title: 13372753 - Col-0+DEX vs DRN+DEX

hyb_protocol: DRN+DEX Cy5 / Col-0+DEX 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: 13372742 - Col-0 vs DRN

status: Public on Sep 26 2008

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Identification of the target genes of the ESR1/DRN TF using dexamethasone induction

hyb_protocol: DRN Cy5 / Col-0 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,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

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: DRN

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 - MS/2, sacharose 7g/L, agar 10g/L 25°C Light 16h/8h

extract_protocol: Pool of extract, DRN_1:0.5ug, DRN_2:0.5ug.

treatment_protocol: Name:Control - control buffer - control buffer,water+silwet:quantity 0.05percent time 2min . 2min and 1h of incubation, 2min and 2h of incubation

tag: Arabidopsis thaliana (columbia)  mutant (DRN) - age:15daydev.stage (Boyes et al. Plant Cell 2001):boyes = 1.04

extract_protocol: Pool of extract, Col-0_1:0.5ug, Col-0_2:0.5ug.

tag: Arabidopsis thaliana (columbia)  - age:15daydev.stage (Boyes et al. Plant Cell 2001):boyes = 1.04


title: ash2I1_larvae_(Replicate2)

city: Barcelona

first: Sergi

last: Beltran

address: Baldiri Reixac 10

department: Serveis Cientificotècnics

country: Spain

institute: Universitat de Barcelona

description: Total RNA from w1118;+;+ larvae was pooled and used as a common reference in four microarrays against w1118;+;ash2I1 total RNA coming from two different extractions to take biological differences into account. Amplified RNA (aRNA) was obtained with the Amino-Allyl Messageamp II aRNA Amplification Kit (Ambion, Inc) from w1118;+;+ and w1118;+;ash2I1 prior to hybridization.

hyb_protocol: Samples were diluted in 2X Hybridization Buffer #5185-5973(Agilent Technologies) and hybridization was carried out at 60ºC for 18 hours with a G2534A SureHyb Chamber in a G2545A Hybridization Oven (Agilent Technologies).

scan_protocol: GenePix Results (GPR) data files were obtained for each microarray with an Axon 4000B scanner and GenePix Pro 6 (Axon Instruments, Inc).

data_processing: GPR files were analyzed with Limma package from BioConductor (Gentleman et al., 2004; Genome Biol 5, R80; Smyth, 2004; Statistical Applications in Genetics and Molecular Biology 3, Article 3) using the same criteria. Data was background corrected with the "normexp" method and normalized with OLIN (Futschik and Crompton, 2005; Bioinformatics 21, 1724-1726). Spots not fulfilling the quality thresholds (based on spot size, foreground versus background signals, saturation, coincidence between differently calculated ratio measures and R2 of regression ratio) were eliminated from further analysis.

organism: Drosophila melanogaster

source_name: w1118;+;ash2I1 isogenized larvae (Biological Replicate 1)

label_protocol: 1.5ug total RNA were amplified and indirectly labelled with Amino-Allyl Messageamp II aRNA Amplification Kit (Ambion, Inc). Fragmentation was done with RNA Fragmentation Reagents #8740(Ambion, Inc).

growth_protocol: Flies were kept on standard media with 0.025% bromophenol blue at 25ºC.

extract_protocol: Larvae were squashed in PBS and total RNA extraction was performed with RNeasy Protect Mini Kit (QIAGEN Inc.). Quality was assessed using the Eukaryote Total RNA Nano Assay on a 2100 Bioanalyzer (Agilent Technologies).

tag: Strain

value: w1118;+;ash2I1 isogenized from wt strain.

tag: Stage

value: third instar larvae (bromophenol blue staged)

tag: Tissue

value: whole larvae

source_name: w1118;+;+ isogenic wt larvae (pool)

value: w1118;+;+ isogenic wt strain (Ryder, E., 2004; Genetics 167, 797-813).


title: Construct Q23 Line 1 1 days (Q23_1_1_1)

status: Public on Sep 29 2008

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: Gene expression data from PC12 cells stably transfected with a doxycylin-inducible exon1 huntingtin fragment with normal-sized or elongated glutamine stretch

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Non-background corrected average intensities across all replicate beads (obtained from Beadstudio) were normalized with vsn

label: biotin

organism: Rattus norvegicus

source_name: PC12 cell culture

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

growth_protocol: RNA was isolated from one 9 cm petriddish

extract_protocol: RNA was isolated with the RNeasy kit

treatment_protocol: Cells were treated with 1ug /ml doxycylin for the indicated number of days

tag: Construct

value: Q23, Line 1

tag: Time after induction

value: 1 days


title: 13372755 - DRN+Cyclo vs DRN+DEX+Cyclo

hyb_protocol: DRN+DEX+Cyclo Cy5 / DRN+Cyclo 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: DRN+DEX+Cyclo

extract_protocol: Pool of extract, DRN+DEX+Cyclo_1:0.5ug, DRN+DEX+Cyclo_2:0.5ug.

treatment_protocol: Name:Cyclo+DEX - compound based treatment - traduction inhibitor+protein activator,cyclo+dex:quantity 0.01mM time 2min . Cyclo 10(u)M +DEX 10(u)M 2min and 1h of incubation, 2min and 2h of incubation

source_name: DRN+Cyclo

extract_protocol: Pool of extract, DRN+Cyclo_1:0.5ug, DRN+Cyclo_2:0.5ug.

treatment_protocol: Name:Cyclo - compound based treatment - traduction inhibitor,cycloheximide:quantity 0.01mM time 2min . 2min and 1h of incubation, 2min and 2h of incubation


title: trxE3/trxB11_larvae_(Replicate1)

description: Total RNA from w1118;+;+ larvae was pooled and used as a common reference in four microarrays against w1118;+;trxE3/trxB11 total RNA coming from two different extractions to take biological differences into account. Two amplifications from w1118;+;+ and one from each w1118;+;trxE3/trxB11 replicate were performed with the Amino-Allyl Messageamp II aRNA Amplification Kit (Ambion, Inc) to obtain amplified RNA (aRNA). The arrays from each replicate pair were hybridized with the same amplified RNA from sample and common reference but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.

growth_protocol: Flies were kept on standard media with 0.025% bromophenol blue at 21ºC.

source_name: w1118;+;trxE3/trxB11 isogenized larvae (Biological Replicate 1)

value: w1118;+;trxE3/trxB11 isogenized from wt strain.


title: 13372743 - DRN vs Col-0

hyb_protocol: Col-0 Cy5 / DRN 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: 13372740 - Col-0 vs Col-0+DEX

hyb_protocol: Col-0+DEX Cy5 / Col-0 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.

extract_protocol: Pool of extract, Col-0+DEX_1:0.5ug, Col-0+DEX_2:0.5ug.

treatment_protocol: Name:DEX - compound based treatment - protein activator,dexamethasone:quantity 0.01mM time 2min . 2min and 1h of incubation, 2min and 2h of incubation


title: P831 35 MRC-5S

status: Public on Sep 25 2008

city: Bethesda

first: Giang Huong

last: Nguyen

state: MD

address: 37 Convent Drive

department: CCR

country: USA

institute: NCI

description: Total RNA was biotin labeled and hybridization on the version 4.0 miR arrays (Ohio State University) as described in (Liu et al, PNAS, 2004).

hyb_protocol: hybridizated on miRNA array chip containing 4104 probes printed in duplicate, corresponding to 474 human and 373 mouse miRNAs. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix.

scan_protocol: The microarrays were processed by using a method of direct detection of biotin-containing transcripts by streptavidin-Alexa647 conjugate. Processed slides were then scanned by using the PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at power 80 and PMT 70 setting and a scan resolution of 10 nm

data_processing:
The raw data was normalized, log2 transformed and averaged for the the duplicate using BRB software (NCI, NIH).
The data were pre-processed by the statistical software  2.5.0 (R Foundation for Statistical Computing, Vienna, Austria) to remove probes with higher intenstiies than background intensities. The data were normalized by locally weighted scatter plot smoothing LOESS and imported intoBiometric Research Branch (BRB) array tools 3.6.0  for subsequent microarray. Class comparison analysis using paired t tests identified microRNAs that were differentially expressed in senescence cells compared to young fibroblast cells.

label: Biotin

organism: Homo sapiens

source_name: Human embryonic fibroblast

label_protocol: Five microgram of total RNA was reversed transcribed and biotin labeling. See in paper published by Lin at al, PNAS, 2004.

growth_protocol: WI-38 and MRC-5 were grown in DMEM 10% FBS until confluence

extract_protocol: RNA was extracted using TRIZOL (Invitrogene) according to the manufacturer protocol

treatment_protocol: To be updated

tag: Senescence


title: P810 14 WI-38S

label_protocol: Five microgram of total RNA was reversed transcribed and biotin labeling. See in paper published by Lin at al, PNAS, 2004.. See in paper published by Lin at al, PNAS, 2004.


title: P813 17 MRC-5Y

tag: Young


title: P809 13 WI-38Y


title: trxE3/trxB11_larvae_(Replicate2)


title: 13489209 - DRN+Cyclo 2 vs DRN+DEX+Cyclo 2

hyb_protocol: DRN+DEX+Cyclo 2 Cy5 / DRN+Cyclo 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,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%

source_name: DRN+DEX+Cyclo 2

source_name: DRN+Cyclo 2


title: Zm_SG200Dpep1_24hpi_I

city: Marburg

first: Gunther

last: Doehlemann

state: Hessen

address: Karl von Frisch Str.

department: Organismic Interactions

country: Germany

institute: Max Planck Institue for Terrestiral Microbiology

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (Expression Analysis Technical Manual, 2001, Affymetrix)

scan_protocol: Microarrays were scanned on an Affymetrix GSC3000.

data_processing: Data were analyzed with Microarray Suite version 5.1 (MAS 5.1) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.

organism: Zea mays

source_name: infected leaf tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Maize plants of the cultivar Early Golden Bantam were grown in a phytochamber in a 15 h / 9 h light-dark cycle; light period started with a continuous increase from 0% to 100% light for 1h, and ended 13h later with a continuous decrease from 100% to 0% light for 1 h. Temperature was 28°C and 20°C, relative humidity 40% and 60% during light and dark periods, respectively, with a 1 h ramping for both values. Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) to avoid shading of the plants.

