title: 14089428 - fie 7dag 2 vs fie 3mon 2

status: Public on Dec 01 2010

type: RNA

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

description: Role of PRC2 repressory complex for differentiation pathways in Arabidopsis thaliana?

hyb_protocol: fie 3mon 2 Cy5 / fie 7dag 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: fie 3mon 2

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - media: 1/2 MS plates, 1% sucrose	 temperature: 19 C	 light: 12h/12h

extract_protocol: fie 3mon 2:10ug.

treatment_protocol: no treatment

tag: strain

value: columbia mutant (fie)

tag: harvest date

source_name: fie 7dag 2

extract_protocol: fie 7dag 2:10ug.

tag: age


title: 14092642 - fie 7dag 1 vs wt 7dag 1

hyb_protocol: wt 7dag 1 Cy5 / fie 7dag 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wt 7dag 1

extract_protocol: wt 7dag 1:10ug.

value: columbia

source_name: fie 7dag 1

extract_protocol: fie 7dag 1:10ug.


title: 14092641 - fie 7dag 1 vs fie 3mon 1

hyb_protocol: fie 3mon 1 Cy5 / fie 7dag 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: fie 3mon 1

extract_protocol: fie 3mon 1:10ug.


title: 14089427 - fie 3mon 2 vs fie 7dag 2

hyb_protocol: fie 7dag 2 Cy5 / fie 3mon 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969284 - wt 20dag 2 vs fie 20dag 2

hyb_protocol: fie 20dag 2 Cy5 / wt 20dag 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: fie 20dag 2

growth_protocol: whole plant - liquid 1/2 MS + 1% sucrose 12h light/12h dark 21°C

extract_protocol: fie 20dag 2:30ug.

source_name: wt 20dag 2

extract_protocol: wt 20dag 2:30ug.


title: 14089429 - fie 7dag 2 vs wt 7dag 2

hyb_protocol: wt 7dag 2 Cy5 / fie 7dag 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wt 7dag 2

extract_protocol: wt 7dag 2:10ug.


title: 14092643 - wt 7dag 1 vs fie 7dag 1

hyb_protocol: fie 7dag 1 Cy5 / wt 7dag 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969285 - fie 20dag 2 vs wt 20dag 2

hyb_protocol: wt 20dag 2 Cy5 / fie 20dag 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: W_1 with array type rice from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

description: The Bacterial Leaf Blight disease of rice is due to Xanthomonas oryzae pv. oryzae. As for many pathogenic bacteria, it relies on a type 3 secretion system that is devoted to the injection of type 3 effectors into the eukaryotic host cell. These proteins are meant to suppress host basal defense responses and/or mimic some host regulatory function promoting bacterial survey in the plant. We are interested in the functional analysis of a subgroup of Xoo T3Es, that are specialized in host cell transcriptome remodelling. These effectors, therefore called TAL for Transcription Activator-Like proteins (also named AvrBs3/PthA-like), are often key virulence factors essential to Xoo pathogenicity such as the effector protein Talc of african Xoo strain BAI3. Our goal is to understand its function during disease development, by identifying rice host genes that are being directly up- or down-regulated by Talc. To that end, we aim at performing Affymetrix transcriptomic analysis, comparing leaf samples of a susceptible rice line inoculated with Xoo to leaves challenged with a Talc-deficient mutant and water-treated leaves. Highly induced genes are likely to be Talc primary targets and therefore potentially good susceptibility gene candidates.

hyb_protocol: labelled extract quantity: 10ug, according to standard protocols.

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1, according to standard protocols.

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Oryza sativa

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug, according to standard protocols.

growth_protocol: aerial - S2 type greenhouse, 26°C, 80 HR

treatment_protocol: Name:Xoo strain BAI3 - syringe-inoculation - pathogen infection,xoo strain bai3:time 24hour. Young leaves of 3 weeks old plantlets are infiltrated with a freshly-grown bacterial suspension at an OD of 0,5 using a syringe.

tag: variety

value: nipponbare

tag: tissue

value: leaves


title: 14092640 - fie 3mon 1 vs fie 7dag 1

hyb_protocol: fie 7dag 1 Cy5 / fie 3mon 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969283 - fie 20dag 1 vs wt 20dag 1

hyb_protocol: wt 20dag 1 Cy5 / fie 20dag 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wt 20dag 1

extract_protocol: wt 20dag 1:30ug.

source_name: fie 20dag 1

extract_protocol: fie 20dag 1:30ug.


title: H_1 with array type rice from Affymetrix

treatment_protocol: Name:Mock - control buffer - control,potyvirus:time 7day. Two to three Arabidopsis leaves are inoculated with grinded plant juice (not infected). Two days after the first one, a second inoculation is realised. Seven days after inoculation, inoculated leaves are collected.


title: H_3 with array type rice from Affymetrix


title: 14092639 - wt 7dag 2 vs fie 7dag 2

hyb_protocol: fie 7dag 2 Cy5 / wt 7dag 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: W_2 with array type rice from Affymetrix


title: Delta_2 with array type rice from Affymetrix

treatment_protocol: Name:Xoo strain BAI3 Delta_talc - syringe-inoculation - pathogen infection,xoo strain bai3 delta_talc:time 24hour. Young leaves of 3 weeks old plantlets are infiltrated with a freshly-grown bacterial suspension at an OD of 0,5 using a syringe


title: Delta_1 with array type rice from Affymetrix


title: Side population cell replicate group SPd

city: Berlin

first: Rosa

last: Schmuck

state: Berlin

address: Cariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite university medicine

description: The total RNA was quantified by UV-spectroscopy and its quality was assessed using a LabChip (BioAnalyzer, AGILENT Technologies, Santa Clara, CA) and by agarose gel electrophoresis.

hyb_protocol: The fragmented cRNA was hybridized to the HG U133A /MG U74Av2 array (Affymetrix, Santa Clara, CA). Hybridization was then carried out at 45°C in a hybridization oven for 16 hours. Subsequent washing and staining of the arrays was performed using the GeneChip fluidics station protocol EukGE-WS2.

scan_protocol: Following washing and staining, probe arrays were scanned twice at 3 μm resolution using the GeneChip System confocal scanner (Hewlett-Packard, Santa Clara, CA).

data_processing: Raw data were analyzed with the Affymetrix GeneChip Operating Software (GCOS 1.4). The detection p-value of a transcript determines the detection call, which indicates whether the transcript is reliably detected (p<0.05; present) or not detected (absent). To enable the comparison between chips the data were scaled to a global intensity of 500. The Data Mining Tool 2.0 (Affymetrix) and GeneSpring software package 7.2 (Silicon Genetics, Redwood City, CA) were used to average results from different samples and perform statistical analysis.

