lowess method ,GeneSpring 10.0 . VALUE:Cy3/Cy5 signal intensity, ratio:Log2 transformed

source_name: Rat iPS M13-3

growth_protocol: Rat iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) in Knockout DMEM supplemented with 10% ES cell qualified fetal bovine serum, 10% KnockOut serum replacer, 0.1 mM non-essential amino acids, 1 mM L-glutamine, and 0.1 mM ß-mercaptoethanol (ES media) (all from Invitrogen, Carlsbad, CA).

tag: SD Rat iPS M13 cells were maintained on irradiated primary murine embryonic feeders (PMEF).


title: 559N.normal.Cy3

city: St. Louis

first: Robert

last: Lesurf

state: MO

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

institute: Washington University in St. Louis

description: RNA isolated from laser capture microdissected mammary tissue.

hyb_protocol: Following fragmentation, 750ng of cRNA was hybridized to Agilent's Whole Mouse Genome expression array (G4122A) according to the protocols provided by the manufacturer.

scan_protocol: Array was scanned using Agilent's dual-laser microarray scanner (Model G2505B), and Cy5/Cy3-signals were quantified using Agilent's Feature Extraction software (Palo Alto, CA).

data_processing: Raw Cy5 and Cy3 intensities were background corrected using the RMA background correction algorithm. Data was transformed to log2 ratios and within array normalization was performed using spatial and intensity-dependent loess.

source_name: Normal epithelial tissue from murine mammary glands

label_protocol: 4ng of extracted RNA was subjected to two rounds of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy3-labeled cRNA was prepared from 4-5ug total RNA using Ambion's MessageAmp kit.

extract_protocol: Phenol-chloroform extraction

tag: Sample identifier

value: 559N; Diagnosis:normal; Sex:Female; Strain:FVB/N

source_name: Stratagene universal mouse reference

label_protocol: 4ng of extracted RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy5-labeled cRNA was prepared from 4-5 ug total RNA using Ambion's MessageAmp kit.

extract_protocol: No extraction


title: Rat iPS F65-2 vs mix1

source_name: Rat iPS F65-2

tag: SD Rat iPS F65 cells were maintained on irradiated primary murine embryonic feeders (PMEF).


title: Rat iPS M13-2 vs mix1

source_name: Rat iPS M13-2


title: Rat iPS F65-3 vs mix1

source_name: Rat iPS F65-3


title: 6696T.tumor.Cy3

source_name: Tumor epithelial tissue from murine mammary glands

value: 6696T; Diagnosis:erbb2-type carcinoma; Sex:Female; Strain:FVB/N


title: Rat iPS M13-1 vs mix1

source_name: Rat iPS M13-1


title: Abomasum control 38 days


title: dye-swap experiment between EG4 and Nipponbare 2

city: Athens

first: Ken

last: Naito

state: GA

address: 4505 Miller Plant Sciences Building

department: Plant Biology

institute: University of Georgia

description: 400 ng RNAs were labeled and 1µg of Cy3- and Cy5-labeled cRNAs were used.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent scanner model G2505B, software G2565BA

data_processing: Data was analyzed by Fearure Extraction software (version 9.1, Agilent)

organism: Oryza sativa Japonica Group

source_name: Gimbozu EG4 replicate 2

label_protocol: Low RNA inout Lineat Amplification/Labeling Lit (Agilent)

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

tag: age

value: 7-day-old seedling

tag: disease state

value: healthy

tag: cultivar

value: Gimbozu EG4

source_name: Nipponbare replicate 2

value: Nipponbare


title: Rat iPS F65-1 vs mix1

source_name: Rat iPS F65-1


title: 559T.tumor.Cy3

value: 559T; Diagnosis:solid nodular, erbb2-type carcinoma; Sex:Female; Strain:FVB/N


title: 6696N.normal.Cy3

value: 6696N; Diagnosis:normal; Sex:Female; Strain:FVB/N


title: dye-swap experiment between EG4 and Nipponbare 1

source_name: Nipponbare replicate 1

source_name: Gimbozu EG4 replicate 1


title: 5033T.tumor.Cy3

value: 5033T; Diagnosis:erbb2-type carcinoma; Sex:Female; Strain:FVB/N


title: 4164T.tumor.Cy3

value: 4164T; Diagnosis:erbb2-type carcinoma; Sex:Female; Strain:FVB/N


title: 3229T.tumor.Cy3

value: 3229T; Diagnosis:adenosquamous carcinoma; Sex:Female; Strain:FVB/N


title: 562N.normal.Cy3

value: 562N; Diagnosis:normal; Sex:Female; Strain:FVB/N


title: 3229N.normal.Cy5.45k

hyb_protocol: Following fragmentation, 825ng of cRNA was hybridized to Agilent's Whole Mouse Genome expression array (G4122F) according to the protocols provided by the manufacturer.

label_protocol: 4ng of extracted RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy3-labeled cRNA was prepared from 4-5 ug total RNA using Ambion's MessageAmp kit.

label_protocol: 4ng of extracted RNA was subjected to two rounds of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy5-labeled cRNA was prepared from 4-5ug total RNA using Ambion's MessageAmp kit.

value: 3229N; Diagnosis:normal; Sex:Female; Strain:FVB/N


title: 4164T.tumor.Cy5.45k


title: 4691N.normal.Cy3

value: 4691N; Diagnosis:normal; Sex:Female; Strain:FVB/N


title: 5154T.tumor.Cy3

value: 5154T; Diagnosis:adenosquamous carcinoma with cellular stroma; Sex:Female; Strain:FVB/N


title: 4691T.tumor.Cy3

value: 4691T; Diagnosis:erbb2-type carcinoma; Sex:Female; Strain:FVB/N


title: 4164N.normal.Cy3

value: 4164N; Diagnosis:normal; Sex:Female; Strain:FVB/N


title: 5154N.normal.Cy3

value: 5154N; Diagnosis:normal; Sex:Female; Strain:FVB/N


title: 4695T.tumor.Cy5.45k

value: 4695T; Diagnosis:scirrhous adenocarcinoma; Sex:Female; Strain:FVB/N


title: 5156T.tumor.Cy3

value: 5156T; Diagnosis:erbb2-type carcinoma; Sex:Female; Strain:FVB/N


title: 5033T4.tumor.Cy5.45k

value: 5033T4; Diagnosis:papillary carcinoma; Sex:Female; Strain:FVB/N


title: 5482T.tumor.Cy5.45k

value: 5482T; Diagnosis:type A microacinar carcinoma with squamous metaplasia; Sex:Female; Strain:FVB/N


title: 559T.tumor.Cy5

label_protocol: 4ng of extracted RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy3-labeled cRNA was prepared from 4-5ug total RNA using Ambion's MessageAmp kit.

label_protocol: 4ng of extracted RNA was subjected to two rounds of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy5-labeled cRNA was prepared from 4-5 ug total RNA using Ambion's MessageAmp kit.