extract_protocol: For RNA isolation, material from 30 plants was pooled and subsequently ground in liquid nitrogen by mortar and pestle. RNA was extracted from the powder with Trizol (Invitrogen) and purified using the Qiagen RNeasy kit, according to the manufacturer’s instructions, respectively.

treatment_protocol: U. maydis strain SG200Dpep1 was grown in liquid culture overnight to an OD600 of 1.0, harvested by centrifugation, and resuspended in water to an OD600 of 3.0; compatible strains were mixed in equal amounts immediately before infection; 0.2 ml of cell suspension mixes were injected into the leaf whorl of 6–7-day-old corn plants (as described in Mol Microbiology 42:1047-1063). Plants were infected 7 days after sowing 1 h before end of the light period with the exception of the 12 hpi samples were plants were infected during the beginning of the light period.

tag: 3. leaf of maize seedlings 24 hours post Ustilago maydis infection. Infection was performed 7 days post sowing. Dissected leaf tissue from 30 plants was pooled. Samples were harvested in the evening.


title: Zm_SG200Dpep1_24hpi_III


title: MMCASE20_NSP

type: genomic

city: salamanca

first: Maria

middle: Eugenia

last: Sarasquete

state: salamanca

address: Paseo San Vicente 58-182

department: Hematology

institute: Hospital Universitario de Salamanca

hyb_protocol: Mapping 500K arrays were hybridized according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using an Affymetrix hybridization oven.

scan_protocol: Mapping 500K arrays were scanned according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using a GS3000 scanner.

data_processing: Genotypes were determined using the BRLMM algorithm (Bayesian Robust Linear Model with Mahalanobis distance classifier) with cases and controls undergoing a joint cluster analysis. Before the analysis, quality filtering tests (of both samples and SNP’s) were carried out to ensure a robust association test. The criteria for exclusion were: 1) call rate<90%, 2) minor allele frequency, MAF<5% and 3) deviations from Hardy-Weinberg equilibrium with a low enough significance (p<0.00001). Sexual chromosomes were not considered in the SNP analysis.

label: BIOTIN

molecule: genomic DNA

source_name: PERIPHERAL BLOOD

label_protocol: Following restriction enzyme digestion, biotin labeled DNA was prepared according to the Affymetrix protocol from 500ng of starting DNA (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005).

extract_protocol: AUTOMATED DNA EXTRACTION MAGNA PURE

tag: PB MM CASE - NSP CHIP

tag: Number

tag: Case

tag: Treatment

value: 1- Pamidronate

tag: Gender

value: female


title: MMCASE22_NSP

value: 5- Zoledronic Acid

value: male


title: Construct Q23 Line 5 0 days (Q23_0_5_1)

value: Q23, Line 5

value: 0 days


title: MMCASE21_NSP


title: trxE3/trxB11_larvae_(Replicate3)

source_name: w1118;+;trxE3/trxB11 isogenized larvae (Biological Replicate 2)


title: 13372741 - Col-0+DEX vs Col-0

hyb_protocol: Col-0 Cy5 / Col-0+DEX 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: MMCASE13_NSP


title: MMCASE18_NSP


title: MMCASE10_NSP


title: Zm_SG200Dpep1_24hpi_II


title: MMCASE15_NSP


title: MMCASE7_NSP


title: MMCASE3_NSP


title: MMCASE16_NSP


title: MMCASE9_NSP


title: MMCONTROL64_NSP

tag: PB MM CONTROL - NSP CHIP

tag: Control


title: MMCASE19_NSP


title: MMCASE11_NSP


title: MMCASE4_NSP


title: MMCASE6_NSP


title: MMCASE5_NSP


title: MMCONTROL63_NSP


title: MMCONTROL65_NSP


title: MMCASE17_NSP


title: MMCASE8_NSP


title: KAT18 - treated with P53 antisense

city: Busan

first: Young

middle: Hyun

last: Yoo

address: 3-1 Dongdaesin-Dong

department: Dept Anatomy and Cell Biology

country: South Korea

institute: Dong-A Univ Coll Med

description: Total RNA collected from KAT-18 cells 24 h after p53-specific AS treatment served as the mRNA sources for microarray analysis.

hyb_protocol: 1. Vortex Hybridization Controls, then centrifuge the tube briefly. 2.If you used the Applied Biosystems Chemiluminescent RT Labeling Kit, add nuclease-free water to the cDNA targets to bring the volume to 150uL 3. For each microarray, prepare hybridization mixture in a 1.5mL nuclease-free microcentrifuge tube. 4. Vortex the hybridization mixture, then centrifuge the tube briefly 5. Take to the hybridization oven 6. Quickly transfer hybridization mixture into microarray cartridge 7. Incubate cartridge(s) in the oven    -  Temperature: 55 oC    -  Agitation: 100 rpm    -  Time: 16 hour

scan_protocol: Image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following the manufacturer’s protocol.

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391).

label: DIG

source_name: Human thyroid cancer cell line

label_protocol: Label cRNA was generated and amplified from 2μg of total RNA using Applied Biosystems Chemiluminescent RT-IVT labeling kit according to the manufacturer's protocol

extract_protocol: Total RNA was extracted from KAT-18 cell using the RNeasyⓇ plus Mini Kit (QIAGEN) following the manufacturer's instructions. The quality and integrity of the total RNA was evaluated on the 2100 Bioanalyzer(Agilent Technologies) and the concentration was measured using a NanoDrop spectrophotometer

tag: KAT 18 is obtained from primary culture of an anaplastic thyroid carcinoma.


title: MMCASE12_NSP


title: MMCONTROL61_NSP


title: KAT18 - control

description: Do not vary the incubation time of hybridization. Variations may affect reproducibility.

tag: KAT 18 is obtained from primary culture of an anaplastic thyroid carcinoma


title: MMCONTROL60_NSP


title: JPA705

city: Houston

first: Kwong-Kwok

last: Wong

state: TX

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

description: Gene expression from juvenile pilocytic astrocytoma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using GeneArray Scanner Model G2500

data_processing: The data were analyzed using GCOS1.4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Trizol followed by RNeasy was performed according to the manufacturer's instructions

tag: Juvenile pilocytic astrocytoma

tag: Age

value: 10 Sex:M

tag: Location

value: posterior fossa

tag: Histopathology


title: Nc321

tag: Normal Cerebellar tissue

value: 8 Sex:F

value: cerebellum

value: normal


title: JPA667

value: 11 Sex:M

value: nd


title: Nc739

tag: normal cerebellar tissue

value: 16 Sex:M

tag: Histopatholgy


title: NcAb

source_name: NcAb

tag: Normal cerebellar tissue

value: 63 Sex:M


title: JPA668


title: MMCONTROL58_NSP


title: Nfb

source_name: Nfb

tag: Normal fetal brain

value: 24 weeks Sex:F

value: whole brain

value: normal fetal brain


title: MMCONTROL57_NSP

tag: Number

value: 1- Pamidronate

value: female


title: MMCONTROL62_NSP


title: MMCONTROL55_NSP

value: 5- Zoledronic Acid

value: male


title: MMCONTROL59_NSP


title: MMCONTROL51_NSP


title: JPA528

value: 3 Sex:F

value: focal vascular proliferation, Ki-67 (3-5%)


title: MMCONTROL56_NSP


title: MMCONTROL54_NSP


title: JPA399

value: 4 Sex:M

value: posterior fossa

value: variable cellularity, rich vascularization


title: JPA562

value: 8 Sex:M

value: variable cellular morphologies


title: JPA564

value: 5 Sex:M


title: JPA276

value: 6 Sex:M

value: no special feature


title: JPA284

value: 9 Sex:F

value: hypocellular, Ki-67(1-4%)


title: JPA637

value: 13 Sex:F


title: JPA567

value: 14 Sex:M

value: vessels with prominent endothelial cells, Ki-67 (1-2%), with progressive disease


title: MMCONTROL52_NSP

value: 1- Pamidronate

value: female


title: JPA317

value: 2 Sex:F


title: JPA281

value: cerebellum

value: highly vascular with vascular proliferation noted


title: MMCONTROL53_NSP

value: male


title: 13373308 - ler vs crc1

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

description: Identification of target genes from three transcription factors involved in gynoecium development

hyb_protocol: crc1 Cy5 / ler 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: flowers - Media : peet-based compost	 hygrometry : 55-75%	 Temperature : 15-20,6°C	 Light : 12000-14000 lux

treatment_protocol: no treatment

tag: Arabidopsis thaliana (landsberg erecta)  mutant (crc1) - dev.stage (Boyes et al. Plant Cell 2001):6.00

source_name: ler

tag: Arabidopsis thaliana (landsberg erecta)  - dev.stage (Boyes et al. Plant Cell 2001):6.00


title: JPA323

value: 2 Sex:M

value: frontal lobe

value: pilomyxoid feature with many small blood vessels, with progressive disease


title: MMCASE14_NSP

tag: PB MM CASE - NSP CHIP

tag: Case

tag: Treatment

tag: Gender


title: 13373309 - crc1 vs ler

hyb_protocol: ler Cy5 / crc1 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: JPA389

