status: Public on Oct 20 2004

city: Trondheim

first: Kristin

last: Nørsett

department: Dept of Cancer Research and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

summary:
Omeprazole stimulated gene expression in rats
Samples and RNA preparation:
The series is composed of 9 hybridizations for analysis of differentially expressed genes in the gastric mucosa of omeprazole dosed vs. control rats. Nine rats (200-250 g) were given (by gavage) 400 micromol/kg of the proton pump inhibitor omeprazole (Astra AB, Gothenburg, Sweden) in Methocel (Dow Corning, Midland, MI) daily for 10 weeks. Seven rats received vehicle only. After 10 weeks the stomachs were removed for sampling of full-thickness corpus from the upper part of the greater curvature. Total RNA extraction was performed first by ultrasentrifugation on a cesium chloride cushion and then using TRIZOL Reagent (GIBCO BRL Life Technologies, New York, NY).
Labeling and hybridization:
Total RNA from 7 untreated rats were pooled and used as a common control. Three micrograms of total RNA from the control pool, and three micrograms of total RNA from each omeprazole dosed rat were reverse transcribed and labeled with capture sequences for subsequent attachment of Cy3- and Cy5-attached dendrimer, respectively, using 3DNA Array 350 Expression Array Detection kit as described in the manufacturer's protocols (Genisphere, Montvale, NJ). The labeling reactions were also spiked with exogenous control RNAs (Stratagene) at ratios of 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 0.5, 0.33, 0.25 and 0.125 for control spike 1, 2, 3, 4, 5, 6, 8, 9, 10 and 7, respectively.
The slides were pre-washed in 2xSSC, 0.2% SDS at 55oC for 20 min, then 0.2x SSC at room temperature for 3 min, and deionized sterile filtered H2O at room temperature for 2 min. The Cy3 and Cy5 labeled samples (combined volume 9 microliter) were mixed with 25 microliter of the hybridization solution containing 0.25 M NaPO4, 1 mM EDTA, 4.5% SDS, 1 x SSC, 2 x Denhardt's solution and 2 microliter LNA dT Blocking reagent (Genisphere). A total hybridization volume of 50 microliter was added onto the array and covered with 24 x 60 mm cover slip. The array was assembled into humidified hybridization chamber (Corning) and hybridized at 60 oC for 18 h by submerging in a water bath. Post-hybridization washes were done once in 2 x SSC, 0.2% SDS at 55 oC for 15 min, then in 2 x SSC at room temperature for 15 min, and finally with 0.2 x SSC at room temperature for 15 min. After washing the fluorescent 3DNA reagent was hybridized to the cDNA at 60 oC for 3 h as described in the manufacturer's protocols. After dendrimer hybridization the slides were washed as described above.
Scanning, image analysis and data processing:
Arrays were scanned at 10 micrometer resolution with a ScanArray Express HT scanner (Packard BioSciences, Billerica, MA). The microarrays were analyzed using GenePix™ Pro 4.1 (Axon Instruments, Inc., Union City, CA). All subsequent statistical analyses were performed using the statistical package R, R Development Core Team. A signal intensity based criterion was applied to remove the spots with median spot signal intensity less than 200. A spot area based criterion was applied to remove the spots with the area less than 50 pixels in either channel. Spots with more than 40% of the pixels saturated in either channel were also removed. Print tip-dependent normalization was applied to the data in order to compensate for systematic errors. The normalized ratios of the duplicated spots were averaged. Further analysis was done on the log2 transformed ratios. In order to assess the significance of up- or downregulation of the genes, tests for differential expression were performed using moderated T-tests, as implemented in the Limma R package of Smyth.
Keywords: repeat sample

first: Mette

last: Langaas

first: Astrid

last: Lægreid

first: Sara

last: Worlund

first: Helge

middle: L

last: Waldum

first: Arne

middle: K

last: Sandvik


title: Dual Ligand Effects

status: Public on Oct 23 2004

city: Pasadena

first: Sangdun

last: Choi

state: CA

address: 1200 E. California Blvd

department: Biology

country: USA

institute: California Institute of Technology

summary:
We identified differentially expressed genes in response to single and double ligand treatments (LPS, IFG, 2MA, LPS plus 2MA, and LPS plus IFG). The majority of the regulated transcripts responded additively to dual ligand treatment. However, a significant fraction responded in a non-additive fashion. Several cytokines showing non-additive transcriptional responses to dual ligand treatment also showed non-additive protein production/secretion responses in separate experiments. Many of the genes with non-additive responses to LPS plus 2MA showed enhanced responses and encoded pro-inflammatory proteins. On the other hand, LPS plus IFG appeared to induce both non-additive enhancement and non-additive attenuation of gene expression. The affected genes were associated with a variety of biological functions. These experiments reveal both dependent and independent regulatory pathways and further analyses may point out the specific nature of the regulatory interactions.