title: 567T.tumor.Cy5.45k

value: 567T; Diagnosis:adenocarcinoma with sclerosis; Sex:Female; Strain:FVB/N


title: 3229N.normal.Cy3


title: 6696N.normal.Cy5


title: 559N.normal.Cy5

value: 559N; Diagnosis:normal; Sex:Female; Strain:FVB/N


title: 4164T.tumor.Cy5


title: 562N.normal.Cy5


title: 6696T.tumor.Cy5

value: 6696T; Diagnosis:erbb2-type carcinoma; Sex:Female; Strain:FVB/N


title: 5033T.tumor.Cy5

value: 5033T; Diagnosis:erbb2-type carcinoma; Sex:Female; Strain:FVB/N


title: Abomasum infected 27 days

value: abomasum

value: St. Croix hair sheep

value: 50% Dorset, 25% Finnsheep, 25% Ramboillet wool sheep composite


title: 3229T.tumor.Cy5

value: 3229T; Diagnosis:adenosquamous carcinoma; Sex:Female; Strain:FVB/N


title: 4425T.tumor.Cy5.45k

value: 4425T; Diagnosis:adenocarcinoma; Sex:Female; Strain:FVB/N


title: 3229N.normal.Cy5

value: 3229N; Diagnosis:Normal; Sex:Female; Strain:FVB/N


title: 5482T.tumor.Cy3.45k

label_protocol: 4ng of extracted RNA was subjected to two rounds of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy3-labeled cRNA was prepared from 4-5 ug total RNA using Ambion's MessageAmp kit.

label_protocol: 4ng of extracted RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy5-labeled cRNA was prepared from 4-5ug total RNA using Ambion's MessageAmp kit.


title: 5154T.tumor.Cy5

value: 5154T; Diagnosis:adenosquamous carcinoma with cellular stroma; Sex:Female; Strain:FVB/N


title: 567T.tumor.Cy3.45k


title: 5612T.tumor.Cy5.45k

value: 5612T; Diagnosis:adenocarcinoma; Sex:Female; Strain:FVB/N


title: 5156N.normal.Cy3

value: 5156N; Diagnosis:normal; Sex:Female; Strain:FVB/N


title: 4164T.tumor.Cy3.45k

value: 4164T; Diagnosis:erbb2-type carcinoma; Sex:Female; Strain:FVB/N


title: 5033N.normal.Cy5

value: 5033N; Diagnosis:normal; Sex:Female; Strain:FVB/N


title: 5156N.normal.Cy5


title: 4691N.normal.Cy5

value: 4691N; Diagnosis:Normal; Sex:Female; Strain:FVB/N


title: 4695T.tumor.Cy3.45k

value: 4695T; Diagnosis:scirrhous adenocarcinoma; Sex:Female; Strain:FVB/N


title: 4691T.tumor.Cy5

value: 4691T; Diagnosis:erbb2-type carcinoma; Sex:Female; Strain:FVB/N


title: 5154N.normal.Cy5

value: 5154N; Diagnosis:Normal; Sex:Female; Strain:FVB/N


title: 562T.tumor.Cy5

value: 562T; Diagnosis:MIN with solid, nodular intra lobular polyps; Sex:Female; Strain:FVB/N


title: 3229N.normal.Cy3.45k

value: 3229N; Diagnosis:normal; Sex:Female; Strain:FVB/N


title: 5156T.tumor.Cy5

value: 5156T; Diagnosis:erbb2-type carcinoma; Sex:Female; Strain:FVB/N


title: 4164N.normal.Cy5

value: 4164N; Diagnosis:Normal; Sex:Female; Strain:FVB/N


title: 5033T4.tumor.Cy3.45k

value: 5033T4; Diagnosis:papillary carcinoma; Sex:Female; Strain:FVB/N


title: 562T.tumor.Cy3

source_name: Tumor epithelial tissue from murine mammary gland


title: Mouse lung-2 vs MEF

source_name: Mouse lung-2

tag: Mouse lung-2 was extracted directed from the mouse lung tissue skived with liquid nitrogen and then solved in Trizol.

source_name: MEF

growth_protocol: MEF was maintained in DMEM (GIBICO) supplemented with 10% heat-inactivated fetal bovine serum (FBS, HyClone Laboratories, Logan, UT), 0.1 mM non-essential amino acids.

tag: primary murine embryonic feeders


title: 5033N.normal.Cy3


title: Mouse heart-1 vs MEF

source_name: Mouse heart-1

tag: Mouse heart-1 was extracted directed from the mouse heart tissue skived with liquid nitrogen and then solved in Trizol.


title: US28-WT (clone 9)

city: Amsterdam

first: David

last: Maussang

address: De Boelelaan 1083

department: Division of Medicinal Chemistry, Faculty of Sciences

country: Netherlands

institute: Vrije Universiteit Amsterdam, Leiden/Amsterdam Center for Drug Research

description: US28-WT transfected

hyb_protocol: Following fragmentation, 20mg of cRNA were hybridized for 16h at 45C on the Affymetrix Fluidics Station 400.

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

data_processing: The array images were quantified with the GeneChip operating system (GCOS) v1.2 software (Affymetrix). The average fluorescence intensity was determined for each microarray and then the output of each experiment was globally scaled to a target value of 200. Further normalization and variance stabilization was performed using RMA in the R statistical software package.

label: Biotin

source_name: Stably transfected NIH-3T3 cells

label_protocol: Biotinylated cRNA were prepared from 3mg total RNA using the MessageAmp II aRNA amplification kit (Ambion), according to the manufacturer's protocol.

growth_protocol: Stable NIH-3T3 cells were grown in DMEM supplemented with 10% calf serum and 400mg/ml neomycin.

extract_protocol: Total RNA was extracted from cell pellets using the Qiagen Rneasy Mini kit according to the manufacturer's instructions.

treatment_protocol: One day prior total RNA extraction, cells were grown in serum-starvation medium (DMEM supplemented with 0.5% calf serum and 400mg/ml neomycin).

tag: US28-WT transfected


title: Mouse lung-1 vs MEF

source_name: Mouse lung-1

tag: Mouse lung-1 was extracted directed from the mouse lung tissue skived with liquid nitrogen and then solved in Trizol.


title: MRC-5-1 vs mix2

growth_protocol: MRC-5 were cultured in DMEM (GIBICO) supplemented with 10% heat-inactivated fetal bovine serum (FBS, HyClone Laboratories, Logan, UT), 0.1 mM non-essential amino acids.

tag: Derived from normal lung tissue of a 14-week-old male fetus by J. P. Jacobs in September 1966 (Nature 227

growth_protocol: CCD-1079sk and IMR90 were cultured in DMEM (GIBICO) supplemented with 10% heat-inactivated fetal bovine serum (FBS, HyClone Laboratories, Logan, UT), 0.1 mM non-essential amino acids.

tag: mix2 are the mixture of CCD-1079sk and IMR90.


title: MRC-5-2 vs mix2


title: US28-WT (clone 23)

description: US28-WT transfected


title: human ES cell-3 vs mix2

source_name: human ES cell-3

growth_protocol: Human ES cells were maintained on irradiated mouse embryonic fibroblasts (MEF) in DMEM/F12 culture medium supplemented with 20% KnockOut serum replacer, 0.1 mM non-essential amino acids, 1 mM L-glutamine, 0.1 mM ß-mercaptoethanol and 100 ng/ml basic fibroblast growth factor (bFGF).