label: biotin

organism: Homo sapiens

source_name: gastric cancer cell line AGS

label_protocol: The arrays were stained for 10 min in streptavidin-phycoerythrin (SAPE) solution (Molecular Probes, Eugene, OR) at 25°C. The post stain wash consisted of 10 cycles at 25°C in the fluidics station using the non-stringent solution. The probe arrays were treated for 10 min. in antibody solution [2 μg/μl acetylated BSA, 0.1 μg/μl normal goat IgG (Sigma, St.Louis, MO), 3 μg/ml goat-anti-streptavidin, biotinylated antibody (Vector Laboratories, Burlingame, CA) in 100mM MES; 1M NaCl, 0.05% Tween20] at 25 °C.

growth_protocol: The cells were grown in VLE 1640 RPMI medium supplemented with 10% (AGS) or 20% (MKN 45) fetal bovine serum (FBS; Biochrom AG, Germany) at 37 ºC in a humidified atmosphere with 5% CO2. For re-cultivation experiments, the cell culture medium was supplemented with 10 µl/ml penicillin/streptomycin (PAA, Austria). Cells were washed with phosphate buffered saline (PBS) and harvested by incubating for 5 min. with trypsin. Trypsin was inhibited by the addition of culture medium and the cells were pelleted by centrifugation (5 min. 800 rpm).  Subsequently the cells were re-suspended in culture medium, counted using the Z1 Beckman Coulter (Krefeld, Deutschland) and aliquoted in portions of 1×106 cells. All experiments were done in a culture hood and all cell culture solutions were preheated to 37 °C before use.

extract_protocol: RNA was extracted using a mirVana™ miRNA Isolation Kit (Ambion, Austin, USA) according to the manufacturer’s instructions.

tag: origin

value: gastric cancer cell lines AGS and MKN 45

tag: cell type

value: side population


title: Unsorted cell population replicate group UCPb

value: unsorted


title: Non-side population cell replicate group SPa

value: non-side population


title: Side population cell replicate group SPb

source_name: gastric cancer cell line


title: Non-side population cell replicate group SPb


title: Non-side population cell replicate group SPc


title: Side population cell replicate group SPa

source_name: gastric cancer cell lines


title: H_2 with array type rice from Affymetrix


title: 13969282 - wt 20dag 1 vs fie 20dag 1

hyb_protocol: fie 20dag 1 Cy5 / wt 20dag 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Delta_3 with array type rice from Affymetrix


title: W_3 with array type rice from Affymetrix


title: T. denticola bone 4

status: Public on Nov 16 2010

city: Gainesville

first: Kesavalu

middle: Naidu

last: Lakshmyya

state: FL

address: 1600 SW Archer road, D11-24

department: Periodontology

country: USA

institute: University of Florida, College of Dentistry

description:
T. denticola_Bone_4B
Gene expression data from T. denticola infected tissue.

hyb_protocol: Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized  using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles

organism: Mus musculus

source_name: T. denticola infected bone 4

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

growth_protocol: T. denticola ATCC 35404 was cultured in GM-1 growth medium under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.

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

treatment_protocol: Infection protocol: T. denticola was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N = 10) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection.  The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.

value: calvarial bone

tag: infection

value: T. denticola

value: 9 weeks


title: Non-side population cell replicate group SPd


title: Transcription comparison of UC26 to wild type G217B

status: Public on Dec 05 2010

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

hyb_protocol: The microarrayed DNA probes were incubated in Prehybridization Buffer (5X SSC, 0.1% SDS, and 1% bovine serum albumin) at 42oC for 90 min. For hybridization, the microarray slides are spotted with 42 ml Hybridization Buffer (25% formamide, 5X SSC, 0.1% SDS, 5 mg/ml COT1-DNA, 5 mg/ml poly(A)-DNA, and 2 mg/ml yeast tRNA) and the fluorescence-labeled target aRNA. Hybridizations were preformed at 48oC using the MAUI hybridization station (BioMicro, Salt Lake City, Utah) for 16 hrs.    The slides were washed using the MAUI wash station.  The slides were first washed in 1X SSC/0.2% SDS at 48°C followed by 0.1X SSC/0.2% SDS, and a final wash in 0.1X SSC at room temperature. The slides were rinsed in water and spun-dried immediately after washing.

scan_protocol: Imaging and data generation were carried out using a GenePix 4000A and GenePix 4000B (Axon Instruments; Union City, CA) and associated software from Axon Instruments, Inc. (Foster City, CA). The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5 fluorescence emittance. Images were captured in JPEG and TIFF files, and DNA spots captured by the adaptive circle segmentation method. Information extraction for a given spot is based on the median value for the signal pixels minus the median value for the background pixels to produce a gene set data file for all the DNA spots. The Cy3 and Cy5 fluorescence signal intensities were normalized.

data_processing: See: Sartor, et al. BMC Bioinformatics. 2006 Dec 19;7:538.

label: Cy3, Cy5

organism: Histoplasma capsulatum

source_name: Total RNA from mycelial phase cultures grown at 25 C on HMM

label_protocol: 100-250 ng of total RNA was amplified twice first with Ambion MessageAmp II Amplification kit (P/N AM1751) followed with Amino Allyl MessageAmp II aRNA amplification kit (P/N AM1753) to synthesize microgram quantities of amino allyl labelled amplified RNA (aRNA) using manufacturer's protocols. 5 ug of aRNA was decorated with monofunctional reactive Cy3 and Cy5 dyes.

extract_protocol: Total RNA was extracted from mycelial cultures grown at 25 C on HMM plate  using Tri-Zol according to the manufacturer's instructions.

value: UC 26


title: ICN 3-5, DP rep 2

status: Public on Nov 14 2010

city: Boston

first: Il-Ho

last: Jang

state: MA

address: Karp Bld, rm 7004, 1 Blackfan circle

department: Hematology/Oncology

institute: Children's Hospital Boston

description: ICN3-5 DP_0808

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Day 6 embryoid body

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Day 6

value: sorted cells from embryoid body


title: T. denticola bone 3

description:
T. denticola_Bone_3B
Gene expression data from T. denticola infected tissue.

source_name: T. denticola infected bone 3


title: ICN 3-5, CD41 sp rep 1

description: ICN3-5 41 sp


title: T. denticola bone 2

description:
T. denticola_Bone_2B
Gene expression data from T. denticola infected tissue.

source_name: T. denticola infected bone 2


title: T. denticola tissue 2

description:
T. denticola_Tissue_2T
Gene expression data from T. denticola infected tissue.

source_name: T. denticola infected tissue 2

value: soft tissue overlying calvarial bone


title: Side population cell replicate group SPc


title: ICN 3-5, VE sp rep 1

description: ICN3-5 VE sp


title: T. denticola tissue 4

description:
T. denticola_Tissue_4T
Gene expression data from T. denticola infected tissue.

source_name: T. denticola infected tissue 4


title: T. denticola bone 1

description:
T. denticola_Bone_1B
Gene expression data from T. denticola infected tissue.