Keywords = Lipopolysaccharide
Keywords = Interferon-gamma
Keywords = 2-Methyl-thio-ATP
Keywords = Dual Ligand Effects
Keywords = Gene Expression
Keywords = RAW 267.4
Keywords = Macrophage
Keywords: repeat sample

first: Misook

last: Chang

first: Amy

last: Pope

first: Jaclyn

last: Zhou

first: Robert

last: Hsueh

first: Mi Sook


title: Community composition of plant biomass-associated bacteria in sheep rumen

status: Public on Oct 15 2004

city: Columbus

first: Zhongtang

last: Yu

state: OH

address: 2027 Coffey Rd.

department: Animal Sciences

institute: The Ohio State University

summary:
Microbiome DNA from the adhering fraction of a sheep rumen.
The RSTs were generated using an improved version of SARST (referred to as iSARST) from the microbiome DNA extracted from the adhering fraction of the rumen content taken from a sheep. The iSARST method is going to be submitted to Nature Biotechnology for publication.
Keywords: other

first: Z

first: Mark

last: Morrison


title: Comparison of liver and kidney from wildtype C3HeB/FeJ mice

city: Munich - Neuherberg

first: Johannes

last: Beckers

state: Bavaria

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: GSF - National Research Center

summary:
Comparison of kidney and liver samples from wildtype C3HeB/FeJ mice.
16 dual-color DNA-chip hybridizations of cDNAs from three age-matched male mice were made. For each individual mouse 6 or 4 replicate hybridizations were done.
Keywords = liver
Keywords = kidney
Keywords = C3HeB/FeJ
Keywords: other

first: Tomek

last: Mijalski


status: Public on Oct 13 2004

city: Baltimore

first: James

middle: T

last: Handa

state: MD

address: 600 N. Wolfe St.

department: Wilmer Eye Institute

institute: Johns Hopkins Medical Institutes

summary:
Description
I.	Exp Design
1.	Type of experiment: Comparison of native versus cultured RPE cells
2.	Experimental factors: Native RPE versus ARPE-19 cells grown in different culture conditions
3.	How many hybridizations in exp: 20
4.	If a common reference used for all the hybs: no
5.	Quality control steps: three independent arrays for each condition, and five different donor globes for native RPE
6.	Description: The expression profile of ARPE-19 cells grown under different culture conditions were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 5 donors.

II.	Samples used, extract prep, and labeling
1.	Biosource: Human donor globes from NDRI and Sierra Eye and Tissue Bank, and ARPE-19 cells.
2.	Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (subconfluent culture density in presence of serum, confluent culture density in presence of serum, confluent culture density with serum withdrawn medium, differentiated (grown for 2.5 months) in serum, and differentiated (grown for 2.5 months) and then serum withdrawn medium).
3.	Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturer's instructions.
4.	Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP.
5.	No external controls were added.

III.	Hybridization procedures and parameters
1.	Sample, array type, batch and serial # used
2.	Hybridization protocol: Hybridization was carried out using the manufacturer's recommendations. Arrays were prehybridized with  Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS.
IV.	Measurement data and specifications of data processing
1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis.
3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis.

Keywords: other


title: Gene Expression Profiling of Host Response in Models of Acute HIV infection

status: Public on Nov 03 2004

city: Toronto

first: Steven

middle: Edward

last: Bosinger

state: Ontario

address: 200 Elizabeth St.

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute, University Health Network

summary:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate

Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Keywords: time-course

middle: E

first: Karoline

middle: A

last: Hosiawa

middle: J

last: Cameron

first: Desmond

last: Persad

first: Longsi

last: Ran

first: Luoling

last: Xu

first: Mohamed

middle: R

last: Boulassel

first: Monique

last: Parenteau

first: Jocelyn

last: Fournier

first: Erling

middle: W

last: Rud

first: David

last: Kelvin


title: Striatum from rats treated with methamphetamine

status: Public on Sep 30 2004

first: Ning-sheng

last: Cai

address: 5500 Nathan Shock Drive

department: Molecular Neuropsychiatry Branch

institute: National Institute on Drug Abuse

summary:
Comparison of striatum from rats treated with either saline or 40mg/kg methamphetamine
Keywords: other

first: Jean Lud

last: Cadet

middle: S

first: Michael

last: McCoy

first: Bruce

last: Ladenheim

first: Johnalyn

last: Lyles


title: Identification of central nervous system genes involved in the host response to the scrapie agent.