tag: The hESC line H1 (NIH code

value: WA01) was maintained on irradiated primary murine embryonic feeders (PMEF).


title: Mouse heart-2 vs MEF

source_name: Mouse heart-2

tag: Mouse heart-2 was extracted directed from the mouse heart tissue skived with liquid nitrogen and then solved in Trizol.


title: 5612T.tumor.Cy3.45k

source_name: Stratagene universal mouse reference


title: 4425T.tumor.Cy3.45k

value: 4425T; Diagnosis:adenocarcinoma; Sex:Female; Strain:FVB/N


title: Mock (clone 13)

description: Mock transfected

tag: Mock transfected


title: mouse ES cell-3 vs MEF

source_name: mouse ES cell-3

growth_protocol: Mouse ES cells were cultured in 85% Knockout DMEM (Invitrogen), 15% defined FBS , 1× MEM nonessential amino acids (Invitrogen), 1× L-glutamine (Invitrogen), 0.1 mM 2-mercaptoethanol , leukemia inhibitory factor.

tag: The mouse ES cells were maintained on irradiated primary murine embryonic feeders (PMEF).


title: mouse ES cell-2 vs MEF

source_name: mouse ES cell-2


title: Mock (clone 12)

description: Mock transfected


title: K14_0036PXT

status: Public on Mar 29 2009

city: Sunnyvale

first: Ljubomir

last: Buturovic

address: 1196 Borregas Avenue

department: Application Development

institute: Pathwork Diagnostics

description: Well differentiated

hyb_protocol: Affymetrix GeneChip standard protocol

scan_protocol: Affymetrix GeneChip standard protocol

data_processing: Pathwork standardization (Dumur et al., JMD 2008, Vol. 10, No. 1)

source_name: Liver

label_protocol: Affymetrix GeneChip 1-cycle IVT labeling and cDNA synthesis kits

extract_protocol: Qiagen RNEasy kit

tag: Anatomical sites

value: Liver

tag: gender

value: F

tag: TNM


title: mouse ES cell-1 vs MEF

source_name: mouse ES cell-1

tag: irradiated primary murine embryonic feeders


title: K14_0049PXT

description: Invasive grade 3 (of 4) adenocarcinoma

source_name: Pancreas

value: Lymph node

value: M

tag: age


title: K14_0038PXT

description: Moderately differentiated grade 2 (of 4) hepatocellular carcinoma forming a 17.0 x 14.0 x 8.5cm mass with extensive necrosis and vascular invasion.


title: human ES cell-2 vs mix2

source_name: human ES cell-2


title: human ES cell-1 vs mix2

source_name: human ES cell-1

growth_protocol: Human ES cells were maintained on irradiated mouse embryonic fibroblasts (MEF) in DMEM/F12  culture medium supplemented with 20% KnockOut serum replacer, 0.1 mM non-essential amino acids, 1 mM L-glutamine, 0.1 mM ß-mercaptoethanol and 100 ng/ml basic fibroblast growth factor (bFGF).

growth_protocol: CCD-1079sk and IMR90 were cultured in DMEM (GIBICO) supplemented with 10% heat-inactivated fetal bovine serum (FBS, HyClone Laboratories, Logan, UT),  0.1 mM non-essential amino acids.


title: K14_0048PXT

description: Invasive grade 4 (of 4) adenocarcinoma forming a 2.0 x 2.0 x 1.7 cm mass in the head of the pancreas.

value: Pancreas


title: K14_0045PXT

description: Invasive grade 4 (of 4) adenocarcinoma forming a 3.2 x 2.7 x 2.0 cm mass in the proximal portion of the specimen.


title: K14_0044PXT

description: Invasive grade 4 (of 4) adenocarcinoma with anaplastic features forming a  circumscribed mass (6.0 x 5.2 x 3.5 cm) arising

value: Stomach


title: K14_0047PXT

description: Invasive grade 2 (of 4) adenocarcinoma forming a 3.5 x 2.5 x 2.0 cm mass in the head of the pancreas.

value: Retroperiteum


title: K14_0035PXT

description: Grade 3 (of 4) hepatocellular carcinoma


title: K14_0034PXT

description: Grade 3 (of 4) hepatocellular  carcinoma


title: K14_0042PXT

description: Invasive Grade 3 (of 4) adenocarcinoma with squamous differentiation forming a 8.8 x 3.6 x 2.6 cm mass with a pseudocyst formation arising in the body of the pancreas and extending into the peripancreatic soft tissue.

value: Mesentary


title: K08_1298P8H

description: Papillary carcinoma of the thyroid

source_name: Thyroid


title: K14_0040PXT

description: Grade 3 (of 4) hepatocellular carcinoma forming a 5.0 x 4.5 x 4.3 cm mass.


title: K14_0039PXT

description: Grade 3 (of 4) hepatocellular carcinoma forming a 9.0 x 7.5 x 7.0 cm solitary right lobe mass.


title: K08_8270P8H

description: Metastatic gastric adenocarcinoma poorly differentiated

source_name: Gastric

value: Ovary


title: K08_1128P8H

description: Papillary carcinoma of the thyroid


title: K08_1297P8H

description: Papillary carcinoma of the thyroid


title: K14_0037PXT

description: Grade 3 (of 4) hepatocellular carcinoma forming a 4.0 x 3.8 x 2.5 cm non-encapsulated mass situated at 1.3 cm from the closest surgical margin.