value: 6 Sex:F

value: posterior fossa


title: MMCONTROL50_NSP

tag: PB MM CONTROL - NSP CHIP

tag: Control


title: MMCONTROL49_NSP


title: MMCONTROL46_NSP


title: MMCONTROL48_NSP


title: MMCONTROL47_NSP


title: MMCONTROL44_NSP


title: MMCONTROL45_NSP


title: JPA266

tag: Juvenile pilocytic astrocytoma

tag: Age

value: 1.3 Sex:M

value: no special feature


title: JPA170

tag: Location

tag: Histopathology

value: variable cellularity, prominent blood vessels


title: MMCASE19_STY

tag: PB MM CASE - STY CHIP


title: JPA159


title: MMCASE22_STY

value: 5- Zoledronic Acid


title: MMCASE21_STY


title: JPA135

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

value: 3 Sex:F

value: conspicuous vascular proliferation in most areas


title: MMCASE18_STY


title: JPA110

value: nd


title: MMCONTROL42_NSP

value: 1- Pamidronate


title: MMCASE17_STY

value: female


title: MMCASE20_STY


title: MMCASE13_STY


title: MMCASE16_STY


title: MMCONTROL41_NSP


title: MMCASE12_STY


title: MMCONTROL39_NSP


title: MMCONTROL36_NSP


title: MMCONTROL37_NSP


title: MMCASE14_STY


title: MMCASE15_STY


title: MMCASE9_STY


title: MMCASE10_STY


title: MMCONTROL34_NSP


title: MMCASE8_STY


title: MMCONTROL40_NSP


title: MMCONTROL38_NSP


title: MMCASE11_STY


title: MMCONTROL35_NSP


title: JPA314

value: cerebellar vermis

value: prominent blood vessels, no mitotic activity


title: MMCASE3_STY


title: MMCASE6_STY


title: MMCASE7_STY

value: male


title: MMCONTROL43_NSP


title: MMCONTROL59_STY

tag: PB MM CONTROL - STY CHIP


title: MMCONTROL33_NSP


title: MMCONTROL32_NSP


title: MMCONTROL62_STY


title: MMCONTROL60_STY


title: MMCONTROL31_NSP


title: MMCONTROL63_STY


title: MMCASE4_STY


title: MMCASE5_STY


title: MMCONTROL65_STY


title: MMCONTROL54_STY


title: MMCONTROL61_STY


title: MMCONTROL58_STY


title: MMCONTROL30_NSP


title: MMCONTROL57_STY


title: MMCONTROL56_STY


title: MMCONTROL27_NSP


title: MMCONTROL25_NSP

scan_protocol: Mapping 500K arrays were scanned according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using a GS3000 scanner


title: MMCONTROL29_NSP


title: MMCONTROL51_STY


title: MMCONTROL55_STY


title: MMCONTROL48_STY


title: MMCONTROL64_STY


title: MMCONTROL50_STY


title: MMCONTROL23_NSP


title: MMCONTROL47_STY


title: MMCONTROL28_NSP


title: MMCONTROL21_NSP


title: MMCONTROL24_NSP


title: MMCONTROL52_STY


title: MMCONTROL45_STY


title: MMCONTROL46_STY


title: MMCONTROL43_STY


title: MMCONTROL44_STY


title: MMCONTROL20_NSP


title: MMCONTROL42_STY


title: MMCONTROL39_STY


title: MMCONTROL38_STY


title: MMCONTROL19_NSP


title: MMCONTROL37_STY


title: MMCONTROL16_NSP


title: MMCONTROL41_STY


title: MMCONTROL53_STY


title: MMCONTROL33_STY


title: MMCONTROL40_STY


title: MMCONTROL18_NSP


title: MMCONTROL36_STY


title: MMCONTROL32_STY


title: MMCONTROL34_STY


title: MMCONTROL14_NSP


title: MMCONTROL15_NSP


title: MMCONTROL11_NSP


title: MMCONTROL35_STY


title: MMCONTROL13_NSP


title: MMCONTROL12_NSP


title: MMCONTROL30_STY


title: MMCONTROL10_NSP


title: MMCONTROL31_STY


title: MMCONTROL29_STY


title: MMCONTROL9_NSP


title: MMCONTROL6_NSP


title: MMCONTROL22_NSP


title: MMCONTROL28_STY


title: MMCONTROL7_NSP


title: MMCONTROL17_NSP

value: 3- OTROS


title: MMCONTROL8_NSP


title: MMCONTROL27_STY


title: MMCONTROL26_STY


title: MMCONTROL26_NSP


title: MMCONTROL24_STY


title: MMCASE2_NSP

hyb_protocol: Mapping 500K arrays were hybridized according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using an Affymetrix hybridization oven


title: 14 days post infarction, array 5

city: Oslo

first: Cathrine

last: Husberg

address: Kirkeveien 166

country: Norway

institute: Institute for experimental medical research

description: Gene expression was examined in non-infarcted left ventricle at 3, 5, 7 and 14 days after myocardial infarction. Left ventricle from sham operated mice was used as controls.

hyb_protocol: Agilent oligo microarray kit hybridization protocol

scan_protocol: The arrays were controlled for spatial and intensity dependent effects by visual inspections of the array images and of ratio/intensity (RI) plots. To retain saturated spots (with more than half of the pixels in saturation) we performed additional lower scans of the arrays and modified the saturated intensities according to the algorithm described in Lyng, Badiee et al (2004). As measures of the spot intensities we used the median of the foreground pixel intensities, and log-transformed them to obtain approximate normality. No further normalisation was done because this is taken care of in our model-based analysis described below

data_processing: Our model is based on a log-linear mixed effect model according to Kerr et al (2000).  The base2 logarithm of each of the measured fluorescent intensity was modelled as a sum of dye, gene and array effects plus effects of the interaction terms array*gene (i.e. spot effects), dye*gene and time*variety*gene (the time-dependent effect of the specific variety – here myocardial infarction or  control - on each gene). The latter is the parameter of main concern, and we note that the difference here for a given gene between myocardial infarction and control is the log2 ratio (normalised for experimental noise) in gene expression between the two types. Parameter estimates were obtained using the MicroArray ANOVA (MAANOVA) package by Wu et al (2002), for the statistical language R. We sat the threshold of significance of 30% change and p<0.05.

organism: Mus musculus

source_name: Mouse left ventricle, non-infarcted tissue, 14 days post infarction

label_protocol: Agilent Low RNA input fluorescent linear amplification kit

extract_protocol: SV total RNA isolation system, Promega

tag: Mouse C57BL6,male, 8 weeks, heart, myocardial infarction

source_name: Mouse left ventricle, sham operated

tag: Mouse C57BL6,male, 8 weeks, heart, sham operated


title: 7 days post infarction, array 4

source_name: Mouse left ventricle, non-infarcted tissue, 7 days post infarction


title: MMCONTROL2_NSP

tag: Number


title: MMCONTROL22_STY


title: MMCONTROL1_NSP


title: MMCONTROL5_NSP


title: MMCONTROL25_STY


title: MMCONTROL23_STY


title: MMCONTROL18_STY


title: MMCONTROL49_STY


title: MMCONTROL4_NSP


title: MMCONTROL21_STY


title: MMCONTROL20_STY


title: MMCONTROL17_STY


title: MMCONTROL15_STY


title: 14 days post infarction, array 4

description: Gene expression was examined in non-infarcted left ventricle at 3, 5, 7 and 14 days after myocardial infarction. Left ventricle from sham operated mice was used as controls


title: MMCONTROL19_STY


title: 14 days post infarction, array 1


title: MMCASE1_NSP


title: MMCONTROL3_NSP

value: 0- NO TTO


title: MMCONTROL11_STY


title: 14 days post infarction, array 2


title: 7 days post infarction, array 3


title: MMCONTROL9_STY


title: 7 days post infarction, array 2


title: 14 days post infarction, array 3


title: 5 days post infarction, array 2

description: Gene expression was examined in non-infarcted left ventricle at 3, 5, 7 and 14 days after myocardial infarction. Left ventricle from sham operated mice were used as controls.

source_name: Mouse left ventricle, non-infarcted tissue, 5 days post infarction


title: MMCONTROL13_STY


title: 7 days post infarction, array 5


title: 5 days post infarction, array 4

tag: Mouse C57BL6,male, 8 weeks, heart, sham operatedMouse

tag: C57BL6,male, 8 weeks, heart, myocardial infarction


title: 5 days post infarction, array 1


title: MMCONTROL7_STY


title: MMCONTROL8_STY


title: 7 days post infarction, array 1


title: 5 days post infarction, array 3


title: MMCONTROL14_STY


title: MMCONTROL10_STY


title: MMCONTROL5_STY


title: MMCONTROL6_STY


title: 3 days post infarction, array 5

source_name: Mouse left ventricle, non-infarcted tissue, 3 days post infarction


title: 3 days post infarction, array 4


title: MMCASE1_STY


title: MMCONTROL4_STY


title: MMCASE2_STY


title: MMCONTROL16_STY


title: mCtx_KCl_1hr_B_1

status: Public on Sep 24 2008

city: Boston

first: Yingxi

last: Lin

state: MA

address: Enders 250, 300 Longwood Avenue

department: Neurology/Neurobiology

institute: Children' Hospital/Harvard Medical School

description: Postnatal day 0 mouse embryonic cortical neuron cultures were depolarized with 55 mM KCl for 0, 1 and 6 hours.

hyb_protocol: Following fragmentation, 2.7 microg of cRNA were hybridized to the Affymetrix MOE-430B chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner.

data_processing: The data were processed with MAS 4.0. The normalization target was set to 500.

source_name: mouse P0 cortical neurons, KCl treatment for 1 hour

label_protocol: Biotinylated cRNA were prepared from 200 ng total RNA using the Enzo IVT labeling kit (Enzo, Farmingdale, NY).

extract_protocol: Total RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

tag: Mouse P0 cortical neurons

tag: 5 DIV, 55 mM KCl treatment for 1 hour


title: mCtx_KCl_0hr_B_1

source_name: mouse P0 cortical neurons, KCl treatment for 0 hour

tag: 5 DIV, 55 mM KCl treatment for 0 hour


title: VTT-C-99318_fermentation 2_hybridization 2.3_glucose_24h

city: Espoo

first: Laura

last: Salusjärvi

address: Tietotie 2

country: Finland

institute: VTT Technical Research Centre of Finland

scan_protocol: The arrays were scanned by Agilent G2500A GeneArray Scanner.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae VTT-C-99318 grown on 50 g/L glucose for 24h

label_protocol: Affymetrix hybridisations and analyses were carried out according to the protocols provided by Affymetrix, Inc. Double-stranded cDNA was synthesised from 5 µg total RNA. An in vitro transcription (IVT) reaction was then carried out to produce biotin-labelled cRNA from the cDNA. The cRNA was fragmented and hybridised to a Test3 array for quality control, then to the Yeast Genome S98 array for 16 h at 45oC. The arrays were washed and stained with streptavidin-phycoerythrin in an Affymetrix Fluidics Station 400 and scanned (Agilent G2500A GeneArray Scanner). The data were extracted with Affymetrix MicroArray Suite 5.0 software.