source_name: T. denticola infected bone 1


title: ICN 3-5, DN rep 3

description: ICN3-5 DN_0821


title: ICN 3-5, DP rep 1

description: ICN3-5 DP


title: ICN 0, DN rep 2

description: ICNO DN_0808


title: T. denticola bone 5

description:
T. denticola_Bone_5B
Gene expression data from T. denticola infected tissue.

source_name: T. denticola infected bone 5


title: T. denticola tissue 1

description:
T. denticola_Tissue_1T
Gene expression data from T. denticola infected tissue.

source_name: T. denticola infected tissue 1


title: T. denticola tissue 5

description:
T. denticola_Tissue_5T
Gene expression data from T. denticola infected tissue.

source_name: T. denticola infected tissue 5


title: ICN 3-5, CD41 sp rep 3

description: ICN3-5 41 sp_0821


title: T. denticola tissue 3

description:
T. denticola_Tissue_3T
Gene expression data from T. denticola infected tissue.

source_name: T. denticola infected tissue 3


title: ICN 3-5, DP rep 3

description: ICN3-5 DP_0821


title: ICN 3-5, DN rep 1

description: ICN3-5 DN


title: Unsorted cell population replicate group UCPa


title: ICN 3-5, VE sp rep 3

description: ICN3-5 VE sp_0821


title: ICN 3-5, VE sp rep 2

description: ICN3-5 VE sp_0808


title: ICN 0, VE sp rep 2

description: ICNO VE sp_0808


title: ICN 0, DP rep 3

description: ICNO DP_0821


title: ICN 3-5, CD41 sp rep 2

description: ICN3-5 41 sp_0808


title: ICN 0, DP rep 1

description: ICNO DP


title: ICN 0, CD41 sp rep 3

description: ICNO 41 sp_0821


title: Comparison of inoculated NIL seeds replicate 3

status: Public on Oct 01 2010

city: New Orleans

first: Meng

last: Luo

state: LA

address: 1100 Robert E Lee Blvd

department: FFS

institute: SRRC, USDA-ARS

description:
Eyl25 Inoculated/Eyl31 Inoculated rep3
Technical replicate 3 of 4.

hyb_protocol: According to the protocols provided by the manufacturer (http://www.maizearray.org/maize_protocols.shtml), 12 μg of Cy3 and Cy5 labeled cRNAs were hybridized to the 46k oligonucleotide array (Version 1).

scan_protocol: Slides were scanned using the Genepix 4000B (Molecular Devices, Sunnyvale, CA). The saturated spots ratio was set as 0.005%.

data_processing: Array images were processed using GENEPIX 6.0. Raw intensity data were imported into GeneSpring GX 10.0 software (Silicon Genetics, Redwood City, CA).  Two criteria were used for selecting positive spots, (Signal – Background) mean > 400 unit as expression intensity filter, and at least two spots existing in the four replicates. Data normalization was performed using a LOWESS filter (locally weighted regression). Differentially expressed genes were identified by performing a one-way ANOVA on the normalized data using a T-test with no assumption of equal variance. A Benjamini and Hochberg correction for multiple testing was applied using a false-discovery rate (FDR) of 0.05. Genes showing a ratio above 2 (below 0.5) in at least three of four replicates of the same experiments were considered up- (down) regulated.

organism: Zea mays

label_protocol: Purified total RNA was amplified and labeled following the aminoallyl method (http://www.maizearray.org/maize_protocols.shtml). The Ambion Message Amp II kit was used to produce cRNA which is indirectly labeled using dye Cy3 or Cy5 coupling reaction.

extract_protocol: Total RNA was extracted from seeds using a Trizol (Invitrogen). RNA was then treated with RNase-free DNase I (Qiagen) according to the manufacturer’s instructions. Treated RNA samples were further purified using an RNAeasy clean up kit (Qiagen) to remove any residual impurities remaining.

treatment_protocol: Seeds were surface sterilized and inoculated with A. flavus (AF13) according to the Kernel Screening Assay developed by Robert Brown. Inoculated and noninoculated seeds were incubated at 31°C and 100% humidity for 72 hours.

tag: near isogenic lines

value: Aspergillus flavus-AF13


title: ICN 0, DN rep 3

description: ICNO DN_0821


title: ICN 0, VE sp rep 1

description: ICNO VE sp


title: Comparison of inoculated NIL seeds replicate 2

description:
Eyl25 Inoculated/Eyl31 Inoculated rep2
Technical replicate 2 of 4.


title: Comparison of noninoculated NIL seeds replicate 4

description:
Eyl25 Noninoculated/Eyl31 Noninoculated rep4
Technical replicate 4 of 4.


title: Aspergillus flavus challenged Eyl31 kernels replicate4

description:
Eyl31 Inoculated/Noninoculated rep4
Technical replicate 4 of 4.


title: Comparison of inoculated NIL seeds replicate 4

description:
Eyl25 Inoculated/Eyl31 Inoculated rep4
Technical replicate 4 of 4.


title: Aspergillus flavus challenged Eyl31 kernels replicate2

description:
Eyl31 Inoculated/Noninoculated rep2
Technical replicate 2 of 4.


title: Aspergillus flavus challenged Eyl31 kernels replicate1

description:
Eyl31 Inoculated/Noninoculated rep1
Technical replicate 1 of 4.


title: Comparison of noninoculated NIL seeds replicate 3

description:
Eyl25 Noninoculated/Eyl31 Noninoculated rep3
Technical replicate 3 of 4.


title: Aspergillus flavus challenged Eyl31 kernels replicate3

description:
Eyl31 Inoculated/Noninoculated rep3
Technical replicate 3 of 4.


title: ICN 0, DN rep 1

description: ICNO DN


title: Comparison of noninoculated NIL seeds replicate 2

description:
Eyl25 Noninoculated/Eyl31 Noninoculated rep2
Technical replicate 2 of 4.


title: Comparison of noninoculated NIL seeds replicate 1

description:
Eyl25 Noninoculated/Eyl31 Noninoculated rep1
Technical replicate 1 of 4.


title: ICN 0, DP rep 2

description: ICNO DP_0808


title: ICN 0, CD41 sp rep 1

description: ICNO 41 sp


title: Comparison of inoculated NIL seeds replicate 1

description:
Eyl25 Inoculated/Eyl31 Inoculated rep1
Technical replicate 1 of 4.


title: ICN 0, CD41 sp rep 2

description: ICNO 41 sp_0808


title: ICN 0, VE sp rep 3

description: ICNO VE sp_0821


title: ICN 3-5, DN rep 2

description: ICN3-5 DN_0808


title: 13832525 - 4°C W1 vs 4°C

status: Public on Aug 01 2010

description: Is there an overlap between PI4-kinase and phospholipase C signaling in cold response ?

hyb_protocol: 4°C Cy5 / 4°C W1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: cell culture - Columbia suspension cells 22°C

treatment_protocol: Name:4°C - environmental treatment - growth conditions,temperature:time 4hour .