title: K09_1342P8H

description: Non-seminomatous Malignant Germ Cell Tumor

source_name: Germ Cell

value: Testis


title: K08_8247P8H

description: Metastasis of the signet ring carcinoma of the gastric


title: K08_1190P8H

description: Papillary carcinoma of the thyroid


title: K08_1123P8H

description: Papillary carcinoma of the thyroid


title: K09_1195P8H

description: Mixed Non-Seminomatous Germ Cell Tumor


title: K08_1285P8H

description: Papillary carcinoma of the thyroid


title: K09_1104P8H

description: Non-seminomatous  Malignant Germ Cell Tumor


title: K09_9317P8H

description: Metastatic cancer AdenocarcinomaPancreas


title: K09_2205P8H

description: Immature Teratoma


title: K09_2138P8H

description: Malignant Non-seminomatous Germ Cell Tumor


title: K07_6094P8H

description: Carcinoma of thyroid

value: Thyroid gland


title: K08_1278P8H

description: Medullary carcinoma of the thyroid


title: K09_2510P8H

description: Teratoma


title: K08_1127P8H

description: Papillary carcinoma follicular variant of the thyroid


title: K09_9131P8H

description: Teratoma Mature Teratoma


title: K09_7905P8H

description: Metastatic cancer Adenocarcinoma Pancreas

value: Lung


title: K07_1208P8H

description: Adenocarcinoma of stomach


title: K09_2079P8H

description: Papillary carcinoma of the thyroid

value: Lymph Node


title: K09_1960P8H

description: Teratoma


title: K09_3319P8H

description: Metastatic Adenocarcinoma Pancreatic Ductal AdenocarcinomaPancreas

value: Adrenal Gland and Soft Tissue


title: K07_1753P8H

description: Adenocarcinoma of stomach


title: K09_2672P8H

description: Mixed (papillary and follicular) carcinoma of the thyroid

value: Thyroid Gland

value: High Grade


title: K09_3108P8H

description: Carcinoma of the thyroid gland

value: Poorly Differentiated


title: K09_2754P8H

description: Adenocarcinoma Metastatic AdenocarcinomaPancreas

value: Liver


title: K09_6286P8H

description: Carcinoma Thyroid


title: K07_1707P8H

description: Adenocarcinoma of stomach


title: K07_7668P8H

description: Malignant melanoma

source_name: Skin

value: Soft tissue

value: F


title: K08_1126P8H

description: Papillary carcinoma of the thyroid

value: Lymph node


title: K09_2132P8H

description: Teratoma

value: M


title: K09_8864P8H

description: Metastatic Adenocarcinoma Pancreas


title: J06_0460P2A

description: Metastatic Melanoma


title: J06_0296P2A

description: Metastatic mixed germ cell tumor consisting of embryonal carcinoma and immature teratoma


title: J06_0288P2A

description: Metastatic melanoma involving full thickness of the gastric wall

value: Stomach


title: J06_0387P2A

description: Metastatic hepatocellular carcinoma w/ angiolymphatic invasion

value: Colon/rectum


title: J06_0290P2A

description: Metastatic malignant melanoma

value: Small bowel


title: J06_0369P2A

description: Papillary

source_name: Ovary

value: Ovary


title: K07_2049P8H

description: Malignant melanoma

value: Lymph node:sentinel


title: J06_0293P2A

description: Moderately to poorly differentiated metastatic gastric carcinoma with focal neuroendocrine differentiation


title: J06_0368P2A

description: Papillary serous adenocarcinoma involving both ovaries

value: 3 to 4


title: J06_0358P2A

description: Papillary carcinoma w/ a few foci of tall cell variant

value: Thyroid


title: J06_0359P2A

description: Multiple nodules of metastatic sarcoma

source_name: Soft Tissue


title: J06_0353P2A

description: Oncocytic carcinoma of the thyroid with clear cell change

value: Muscle/soft tissue


title: J06_0328P2A

description: Metastatic adenocarcinoma consistent w/ prostatic origin

source_name: Prostate


title: J06_0352P2A

description: Metastatic


title: J06_0327P2A

description: Moderately differentiated metastatic hepatocellular carcinoma

value: Subcutaneous Tissue


title: J06_0324P2A

description: High-grade sarcoma consistent w/ metastatic leiomyosarcoma from small intestine primary


title: J06_0351P2A

description: Metastatic hepatocellular carcinoma with cellular anaplasia


title: J06_0329P2A

description: Poorly differentiated carcinoma with clear cell and oncocytic diferentiation and massive necrosis

source_name: Kidney


title: J06_0325P2A

description: Metastatic osteosarcoma

value: Lung


title: J06_0367P2A

description: Poorly diff. papillary serous carcinoma most likely of ovarian origin

value: Mesentary/small bowel


title: J06_0292P2A

description: Metastatic high-grade urothelial carcinoma involving the visceral pleura with angiolymphatic invasion

source_name: Bladder


title: J06_0333P2A

description: Metastatic renal cell carcinoma

value: Adrenal gland


title: J06_0323P2A

description: Metastatic prostatic adenocarcinoma


title: J06_0317P2A

description: Metastatic follicular carcinoma

value: Neck mass


title: P09_2407P1H

description: Hepatocellular Carcinoma

value: Liver


title: J06_0300P2A

description: Metastatic urothelial carcinoma with extranodal extension and blood vessel deposits


title: P09_9685P1H

description: Hepatocellular Carcinoma

value: F


title: P09_9665P1H

description: Malignant teratoma

value: Testis


title: P09_2511P1H

description: Hepatocellular Carcinoma

value: M


title: P09_2139P1H

description: Transitional cell carcinoma of the urinary bladder

value: Bladder


title: P09_1625P1H

description: Adenocarcinoma

value: Prostate

value: Gleason 7


title: P09_2353P1H

description: Transitional cell carcinoma of the bladder


title: P09_2040P1H


title: P09_1495P1H

description: Bladder urothelial carcinoma (transitional)


title: P09_1290P1H

description: Hepatocellular Carcinoma


title: P09_1620P1H

description: Transitional urothelial carcinoma of the bladder


title: P09_1288P1H

description: Hepatocellular Carcinoma


title: P09_1170P1H

description: Hepatocellular Carcinoma


title: P06_0400U2H

description: Metastatic malignant neoplasm, morphologically consistent w/seminoma

value: Lymph node


title: P09_1626P1H

description: Transitional cell carcinoma of urinary bladder


title: P09_1182P1H

description: Papillary transitional cell carcinoma of the urinary bladder


title: P09_1215P1H

description: Papillary urothelial carcinoma (transitional) of the bladder


title: U06_0459UXA

description: Anaplastic Large Cell Lymphoma (CD30)

source_name: Lymph Node

value: Extradural Mass (Cranium)


title: U06_0439U2A

description: Metastatic fibrolamellar hepatocellular carcinoma

value: Mediastinal mass


title: U06_0428U2A

description: Metastatic alveolar soft part sarcoma


title: U06_0432U2A

description: Invasive transitional cell carcinoma

value: Ureter

value: 3 to 4


title: U06_0426U2A

description: Metastatic poorly diff. adenocarcinoma consistent with ovarian primary

value: Chest wall


title: U06_0438U2A

description: Metastatic hepatocellular carcinoma


title: U06_0420U2A

description: Metastatic carcinoma consistent w/renal primary (clear cell type)

value: Lung


title: U06_0499U2A

description: Invasive poorly differentiated prostatic adenocarcinoma


title: U06_0413U2A

description: Metastatic high-grade sarcoma w/ angiolymphatic invasion


title: U06_0431U2A

description: Moderately to poorly diff. papillary carcinoma


title: U06_0408U2A

description: Mixed malignant germ cell tumor with embroyonal carcinoma

value: Testicle


title: U06_0373U2A

description: Metastatic moderately to poorly differentiated adenocarcinoma morphologically similar to esophageal adenocarcinoma

value: Chest Wall


title: U06_0372U2A

description: Metastatic poorly diff. adenocarcinoma consistent w/ krukenberg tumor

value: Ovary


title: U06_0382U2A

description: High grade spindle cell and pleomorphic sarcoma with leimyosarcomatous and focal liposarcomatous diff.