growth_protocol: VTT-C-99318 was grown at 30°C in 1.8-litre bioreactors (Chemap CMF Bioreactor, Chemap AG, Volketswil, Switzerland) with a working volume of 1.5 litres. The pH was kept constant at 5.5 by automatic addition of 2M KOH, and the stirrer speed was maintained at 500 rpm. Mass flow controllers (Bronkhorst High-Tech B.V, Ruurlo, Netherlands) regulated the total gas flow rate, at 0.5 standard litres per minute (SLPM). The composition of the fermentor off-gas was analysed using a QMG 421C quadrupole mass spectrometer (Balzers Pfeiffer Scandinavia AB, Sweden). The medium was synthetic complete (modified from Sherman, 1983) supplemented with 0.5 ml silicone antifoam l-1 (AnalaR BDH, UK) and 50 g l-1 glucose. Triplicate cultures (F0, F1, and F2) were carried out. Cultures were started with an initial OD600 of 1 to 1.5.

extract_protocol: Cells were broken by glass beads in the Trizol reagent (Gibco BRL, Life Technologies, USA). After the extraction, RNA was precipitated by isopropyl alcohol and the RNA pellet was rinsed with 80% (v/v) ethanol and resuspended in RNAse-free water.

treatment_protocol: The 25 ml sample for transcriptome analysis was harvested by centrifugation (2 min., 5000g) after 5 h growth and frozen in liquid nitrogen.

tag: CEN.PK2-1D ura3::XYL1 XYL2 his3::XKS1 kanMX


title: VTT-C-99318_fermentation 2_hybridization 2.1_xylose_72h

hyb_protocol: Affymetrix hybridisations and analyses were carried out according to the protocols provided by Affymetrix, Inc.

data_processing: The data were extracted with Affymetrix MicroArray Suite 5.0 software.

source_name: Saccharomyces cerevisiae VTT-C-99318 grown on 50 g/L xylose for 72h

growth_protocol: VTT-C-99318 was grown at 30°C in 1.8-litre bioreactors (Chemap CMF Bioreactor, Chemap AG, Volketswil, Switzerland) with a working volume of 1.5 litres. The pH was kept constant at 5.5 by automatic addition of 2M KOH, and the stirrer speed was maintained at 500 rpm. Mass flow controllers (Bronkhorst High-Tech B.V, Ruurlo, Netherlands) regulated the total gas flow rate, at 0.5 standard litres per minute (SLPM). The composition of the fermentor off-gas was analysed using a QMG 421C quadrupole mass spectrometer (Balzers Pfeiffer Scandinavia AB, Sweden). The medium was synthetic complete (modified from Sherman, 1983) supplemented with 0.5 ml silicone antifoam l-1 (AnalaR BDH, UK) and 50 g l-1 xylose. Triplicate cultures (F0, F1, and F2) were carried out. Cultures were started with an initial OD600 of 1 to 1.5.


title: 5 days post infarction, array 5


title: mCtx_KCl_6hr_B_2

source_name: mouse P0 cortical neurons, KCl treatment for 6 hour

tag: 5 DIV, 55 mM KCl treatment for 6 hour


title: 3 days post infarction, array 2


title: 3 days post infarction, array 3


title: VTT-C-99318_fermentation 2_hybridization 2.1_glucose_24h


title: VTT-C-99318_fermentation 2_hybridization 2.2_glucose_24h


title: VTT-C-99318_fermentation 2_hybridization 2.2_xylose_72h


title: mCtx_KCl_1hr_B_3


title: MMCONTROL2_STY

tag: Control

tag: Treatment

tag: Gender


title: VTT-C-99318_fermentation 2_hybridization 2.3_xylose_72h


title: mCtx_KCl_6hr_B_1


title: MMCONTROL3_STY


title: VTT-C-99318_fermentation 2_hybridization 2.1_glucose_5h

source_name: Saccharomyces cerevisiae VTT-C-99318 grown on 50 g/L glucose for 5h


title: mCtx_KCl_1hr_B_2


title: mCtx_KCl_0hr_B_3


title: VTT-C-99318_fermentation 2_hybridization 2.3_glucose_5h


title: VTT-C-99318_fermentation 1_hybridization 1_xylose_72h


title: mCtx_KCl_0hr_B_2


title: VTT-C-99318_fermentation 1_hybridization 1_glucose_24h


title: mCtx_KCl_6hr_B_3


title: VTT-C-99318_fermentation 1_hybridization 1_glucose_5h


title: VTT-C-99318_fermentation 2_hybridization 2.2_glucose_5h


title: 3 days post infarction, array 1

tag: Mouse C57BL6,male, 8 weeks, heart, sham operated, control animals

tag: Mouse C57BL6, male, 8 weeks, heart, myocardial infarction


title: MMCONTROL1_STY

source_name: PERIPHERAL BLOOD

tag: PB MM CONTROL-STY CHIP


title: VTT-C-99318_Fermentation 0_Hybridisation 0_glucose_5h

growth_protocol: VTT-C-99318 was grown at 30°C in 1.8-litre bioreactors (Chemap CMF Bioreactor, Chemap AG, Volketswil, Switzerland) with a working volume of 1.5 litres. The pH was kept constant at 5.5 by automatic addition of 2M KOH, and the stirrer speed was maintained at 500 rpm. Mass flow controllers (Bronkhorst High-Tech B.V, Ruurlo, Netherlands) regulated the total gas flow rate, at 0.5 standard litres per minute (SLPM). The composition of the fermentor off-gas was analysed using a QMG 421C quadrupole mass spectrometer (Balzers Pfeiffer Scandinavia AB, Sweden). The medium was synthetic complete (modified from Sherman, 1983) supplemented with 0.5 ml silicone antifoam l-1 (AnalaR BDH, UK) and 50 g l-1 50 g l-1glucose. Triplicate cultures (F0, F1, and F2) were carried out. Cultures were started with an initial OD600 of 1 to 1.5.


title: VTT-C-99318_fermentation 0_hybridization 0_glucose_24h

growth_protocol: VTT-C-99318 was grown at 30°C in 1.8-litre bioreactors (Chemap CMF Bioreactor, Chemap AG, Volketswil, Switzerland) with a working volume of 1.5 litres. The pH was kept constant at 5.5 by automatic addition of 2M KOH, and the stirrer speed was maintained at 500 rpm. Mass flow controllers (Bronkhorst High-Tech B.V, Ruurlo, Netherlands) regulated the total gas flow rate, at 0.5 standard litres per minute (SLPM). The composition of the fermentor off-gas was analysed using a QMG 421C quadrupole mass spectrometer (Balzers Pfeiffer Scandinavia AB, Sweden). The medium was synthetic complete (modified from Sherman, 1983) supplemented with 0.5 ml silicone antifoam l-1 (AnalaR BDH, UK) and 50 g l-1glucose. Triplicate cultures (F0, F1, and F2) were carried out. Cultures were started with an initial OD600 of 1 to 1.5.

treatment_protocol: The 25 ml sample for transcriptome analysis was harvested by centrifugation (2 min., 5000g) after 24 h growth and frozen in liquid nitrogen.


title: E.coli_RviaT8_SR3

status: Public on Sep 23 2008

city: Stuttgart

first: Karin

last: Lemuth

address: Allmandring 31

institute: Universität Stuttgart

description: no additional information left

hyb_protocol: The slides were hybridized in the fully automatic hybridization station HS400 (Tecan Deutschland GmbH, Crailsheim, Germany). Labeled cDNA samples were prepared by heating them to 95 °C for 3 min. The hybridization lasted for 12 h at 42 °C. 6 x SSPE (20 x stock: NaCl 175.3 g; NaH2PO4 x 1H2O 27.6 g; Na2EDTA 7.4 g; bidestilled H2O ad 1 l) was used for pre-wetting; washing buffer 1 (NaCl 17.6 g; sodium citrate 8.8 g; SDS 1 g; ddH2O ad 1 l) and washing buffer 2 (NaCl 0.88 g; NaCitrate 4.4 g; bidestilled H2O ad 1 l) were used for washing the hybridized slides which were subsequently dried with nitrogen gas for two minutes.

scan_protocol: The completely dryed DNA microarrays were scanned using the ScanArray Express Microarray Scanner (Perkin Elmer, Massachusetts, USA) (resolution: 5 µM; PMT setting: 70). Pictures of both channels were saved as 16- bit tiff files.

data_processing:
Raw data were created by analyzing 16-bit tiff files with the Scan Array Express imaging software (microarray analysis system, version 3.0.0.0016, PerkinElmer, Massachusetts, USA; adaptive treshold method, total normalization method).
Adaptive threshold (quantitation method) uses the parameters of the spot diameter and background inner and outer dimensions to create a spot mask and background mask, then refines the mask on a pixel-by-pixel basis. Total (normalization method), uses the intensity of each spot in relation to all spots.
The VALUE data are normalized log2(test/ref) ratios which were normalized 'print-tip-loess' using the software R (R, 2005) and the Limma package included (Smyth, 2005). Additionally, spots, which were classified as not found by the image analysis software, were down weighted to 10%.

organism: Escherichia coli str. K-12 substr. W3110

source_name: E. coli, unlimited growth (batch)

label_protocol:
Concentrated total RNA was reverse transcribed using Superscript II RNase H- Reverse Transcriptase (Invitrogen, Karlsruhe, Germany) and labeled at the same time. Cy3-dCTPs and Cy5-dCTPs were incorporated and the reverse transcribed probes hybridized on the arrays as described in “Hybridization protocol”.
Reverse transcription was carried out as follows: 3 µl random hexanucleotide primers (6 N) and 16.5 µl precipitated RNA were mixed and incubated at 65 °C for 10 min. The reaction mix was then incubated at room temperature for further 10 min and on ice for 2 min. Now 8 µl 5 x RT reaction buffer (Superscript II Kit, Invitrogen), 4 µl dNTP Mastermix (dATP - 100 mM, 5 µl; dGTP - 100 mM, 5 µl; dTTP - 100 mM, 5 µl; dCTP - 100 mM, 2 µl ad 100 µl bidestilled RNase free H2O), 4 µl Cy3-dCTP and Cy5-dCTP (1 mM) respectively, 4 µl DTT (0.1 M, Superscript II Kit, Invitrogen) and 1.5 µl Superscript II (200 U, Invitrogen) were added. This mixture was incubated for 2 h at 42 °C. The reaction was stopped by adding 10 µl of a sodium hydroxide solution (1 M) and heating to 65 °C for 10 min. The solution was neutralized by adding 10 µl of hydrochloric acid (1 M). 200 µl 1 x TE buffer was added and the mixture purified using the PCR Purification Kit as recommended by the manufacturer (Qiagen). cDNA concentration was determined photometrically (Nanodrop ND 1000, NanoDrop Technologies, Inc.) and identical amounts of labeled cDNA were combined and vacuum dried at 30 °C until nearly dry. The cDNA was redissolved in 65 µl prewarmed (42 °C) hybridization buffer (MWG) and stored for subsequent use - either on ice for less than 1 h or at -20 °C when stored overnight.