tag: dev.stage (boyes et al. plant cell 2001)

value: suspension cells

source_name: 4°C W1

treatment_protocol: Name:4°C W1 - compound based treatment - compound addition,wortmannin:quantity 1uM time 4hour . Wortmannin (6 mM in methanol) was used at 1 microM final concentration. Chemicals were added 15 min before cold treatment. Cold treatments were performed putting cell flasks in room at 4°C maintaining light and agitation. Cells were harvested 4h after cold treatment, and RNA were extracted.


title: Aspergillus flavus challenged Eyl25 kernels replicate3

description:
Eyl25 Inoculated/Noninoculated rep3
Technical replicate 3 of 4.


title: Aspergillus flavus challenged Eyl25 kernels replicate2

description:
Eyl25 Inoculated/Noninoculated rep2
Technical replicate 2 of 4.


title: 13832631 - 4°C_2 vs 4°C W1_2

hyb_protocol: 4°C W1_2 Cy5 / 4°C_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690897 - 4°C Edelfosine_2 vs 4°C_2

hyb_protocol: 4°C_2 Cy5 / 4°C Edelfosine_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 4°C Edelfosine_2

extract_protocol: 4°C Edelfosine_2:30ug.

treatment_protocol: Name:4°C Edelfosine - compound based treatment - compound addition,edelfosine:quantity 150uM time 4hour . Edelfosine (15 mM in water) was used at 150 microM final concentration. Chemicals were added 15 min before cold treatment. Cold treatments were performed putting cell flasks in room at 4°C maintaining light and agitation. Cells were harvested 4h after cold treatment, and RNA were extracted


title: 13832615 - 4°C W1_2 vs 4°C_2

hyb_protocol: 4°C_2 Cy5 / 4°C W1_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690906 - 22°C Edelfosine_2 vs 22°C_2

hyb_protocol: 22°C_2 Cy5 / 22°C Edelfosine_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 22°C Edelfosine_2

extract_protocol: 22°C Edelfosine_2:30ug.

treatment_protocol: Name:22°C Edelfosine - compound based treatment - compound addition,edelfosine:quantity 150uM time 4hour . Edelfosine (15 mM in water) was used at 150 microM final concentration. Cells were harvested 4h after cold treatment, and RNA were extracted.


title: 13690901 - 4°C W1_2 vs 4°C W30_2

hyb_protocol: 4°C W30_2 Cy5 / 4°C W1_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:4°C W30 - compound based treatment - compound addition,wortmannin:quantity 30uM time 4hour . Wortmannin (6 mM in methanol) was used at 30 microM final concentration. Chemicals were added 15 min before cold treatment. Cold treatments were performed putting cell flasks in room at 4°C maintaining light and agitation. Cells were harvested 4h after cold treatment, and RNA were extracted.


title: 13832524 - 4°C vs 4°C W1

hyb_protocol: 4°C W1 Cy5 / 4°C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690905 - 22°C_2 vs 22°C Edelfosine_2

hyb_protocol: 22°C Edelfosine_2 Cy5 / 22°C_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690753 - 4°C W30 vs 4°C W1

hyb_protocol: 4°C W1 Cy5 / 4°C W30 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 4°C W30


title: 13690892 - 22°C vs 22°C DMSO

hyb_protocol: 22°C DMSO Cy5 / 22°C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 22°C DMSO

extract_protocol: 22°C DMSO:30ug.

treatment_protocol: Name:22°C DMSO - control buffer - control buffer,dmso:time 4hour .


title: 13690754 - 4°C_2 vs 22°C_2

hyb_protocol: 22°C_2 Cy5 / 4°C_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690748 - 4°C vs 22°C

hyb_protocol: 22°C Cy5 / 4°C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Aspergillus flavus challenged Eyl25 kernels replicate1

description:
Eyl25 Inoculated/Noninoculated rep1
Technical replicate 1 of 4.


title: 13690896 - 4°C_2 vs 4°C Edelfosine_2

hyb_protocol: 4°C Edelfosine_2 Cy5 / 4°C_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690894 - 4°C vs 4°C Edelfosine

hyb_protocol: 4°C Edelfosine Cy5 / 4°C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 4°C Edelfosine

extract_protocol: 4°C Edelfosine:30ug.


title: 13690749 - 22°C vs 4°C

hyb_protocol: 4°C Cy5 / 22°C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690763 - 22°C_2 vs 4°C_2

hyb_protocol: 4°C_2 Cy5 / 22°C_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690751 - 22°C Edelfosine vs 22°C

hyb_protocol: 22°C Cy5 / 22°C Edelfosine Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 22°C Edelfosine


title: 13690893 - 22°C DMSO vs 22°C

hyb_protocol: 22°C Cy5 / 22°C DMSO Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690752 - 4°C W1 vs 4°C W30

hyb_protocol: 4°C W30 Cy5 / 4°C W1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690895 - 4°C Edelfosine vs 4°C

hyb_protocol: 4°C Cy5 / 4°C Edelfosine Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690750 - 22°C vs 22°C Edelfosine

hyb_protocol: 22°C Edelfosine Cy5 / 22°C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Aft/Aft atv/atv double mutant, biological rep1

status: Public on Jul 31 2010

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

country: Italy

institute: Sant'Anna School of Advanced Studies

description: No additional description required

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: GC-RMA Algorithm

organism: Solanum lycopersicum

source_name: Mature green tomato fruit

label_protocol: Affymetrix standard labeling protocol

growth_protocol: Selected tomato genotypes were grown during the winter season in a controlled heated greenhouse (minimal temperature 12°C). Fruits were collected at mature green, turning red and red stages of development.

extract_protocol: The total RNA was extracted using the SpectrumTM  Plant Total RNA Kit (SIGMA)

treatment_protocol: No treatment

tag: phenotype

value: Strong anthocyanin pigmentation

value: Fruit peel

tag: genotype

value: Double mutant Aft/Aft atv/atv

value: Green fruit


title: atv (atroviolacea) mutant, biological rep2

description: No additional description required

value: No significant anthocyanin presence

value: atroviolacea (atv) mutant (accession number LA0797)


title: atv (atroviolacea) mutant, biological rep1

description: No additional description required


title: Aft (Anthocyanin fruit) mutant, biological rep2

description: No additional description required

value: Limited amount of anthocyanins (spots)

value: Anthocyanin fruit (Aft) mutant (accession number LA1996)


title: Aft (Anthocyanin fruit) mutant, biological rep1

description: No additional description required


title: wild type (cv. Ailsa Craig), biological rep1

description: No additional description required

value: wild type cv. Ailsa Craig (accession number LA2838A)


title: MicMa 085

status: Public on Jul 01 2010

type: genomic

city: Oslo

first: Jørgen

middle: Mømb

last: Aarøe

address: Montebello

department: Genetics

country: Norway

institute: The Norwegian Radium Hospital

description: The arrays were scanned within 30 minutes after washing, using an Agilent Microarray Scanner. Data extraction, filtering and normalization were conducted using the Feature Extraction software version A.7.5.1 from Agilent Technologies