city: Winnipeg

first: Garrett

last: Sorensen

institute: Canadian Science Centre for Human and Animal Health

summary:
In this study we identified genes differentially expressed in the central nervous system (CNS) of mice during infection with mouse-adapted scrapie agents. We used cDNA microarrays to examine gene expression profiles at early, mid (pre-clinical) and late (clinical) time points after inoculation.
Keywords = scrapie
Keywords = prion
Keywords = CNS
Keywords = BMAP
Keywords: other

first: S

last: Booth

first: Christopher

last: Bowman

first: Richard

last: Baumgartner

first: G

first: C

last: Robtertson

first: M

last: Coulthart

last: Phillipson

first: Rajmund

last: Somorjai


title: Bovine blood gamma/delta T cell stimulation study

status: Public on Oct 28 2004

city: Saint Paul

first: Mingqi

last: Deng

state: MN

address: 1988 Fitch Avenue

department: Veterinary and Biomedical Sciences

institute: University of Minnesota

summary:
Blood gamma/delta T cells were purfiied from holstein calves less than six months old. Blood from 4 individual calves were pooled and gamma/delta T cells were purified by immunomagnetic separation, rested in RPMI medium for 12h, and underwent ConA & hIL-2 stimulation. Total RNAs were extracted by using Trizol reagents. 15 ug of total RNA was used for cDNA synthesis and microarray hybridization.

Table 1: regulated genes

These genes were identified, in GeneSpring software, via filtering of genes with relative expression ratio of 1.5 and over or 0.667 or below, equivalent to up- and down-regulation by fold change 1.5 or more, in both experiments.

Table 2: down-regulated genes

These genes were identified, in GeneSpring software, via filtering of genes with relative expression ratio of 0.667 or below, equivalent to down-regulation by fold change 1.5 or more, in both experiments. The avergae fold change was then converted to negative value. Gene annotation was performed by using GeneSpring's "Build Simplified Ontology" constructor.

Table 3: up-regulated genes

These genes were identified, in GeneSpring software, via filtering of genes with relative expression ratio of 1.5 or over, equivalent to up-regulation by fold change 1.5 or more, in both samples. Gene annotation was performed by using GeneSpring's "Build Simplified Ontology" constructor.

Keywords: other

first: Jin

last: Liu

first: Cheryl

last: Lancto

first: Colleen

middle: N

last: Pelak

first: Mitchell

last: Abrahamsen


title: NCH_SLK_GBM_Predonisolone

status: Public on Oct 01 2004

city: Kyoto

first: Tadashi

last: Kadowaki

country: Japan

institute: Kyoto University

summary:
Animals: Specific pathogen-free male Wistar-Kyoto rats weighing 300 to 350 g (Charles River Japan, Kanagawa, Japan) were used.
Experiments were performed according to institutional guidelines.
Anti-GBM GN: GBM antigen for the rats was prepared as described previously(1,2).
Five albino rabbits were immunized subcutaneously with GBM antigen emulsified with Freund's complete adjuvant (Difco Laboratories, Detroit, MI, USA).
A booster was given three times every two weeks using the same antigen.
Four days after the final booster, the rabbits were bled from the carotid artery under anesthesia.
Anti-GBM sera were heat-decomplemented for 30 min at 56 degrees Celsius and absorbed with freshly harvested rat erythrocytes.
Rats were divided into several groups, each of which consisted of 4 to 8 rats.
The rats assigned to the GN groups were injected in the dorsal tail vein with 3 ml/kg of anti-GBM serum diluted ten-fold with saline under ether anesthesia.
The day of the anti-GBM serum injection was defined as day 0.
The rats assigned to the control groups were injected intravenously with the same volume of non-immune rabbit control serum, for comparison with the anti-GBM GN rats.
The general condition and body weight of the rats was observed over the course of the experiments.
Drug Treatment: Prednisolone (Shionogi Pharmaceutical, Osaka, Japan) was administered orally at 1 mg/kg body weight twice a day from day 14 of anti-GBM serum injection until sacrifice.
cDNA microarray analysis: NCH_RAT_SLK array contains about 3000 distinct cDNAs from a normalized rat kidney cDNA library.
cDNAs were spotted on the slide glass with MAS coated surface (Matsunami, Osaka, Japan) and irradiate UV for cross-linking.
Non-spotted surface was blocked with succinic anhydride.
Total RNA was prepared from each renal cortex by a guanidinium isothiocyanate method using ISOGEN reagent (Nippon Gene, Tokyo, Japan), and mRNA was prepared by using Oligotex-dT30 (Takara, Shiga, Japan), according to the manufacturer's instructions.
We hybridized labeled target DNAs on the cDNA microarrays with overnight incubation at 65 degrees Celsius.
Hybridization images were scanned using a GenePix 4000A scanner (Axon Instruments, Union City, CA), and the signal intensities were quantified with GenePix Pro 3.0 software (Axon Instruments).
Data analysis was performed(3,4).
In brief, quantified signal intensities were converted by taking logarithms in base two.
Using transformed data derived from each pair of competitive hybridization images, we drew scatter diagrams to compare sample signal intensities with those derived from controls, and executed regression analysis.
The given residuals explain logarithmic gene expression ratios.
Therefore, we selected genes whose average residuals were more than 1 or less than –1, i.e. they represented a two-fold difference in expression level.
References
1. Yamada, M., Sasaki, R., Sato, N., Suzuki, M., Tamura, M., Matsushita, T., Kurumatani, H.Amelioration by beraprost sodium, a prostacyclin analogue, of established renal dysfunction in rat glomerulonephritis model. Eur. J. Pharmacol. 449, 167-176 (2002).
2. Krakower, C.A., Nicholes, B.K., Greenspon, S.A. Proteinuria and the fragility of normal and diseased glomerular basement membrane. Proc. Soc. Exp. Biol. Med. 159, 324-334 (1978).
3. Katsuma, S., Shiojima, S., Hirasawa, A., Suzuki, Y., Takagaki, K., Murai, M., Kaminishi, Y., Hada, Y., Koba, M., Muso, E., Miyawaki, S., Ohgi, T., Yano, J., Tsujimoto, G. Genomic analysis of a mouse model of immunoglobulin A nephropathy reveals an enhanced PDGF-EDG5 cascade. Pharmacogenomics J. 1, 211-217 (2001).
4. Dong, G., Loukinova, E., Chen, Z., Gangi, L., Chanturita, T.I., Liu, E.T., Van Waes, C. Molecular profiling of transformed and metastatic murine squamous carcinoma cells by differential display and cDNA microarray reveals altered expression of multiple genes related to growth, apoptosis, angiogenesis, and the NF-kappaB signal pathway. Cancer Res. 61, 4797-4808 (2001).