value: Soft Tissue


title: U06_0403U2A

description: Massive replacement by poorly differentiated malignant neoplasm

value: Liver


title: U06_0388U2A

description: Malignant mixed germ cell tumor w/ components of embryonal carcinoma (80%) and seminoma (20%)


title: U06_0378U2A

description: Metastatic papilary serous carcinoma of ovary

value: Omentum


title: U06_0366U2A

description: Metastatic urothelial carcinoma

value: F


title: U06_0391U2A

description: Metastatic urothelial carcinoma

value: M


title: U06_0362U2A

description: Metastatic prostatic adenocarcinoma

value: Lymph Node


title: U06_0337U2A

description: Adenocarcinoma consistent with gastroesophageal origin


title: U06_0265U2A

description: Diffuse large B Cell lymphoma w/ prominent epithelioid cells


title: U06_0267U2A

description: Non-Hodgkin's lymphoma


title: U06_0263U2A

description: Metastatic squamous cell carcinoma

source_name: Lung


title: U06_0365U2A

description: Invasive poorly differentiated adenocarcinoma

value: Prostate


title: X06_0417UXA

description: Poorly differentiated metastatic renal clear cell carcinoma with marked desmoplatic response

value: Lymph node


title: X06_0364UXA

description: Metastatic poorly adenocarcinoma consistent w/ prostatic primary


title: P06_0335U2H

description: Poorly differentiated transitional cell carcinoma with squamous cell differentiation and focal mucin production

value: Small bowel


title: U06_0326U2A

description: Metastatic adenocarcinoma consistent w/ prostatic origin


title: X06_0384UXA

description: Metastatic pleomorphic sarcoma w/extensive vascular invasion


title: P06_0332U2H

description: Invasive urothelial carcinoma

value: Bladder


title: K08_8250P8H

description: Gastric adenocarcinoma poorly differentiated


title: P06_0322U2H

description: Metastatic high grade urothelial carcinoma


title: P06_0330U2H

description: Metastatic malignant germ cell neoplasm


title: P06_0334U2H

description: Metastatic urothelial carcinoma


title: P06_0294U2H

description: Invasive poorly differentiated adenocarcinoma with signet ring features

value: Stomach


title: P07_7830U4H

description: Adenocarcinoma of pancreas

value: Pancreas


title: P06_0298U2H

description: Metastatic melanoma with multiple foci


title: P06_0303U2H

description: Metastatic malignant melanoma


title: P06_0284U2H

description: Metastatic melanoma with extensive angiolymphatic and visceral pleaural invasion


title: P06_0295U2H

description: Metastatic melanoma


title: P07_1484U4H

description: Tumor of testis

value: Testis


title: P07_6551U4H

description: Carcinoma of thyroid

value: Neck


title: P06_0282U2H

description: Metastatic adenocarcinoma

source_name: Colorectal

value: Pelvic mass


title: P07_1879U4H

description: Tumor of testis


title: P06_0304U2H

description: Metastatic urothelial carcinoma


title: P07_6029U4H

description: Tumor of testis


title: P07_1627U4H

description: Tumor of testis


title: P07_0401U4H

description: Adenocarcinoma of pancreas


title: P07_1213U4H

description: Carcinoma of liver

source_name: Liver


title: P07_0132U4H

description: Carcinoma of thyroid


title: P07_8520U5H

description: Adenocarcinoma of prostate

value: Gleason = 6/10


title: P07_6086U4H

description: Carcinoma of bladder


title: P07_0824U4H

description: Tumor of testis


title: P07_5828U5H

description: Tumor of testis


title: P07_1222U4H

description: Tumor of testis


title: P07_5253U5H

description: Adenocarcinoma of prostate

value: Gleason = 7/10


title: P07_5377U4H

description: Adenocarcinoma of pancreas


title: P07_5248U5H

description: Adenocarcinoma of prostate


title: P07_1480U4H

description: Carcinoma of Lung


title: P07_1473U4H

description: Carcinoma of lung


title: P07_2118U5H

description: Adenocarcinoma of prostate


title: P07_1861U5H

description: Tumor of testis


title: P07_0386U4H

description: Adenocarcinoma of pancreas


title: P07_1714U4H

description: Carcinoma of pancreas


title: P07_0191U5H

description: Tumor of testis


title: P07_0463U5H

description: Adenocarcinoma of prostate


title: P07_1300U4H

description: Carcinoma of liver


title: P08_2180U4H

description: adenocarcinoma  poorly differentiated

value: Gastric


title: P07_5002U4H

description: Adenocarcinoma of lung


title: P07_9333U4H

description: Carcinoma


title: P08_2002U4H

description: adenocarcinoma  poorly differentiated


title: P07_1307U4H

description: Tumor of pancreas


title: P08_1020U4H

description: signet ring carcinoma

value: Ovary


title: P08_1670U4H

description: adenocarcinoma moderately to poorly differentiated


title: P08_1970U4H

description: adenocarcinoma  poorly differentiated


title: P07_9585U3H

description: Carcinoma of kidney

value: Lung


title: P07_0353U5H

description: Adenocarcinoma of prostate


title: P07_5765U3H

description: Lymphoma


title: P07_5669U3H

description: Lymphoma

value: Thyroid gland

value: F


title: P07_5522U3H

description: Lymphoma

value: Small intestine

value: WHO grade II


title: P07_5334U3H

description: Lymphoma

value: lleum


title: P07_1165U3H

description: Carcinoma of kidney

value: Lymph node

value: Fuhrman G4


title: P07_5235U3H

description: Lymphoma


title: P07_0584U3H

description: Lymphoma

value: WHO grade 1


title: P07_5382U3H

description: Lymphoma

value: Groin

value: M


title: P07_0164U3H

description: Lymphoma

value: Spleen


title: P07_1625U3H

description: Lymphoma


title: P07_0045U3H

description: Lymphoma


title: P07_0100U3H

description: Malignant melanoma


title: P07_5564U3H

description: Lymphoma


title: P07_1141U3H

description: Adenocarcinoma of stomach


title: P07_0876U3H

description: Malignant melanoma

value: Omentum


title: P07_0011U3H

description: Lymphoma

value: Stomach


title: P07_0162U3H

description: Carcinoma of kidney

value: Fuhrman G3


title: P07_1279U3H

description: Carcinoma of bladder


title: P07_0043U3H

description: Carcinoma of kidney


title: P07_1260U3H

description: Malignant melanoma


title: P07_5107U3H

description: Lymphoma


title: P07_9399U3H

description: Carcinoma of thyroid


title: P07_0698U3H

description: Malignant melanoma

value: Jejunum


title: M06_0340U1A

description: Metastatic malignant melanoma

value: Skin


title: P06_0424U2H

description: Infiltrating ductal carcinoma

source_name: Breast

value: Breast


title: P07_0322U3H

description: Malignant melanoma

value: Lung


title: P07_0213U3H

description: Malignant melanoma


title: P06_0427U2H

description: Medullary thyroid carcinoma w/ focal c-cell hyperplasia

value: Thyroid

value: F


title: P06_0418U2H

description: Metastatic lung adenocarcinoma

value: Adrenal gland


title: P07_0543U3H

description: Malignant melanoma

value: Liver


title: P06_0416U2H

description: Metastatic melanoma


title: P06_0410U2H

description: Multifocal moderately to poorly diff. hepatocellular carcinoma

value: 2 to 3


title: P06_0376U2H

description: Recurrent high grade sarcoma involving mesenteric fat and focally muscle of small bowel