hyb_protocol: For each experiment, 10 μg labeled tumor DNA, 10 μg labeled reference DNA, Agilent blocking agent, Cot-1 DNA and Agilent hybridization buffer were loaded onto the arrays and assembled in hybridization chambers according to manufacturer’s protocol.Arrays were incubated at 65ºC for 40 hours in a Robbins Scientific oven with rotary motion (20 rpm).Hybridization chambers were taken out of the oven, arrays quickly disassembled in washing solution 1 (0.5 x SSPE, 0.005% N-lauroylsarcosine) and placed in slide-rack submerged in fresh washing solution 1.Arrays were manually washed in batches of four; five minutes in washing solution 1, one minute in washing solution 2 (0.1 x SSPE 0.005% N-lauroylsarcosine) at 37ºC, one minute in 100% acetonitrile (Merck) and 30 seconds in Stabilization & Drying solution (Agilent Technologies).Arrays were protected from light until scanning.

scan_protocol: ScannerName: Agilent Technologies Scanner G2505B US22502513 NumChannels: 2 MicronsPerPixel: 10 FeatureExtractor_ScanFileGUID: e4fe23c9-8c99-4157-b681-88b0ff1d7e7a

data_processing:
VALUE = LogRatio (base 10): (REDsignal/GREENsignal) per feature (processed signals used).
Processed signals: Raw intensities are background corrected using local background subtraction. A linear normalization is applied to correct for dye bias.

molecule: genomic DNA

source_name: primary breast carcinoma, MicMa 085

label_protocol: 100 ng genomic DNA was amplified using phi29 DNA polymerase at 30ºC, 16 hours over night. Amplified DNA was digested using 50 units AluI and 50 units RsaI nucleases, 2 hours incubation at 37ºC. The amplified and digested DNA was purified using QIAprep Miniprep Kit (QIAGEN) according to manufacturer's protocol, and quantified using a NanoDrop ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies).  10 μg amplified and digested DNA was labeled with Cy5-dUTP (PerkinElmer) using the BioPrime Labeling System (Invitrogen). Cy3 and Cy5 reactions were combined and purified using Microcon YM-30 Filters (Amicon).

extract_protocol: Tumor DNA was extracted at The Norwegian Radium Hospital using an ABI 341 Nucleic Acid Purification System (Applied Biosystems) according to manufacturer’s protocol. Fresh frozen tumor tissue were homogenized and digested before phenol chloroform extraction on the ABI 341 system. DNA was stored at 4ºC until use.

tag: Tissue

value: breast carcinoma, part of a larger cohort of stage I and II primary tumors.

tag: Gender

value: female

source_name: Human Male Genomic DNA

label_protocol: 100 ng genomic DNA was amplified using phi29 DNA polymerase at 30ºC, 16 hours over night. Amplified DNA was digested using 50 units AluI and 50 units RsaI nucleases, 2 hours incubation at 37ºC. The amplified and digested DNA was purified using QIAprep Miniprep Kit (QIAGEN) according to manufacturer's protocol, and quantified using a NanoDrop ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies).  10 μg amplified and digested DNA was labeled with Cy3-dUTP (PerkinElmer) using the BioPrime Labeling System (Invitrogen). Cy3 and Cy5 reactions were combined and purified using Microcon YM-30 Filters (Amicon).

extract_protocol: Genomic DNA are purified (extraction method unknown), and greater than 90% of the DNA is longer than 50kb in size as measured by pulsed-field gel electrophoresis. The DNA is stored in 10mM Tris-HCl (pH 8.0), 1mM EDTA.

tag: Purified human genomic DNA from multiple anonymous donors. Promega Cat.# G1471


title: wild type (cv. Ailsa Craig), biological rep2

description: No additional description required


title: MicMa 148

source_name: primary breast carcinoma, MicMa 148


title: MicMa 185

source_name: primary breast carcinoma, MicMa 185


title: MicMa 132

source_name: primary breast carcinoma, MicMa 132


title: MicMa 263

source_name: primary breast carcinoma, MicMa 263


title: MicMa 067

source_name: primary breast carcinoma, MicMa 067


title: MicMa 091

source_name: primary breast carcinoma, MicMa 091


title: 13690902 - 4°C W30_2 vs 4°C W1_2

hyb_protocol: 4°C W1_2 Cy5 / 4°C W30_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: columbia


title: MicMa 709

source_name: primary breast carcinoma, MicMa 709


title: MicMa 053

source_name: primary breast carcinoma, MicMa 053


title: MicMa 122

source_name: primary breast carcinoma, MicMa 122


title: MicMa 031

source_name: primary breast carcinoma, MicMa 031


title: MicMa 101

source_name: primary breast carcinoma, MicMa 101


title: MicMa 146

source_name: primary breast carcinoma, MicMa 146


title: MicMa 065

source_name: primary breast carcinoma, MicMa 065


title: MEF HDAC1 fl/fl + siRNA + Tamoxifen rep3

city: Basel

first: Patrick

last: Matthias

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomed. Research

description: gene expression data from HDAC1/2 KO/Kd cells

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix precedure

data_processing: Affymetrix and Expressionist

source_name: MEF HDAC1 fl/fl + siRNA + Tamoxifen

label_protocol: 1-cycle IVT protocol for Affymetrix Mouse 430v2GeneChips

growth_protocol: MEF cultures were grown at 37°C in Dulbecco’s-modified Eagle’s medium supplemented with 10% heat-inactivated FBS and split 1:3.

extract_protocol: Total RNA was extracted with RNeasy Minikit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: cells were treatment with either Ethanol or Tamoxifen at 200 nanoMolar

tag: cells

value: primary MEF

tag: gender

value: Male

value: HDAC1 KO/HDAC2 Kd


title: MEF HDAC1 fl/fl + siRNA + EtOH rep3

description: gene expression data from HDAC2 Kd cells

source_name: MEF HDAC1 fl/fl + siRNA + EtOH

value: HDAC2 Kd


title: MEF HDAC1 fl/fl + siRNA + EtOH rep2


title: MEF HDAC1 fl/fl + siRNA + Tamoxifen rep2


title: MEF HDAC1 fl/fl + siRNA + Tamoxifen rep1


title: MicMa 088

source_name: primary breast carcinoma, MicMa 088


title: MicMa 042

source_name: primary breast carcinoma, MicMa 042

source_name: Human Male Genomic DNA


title: MicMa 079

source_name: primary breast carcinoma, MicMa 079


title: Aft/Aft atv/atv double mutant, biological rep2

description: No additional description required

source_name: Mature green tomato fruit


title: MicMa 020

source_name: primary breast carcinoma, MicMa 020


title: MicMa 632

source_name: primary breast carcinoma, MicMa 632


title: MEF HDAC1 fl/fl + siRNA + EtOH rep1


title: OS4 Replicate 1; osteosarcoma lung metastasis tissue

status: Public on Jun 30 2010

first: Raphaela

last: Fritsche

address: Chariteplatz 1

institute: Charitè Universitätsklinikum Charite

description: Scanning was carried out by Agilent G2500A GeneArrayScanner (Konfocal argon laser). Software of Affymetrix MAS (MicroArraySuite) 5.0 and DATA-mining-tool 2.0 and Silicongenetics GeneSpring 6.0 were used.