Keywords: repeat sample


title: Reloaded 7 days

city: Bern

first: Christoph

last: Däpp

department: Functional Anatomy

country: Switzerland

institute: University of Bern

summary:
Hindlimb suspension for 7 days, subsequent reloading for 7 days
Keywords: repeat sample

first: Silvia

last: Schmutz

first: Hans

last: Hoppeler

first: Martin

last: Flück


title: Hindlimb suspension

summary:
Hindlimb suspended for 7 days
Keywords: repeat sample


title: Control

summary:
Control mice, 14 days
Keywords: repeat sample


title: The expression profile of Escherichia coli K-12 in response to minimal, optimal and excess copper concentrations

status: Public on Sep 22 2004

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

summary:
The gene expression profile of E. coli K-12 MG1655 grown in minimal medium supplemented with elevated copper concentrations (as copper-glycine) has been analysed using whole genome oligonucleotide microarrays.  “Pool” RNA was isolated from five independently grown 50ml DMA cultures of E. coli K-12 MG1655. “Test” RNA was isolated from three independently grown 50ml DMA cultures of E. coli K-12 MG1655, for each growth condition (no added CuSO4, or supplemented with either 0.75mM or 2mM copper glycine).  A sample of each culture was taken at mid to late exponential growth phase at OD600 0.8 (measured using a Pharmacia Biotech Ultrospec 2000 in a cuvette with a path length of 10mm).
Keywords: dose response

last: Kershaw

first: Nigel

last: Brown

first: Mala

last: Patel

first: Jon

last: Hobman


title: Luteinisation genes

status: Public on Sep 17 2004

city: Glasgow

first: Peter

middle: James

last: O'Shaughnessy

address: Bearsden Rd

department: Veterinary Preclinical Studies

institute: University of Glasgow Veterinary School

summary:
Two SAGE libraries generated before (PMSG) or after (PMSG/hCG) the onset of granulosa cell luteinisation induced by hCG
Keywords = granulosa
Keywords = PMSG
Keywords = hCG
Keywords = luteinisation
Keywords: other

first: R. Scott

last: McRae

first: Heather

middle: M

last: Johnston

first: Monika

last: Mihm


title: Dexamethasone treatment of gut cells

status: Public on Oct 08 2004

city: Houston

first: Henning

last: Susan

state: TX

address: 1 Baylor Plaza

department: Pediatrics

institute: Baylor College of Medicine

summary:
Reference pool RNA versus RNA from dexamethasone treated gut cells.
Keywords: other

first: Barbara

last: Agmafle

first: Thomas

last: Oesterreicher

first: Chad

last: Shaw

first: Susan

last: Henning


title: Parasite resistance in the small intestine of sheep

status: Public on Oct 05 2004

city: Dunedin

first: Theresa

last: Wilson

address: 710 Cumberland Street

country: New Zealand

institute: AgResearch

summary:
This experiment details the gene expression data from the small intestine from a set of parasite resistant and a set of parasite susceptible sheep.
Keywords = parasite resistance
Keywords: other

first: Cristina

last: Diez-Tascon

first: Orla

last: Keane

first: David

last: Baird

first: John

last: McEwan


title: Temperature shift time-course of Pre-mRNA splicing factor mutants

status: Public on Sep 25 2004

city: Bangalore

first: Aparna

middle: Katoch

last: Sapra

state: Karnataka

address: C.V. Raman Avenue

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

summary:
Measurement of expression levels as a time course after shifting temperature-sensitive splicing factor mutant cells from 23C to 37C.
Analysis of WT SS330, prp17 null, prp17-1 and prp22-1 cells.
Samples were analyzed at 0, 5, 15, 30, 60 and 120 min.
Keywords = pre-mRNA splicing
Keywords = time course
Keywords = intron
Keywords: time-course

first: Yoav

last: Arava

first: Piyush

last: Khandelia

first: Usha

last: Vijayraghavan


title: Innervated and 2 month Denervated Rat EDL muscles

status: Public on Sep 10 2004

city: Ann Arbor

first: Tatiana

middle: Y.