value: Adominal sarcoma

value: 3 to 4


title: P06_0379U2H

description: Renal cell carcinoma

value: Kidney


title: P07_0144U3H

description: Malignant melanoma

value: M


title: P06_0393U1H

description: Testicular germ cell tumor consisting only of embryonal carcinoma

value: Testicle


title: P06_0375U2H

description: Poorly differentiated serous papillary adenocarcinoma

value: Colon


title: P06_0374U2H

description: Poorly differentiated adenocarcinoma compatible w/ ovarian primary serous papillary type


title: P06_0411U2H

description: Metastatic papillary carcinoma of the thyroid

value: Lymph Node


title: P06_0405U2H

description: Clear cell carcinoma consistent with metastatic renal cell carcinoma

value: Adrenal Gland


title: P06_0402U2H

description: Mixed germ cell carcinoma composed of embryonal carcinoma

value: Lymph node


title: P06_0383U1H

description: Poorly diff. papillary adenocarcinoma confined to the thyroid gland


title: P06_0392U1H

description: Mixed germ cell tumor composed of embryonal carcinoma (70%)


title: P06_0422U2H

description: Metastatic adenocarcinoma

value: Umbilical nodule


title: P06_0381U2H

description: High grade sarcoma (pleomorphic liposarcoma)

value: Soft Tissue


title: P06_0406U2H

description: Invasive poorly differentiated gastric adenocarcinoma

value: Stomach


title: P06_0354U2H

description: Malignant lymphoma

value: Spleen


title: P06_0291U3H

description: Metastatic malignant melanoma

value: Lung


title: P06_0355U2H

description: Invasive moderately diff. ductal adenocarcinoma of the head of the pancreas

source_name: Pancreas

value: Stomach/Duod/Pancreas


title: P06_0348U2H

description: Malignant lymphoma

value: Small bowel


title: P07_8275U3H

description: Carcinoma of liver

value: Liver


title: P07_6525U3H

description: Carcinoma of kidney

value: F

value: Fuhrman G3


title: P06_0357U2H

description: Poorly differentiated adenocarcinoma


title: P07_0420U3H

description: Carcinoma of kidney

value: Adrenal gland


title: P07_1680U3H

description: Carcinoma of kidney

value: M


title: P08_1119U3H

description: medullary carcinoma


title: P06_0336U2H

description: Metastatic urothelial carcinoma


title: P07_1759U3H

description: Carcinoma of liver


title: P08_1117U3H

description: papillary carcinoma


title: P08_1120U3H

description: papillary carcinoma follicular variant


title: H03_1490U2H

description: Adenocarcinoma of breast


title: P08_8175U3H


title: P08_8195U3H


title: P08_8208U3H


title: H03_1243U2H

description: Adenocarcinoma of breast


title: H03_7975U2H

description: Adenocarcinoma of breast

value: Ovary


title: H03_5005U2H

description: Carcinoma of lung

value: Small intestine


title: H03_6153U2H

description: Lymphoma

value: WHO grade 1


title: H03_6111U2H

description: Carcinoma of lung

value: Skin


title: P08_8200U3H

description: adenocarcinoma  poorly differentiated

value: Lymph node


title: H03_5971U2H

description: Carcinoma of lung


title: H03_5289U2H

description: Adenocarcinoma of colon


title: H03_5096U2H

description: Adenocarcinoma of colon


title: H03_5083U2H

description: Lymphoma


title: H03_1160U2H

description: Lymphoma

value: Thyroid gland


title: P07_0748U3H

description: Malignant melanoma


title: J06_0270U1A

description: Metastatic moderately differentiated adenocarcinoma


title: J06_0347U1A

description: Moderately to poorly diff. mucinous adenocarcinoma w/signet ring cell features

value: Pancreas/Duod.


title: J06_0269U1A

description: Metastatic carcinoma consistent with metastasis from the breast


title: J06_0356U1A

description: Invasive pleomorphic carcinoma w/adenocarcinoma and spindle cell carcinoma

value: 3 to 4


title: J06_0339U1A

description: Moderately diff. adenocarcinoma consistent w/ metastatic ductal adenocarcinoma of breast


title: J06_0349U1A

description: Diffuse large B-cell Lymphoma

value: Spleen/soft tissue


title: H03_0237U2H

description: Adenocarcinoma of pancreas


title: J06_0271U1A

description: Malignant neoplasm


title: J06_0275U1A

description: Pancreatic adenosquamous carcinoma

value: Pancreas


title: H03_1001U2H

description: Adenocarcinoma of pancreas

value: Omentum


title: J06_0343U1A

description: Moderately to poorly diff. pancreatic adenocarcinoma of head of pancreas


title: J06_0320U1A

description: Invasive


title: J06_0344U1A

description: Metastatic carcinoma


title: J06_0273U1A

description: Poorly differentiated lung adenocarcinoma


title: H03_0223U2H

description: Adenocarcinoma of colon


title: J06_0338U1A

description: Moderately to poorly differentiated pancreatic adenocarcinoma arising in head of pancreas


title: J06_0260U1A

description: Moderate to poorly differentiated adenocarcinoma extending into the subserosal fat

value: Colon


title: J06_0360U1A

description: Metastatic Colorectal Adenocarcinoma

value: Lung


title: J06_0274U1A

description: Metastatic poorly differentiated carcinoma

value: F


title: J06_0272U1A

description: Malignant lymphoma

value: Thigh mass


title: J06_0276U1A

description: Malignant lymphoma of B-cell type w/ low and intermediate grade components

value: Thyroid


title: J06_0262U1A

description: Invasive moderately to poorly differentiated adenocarcinoma of colon mucinous differentiation


title: J06_0261U1A

description: Poorly differentiated non-small cell carcinoma


title: M06_0202U1A

description: Clear Cell Carcinoma of the Ovary


title: M06_0222U1A

description: Invasive Ductal Carcinoma

value: Breast


title: M06_0208U1A

description: Invasive Ductal Carcinoma


title: Mouse dietary model of type II diabetes, 6 wks, dye reversal

status: Public on Mar 28 2009

city: Honolulu

first: John

last: Maresh

state: HI

address: 651 Ilalo

department: Medicine

institute: University of Hawaii

description: The GPR data was uploaded to Acuity, normalized, and a dataset was generated with 2 biological replicate experiments, each of which was analyzed with 2 microarrays including a dye reversal.

hyb_protocol: The microarrays were hybridized with the Ambion hybridization buffer 16 hours at 50 degrees C. Washing was at room temp: 5 minutes in 2X SSC, 0.1% SDS, then 5 minutes in .1 X SSC, 0.1% SDS, then 5 minutes in .1 X SSC.

scan_protocol: Slides were scanned with Genepix 4000B using standard default settings and autoscan mode

data_processing: The log 2 fold change represents the log 2 of experimental/control ratio of normalized 2 channel feature values (ratio of median normalization determined with the default settings of Acuity).

source_name: aortic endothelium after 6 weeks of high fat diet

label_protocol: Amersham reactive sulfo NHS ester coupled to Cy dye

growth_protocol: Male, Tie 2 GFP mice, beginning at age 8 weeks of age, were placed on Bio-Serv#S3282 diet for 6 weeks

extract_protocol: TRIZOL, Qiagen microRNeasy colum

treatment_protocol: RNA was extracted, amplified with amino ally Message Amp II System and post labeled with Amersham reactive Cy3 dye.