hyb_protocol: According to the standard Affymetrix protocol

data_processing: According to Gcos1.4 protocol

source_name: human osteosarcoma tissue

growth_protocol: Fresh tissue specimens were collected from the consented patients in the operating room and processed immediately after extraction to minimize RNA degradation. Osteosarcoma tissue samples were collected in liquid nitrogen and stored at -80°C until use.

extract_protocol: RNA was isolated using Tri-Reagent (Sigma) as well as the RNeasy-mini-kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: The tissue specimens were fixed in 4% neutral buffered formaldehyde, bone containing tisuue was EDTA-decalcified and embedded in paraffin. Each slide was stained with H&E for Pathologist evaluation to determine tumor content. The diagnosis of the tumor was confirmed according to WHO criteria.

tag: osteosarcoma lung metastasis tissue, male, 40 years, lung, grade 3


title: OS6 Replicate 1; osteosarcoma lung metastasis tissue

scan_protocol: According to the standard Affymetrix protocol

tag: osteosarcoma lung metastasis tissue, female, 21 years, lung, grade 3


title: OS9 Replicate 2; conventional osteosarcoma tissue

label_protocol: According to the standard Affymetrix protocol

tag: conventional osteosarcoma tissue, male, 23 years, tibia, grade 3


title: MEF HDAC1 fl/fl + siRNA scrambled + Tamoxifen rep1

description: gene expression data from HDAC1 KO cells

value: HDAC1 KO


title: MEF HDAC1 fl/fl + siRNA scrambled + Tamoxifen rep2


title: MEF HDAC1 +/+ + Tamoxien rep3

description: gene expression data from control cells treatment with tamoxifen

source_name: MEF HDAC1 +/+ + Tamoxien

value: WT


title: MEF HDAC1 +/+ + Tamoxien rep1


title: MEF HDAC1 fl/fl + siRNA scrambled + EtOH rep3

description: gene expression data from WT cells


title: MEF HDAC1 +/+ + Tamoxien rep2


title: MEF HDAC1 fl/fl + siRNA scrambled + EtOH rep2

description: gene expression data from WT cells


title: OS4 Replicate 2; osteosarcoma lung metastasis tissue


title: OS6 Replicate 2; osteosarcoma lung metastasis tissue


title: OS15 Replicate 2; conventional osteosarcoma tissue

tag: conventional osteosarcoma tissue, female, 74 years, femur, grade 2


title: OS24 Replicate 1; conventional osteosarcoma tissue

tag: conventional osteosarcoma tissue, male, 17 years, femur, grade 3


title: OS16 Replicate 1; osteosarcoma lung metastasis tissue

tag: osteosarcoma lung metastasis tissue, female, 37 years, lung, grade 2


title: OS18 Replicate 1; conventional osteosarcoma tissue

tag: conventional osteosarcoma tissue, male, 7 years, femur, grade 2


title: OS18 Replicate 2; conventional osteosarcoma tissue


title: OS16 Replicate 2; osteosarcoma lung metastasis tissue


title: OS24 Replicate 2; conventional osteosarcoma tissue


title: OS11 Replicate 2; osteosarcoma lung metastasis tissue

tag: osteosarcoma lung metastasis tissue, female, 45 years, lung, grade 1


title: Aspergillus flavus challenged Eyl25 kernels replicate4

description:
Eyl25 Inoculated/Noninoculated rep4
Technical replicate 4 of 4.

hyb_protocol: According to the protocols provided by the manufacturer (http://www.maizearray.org/maize_protocols.shtml), 12 μg of Cy3 and Cy5 labeled cRNAs were hybridized to the 46k oligonucleotide array (Version 1).

tag: near isogenic lines

tag: infection

value: Aspergillus flavus-AF13


title: MicMa 267

source_name: primary breast carcinoma, MicMa 267


title: OS11 Replicate 1; osteosarcoma lung metastasis tissue


title: MEF HDAC1 fl/fl + siRNA scrambled + Tamoxifen rep3


title: Iron radula rep4

status: Public on Jun 25 2010

city: Pacific Grove

first: Luke

last: Gardner

state: California

address: 120 Ocean View Blvd, Hopkins Marine Station

institute: Stanford University

hyb_protocol: Hybridization was performed according to the standard CombiMatrix protocol for single channel 4x2k arrays described in detail at www.combimatrix.com.

scan_protocol: The Cy5- hybridized chip was then scanned using Genepix 4000B microarray scanner (Axon Instruments, CA, USA) according to manufacturer's instructions.

data_processing: Data was pre-processed by global means normalisation.

organism: Liolophura hirtosa

source_name: Pooled iron depositing radula sac tissue

label_protocol: One microgram of total RNA from chiton radule sac was labeled using the Kreatech ampULSe kit to generate Cy5 labeled targets.

extract_protocol: Trizol solution was used to extract total RNA from the chiton radula sac

tag: origin

value: Wild

tag: tissue

value: Iron radula sac

tag: age

value: Adult


title: OS1 Replicate 1; conventional osteosarcoma tissue

tag: conventional osteosarcoma tissue, female, 15 years, femur, grade 3


title: Foot muscle rep1

source_name: Pooled foot muscle sac tissue

value: Foot muscle


title: Foot muscle rep3


title: Calcium radula rep4

source_name: Pooled calcium depositing radula sac tissue

value: Calcium radula sac


title: Iron radula rep1


title: Iron radula rep2


title: Foot muscle rep2


title: Foot muscle rep4


title: OS15 Replicate 1; conventional osteosarcoma tissue


title: OS1 Replicate 2; conventional osteosarcoma tissue


title: Calcium radula rep1


title: OS9 Replicate 1; conventional osteosarcoma tissue


title: Immature radula rep4

source_name: Pooled immature radula sac tissue

value: Immature radula sac


title: Iron radula rep3


title: Immature radula rep3


title: Calcium radula rep3


title: Immature radula rep1


title: MEF HDAC1 fl/fl + siRNA scrambled + EtOH rep1

description: gene expression data from WT cells

tag: genotype


title: HOBc Replicate 2; Non-neoplastic primary osteoblast cells

source_name: Non-neoplastic primary human osteoblasts

growth_protocol: HOBc was maintained in special osteoblast growth medium (PromoCell, Heidelberg, Germany) with 10% FCS and 1% penicillin/streptomycin