last: Kostrominova

state: MI

address: 300 N. Ingalls st.

department: Institute of Gerontology

institute: University of Michigan

summary:
The right legs of 8 Brown-Norway male rats were denervated by a high sciatic nerve section in the hip region of the hind limb.Two months after denervation (6 months of age), extensor digitorum longus (EDL) muscles were removed from the operated legs. The EDL muscles from 8 age-matched non-operated rats served as innervated controls. Total RNA was isolated, labeled cDNA was prepared and hybridized to the Rat Atlas 1.2 Array II membranes (Clontech Laboratories, Palo Alto, CA).
Keywords: other

middle: Y

first: Douglas

middle: D

last: Dow

first: Robert

middle: G

last: Dennis

first: Richard

last: Miller

last: Faulkner


title: Reloaded 1 day

first: Christoph

last: Däpp

summary:
Hindlimb suspended for 7 days, subsequent reloading for 1 day
Keywords: repeat sample

first: Silvia

last: Schmutz

first: Hans

last: Hoppeler

first: Martin

last: Flück


title: Hindlimb suspension and reloading study

summary:
Analysis of effect of hindlimb suspension and reloading on C57Bl/6 mouse soleus muscle.

Experimental groups examined:
-Control mice, 14 days
-Hindlimb suspension for 7 days
-Hindlimb suspension for 7 days, and subsequent reloading for 1 day
-Hindlimb suspension for 7 days, and subsequent reloading for 7 days
Keywords: other


title: Gyrase binding in wild type and gyrA D82G mutant

status: Public on Sep 09 2004

first: Kyeong Soo

last: Jeong

type: Genome binding/occupancy profiling by array

summary:
Raw data for spatial pattern analysis of gyrase binding in E. coli MG1655 wild type and gyrA D82G mutant (ChIP-chip data)
Keywords: other

first: Jaeyong

last: Ahn

first: Arkady

last: Khodursky


title: mRNA abundance from wild type

summary:
- mRNA abundance from wild type grown in LB or M9 (mRNA vs. Genomic DNA) : GSM30231 - GSM30238, GSM30338-GSM30341
- mRNA abundance grown in LB with norfloxacin treatment for 10 min or 30 min (mRNA vs. Genomic DNA): GSM30247-GSM30262
- mRNA abundance from gyrA (D82G) mutant grown in LB (mRNA vs. Genomic DNA):GSM30239-GSM30246
- Transcription profile between wild type and gyrA (D82G) mutant: GSM30330-GSM30337
Keywords: other


title: Phytophthora sojae, race 2, infection of soybean hypocotyls

status: Public on Sep 14 2004

city: London

first: Mark

last: Gijzen

state: ON

address: 1391 Sandford St

department: Agriculture & AgriFood Canada

institute: SCPFRC London

summary:
Examination of soybean hypocotyls, G. max cv. Harosoy (Rps7), at 3, 6, 12, 24 and 48 hours after inoculation with P. sojae, race 2, isolate P6497

Patterns of Gene Expression Upon Infection of Soybean Plants by Phytophthora sojae. P. Moy, D. Qutob, B. P. Chapman, I. Atkinson, and M. Gijzen. Pages 1051-1062. Publication no. M-2004-0728-01R. Molecular Plant-Microbe Interactions, October 2004, Volume 17, Number 10.
Keywords: time-course

sample_organism:
Glycine max
Phytophthora sojae

platform_organism:
Glycine max
Phytophthora sojae

first: Pat

last: Moy

first: Dinah

last: Qutob

first: B

middle: P

last: Chapman

first: Ian

last: Atkinson


title: Mouse cerebellum

status: Public on Oct 26 2004

first: Magdalena

last: Popesco

institute: The Ohio State Universiy

summary:
Serial analysis of gene expression (SAGE) was used to identify and quantify all expressed cerebellar genes in the adult (P92; GSM17430) and aged (P810; GSM17226) C57BL/6J mouse cerebellum. A "closest-neighbor" algorithm was used to differentiate low abundance tags from possible sequencing errors in both libraries. Unique tags were categorized into four groups: (1) novel genes; (2) ESTs; (3) RIKEN, KIA, and hypothetical genes; and (4) known genes. Known genes were further subdivided into functional categories based on the gene ontology classification, using a web-based program developed in this laboratory (MmSAGEClass). Comparison of adult and aged cerebellar libraries revealed several genes that were differentially expressed, including growth hormone and prolactin, both of which were markedly decreased in the aged cerebellum. In addition, several tags showing differential expression were not identified in the Unigene database and are likely to represent novel genes. The present SAGE data on the aged cerebellar transcriptome may reveal candidate genes involved in the aging process.
Keywords: other

middle: C

first: Adrienne

last: Frostholm

first: Andrej

last: Rotter


title: 14028 versus che mutants

status: Public on Sep 02 2004

city: Austin

first: Rasika

last: Harshey

department: Section of Molecular Genetics and Microbiology

institute: Institute of Cellular and Molecular Biology

summary:
Salmonella wild type strain 14028 compared with chemotaxis mutants, cheA, cheB, cheY, and cheZ at various time points both in broth medium and on swarming plates
Keywords: other