growth_protocol: The fed-batch cultivations were carried out with the bacterial strain E. coli K-12 W3110 (DSM 5911, German Collection of Microorganisms and Cell Cultures) in a 30-l bioreactor (Bioengineering AG, Wald, Switzerland). Minimal medium supplemented with glucose as the carbon source was used. The batch medium (batch volume VR,0 =17 l) consisted of 8.8 g l−1 glucose•H2O, 2.0 g l−1 Na2SO4•10H2O, 2.68 g l−1 (NH4)2SO4, 1.0 g l−1 NH4Cl, 14.6 g l−1 K2HPO4, 4.02 g l−1 NaH2PO4•2H2O, 0.01 g l−1 thiamine HCl; 0.3mM CaCl2•2H2O, 2mM MgSO4•7H2O; 3ml l−1 of trace element solution (TES: 16.7 g l−1 FeCl3•6H2O, 20.1 g l−1

extract_protocol: Total RNA from 8.1*10exp9 cells was isolated using the RNeasy Kit (Qiagen) according to the manufacturer’s protocol. On-column DNase digestion was performed (RNase free DNase set, Qiagen). RNA concentration and quality were assessed photometrically (Nanodrop ND 1000, NanoDrop Technologies, Inc., Delaware, USA), by formaldehyde gel electrophoresis and bioanalyzer analysis (RNA 6000 Nano LabChip Kit, Agilent Bioanalyzer 2100, Agilent Technologies, California, USA). Only RNA with 260 nm / 280 nm ratio of 1.8 - 2 as well as 260 nm / 230 nm ratio > 1.8 was used for precipitation. The RNA was precipitated and resolved at the final concentration of 6 µg / µl required for reverse transcription and labeling with fluorescent dyes. Total RNA isolate was mixed with 1/10 volume of NaCl solution (3 M) and 2 volumes of ethanol (100 %) and stored at -20 °C overnight. The samples were subsequently centrifuged (14000 rpm; 20800 g) and the supernatant was discarded. The RNA was washed with ethanol (70 %) and vacuum dried. 100 µg of RNA were used for reverse transcription.

treatment_protocol:
The culture medium samples were withdrawn with a capillary sampling probe as developed by Theobald et al. (1997), however, without using membrane-covered glass tubes.
The cell samples were collected directly into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) to avoid RNA degradation. The samples were centrifuged according to the manufacturer’s protocol and frozen at - 80 °C until RNA isolation.
Theobald, U., Mailinger,W., Baltes, M., Rizzi, M., Reuss, M., 1997. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae. 1. Experimental observations. Biotechnol. Bioeng. 55, 305–316.

tag: E. coli K12 (W3110), fed-batch/linear feed, unlimited growth (batch)

source_name: E. coli, glucose limitation, 350 min after depletion of extracellular acetate

tag: E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, 350 min after depletion of extracellular acetate


title: E.coli_T8viaR_SR3

description: no additional information left


title: mCtx_KCl_1hr_A_2

hyb_protocol: Following fragmentation, 2.7 microg of cRNA were hybridized to the Affymetrix MOE-430A chip according to the protocols provided by the manufacturer.


title: mCtx_KCl_6hr_A_1


title: mCtx_KCl_1hr_A_3


title: E.coli_T7viaR_SR3

description: no additional information left

source_name: E. coli, glucose limitation, 230 min after depletion of extracellular acetate

tag: E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, 230 min after depletion of extracellular acetate


title: E.coli_RviaT7_SR3

description: no additional information left


title: VTT-C-99318_fermentation 0_hybridization 0_xylose_72h


title: mCtx_KCl_0hr_A_3


title: mCtx_KCl_6hr_A_3


title: mCtx_KCl_0hr_A_2


title: mCtx_KCl_6hr_A_2


title: E.coli_T6viaR_SR3

description: no additional information left

source_name: E. coli, glucose limitation, 170 min after depletion of extracellular acetate

tag: E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, 170 min after depletion of extracellular acetate


title: mCtx_KCl_0hr_A_1

tag: mouse P0 cortical neurons

tag: 5 DIV, 55 mM KCl treatment for 0 hr


title: E.coli_RviaT6_SR3

description: no additional information left


title: mCtx_KCl_1hr_A_1

tag: Mouse P0 cortical neurons


title: E.coli_T2viaR_SR3

description: no additional information left

source_name: E. coli, glucose limitation, acetate concentration ≤ 0.35 gL-1

tag: E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, acetate concentration ≤ 0.35 gL-1


title: E.coli_T4viaR_SR3

description: no additional information left

source_name: E. coli, glucose limitation, 50 min after depletion of extracellular acetate

tag: E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, 50 min after depletion of extracellular acetate


title: E.coli_RviaT8_SR2

description: no additional information left


title: E.coli_RviaT3_SR2

description: no additional information left

source_name: E. coli, glucose limitation, 30 min after depletion of extracellular acetate

tag: E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, 30 min after depletion of extracellular acetate


title: E.coli_RviaT1_SR3

description: no additional information left

source_name: E. coli, glucose limitation (glucose concentration < 0.05 gL-1)

tag: E. coli K12 (W3110), fed-batch/linear feed, glucose limitation (glucose concentration < 0.05 gL-1)


title: E.coli_RviaT4_SR3

description: no additional information left


title: E.coli_T8viaR_SR2

description: no additional information left


title: E.coli_T3viaR_SR3

description: no additional information left


title: E.coli_RviaT2_SR3

description: no additional information left


title: E.coli_T1viaR_SR3

description: no additional information left


title: E.coli_RviaT1_SR2

description: no additional information left


title: E.coli_T5viaR_SR3

description: no additional information left

source_name: E. coli, glucose limitation, 110 min after depletion of extracellular acetate

tag: E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, 110 min after depletion of extracellular acetate


title: E.coli_T3viaR_SR2

description: no additional information left


title: E.coli_RviaT7_SR2

description: no additional information left


title: E.coli_RviaT5_SR3

description: no additional information left


title: E.coli_T1viaR_SR2

description: no additional information left


title: E.coli_RviaT3_SR3

description: no additional information left


title: E.coli_RviaT6_SR2

description: no additional information left


title: E.coli_T7viaR_SR2

description: no additional information left


title: MMCONTROL12_STY

tag: PB MM CONTROL - STY CHIP

tag: Number

tag: Control

tag: Treatment


title: E.coli_T5viaR_SR2

description: no additional information left


title: E.coli_RviaT5_SR2

description: no additional information left


title: E.coli_T4viaR_SR2

description: no additional information left


title: E.coli_RviaT2_SR1

description: no additional information left


title: MICMA263

first: Hilde

last: Johnsen

address: Montebello

department: Genetics

institute: Norwegian Radium Hospital

description: no additional information

hyb_protocol: Agilent miRNA Labeling and Microarray Hybridization Protocol version 0.1 (November 2006)

scan_protocol: Agilent Microarray Scanner (G2565A). Scanned at 100% and 5% PMT

data_processing: The data was extracted from the image files using Feature Extraction 9.1.3.44. The matrix was created using Genespring.7.3 software based on the Geneview files.  Preprocessing: Signals below 0.01 was set to 0.01. No normalization was done. For replicated samples the arithmetic mean value for each miRNA were calculated

source_name: Primary human breast cancer sample

extract_protocol: Samples were fresh frozen immediately after surgery and stored at -80°C. All specimens analyzed contained more than 40% tumor cells (of the total number of cells counted). The majority of tumors were invasive ductal carcinomas, T1/T2, N0/N1,and histological grade 2 and 3. Total RNA was isolated by phenol-chloroform extraction (TRIzol reagent, Invitrogen), the quality and integrity of the total RNA was evaluated on the 2100 Bioanalyzer (Agilent Technologies) and the concentration was measured using a NanoDrop spectrophotometer (NanoDrop Technologies).

value: 0 [(wild type=0, mutated=1)]

tag: sequence change

value: no information provided

tag: molecular tumor subtype

value: 1 [(1=Lum A, 2= Lum B, 3=ERBB2+, 4= Basal-like, 5= Normal-like)]

tag: tumor size

tag: ncat

value: 1 [(N0=0, N1=1, not classifiable =7)]

tag: grade

tag: % tumor cells (of no. of cells counted)


title: MICMA632

description: no additional information

label_protocol: Agilent miRNA Labeling and Microarray Hybridization Protocol version 0.1 (November 2006)


title: E.coli_RviaT2_SR2

description: no additional information left

tag: E. coli K12 (W3110), fed-batch/linear feed, unlimited growth (batch)


title: E.coli_T6viaR_SR2

description: no additional information left

tag: E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, 170 min after depletion of extracellular acetate


title: E.coli_T4viaR_SR1

description: no additional information left


title: E.coli_RviaT4_SR1

description: no additional information left


title: E.coli_T3viaR_SR1

description: no additional information left


title: E.coli_T2viaR_SR2

description: no additional information left

tag: E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, acetate concentration ≤ 0.35 gL-1


title: MICMA267

description: no additional information

value: 1 [(wild type=0, mutated=1)]

value: C213:CGA - TGA

value: 4 [(1=Lum A, 2= Lum B, 3=ERBB2+, 4= Basal-like, 5= Normal-like)]


title: MICMA709

description: no additional information

value: 1 bp del (start C195)

value: 0 [(N0=0, N1=1, not classifiable =7)]


title: E.coli_RviaT4_SR2

description: no additional information left

tag: E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, 50 min after depletion of extracellular acetate