treatment_protocol: cells were grown to 70-80% confluence before RNA extraction

tag: Non-neoplastic primary osteoblast cells with limited live span in vitro


title: Calcium radula rep2


title: Immature radula rep2


title: UC_0466_1a_Hv3_35k_h1

status: Public on Jun 14 2010

city: Lund

first: David

last: Lindgren

address: Building 404 A3, Scheelevägen 2, Medicon Village

department: Dept of Laboratory Medicine

country: Sweden

institute: Lund University

hyb_protocol: Samples were dissolved in 42 microliter Universal Hybridization Solution (Corning) and hybridizations were carried out in a CMT-Hybridization Chamber (Corning) for 18 h at 42°C. Pre-hybridization of slides and post-hybridization washes were performed using the Pronto Plus System (Promega)

scan_protocol: Fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies). Image analysis on scanned arrays was performed with GenePix 4.0 (Axon Instruments)

data_processing: Data was processed in the BioArray Software Environment (BASE). For each channel, the Mean FG - Median BG intensity value was used. Features flagged bad, missing or saturated during image analysis were removed. Poorly measured features with ch1 or ch2 intensities <15 were removed. Data was normalized using pin-based LOWESS algorithm.

source_name: Urinary bladder tumor UC_0466_1a

label_protocol: Labeling of 5 micrograms of sample RNA was performed using the Pronto Plus System (Promega)

extract_protocol: Tissue homogenization and RNA recovery using TRIzol reagent (Invitrogen), followed by purification of total RNA using RNeasy kit (Qiagen).

tag: sample histology

value: Urothelial carcinoma

tag: tumor stage

tag: tumor grade

source_name: Stratagene Universal Human Reference

tag: reference

value: RNA pooled from ten human cell lines


title: UC_0458_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0458_1

tag: dead of disease

value: NO

tag: follow up time (months)

tag: cystectomy

value: YES


title: HOBc Replicate 1; Non-neoplastic primary osteoblast cells

source_name: non-neoplastic human primary osteoblasts


title: UC_0410_1b_Hv3_35k_h2

source_name: Urinary bladder tumor UC_0410_1b


title: UC_0442_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0442_1

tag: tat1 progress^to minv/cystectomy/dead


title: UC_0349_2_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0349_2


title: UC_0301_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0301_1


title: UC_0339_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0339_1

tag: distant metastasis

value: M+


title: UC_0372_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0372_1


title: UC_0302_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0302_1


title: UC_0376_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0376_1


title: UC_0394_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0394_1


title: UC_0312_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0312_1


title: UC_0321_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0321_1


title: UC_0242_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0242_1


title: UC_0323_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0323_1


title: UC_0329_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0329_1


title: UC_0283_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0283_1

source_name: Stratagene Universal Human Reference


title: UC_0263_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0263_1

value: Ta


title: UC_0250_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0250_1


title: UC_0237_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0237_1

value: Tx


title: UC_0290_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0290_1


title: UC_0265_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0265_1


title: UC_0267_3_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0267_3


title: UC_0241_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0241_1


title: UC_0215_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0215_1


title: UC_0207_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0207_1


title: UC_0235_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0235_1


title: UC_0214_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0214_1


title: UC_0455_1_BAC_32k_h1

hyb_protocol: Differentially labeled DNA was pooled, mixed with 100 microgram Human Cot-1 DNA (Invitrogen), and lyophilized prior to resuspension in 55 microliter hybridization solution (50% formamide, 10% dextran sulfate, 2x SSC, 2% SDS, 10 mg/ml yeast tRNA). Probes were heated at 70°C for 15 minutes and at 37°C for 30 minutes before hybridization to micro arrays for 48-72 hours at 37°C. Prior to hybridization, micro arrays were UV-cross linked at 500 mJ/cm2 and pretreated using the Universal Micro array Hybridization Kit (Corning, Acton, MA) according to the manufacturer's instructions. The slides were washed in 2 x SSC, 0.1% SDS for 15 min, followed by 2 x SSC, 50% formamide (pH 7.0) for 15 min at 45°C, 2 x SSC, 0.1% SDS for 30 min at 45°C, and 0.2 x SSC for 15 min at room temperature.

data_processing: Data was processed in the BioArray Software Environment (BASE). For each channel, the Mean FG - Median BG intensity value was used. Features flagged bad/missing or saturated during image analysis were removed. Poorly measured features with Ch1 or Ch2 signal to noise ratio (SNR) <5 were removed. Data was normalized using the popLowess method (Staaf, et al, BMC Genomics, 2007, 8:382)

source_name: Urinary bladder tumor UC_0455_1

label_protocol: 1.5 microgram sample and reference genomic DNA was labeled with Cy5-dCTP or with Cy3-dCTP (Amersham Biosciences) using random primer labeling (Bioprime array CGH genomic Labeling module, Invitrogen), and purified using filter-based spin columns (Cyscribe GFX Purification kit, Amersham Biosciences).

extract_protocol: Genomic DNA was extracted using the Dneasy Tissue kit (Qiagen)

source_name: Reference male DNA

value: Reference male DNA


title: UC_0399_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0399_1


title: UC_0399_1_BAC_32k_h1

label_protocol: 1.5 microgram sample and reference genomic DNA was fluorescently labeled with Cy3-dCTP and Cy5-dCTP (Amersham Biosciences), respectively, using the Array CGH labeling kit (Invitrogen), and purified using filter-based spin columns (Cyscribe GFX Purification kit, Amersham Biosciences).


title: UC_0322_2_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0322_2


title: UC_0224_1_Hv3_35k_h2

source_name: Urinary bladder tumor UC_0224_1


title: UC_0203_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0203_1

source_name: Stratagene Universal Human Reference


title: UC_0223_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0223_1


title: UC_0199_2_Hv3_35k_h2

source_name: Urinary bladder tumor UC_0199_2


title: UC_0226_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0226_1


title: UC_0195_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0195_1


title: UC_0372_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0372_1


title: UC_0196_1_Hv3_35k_h2

source_name: Urinary bladder tumor UC_0196_1


title: UC_0376_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0376_1


title: UC_0187_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0187_1


title: UC_0339_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0339_1


title: UC_0200_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0200_1


title: UC_0184_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0184_1

value: YES^cystectomy


title: UC_0349_2_BAC_32k_h1

source_name: Urinary bladder tumor UC_0349_2

source_name: Reference male DNA


title: UC_0230_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0230_1


title: UC_0185_1_Hv3_35k_h2

source_name: Urinary bladder tumor UC_0185_1


title: UC_0329_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0329_1


title: UC_0335_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0335_1


title: UC_0322_2_BAC_32k_h1

source_name: Urinary bladder tumor UC_0322_2


title: UC_0179_1_Hv3_35k_h1

description:
UC_0179_1_Hv3_35k_h1
This is one of two samples that were hybridized to both 27k and 35k platforms. They were only used for merging of the two expression datasets.