tag: strain

source_name: aortic endothelium after 6 weeks of control diet (normal chow)

growth_protocol: Male, Tie 2 GFP mice, beginning at age 8 weeks of age, were maintained on control diet (normal chow) for 6 weeks.

extract_protocol: TRIZOL, Qiagen microRNeasy column

treatment_protocol: RNA was extracted, amplified with amino ally Message Amp II System and post labeled with Amersham reactive Cy5 dye.


title: Mouse dietary model of type II diabetes, at 6 wk


title: M06_0204U1A

description: Invasive Ductal Carcinoma


title: J06_0259U1A

description: Metastatic adenocarcinoma consistent with breast primary

value: Ovary


title: M06_0203U1A

description: Poorly Differentiated Serous Carcinoma of Ovary


title: J06_0258U1A

description: Invasive poorly differentiated adenosquamous cell carcinoma

value: M


title: Mouse dietary model of type II diabetes, 8 wks, dye reversal

data_processing: The log 2 fold change represents the log 2 of experimental/control ratio of normalized 2 channel feature values (ratio of median normalization determined with the default settings of Acuity

source_name: aortic endothelium after 8 weeks of high fat diet

growth_protocol: Male, Tie 2 GFP mice, beginning at age 8 weeks of age, were placed on Bio-Serv#S3282 diet for 8 weeks

source_name: aortic endothelium after 8 weeks of control diet (normal chow)


title: Mouse dietary model of type II diabetes, biological replicate #1, dye reversal

source_name: aortic endothelium after 4 weeks of high fat diet

growth_protocol: Male, Tie 2 GFP mice, beginning at age 8 weeks of age,  were  placed on Bio-Serv#S3282 diet for 4 weeks

source_name: aortic endothelium after 4 weeks of control diet (normal chow)

growth_protocol: Male, Tie 2 GFP mice, beginning at age 8 weeks of age,  were maintained on control diet (normal chow) for 4 weeks.


title: Mouse dietary model of type II diabetes, biological replicate #2

growth_protocol: Male, Tie 2 GFP mice, beginning at age 8 weeks of age, were placed on Bio-Serv#S3282 diet for 4 weeks

growth_protocol: Male, Tie 2 GFP mice, beginning at age 8 weeks of age, were maintained on control diet (normal chow) for 4 weeks.


title: Mouse dietary model of type II diabetes, at 8 wk

growth_protocol: Male, Tie 2 GFP mice, beginning at age 8 weeks of age, were maintained on control diet (normal chow) for 8 weeks.


title: Mouse dietary model of type II diabetes, biological replicate #2, dye reversal


title: Mouse dietary model of type II diabetes, biological replicate #1


title: M06_0205U1A

description: High Grade Serous Carcinoma of Ovary

source_name: Ovary


title: NIH-CAR AdEmpty replicate3

status: Public on Mar 27 2009

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

hyb_protocol: After fragmentation at 94°C for 35 min in fragmentation buffer (40 mM Tris, 30 mM magnesium acetate, 10 mM potassium acetate), 15 μg of labeled cRNA was hybridized for 16 h to the Mouse 430 2.0 array (Affymetrix Inc.)

scan_protocol: Hybridized arrays were scanned using the Affymetrix GeneChip® Scanner 3000

data_processing: The raw intensity data was normalized using the RMA algorithm implemented with the Bioconductor affy package using R version 2.5.0.

source_name: NIH-CAR cells transduced with adenovirus containing empty vector followed by addition of vehicle (DMSO)

label_protocol: Two micrograms of total RNA was used to synthesize double-stranded cDNA with the one-cycle cDNA synthesis Kit (Affymetix Inc.) using an oligo(dT) primer containing a T7 RNA polymerase promoter (Affymetrix Inc.). The cDNA was purified using the GeneChip clean-up module (Affymetrix Inc.) and used as the template for an in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (IVT labeling Kit; Affymetrix Inc.).

growth_protocol: NIH-CAR cells were cultured in DMEM (Gibco) supplemented with 10% calf serum (Fischer Scientific PAA)

extract_protocol: The adenovirally transduced NIH-CAR cells were harvested in 500 μl TRIzol. Total RNA was extracted by addition of chloroform and precipitated with isopropanol and centrifugation. The pellet was washed with 75 % ethanol and redissolved in diethyl pyrocarbonate (DEPC) treated water. The RNA samples were purified further on RNAeasy columns (Qiagen) and the  integrity and purity of the RNA was verified with an Agilent Bioanalyzer

treatment_protocol: Adenovirus was suspended in medium and added to NIH-CAR cells at 80% confluency. After 2 h of transduction, the virus-containing medium was removed and new medium containing either only the vehicle dimethyl sulfoxide (DMSO) or 1 μM of the PPARg-specific agonist rosiglitazone/BRL49653.

value: passage 12

tag: cell line

value: NIH 3T3


title: NIH-CAR AdHA-PPARgCDE replicate3

source_name: NIH-CAR cells transduced with adenovirus expressing truncated PPARgamma2 lacking the A/B-domain treated with rosiglitazone


title: NIH-CAR AdHA-PPARgCDE replicate1


title: NIH-CAR AdHA-PPARgCDE replicate2


title: NIH-CAR AdEmpty replicate2


title: NIH-CAR AdHA-PPARg2 replicate3

source_name: NIH-CAR cells transduced with adenovirus expressing full length PPARg2 treated with rosiglitazone


title: NIH-CAR AdEmpty replicate1


title: NIH-CAR AdHA-PPARg2 replicate1


title: NIH-CAR AdHA-PPARg2 replicate2


title: C57_LPS_C_240min

city: Seattle

first: Bruz

last: Marzolf

state: WA

institute: Institute for Systems Biology

description: LPS 240 minutes

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor

source_name: Mouse bone-marrow macrophages - LPS 240 minutes

label_protocol: GeneChip® One-Cycle Target Labeling Kit

growth_protocol: BMDM were grown for 7days in DMEM suppplemented with 50µg/mL rh-MCSF