title: E.coli_RviaT1_SR1

description: no additional information left

source_name: E. coli, glucose limitation (glucose concentration < 0.05 gL-1), fed-batch


title: E.coli_T2viaR_SR1

description: no additional information left


title: E.coli_T1viaR_SR1

description: no additional information left


title: MICMA185

description: no additional information

value: C173:GTG - ATG


title: MICMA122

description: no additional information


title: MICMA148

description: no additional information

value: C274:GTT - GAT

value: 2 [(1=Lum A, 2= Lum B, 3=ERBB2+, 4= Basal-like, 5= Normal-like)]


title: MICMA146

description: no additional information

value: C273:CGT - TGT

value: 3 [(1=Lum A, 2= Lum B, 3=ERBB2+, 4= Basal-like, 5= Normal-like)]


title: MICMA088

description: no additional information

value: C220:TAT - TGT


title: MICMA079

description: no additional information

value: 2 bp del (Start C209)


title: MICMA101

description: no additional information


title: MICMA091

description: no additional information

value: G - A 1bp downstream of ex9

value: Uc [ (1=Lum A, 2= Lum B, 3=ERBB2+, 4= Basal-like, 5= Normal-like)]


title: MICMA065

description: no additional information

value: 0 [(wild type=0, mutated=1)]

value: no information provided


title: MICMA053

description: no additional information

value: C141:TGC - TAC


title: MICMA067

description: no additional information

value: 1 [(wild type=0, mutated=1)]

value: C274:GTT - TTT

value: 1 [(N0=0, N1=1, not classifiable =7)]


title: MICMA031

description: no additional information

value: C234:TAC - TG

value: 4 [(1=Lum A, 2= Lum B, 3=ERBB2+, 4= Basal-like, 5= Normal-like)]


title: MICMA042

description: no additional information

value: C248:CGG - CAG

value: 0 [(N0=0, N1=1, not classifiable =7)]


title: MICMA020

description: no additional information

value: 5 [ (1=Lum A, 2= Lum B, 3=ERBB2+, 4= Basal-like, 5= Normal-like)]


title: E.coli_RviaT3_SR1

description: no additional information left

tag: E. coli K12 (W3110), fed-batch/linear feed, glucose limitation, 30 min after depletion of extracellular acetate


title: 6th-57, reference sample (normal eye-antennal discs) vs. posterior fragments from eye discs from w1118 larvae

city: Berlin

first: Ansgar

last: Klebes

address: Chausseestr. 117

department: Biology

institute: Humboldt University Berlin

description: Microarray experiments were conducted as previously described (Xu et al., 2003; Klebes et al., 2005). In brief, custom made glass microarrays with 14,151 PCR products of 100-600 bp length that were amplified with specific primer pairs (Incyte Genomics) were hybridized with Cy3 or Cy5 labeled cDNA probes. Each experimental sample was simultanously hybridized with a common reference sample that was produced from eye-antennal discs from third instar larvae of an isogenized w1118 stock. Experimental samples were produced from the dissected eye discs of third instar larvae of the indicated genotypes. All samples were produced from a few discs using linear RNA amplification (for a detailed protocol: Klebes and Kornberg, 2008). Microarray data was processed as relative expression ratios.

hyb_protocol: Hybridization was performed in a DeRisi-style hybridization chamber in a waterbath at 64°C over night (hybridization mix: 34 microl labeled probe, 6.8 microl 20x SSC, 3.5 microl polyA RNA, 1 microl 10% SDS, 1.1 microl 0.5M HEPES, pH7.5).

scan_protocol: GenePix 4000B, Axon Instruments and GenePix Pro software.

data_processing: Median of ratio values from the experiment were subjected to linear normalization in NOMAD (http://ucsf-nomad.sourceforge.net/). Log2 transformation was performed with Cluster 3.0 (Michiel de Hoon, Seiya Imoto and Satory Miyano, University of Tokyo) and if necessary dye orientation was converted in Excel.

label: Hybridization was performed with Cy3.

source_name: test sample: posterior fragment from eye discs

extract_protocol: Total RNA extraction was performed with the RNA mini isolation kit (Zymo, Inc.) and submitted to two rounds of linear amplification (Klebes, A., and Kornberg, T. B. (2008). Linear RNA amplification for the production of microarray hybridization probes. Methods Mol Biol 420, 303-317). The amplified-RNA was indirectly labeled with the flourophore (Cy3 or Cy5) by RT and amino-allyl coupling.

treatment_protocol: Few imaginal discs were dissected in PBS and the eye part was cut along the morphogenetic furrow (MF). The fragments posterior of the MF were submitted to two rounds of linear T7-based RNA amplification as described in: Klebes, A., and Kornberg, T. B. (2008). Linear RNA amplification for the production of microarray hybridization probes. Methods Mol Biol 420, 303-317.

tag: Posterior fragment from eye imaginal discs from 3rd instar wandering larvae of w1118 mutant flies. Dye was Cy3.

label: Hybridization was performed with Cy5.

treatment_protocol: Imaginal discs were dissected in PBS and submitted to one round of linear T7-based RNA amplification as described in: Klebes, A., and Kornberg, T. B. (2008). Linear RNA amplification for the production of microarray hybridization probes. Methods Mol Biol 420, 303-317.

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of white<1118> (w1118) homzygous mutant flies. These flies develop normally except for eye pigmentation. Dye was Cy5.


title: 7th-121, reference sample (normal eye-antennal discs) vs. posterior fragments from eye discs from w1118 larvae

label: Hybridization was performed with Cy5, but ratios were converted to comply with: test-Cy3/reference-Cy5.

label_protocol: The amplified-RNA was indirectly labeled with the flourophore (Cy3 or Cy5) by RT and amino-allyl coupling.

tag: Posterior fragment from eye imaginal discs from 3rd instar wandering larvae of w1118 mutant flies. Dye was Cy5, but ratios were converted to comply with

value: test-Cy3/reference-Cy5 (raw data is in the original orientation:reference-Cy3, test-Cy5).

label: Hybridization was performed with Cy3, but ratios were converted to comply with: test-Cy3/reference-Cy5.

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of white<1118> (w1118) homzygous mutant flies. These flies develop normally except for eye pigmentation. Dye was Cy3, but ratios were converted to comply with


title: 7th-24, reference sample (normal eye-antennal discs) vs. posterior fragments from eye discs from w1118 larvae


title: 7th-223, reference sample (normal eye-antennal discs) vs. eye antennal discs from 519 larvae

source_name: test sample: 519 eye-antennal discs

treatment_protocol: Few imaginal discs were dissected in PBS and submitted to two rounds of linear T7-based RNA amplification as described in: Klebes, A., and Kornberg, T. B. (2008). Linear RNA amplification for the production of microarray hybridization probes. Methods Mol Biol 420, 303-317.

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of 519 mutant flies. This mutation was identified as a suppressor of roDom (Chanut et al., 2000) and causes a multiple R8 phenotype. Dye was Cy5, but ratios were converted to comply with


title: 7th-120, reference sample (normal eye-antennal discs) vs. eye antennal discs from 519 larvae


title: 7th-135, reference sample (normal eye-antennal discs) vs. posterior fragments from eye discs from w1118 larvae


title: T. rubrum 5-Flucytosine rep-3

city: Beijing

first: Qi

last: Jin

state: Beijing

address: BDA Rong Jing east street No.6, 3rd floor

department: National Institute for Viral Disease Control and Prevention

country: China

institute: Chinese Center for Disease Control and Prevention

description:
Replicate 3 of 3.
T. rubrum Expression database http://www.mgc.ac.cn/TrED/

hyb_protocol: Labeled cDNA was purified using QIAquick columns and mixed with 2μl poly(A); 5× Denharts; 3× SSC; 24 μg yeast tRNA; 25 mM HEPES, pH 7.0; 0.25% SDS, the mixture was heated at 100 °C for 2 min and cooled to room temperature and applied to the array slides under glass coverslips. Hybridization was performed at 65°C overnight in a Micro hybridization incubator (Robbins Scientific; Sunnyvale, CA).

scan_protocol: GenePix 6.0 software (Axon Instruments, Inc.) was used for image analysis and data visualization. Signals were normalized using a locally weighted scatterplot smoothing regression (LOWESS) algorithm in the MIDAS software package.

data_processing: Genes were considered to be differentially expressed if (i) average expression changed by at least 1.5-fold in three independent experiments performed with triplicate RNA samples or (ii) the change in gene expression was in the same direction (“increased” or “decreased”) in three experiments.

molecule: polyA RNA

organism: Trichophyton rubrum

source_name: T. rubrum 5-Flucytosine rep-3

label_protocol: Double strand cDNA were then fluorescently labeled using BioPrime. DNA Labeling System (Life Technologies/Invitrogen; Carlsbad, CA) following the manufacturer’s instructions. ds cDNA was added to 2.5× random primers solution (50 mM Tris-HCl, pH6.8; 5 mM MgCl2; 10 mM 2-mercaptoethanol; 300 μg/ml oligodeoxyribonucleotide primer), boiled at 100 °C for 5 min and then chilled on ice. 10× dNTP Mix for DNA labelling (0.12 mM dATP, dGTP,dTTP; 0.06 mM dCTP; 1 mM Tris-HCl, pH 8.0; 0.1 mM EDTA); Cy5-dCTP (0.06 mM); Klenow fragment (40 U) were added. The mixture was briefly centrifugated and was incubated at 37°C overnight away from light. 5μl 0.5 M EDTA (pH 8.0) was used to stop reaction.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy. Plant Mini Kit (Qiagen, Inc., Valencia, CA) according to the manufacturer's instructions. Poly(A)+ mRNA was isolated with Oligotex mRNA Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: T.rubrum treated with 5-FC

source_name: T. rubrum_DMSO


title: 7th-215, reference sample (normal eye-antennal discs) vs. eye antennal discs from 519 larvae

source_name: test sample: 519> eye-antennal discs

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of 519 mutant flies. This mutation was identified as a suppressor of roDom (Chanut et al., 2000) and causes a multiple R8 phenotype. Dye was Cy3.


title: 7th-61, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous hh<1> larvae

source_name: test sample: hh<1> homozygous eye-antennal discs

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of hedgehog<1> mutant flies. Dye was Cy5, but ratios were converted to comply with


title: 7th-45, reference sample (normal eye-antennal discs) vs. eye antennal discs from ro<X63> larvae

source_name: test sample: ro<X63> eye-antennal discs

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of rough<X63> mutant flies. Dye was Cy5, but ratios were converted to comply with


title: 7th-75, reference sample (normal eye-antennal discs) vs. eye antennal discs from ro<X63> larvae


title: 7th-232, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous hh<1> larvae

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of hedgehog<1> homozygous mutant flies. Dye was Cy3.


title: 7th-42, reference sample (normal eye-antennal discs) vs. eye antennal discs from ro<X63> larvae

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of rough<X63> mutant flies. Dye was Cy3.