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

first: Qingfeng

last: Wang

first: Jonathan

last: Frye

first: Michael

last: McClelland

first: Tim

middle: Q

first: Steffen

last: Porwollik


title: growth culture comparisons

summary:
All the other array data are here, including plate culture versus broth culture, swarming agar culture versus hard agar culture, wildtype versus mutants other than che, and so on
Keywords: other


title: 14028 time course in broth medium

summary:
Salmonella strain 14028, time course in broth medium, array were done between mRNA from various time point in broth and reference mRNA, which is from swarmer cells at 3 hour on swarming plates
Keywords: other


title: Transcriptional Responses of M. tuberculosis to inhibitors of metabolism

status: Public on Sep 01 2004

city: Rockville

first: Helena

middle: I

last: Boshoff

address: 12441 Parklawn Drive

department: LIG

institute: NIAID/ NIH

summary:
Transcriptional profiling of M.tuberculosis was performed using 430 whole-genome microarrays to measure the effects of 75 different drugs, drug combinations or different growth conditions at various times relative to a sample of logarithmically growing MTb. Analysis of this data set revealed 150 underlying clusters of coordinately regulated genes as described in Boshoff et al., 2004.
Keywords = Gene clusters
Keywords = Mechanism of action
Keywords = tuberculosis
Keywords = antimycobacterial drugs
Keywords = natural product
Keywords = respiration
Keywords: other

first: Timothy

last: Myers

first: Brent

last: Copp

last: McNeil

last: Wilson

first: Clifton

middle: E

last: Barry


title: MicroRNA expression patterns in mouse tissues and staged embryos

city: Chapel Hill

first: Scott

last: Hammond

state: NC

department: Dept Cell and Developmental Biology

institute: University of North Carolina

summary:
RNA from seven adult mouse tissues, four staged whole mouse embryos, ES cells, 3 day and 28 day embryoid bodies was profiled against the microRNA microarray.

A custom microarray platform for analysis of microRNA gene expression; Nature Methods  1, 47 - 53 (2004)

Keywords = microRNA
Keywords = miRNA
Keywords: other

platform_organism:
Homo sapiens
Mus musculus

first: John

last: Thomson

first: Joel

last: Parker

first: Charles

last: Perou


title: 14028 time course on non-swarming plates

summary:
Salmonella strain 14028, time course, on non-swarming agar plates (1.5%), array were done between reference mRNA (from swarmer cells at 3 hour) and mRNA from various time points on non-swarming plates.
Keywords: other


title: 14028 time course on swarming plates

summary:
Salmonella 14028 time course on swarming agar (0.6%) plates
mRNA from 3 h time point on swarming plates used as reference for all the time course arrays
Keywords: other


title: DNA vaccination series 1

city: Stockholm

first: Anna

last: Lobell

address: CMM, L8:04, Karolinska Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institute

summary:
Repeated comparisons of gene expression between individual RNA samples from DNA vaccinated rats vs controls.
Keywords: repeat sample

first: Amilcar

last: Flores-Morales

first: Judit

last: Wefer

first: Asa

last: Andersson

first: Robert

middle: A

last: Harris


title: Various mouse cell lines and tissues

city: Toulouse

first: Guillaume

last: Charriere

country: France

summary:
Samples from preadipocyte cell lines, peritoneal macrophages, myoblast cell lines, tibialis muscle, mesenchymal stem cell lines, macrophage cell lines, liver tissue, embryonic stem cell line, and inguinal white adipose tissue
Keywords: other

first: Louis

last: Casteilla

first: Emmanelle

last: Arnaud

first: Beatrice

last: Cousin

first: Mireille

last: Andre

first: Luc

last: Penicaud


title: MelR experiment 1

first: Chrystala

last: Constantinidou

summary:
Three independent repeats of the same experiment, comparing gene expression in E. coli cultures expressing either no MelR, or a constitutively active MelR* protein.
Keywords: repeat sample

first: David

last: Grainger

first: Timothy

last: Overton

first: Jon

middle: L

last: Hobman

first: Stephen

middle: J

last: Busby


title: prors1_dark_vs_WT_dark

city: Chicago

first: christos

last: Noutsos

institute: University of Chicago

summary:
Series of 6 repetitions of hybridization of treatment (prors1_dark) and control (WT_dark) each. Comparison of the dark adapted Arabidopsis prors1 mutant lacking prolyl tRNA synthetase versus the dark adapted WT. P. Pesaresi, D. Leister, unpublished
Keywords: repeat sample