extract_protocol: essentially as described in PMID: 16688188

treatment_protocol: LPS 10ng/ml for 240 min

value: female

tag: tissue

value: Femur Bone Marrow-Derived Macrophages


title: LPS3-20

description: LPS 20 minutes

source_name: Mouse bone-marrow macrophages - LPS 20 minutes

treatment_protocol: LPS 10ng/ml for 20 min


title: C57_A_LPS_240_min

description: LPS 240 minutes


title: WT_LPS_240_min

description: LPS 240 minutes


title: LPS2-0

description: NoStim

source_name: Mouse bone-marrow macrophages - No stimulation

treatment_protocol: NoStim


title: LPS3-120

description: LPS 120 minutes

source_name: Mouse bone-marrow macrophages - LPS 120 minutes

treatment_protocol: LPS 10ng/ml for 120 min


title: LPS3-40

description: LPS 40 minutes

source_name: Mouse bone-marrow macrophages - LPS 40 minutes

treatment_protocol: LPS 10ng/ml for 40 min


title: C57_A_LPS_360_min

description: LPS 360 minutes

source_name: Mouse bone-marrow macrophages - LPS 360 minutes

treatment_protocol: LPS 10ng/ml for 360 min


title: LPS2-60

description: LPS 60 minutes

source_name: Mouse bone-marrow macrophages - LPS 60 minutes

treatment_protocol: LPS 10ng/ml for 60 min


title: C57_B_LPS-360

description: LPS 360 minutes


title: LPS3-0

description: NoStim


title: LPS3-60

description: LPS 60 minutes


title: C57_LPS_B_240_min

description: LPS 240 minutes


title: LPS2-120

description: LPS 120 minutes


title: LPS2-40

description: LPS 40 minutes


title: LPS1-80

description: LPS 80 minutes

source_name: Mouse bone-marrow macrophages - LPS 80 minutes

treatment_protocol: LPS 10ng/ml for 80 min


title: LPS2-80

description: LPS 80 minutes


title: LPS3-80

description: LPS 80 minutes


title: LPS2-20

description: LPS 20 minutes


title: J06_0278U1A

description: Moderately differentiated adenocarcinoma with infiltrating gastric mucosa

source_name: Colorectal

value: Stomach


title: LPS1-120

description: LPS 120 minutes


title: LPS1-0

description: No stimulation


title: iPS cells from episomal vectors (Defined Factor sub-clone) DF6_9_12T (set of 12)

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

hyb_protocol: All arrays were hybridized at 45ºC for 16 hours and scanned using an AFX GC3000 G7 scanner

scan_protocol: AFX GC3000 G7 scanner

data_processing: RMA

label_protocol: Approximately 3 µg of RNA from each sample was labeled using the MessageAmp™ Biotin II-Enhanced IVT kit (Ambion) following manufacturer’s instructions.

growth_protocol: iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion or Tri-Reagent (Sigma).

treatment_protocol: IPS cells treated with episomal vectors

tag: cell type


title: LPS1-20

description: LPS 20 minutes


title: LPS1-40

description: LPS 40 minutes


title: Foreskin Cells Parental Foreskin (set of 12)

source_name: Foreskin Cells Parental

value: Foreskin Cells Parental


title: Chip 13104002 transgenic ΔDDKPtRR13-line16 6hr

city: Gainesville

first: Christopher

last: Dervinis

state: FL

address: 2033 Mowry Road, rm 320

department: SFRC

institute: University of Florida

description: Populus tremula x Populus alba INRA-clone No. 717-1-B4 plants expressing a constitutively active form of the Populus type-B response regulator PtRR13 (ΔDDKPtRR13)were generated via an Agrobacterium-mediated protocol developed by Han et al. (2000). Non-transgenic and ΔDDKPtRR13 line were grown to a height of 60 cm. A 14 cm tall apical cuttings were collected from the mother plants. Cuttings were placed in 25 cm2 pots Fafard mix #4 and placed on a mist bench with intermittent mist to prevent shoot desiccation. Samples were collected at the indicated time points and consisted of a 5 mm section measured up from the base of the cutting (one sample per cutting).

hyb_protocol: 1.5ug labeled ds-cDNA was denatured at 95C for 5min and hybridized to custom in situ synthesized oligonucleotide microarrays (produced by NimbleGen, Madison, WI) at 42C overnight (16-20h). Hybridization and wash buffers are described elsewhere (http://www.nimblegen.com/products/lit/exp_userguide_2008_05_21.pdf)

scan_protocol: As described elsewhere (http://www.nimblegen.com/products/lit/exp_userguide_2008_05_21.pdf).

data_processing: Raw intensity data was background corrected (Irizarry et al. 2003, Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264) and normalized using the Quantile normalization method (Bolstad et al. 2003, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193).

organism: Populus tremula x Populus alba

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 6 hours after excision from a ΔDDKPtRR13-line16 transgenic donor plant.

label_protocol: RNA extracted from each progeny was converted to double-stranded (ds-) cDNA (SuperScript Double Strand cDNA Synthesis Kit, Invitrogen USA, Carlsbad, CA) with oligo-dT primer (Promega USA) according to the manufacturerÆs protocol, except that synthesis of first and second strands were extended to 16h. Resultant ds-cDNA was labeled using cy3-tagged random 9mers and Klenow fragment for 2h at 37C

growth_protocol: Experiments were conducted in a greenhouse at ambient temperature between the months of September and December in Gainesville, Florida. Populus balsamifera ssp. trichocarpa (Torr. and Gray) genotype Nisqually-1 and Populus tremula x Populus alba INRA-clone No. 717-1-B4 plants were given 12-14 hours of natural light, supplemented in the winter with artificial illumination to maintain indeterminate growth. Plants were grown in 11.4 liter pots on flood benches subirrigated once daily with a nutrient solution containing Peters Professional Blend 20-10-20 fertilizer solution (adjusted to 4 mM nitrogen). When plants reached 60-80 cm tall, single cuttings per plant were collected, planted in 25 cm2 pots containing Fafard #4 mix and placed under mist until harvested.

extract_protocol: Total RNA was isolated using a cetyltrimethylammonium bromide (CTAB) method (Chang S, J. Puryear, J. Cairney 1993, A simple and efficent method for isolating RNA from pine trees. Plant Mol Biol Rep 11: 113-116). RNA samples were subjected to DNase treatment with RQ1 RNase-free DNase (Promega, Madison, WI, USA) and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA)

treatment_protocol: For these analyses, 14 cm tall apical cuttings were collected from 60cm tall mother plants (from non-transgenic and ΔDDKPtRR13). Cuttings were placed in 25 cm2 pots Fafard mix #4 and placed on a mist bench with intermittent mist to prevent shoot desiccation. Samples were collected at the indicated time points and consisted of a 5 mm section measured up from the base of the cutting (one sample per cutting).

tag: isolate

value: INRA-clone No. 717-1-B4


title: iPS cells from episomal vectors (Defined Factor) DF19_9 (set of 16)


title: Chip 13103902 transgenic ΔDDKPtRR13-line16 0hr

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 0 hours after excision from a ΔDDKPtRR13-line16 transgenic donor plant.


title: Chip 12715102 Non-transgenic 0hr

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 0 hours after excision from a non-transgenic donor plant.


title: iPS cells from episomal vectors (Defined Factor) DF19_8 (set of 16)


title: Day 7 Chick Breast Muscle- Replicate #2

city: Beltsville

first: Mark

middle: P

last: Richards

address: 10300 Baltimore Avenue

department: ANRI

institute: USDA, ARS

description: Gene expression data for breast muscle from 7 day-old broiler chicken.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 42C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 using the EukGE-WS2v5_450 script.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner using factory set PMT settings.

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 set to the default value of 500.

organism: Gallus gallus

source_name: 7 day-old Chick

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Broiler chicken eggs were hatched and chicks were sampled immediately after emergence from the egg (day 0) and at 7 days post-hatch.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Samples of liver, duodenum, breast muscle and whole brain were collected on days 0 and 7 post-hatch, snap frozen in liquid nitrogen and stored at -80C prior to isolation of total RNA.

value: Breast Muscle

tag: genotype

value: Ross broiler chicken

value: male

value: 7 day-old