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of white<1118> (w1118) homzygous mutant flies. These flies develop normally except for eye pigmentation. Dye was Cy


title: T. rubrum 5-Flucytosine rep-1

description:
Replicate 1 of 3.
T. rubrum Expression database http://www.mgc.ac.cn/TrED/

source_name: T. rubrum 5-Flucytosine rep-1


title: 7th-253, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous hh<1> larvae

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of hedgehog<1> mutant flies. Dye was Cy3.


title: 7th-104, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous ato<1> larvae

source_name: test sample: ato<1> homozygous eye-antennal discs

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of atonal<1> homozygous mutant flies. Dye was Cy5, but ratios were converted to comply with


title: T. rubrum 5-Flucytosine rep-2

description:
Replicate 2 of 3.
T. rubrum Expression database http://www.mgc.ac.cn/TrED/

source_name: T. rubrum 5-Flucytosine rep-2


title: 7th-217, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous ato<1> larvae

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of atonal<1> homozygous mutant flies. Dye was Cy3.


title: 7th-36, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous 2033 larvae

source_name: test sample: 2033 homozygous eye-antennal discs

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of 2033 (Chanut et al., 2000) heterozygous mutant flies. This uncharacterized mutation causes a mild stop furrow phenotype. Dye was Cy5, but ratios were converted to comply with


title: Myometrium During Labor Sample 3

city: Los Angeles

first: Enrico

last: Stefani

state: CA

address: 650 Charles Young Dr

department: Anesthesiology

institute: David Geffen School of Medicine at UCLA

description: Uteri were dissected from late pregnant rats (21 days, LP) (three individuals, two replicates of sample 1) and rats during labor (DL) after the expulsion of the second pup (three individuals, two replicates of sample 1).

hyb_protocol: cRNA biotin-labeled was fragmented and hybridized to Affymetrix Rat RG U34-A GeneChip containing 8740 probe sets targeting different sequences.

scan_protocol: The arrays were washed, stained, and scanned with Fluidics Station 400 (Affymetrix, Santa Clara, CA) and Agilent Scanner (Hewlett–Packard, USA).

data_processing: To determine the presence or absence for each sequence in the experimental cRNA, microarray data were initially processed with Affymetrix Microarray suite 5.0.  Since microarrays may differ in their hybridization patterns, to quantify cRNA sequence expression levels, the values of each cell intensity was calculated using the Li and Wong statistical model applied to all the microarrays (dChip software)

source_name: Myometrium During Labor Sample 3

label_protocol: cDNA was synthesized with the SuperScript Choice System (Life Technologies, Grand Island, NY) using an oligo-dT primer containing the sequence of the T7 promoter region (Genset, La Jolla, CA). The cDNA was then used to perform in vitro transcription incorporating biotin-labeled nucleotides with the Enzo BioArray kit (Enzo Biochem, CA).

extract_protocol: After dissection, uteri were placed immediately in cold Ca2+-free PBS buffer and peripheral large blood vessels, external surrounding connective tissue and placenta were removed. The endometrium superficial layer was separated by gentle scraping.  The myometrium was weighted, finely minced and homogenized with a polytron (Polytron PT3000, Brinkmann, Switzerland).  To extract total RNA the Ambion Totally RNA kit (Ambion, Austin, TX) was used.  RNA concentration was determined with a spectrophotometer at 260 nm OD. The RNA purity was assessed by the OD ratio 260 nm/280 nm and the RNA integrity by the comparison of the 28S and 18S bands from 1 ug total RNA in 0.8% agarose gels in Tris-borate EDTA buffer with 0.5ug/ml ethydium bromide.

tag: Strain

value: Wistar, female 3 month old, During Labor after second pup


title: 7th-63, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous 2033 larvae


title: 5th-220, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous hh<1> larvae


title: Myometrium During Labor Sample 2

source_name: Myometrium During Labor Sample 2


title: Myometrium During Labor Rep. 2 of Sample 1


title: 7th-111, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous ato<1> larvae


title: Wpa-amplified gDNA, 5ng, 05-050

city: New Haven

first: Xinghua

last: Pan

state: CT

address: 300 Cedar Street, TAC-S320

department: Department of Genetics

institute: Yale University School of Medicine

description: SNP genotyping was performed at the Yale Keck Laboratory.

hyb_protocol: Hybridization was performed at the Yale Keck Laboratory.

scan_protocol: Scan was performed at the Yale Keck Laboratory.

data_processing: Data processing was performed using BeadStudio software (Illumina) v3.

label: C-Bio and A-DNP

source_name: 5 ng of 05-050 gDNA, amplified using Wpa

label_protocol: SNPs were identified by single-base extension. SNPs were analyzed at the Yale Keck Laboratory (http://keck.med.yale.edu/)

extract_protocol: Genomic DNA was isolated using an extraction kit.

treatment_protocol: The gDNA was amplified with Wpa (a new WGA procedure as described in the citation) with 5 ng gDNA as input. The amplicon was purified with the QIAEXII kit from Qiagen.

tag: Good-quality genomic DNA sample 05-050 has known CNVs.


title: GenomoPhi-amplified gDNA, 0.5ng, 05-050

source_name: 0.5 ng of 05-050 gDNA, amplified using GenomoPhi v2

treatment_protocol: The gDNA was amplified with the GenomiPhi v2 kit (GE Healthcare Life Science) with 0.5 ng gDNA as input, using the protocol provided with the kit. The amplicon was purified with the QIAEXII kit from Qiagen.


title: 7th-197, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous 2033 larvae

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of 2033 (Chanut et al., 2000) homozygous mutant flies. This uncharacterized mutation causes a mild stop furrow phenotype. Dye was Cy3


title: GenomoPhi-amplified gDNA, 0.5ng, 04-018

source_name: 0.5 ng of 04-018 gDNA, amplified using GenomoPhi v2

treatment_protocol: The gDNA was amplified with the GenomiPhi v2 kit (GE Healthcare Life Sciences) with 0.5 ng gDNA as input, using the protocol provided with the kit. The amplicon was purified with the QIAEXII kit from Qiagen.

tag: Partially degraded genomic DNA sample 04-018 has known CNVs.


title: Native gDNA, 05-050

source_name: Native 05-050 gDNA

treatment_protocol: No treatment.


title: Myometrium During Labor Rep. 1 of Sample 1


title: 7th-221, reference sample (normal eye-antennal discs) vs. eye antennal discs from heterozygous 2033 larvae

source_name: test sample: 2033 heterozygous eye-antennal discs


title: Wpa-amplified gDNA, 0.5ng, 05-050

source_name: 0.5 ng of 05-050 gDNA, amplified using Wpa

treatment_protocol: The gDNA was amplified with Wpa (a new WGA procedure as described in the citation) with 0.5 ng gDNA as input. The amplicon was purified with the QIAEXII kit from Qiagen.


title: GenomoPhi-amplified gDNA, 5ng, 05-050

source_name: 5 ng of 05-050 gDNA, amplified using GenomoPhi v2

treatment_protocol: The gDNA was amplified with the GenomiPhi v2 kit (GE Healthcare Life Science) with 5 ng gDNA as input, using the protocol provided with the kit. The amplicon was purified with the QIAEXII kit from Qiagen.


title: 7th-107, reference sample (normal eye-antennal discs) vs. eye antennal discs from heterozygous 2033 larvae

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of 2033 (Chanut et al., 2000) heterozygous mutant flies. This uncharacterized mutation causes a mild stop furrow phenotype. Dye was Cy3.

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of white<1118> (w1118) homzygous mutant flies. These flies develop normally except for eye pigmentation. Dye was Cy5.


title: Myometrium Late Pregnant Rep. 1 of Sample 1

value: Wistar, female 3 month old, 21 days late pregnant


title: Myometrium During Labor Sample 1

source_name: Myometrium During Labor Sample 1


title: 7th-177, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous roughDominant larvae

source_name: test sample: roDom eye-antennal discs

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of rough<Dominant> (roDom) homzygous mutant flies. Dye was Cy3.

tag: Imaginal discs were dissected in PBS and submitted to one round of linear T7-based RNA amplification as described in

value: Klebes, A., and Kornberg, T. B. (2008). Linear RNA amplification for the production of microarray hybridization probes. Methods Mol Biol 420, 303-317.


title: Myometrium Late Pregnant Sample 2

source_name: Myometrium Late Pregnant Sample 2


title: Myometrium Late Pregnant Sample 3

source_name: Myometrium Late Pregnant Sample 3


title: 5th_64, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous roughDominant larvae


title: 5th-62, reference sample (normal eye-antennal discs) vs. eye antennal discs from homozygous roughDominant larvae

extract_protocol: Total RNA extraction was performed with the RNA mini isolation kit (Zymo, Inc.) and submitted to two rounds of linear amplification (Klebes, A., and Kornberg, T. B. (2008). Linear RNA amplification for the production of microarray hybridization probes. Methods Mol Biol 420, 303-317).