first: A

last: Biehl

first: E

last: Richly

first: C

last: Dietzmann

first: J

last: Kurth

first: F

last: Salamini

first: D

last: Leister


title: prors2_dark_vs_WT_dark

summary:
Series of 6 repetitions of hybridization of treatment (prors2_dark) and control (WT_dark) each. Comparison of the dark adapted Arabidopsis prors2 mutant lacking prolyl tRNA synthetase versus the dark adapted WT. P. Pesaresi, D. Leister, unpublished
Keywords: repeat sample


title: Epithelial cells in contact with bacterial supernatant

status: Public on Aug 26 2004

city: Sophia Antipolis

first: Chimene

last: Moreilhon

institute: CNRS

summary:
Epithelial cells were in contact with bacteria supernatant during different times of incubation.

time course supernatant 10 % MM39
Keywords: time-course


title: Bone marrow grown with vitamin D compared to bone marrow grown with vitamin D plus M-CSF

status: Public on Aug 31 2004

city: Mineola

first: Siham

last: Accacha

state: NY

address: 222, Station Plaza, suite 501

department: Medicine

institute: Winthrop University Hospital

summary:
Osteoclast differentiation and activation requires the presence of osteoblast-derived factors such as Macrophage colony stimulating factor (M-CSF) and receptor activator of nuclear factor-kappaB ligand (RANKL). RANKL is influenced by osteotropic hormones such as calcitriol 1,25(OH)2D3 (vitamin D).The aim of this study is to evaluate the combined effect of vitamin D and M-CSF on murine bone marrow and on murine spleen cell, to define when the inhibitory effect of vitamin D plus M-CSF is maximum and what are the mechanisms involved in this inhibition. When murine bone marrow cells were cultured with 10-8 M vitamin D and 60 ng/ml M-CSF, there was a significant decrease in osteoclasts formation (3.13±3.44),compared to bone marrow cells cultured with vitamin D alone (80.86 ±45.02; p<0.05). Even when the amount of M-CSF added to the bone marrow cell culture was 1 ng/ml there was a 40% decrease in osteoclasts formation. Since bone marrow contains also stromal cells, we eliminate their influence by culturing murine spleen cells with 10-8 M vitamin D, 60 ng/ml M-CSF and RANKL 20 ng/ml. There was a significant decrease in osteoclasts formation (41±14.14) compared to spleen cells cultured with M-CSF and RANKL (215.67±46.44); p<0.05).  These data lead to hypothesize that vitamin D and M-CSF together exert an inhibitory effect on osteoclast differentiation and development. To define the cellular mechanism involved in this inhibition we analyzed gene array data of bone marrow cells cultured with vitamin D and compare them with the cells cultured with vitamin D and M-CSF. Activation Toll like receptors after addition of vitamin D plus M-CSF to bone marrow cells appears to be involved in the inhibition of osteoclast differentiation.
Keywords: parallel sample

first: Jodi

middle: F

last: Evans

first: Quing-tian

last: Niu

first: Mariano

last: Castro-Magana

first: James

middle: K

last: Yeh


title: Synechocystis sp. PCC 6803 response to inorganic carbon limitation

status: Public on Aug 24 2004

city: Stillwater

first: Robert

last: Burnap

state: OK

institute: Oklahoma State University

summary:
Synechocystis 6803 cells was grown photoautotrophically at 32 °C buffered  in BG-11 and bubbled with 3% CO2. A relatively mild Ci stress was applied by switching the aeration from 3% CO2 to air alone. After incubation under designated conditions, a 100-ml aliquot of culture was immediately combined with an equal volume of ice-cold mixture of phenol and ethanol (1:10, w/v) in an ice bath. The resultant cells were collected by centrifugation at 1000 x g for 10 min at 4 °C. Total RNA was isolated with RNeasy Midi Kit (Qiagen, Valencia, CA) and further treated with the DNA-free kit (Ambion, Austin, TX). Fluorescently labeled cDNA was produced via a two-step indirect procedure involving cDNA synthesis from 16 µg of total RNA in a reverse transcriptase reaction incorporating aminoallyl-modified deoxynucleotide, followed by the second step involving chemical coupling of fluorescent dye to the introduced amino moieties of the synthesized cDNA. Labeled cDNA were adjusted to 14.75 µl, and the remainder of the hybridization components containing 2.5 µl of 10 µg µl-1 salmon sperm DNA, 8.75 µl of 20x SSC, 0.25 µl of 10% SDS, and 8.75 µl of formamide were added. The mixture was then heated for 2 min at 99 °C and maintained at 42 °C until hybridization. Hybridizations were preformed in a static incubator at 42 °C for 12-16 h then washed by placing in a 250-ml solution of 2x SSC and 0.1% SDS at 42 °C for 5 min with gentle agitation provided by rotation of a magnetic stir bar. The slide was transferred quickly to a 250-ml solution of 0.1x SSC and 0.1% SDS, incubated for 10 min at room temperature with gentle agitation, and washed five additional times in 0.1x SSC for 1 min at room temperature. Hybridization signals from the microarray were quantified using GenePix Pro 4.1 (Axon Instruments, Union City, CA). The quality control procedures were conducted in the image analysis software, and then data were saved to Acuity 3.1 (Axon Instruments).
Keywords: time-course