source_name: Urinary bladder tumor UC_0179_1

value: Upper urinary tract urothelial carcinoma

source_name: Stratagene Universal Human Reference


title: UC_0323_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0323_1


title: UC_0166_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0166_1


title: UC_0169_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0169_1


title: UC_0312_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0312_1


title: UC_0335_1_Hv3_35k_h1


title: UC_0159_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0159_1


title: UC_0152_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0152_1


title: UC_0302_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0302_1


title: UC_0290_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0290_1


title: CBA/J

status: Public on Jun 26 2010

city: Saint Louis

first: Darryl

last: Higuchi

state: MO

address: 660 S. Euclid Ave

department: Internal Medicine

institute: Washington University

hyb_protocol: Hybridizations were carried out for 18 hr at 42 celsus in the NimbleGen Service Laboratory. The arrays were washed using a NimbleGen Wash Buffer System and immediately dried down by centrifugation.

scan_protocol: Arrays were scanned at 5-um resolution using the GenePix4000B scanner (Axon Instruments, Molecular Devices Corp., Sunnyvale, CA). Data were extracted using NimbleScan extraction software.

data_processing: Each array set was imported into R for normalization. The normalize.qspline method from the affy Bioconductor package was used to normalize and computes the log2 ratios of the signal intensities of the test vs. reference. see PMID 16075461

source_name: CBA/J

label_protocol: The labeling of genomic DNA samples for oligonucleotide microarray CGH analysis was performed using the method of Brennen et al., (2004)

extract_protocol: Phenol-chloroform extraction of DNA from kidney tissue.  DNA pooled from 2-6 animals.

tag: strain

value: CBA/J

value: kidney


title: UC_0321_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0321_1

source_name: Reference male DNA


title: UC_0301_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0301_1


title: UC_0283_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0283_1


title: UC_0138_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0138_1


title: NZW/LacJ

source_name: NZW/LacJ

value: NZW/LacJ


title: UC_0231_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0231_1


title: UC_0134_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0134_1

source_name: Stratagene Universal Human Reference


title: UC_0267_3_BAC_32k_h1

source_name: Urinary bladder tumor UC_0267_3


title: UC_0154_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0154_1


title: UC_0265_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0265_1


title: UC_0455_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0455_1


title: UC_0120_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0120_1


title: UC_0394_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0394_1


title: UC_0249_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0249_1


title: UC_0117_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0117_1


title: UC_0249_1_BAC_32k_h1


title: UC_0111_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0111_1


title: UC_0170_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0170_1


title: UC_0263_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0263_1

source_name: Reference male DNA


title: UC_0241_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0241_1


title: UC_0242_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0242_1


title: UC_0139_2_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0139_2


title: UC_0101_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0101_1


title: UC_0122_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0122_1

source_name: Stratagene Universal Human Reference


title: UC_0237_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0237_1


title: UC_0231_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0231_1


title: UC_0102_2_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0102_2


title: UC_0235_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0235_1


title: UC_0093_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0093_1


title: UC_0224_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0224_1


title: UC_0095_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0095_1


title: UC_0226_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0226_1


title: UC_0215_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0215_1


title: UC_0223_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0223_1


title: UC_0109_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0109_1


title: UC_0207_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0207_1

source_name: Reference male DNA


title: UC_0073_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0073_1


title: UC_0097_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0097_1


title: UC_0086_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0086_1


title: UC_0089_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0089_1

source_name: Stratagene Universal Human Reference


title: UC_0067_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0067_1


title: UC_0069_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0069_1


title: UC_0230_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0230_1


title: UC_0203_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0203_1


title: UC_0057_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0057_1


title: UC_0059_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0059_1


title: UC_0053_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0053_1

value: YES^cystectomy+met


title: UC_0046_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0046_1


title: UC_0060_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0060_1


title: UC_0214_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0214_1


title: UC_0195_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0195_1


title: UC_0200_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0200_1

source_name: Reference male DNA


title: UC_0199_2_BAC_32k_h1

source_name: Urinary bladder tumor UC_0199_2


title: UC_0040_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0040_1


title: UC_0039_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0039_1


title: UC_0035_1_Hv3_35k_h1

description:
UC_0035_1_Hv3_35k_h1
This is one of two samples that were hybridized to both 27k and 35k platforms. They were only used for merging of the two expression datasets.

source_name: Urinary bladder tumor UC_0035_1

value: Gx

source_name: Stratagene Universal Human Reference


title: UC_0172_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0172_1

extract_protocol: Genomic DNA was extracted using Trizol reagent (Invitrogen) and further purified using the Wizard kit (Promega)

source_name: Reference female DNA

value: Reference female DNA


title: UC_0196_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0196_1


title: UC_0192_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0192_1


title: UC_0023_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0023_1


title: UC_0187_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0187_1


title: UC_0034_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0034_1


title: UC_0166_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0166_1


title: UC_0169_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0169_1


title: UC_0170_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0170_1


title: UC_0173_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0173_1


title: UC_0042_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0042_1


title: UC_0022_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0022_1


title: UC_0009_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0009_1


title: UC_0016_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0016_1


title: UC_0159_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0159_1

source_name: Reference male DNA


title: UC_0165_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0165_1


title: UC_0010_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0010_1

source_name: Stratagene Universal Human Reference


title: UC_0152_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0152_1


title: UC_0077_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0077_1


title: UC_0149_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0149_1

source_name: Reference female DNA


title: UC_0147_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0147_1


title: UC_0162_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0162_1


title: UC_0007_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0007_1


title: UC_0185_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0185_1


title: UC_0002_1_Hv3_35k_h2

source_name: Urinary bladder tumor UC_0002_1


title: UC_0138_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0138_1


title: N_013_Hv3_35k_h1

source_name: Urinary bladder tumor N_013

value: Normal bladder


title: N_009_Hv3_35k_h1

source_name: Urinary bladder tumor N_009


title: UC_0122_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0122_1

value: Urothelial carcinoma


title: UC_0001_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0001_1

value: RNA pooled from ten human cell lines


title: N_007_Hv3_35k_h1

source_name: Urinary bladder tumor N_007


title: UC_0129_1_BAC_32k_h2

source_name: Urinary bladder tumor UC_0129_1

value: NO


title: N_008_Hv3_35k_h1

source_name: Urinary bladder tumor N_008

source_name: Stratagene Universal Human Reference


title: N_006_Hv3_35k_h1

source_name: Urinary bladder tumor N_006


title: UC_0003_1_Hv3_35k_h1

source_name: Urinary bladder tumor UC_0003_1

value: YES


title: N_003_Hv3_35k_h1

source_name: Urinary bladder tumor N_003


title: UC_0137_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0137_1

source_name: Reference female DNA


title: UC_0120_1_BAC_32k_h2

source_name: Urinary bladder tumor UC_0120_1


title: UC_0117_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0117_1

source_name: Reference male DNA