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of rough<Dominant> (roDom) homzygous mutant flies. Dye was Cy5, but ratios were converted to comply with

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of white<1118> (w1118) homzygous mutant flies. These flies develop normally except for eye pigmentation. Dye was Cy3, but ratios were converted to comply with


title: Wpa-amplified gDNA, 0.5ng, 04-018

source_name: 0.5 ng of 04-018 gDNA, amplified using Wpa


title: 7th-246, reference sample (normal eye-antennal discs) vs. eye antennal discs from heterozygous roughDominant larvae

source_name: test sample: roDom (hetorzygous) eye-antennal discs

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of rough<Dominant> (roDom) heterozygous mutant flies. Dye was Cy3.


title: GenomoPhi-amplified gDNA, 5ng, 04-018

source_name: 5 ng of 04-018 gDNA, amplified using GenomoPhi v2

treatment_protocol: The gDNA was amplified with the GenomiPhi v2 kit (GE Healthcare Life Sciences) with 5 ng gDNA as input, using the protocol provided with the kit. The amplicon was purified with the QIAEXII kit from Qiagen.


title: 7th-39, reference sample (normal eye-antennal discs) vs. eye antennal discs from heterozygous roughDominant larvae

tag: Eye-antennal imaginal discs from 3rd instar wandering larvae of rough<Dominant> (roDom) heterozygous mutant flies. Dye was Cy5, but ratios were converted to comply with


title: Native gDNA, 04-018

source_name: Native 04-018 gDNA


title: Myometrium late pregnant Sample 1

source_name: Myometrium late pregnant

value: Wistar, Female, 3 month old, 21 days


title: Myometrium Late Pregnant Rep. 2 of Sample 1


title: Ovary_Line DUKsi_biological rep5_technical rep1

status: Public on Sep 22 2008

city: Dummerstorf

first: Jens

last: Vanselow

address: Wilhelm-Stahl-Allee 2

department: Reproductive Biology

institute: Leibniz Institute for Farm Animal Biology

description: Ovaries from 30 animals of line FL1 and of the control line DUKsi were collected at the metestrous stage to identify genes that are involved in increasing the ovulation number.

hyb_protocol: The fragmented cRNA was hybridized overnight (45°C) to the Affymetrix GeneChip MOE 430A mouse expression arrays. Each sample pool was hybridized to two arrays to reduce the technical variation. Arrays were then washed using the GeneChip Fluidics Station (Affymetrix) according to the manufacturer’s protocol and stained by R-Phycoerythrin Streptavidin (Molecular Probes). This was followed by an antibody amplification procedure using a biotinylated anti-streptavidin antibody (Vector laboratories) and goat IgG (Sigma).

scan_protocol: Scanning was carried out with 3µm resolution, 488nm excitation and 570nm emission wavelengths employing the GeneArray Scanner 2500 (Hewlett Packard)

data_processing: For calculation of signal intensity the Affymetrix Microarray Suite 5.0 Software (MAS5) was used. All arrays were normalized by scaling to reach a common target intensity.

source_name: Sample pools, ovaries from six animals, metestrous stage

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

growth_protocol: Mice were kept in Makrolon-cages of 30 x 12.5 x 12.5 cm with free access to pellet concentrate and water. The light regime was LD 12:12, the room temperature was standardized to 22.5 °C.

extract_protocol: Total RNA was prepared with the RNeasey Mini Kit with simultaneous removal of genomic DNA with RNAse free DNAse (Qiagen)

treatment_protocol: Line FL1 was selected for an index trait, combining litter size (LS0) and litter weight (LW0) at birth in primiparous females (Index (I) = 1.6 x LS0 + LW0)) to generation 130

tag: non-selected control line

tag: about six week old females at metestrous stage


title: Ovary_Line DUKsi_biological rep5_technical rep2


title: Ovary_Line DUKsi_biological rep4_technical rep1


title: Ovary_Line DUKsi_biological rep4_technical rep2


title: Ovary_Line DUKsi_biological rep3_technical rep2


title: Ovary_Line DUKsi_biological rep3_technical rep1


title: Ovary_Line DUKsi_biological rep2_technical rep2


title: Wpa-amplified gDNA, 5ng, 04-018

source_name: 5 ng of 04-018 gDNA, amplified using Wpa


title: Ovary_Line DUKsi_biological rep6_technical rep1


title: Ovary_Line DUKsi_biological rep2_technical rep1


title: Ovary_Line DUKsi_biological rep6_technical rep2


title: Ovary_Line FL1_biological rep6_technical rep2

tag: mouse line selected for high fertility performance


title: Ovary_Line DUKsi_biological rep1_technical rep2


title: Ovary_Line FL1_biological rep6_technical rep1


title: Ovary_Line DUKsi_biological rep1_technical rep1


title: Ovary_Line FL1_biological rep5_technical rep1


title: Ovary_Line FL1_biological rep2_technical rep2


title: Ovary_Line FL1_biological rep2_technical rep1


title: Ovary_Line FL1_biological rep3_technical rep1


title: zincsulfate-100ug-heart-62

city: Research Triangle Park

first: beena

last: vallanat

address: 109 Tw Alexanser Dr

institute: EPA

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

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000G

data_processing: The data were analyzed with Rosetta Resolver 6.0  using Affymetrix default profile builder analysis settings.

source_name: Rat whole heart-16 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Target RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA) and further purified using the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA).

tag: Healthy male Wistar Kyoto (WKY) rats, 12 weeks old, were purchased from Charles River Laboratories Inc., Raleigh, NC.  Animals were double housed in polycarbonate cages with beta chips bedding and acclimatized for at least one week in an AAALAC-approved animal facility (21 ± 1OC, 50 ± 5% relative humidity, 12:12 h light/dark cycle) prior to the experimental period. All animals received standard Purina rat chow (Brentwood, MO) and water ad libitum, except during exposures.Rats were randomly assigned to four groups (n = 15 per group) according to body weight, and exposed by nose-only inhalation (Ledbetter et al., 1998) to either filtered air or aerosolized zinc sulfate (10, 30 or 100 ug Zn/m3) for 5 h/day, 3 days/week for 16 weeks.  The aerosol was generated by aerosolizing solutions of zinc sulfate heptahydrate (Sigma Aldrich Chemicals), mixed at different starting concentrations with a TSI Model 3076 atomizer operating at 30 PSIG.  The output was mixed with dry air and directed to the exposure chamber (air flow of 98-105 liters/minute).  Chamber concentration data was determined by gravimetric analysis, with Inductively Coupled Plasma-Optical Emission Spectroscopy (ICP-OES) to determine zinc concentration.


title: Ovary_Line FL1__biological rep1_technical rep1


title: Ovary_Line FL1_biological rep4_technical rep2


title: Ovary_Line FL1_biological rep4_technical rep1


title: zincsulfate-30ug-heart-42


title: Ovary_Line FL1_biological rep3_technical rep2


title: Ovary_Line FL1_biological rep1_technical rep2


title: zincsulfate-100ug-heart-66


title: zincsulfate-30ug-heart-41


title: zincsulfate-100ug-heart-65


title: zincsulfate-30ug-heart-45


title: zincsulfate-30ug-heart-46


title: zincsulfate-10ug-heart-25


title: zincsulfate-100ug-heart-63


title: zincsulfate-10ug-heart-26


title: zincsulfate-100ug-heart-61


title: zincsulfate-100ug-heart-64


title: Nipponbare, 11 days after infection with S. hermonthica, biological replicate #2

city: Sheffield

first: Julie

last: Scholes

address: Western Bank

department: Animal and Plant Sciences

country: United Kingdom

institute: University of Sheffield

description: Gene expression data from Oryza sativa (cultivar Nipponbare) roots infected with Striga hermonthica at 11 days post-inoculation

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using an Affymetrix GeneChip scanner 3000 7G

data_processing: Data were analysed using Affymetrix GCOS, with global scaling to a target of 100

organism: Oryza sativa Japonica Group

source_name: Oryza sativa roots infected with Striga hermonthica at 11 days post-inoculation

label_protocol: 3'IVT Affymetrix protocol using 5 ug total RNA

growth_protocol: Seedlings of the rice cultivars Nipponbare and IAC 165 (Oryza sativa subspecies japonica) were grown for three weeks in a controlled environment growth room under a 14 hour photoperiod with an irradiance of 400 μmol m-2 s-1, a daytime and night-time temperature of 27 oC and 23 oC respectively and 60% relative humidity.

extract_protocol: RNA was isolated using TRI reagent (Ambion) and then purified using an RNA purification column kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Twenty one day-old seedlings were infected with 25 mg of preconditioned and pre-germinated Striga hermonthica seeds by aligning them along the roots.  Control plants were treated in a similar manner (mock-inoculated).

tag: synonym

value: Oryza sativa subsp. japonica

tag: cultivar

value: Nipponbare

tag: Age

value: 32 days


title: zincsulfate-30ug-heart-44


title: zincsulfate-30ug-heart-43


title: zincsulfate-10ug-heart-23


title: Nipponbare, 11 days after infection with S. hermonthica, biological replicate #1


title: zincsulfate-10ug-heart-24


title: Ovary_Line FL1_biological rep5_technical rep2


title: zincsulfate-10ug-heart-22


title: Nipponbare, 11 days after mock-infection, biological replicate #2

description: Gene expression data from Oryza sativa (cultivar Nipponbare) uninfected roots, 11 days after mock-inoculation

source_name: Oryza sativa uninfected roots, 11 days after mock-inoculation


title: Nipponbare, 11 days after mock-infection, biological replicate #1


title: Nipponbare, 4 days after infection with S. hermonthica, biological replicate #2

description: Gene expression data from Oryza sativa (cultivar Nipponbare) roots infected with Striga hermonthica at 4 days post-inoculation

source_name: Oryza sativa roots infected with Striga hermonthica at 4 days post-inoculation

value: 25 days


title: Nipponbare, 4 days after mock-infection, biological replicate #2

description: Gene expression data from Oryza sativa (cultivar Nipponbare) uninfected roots, 4 days after mock-inoculation

source_name: Oryza sativa uninfected roots, 4 days after mock-inoculation


title: Nipponbare, 4 days after mock-infection, biological replicate #1


title: Nipponbare, 4 days after infection with S. hermonthica, biological replicate #1


title: zincsulfate-Ctrl6-heart


title: zincsulfate-Ctrl3-heart


title: zincsulfate-10ug-heart-21


title: zincsulfate-Ctrl2-heart


title: zincsulfate-Ctrl5-heart


title: Nipponbare, 2 days after mock-infection, biological replicate #1

description: Gene expression data from Oryza sativa (cultivar Nipponbare) uninfected roots, 2 days after mock-inoculation

source_name: Oryza sativa uninfected roots, 2 days after mock-inoculation

value: 23 days