first: Hong-Liang

last: Wang

first: Bradley

last: Postier


title: Li-treatment-induced NDI (Li-NDI) in rats

city: Aarhus C

first: Aleksandra

last: Rojek

address: building 233/234

country: Denmark

institute: Institute of Anatomy, Aarhus University

summary:
5 rats were offered food containing 40mM Li/Kg dry weight for 4 weeks, and 5 control rats obtained standard food. The RNA from the inner medulla of the Li-treated rats was labeled red (channel 1), and from the control rats labeled green (channel 2). The samples from  Li-treated rats 1+2 and control rats 1+2 were hybridized to array Li-NDI 1. The samples from  Li-treated rats 3+4 and control rats 3+4 were hybridized to array Li-NDI 2. The samples from  Li-treated rat 5 and control rat 5 were hybridized to array Li-NDI 3.
Keywords: parallel sample

first: Jakob

last: Nielsen

first: Hong

last: Gong

first: Young-Hee

last: Kim

first: Tae-Hwan

last: Kwon

first: Jørgen

last: Frøkiær

first: Søren


title: Sporulation in Bacillus subtilis (mother cell)

city: Cambridge

first: Patrick

middle: Yves

last: Eichenberger

state: MA

address: 16 Divinity Avenue

department: Molecular and Cellular Biology

institute: Harvard University

summary: This series of experiments was designed to identify the program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. The mother cell is one of two cell types generated by asymmetric division of sporulating cells approximately two hours after initiation of sporulation. The program is governed by a hierarchical cascade consisting of the transcription factors: sigmaE, sigmaK, GerE, GerR (YlbO) and SpoIIID. The characterization of the sigmaE regulon was reported in Eichenberger et al. (2003), J. Mol. Biol. 327, 945-972. Here we report the data for sigmaK, GerE, GerR and SpoIIID.

first: Masaya

last: Fujita

first: Shane

middle: T

last: Jensen

first: Erin

last: Conlon

first: David

middle: Z

last: Rudner

first: Stephanie

first: Caitlin

last: Ferguson

first: Koki

last: Haga

first: Tsutomu

last: Sato

first: Jun

middle: S

last: Liu

first: Richard

last: Losick


title: Unfolded protein response in wildtype, ire1, gcn4, gcn2

status: Public on Aug 19 2004

city: San Francisco

first: Chris

last: Patil

address: 600 16th Street, N312

department: Biochemistry and Biophysics

institute: UCSF

summary:
We measured steady-state mRNA levels by microarray hybridization, comparing WT, (delta)ire1, (delta)gcn4, and (delta)gcn2 cells treated with 2 mM DTT for 30 min (by which time the UPR is qualitatively complete) to untreated samples of the same genotype. WT cells were taken as a positive control for UPR induction, and (delta)ire1 cells as a negative control. Fold change in expression of a given gene was computed as the ratio of mRNA level in the treated sample to the level in an untreated sample of the same genotype. Values reported here are the log2 fold change.
Keywords = unfolded protein response
Keywords = UPR
Keywords = ire1
Keywords = gcn4
Keywords = gcn2
Keywords: parallel sample

first: Christopher

first: Hao

last: Li

first: Peter

last: Walter


title: Isometric contractions in skeletal muscle of adult mice

status: Public on Aug 17 2004

city: Liverpool

first: Anne

last: McArdle

department: School of Clinical Science

institute: University of Liverpool

summary:
Study to examine the effect of a demanding 15 minute whole hindlimb isometric contraction protocol in vivo on changes in gene expression, 4 hours post-contraction.
Keywords = skeletal muscle
Keywords = isometric contractions
Keywords: parallel sample


title: H2O2 treatment of myotubes

summary:
Study to examine changes in gene expression in C2C12 myotubes at 5 days post-differentiation following treatment with a non-damaging concentration of hydrogen peroxide)
Keywords: parallel sample


title: Gene expression profile of CD56dimCD16+, CD56brightCD16- and activated CD56+CD16+ human NK subsets

status: Public on Aug 02 2004

city: Jerusalem

first: Ofer

last: Mandelboim

department: The Lautenberg Center for General and Tumor Immunology

country: Israel

institute: The Hebrew University of Jerusalem

summary:
Pooled purified peripheral blood derived CD56dimCD16+ NK, CD56brightCD16- NK and in vitro activated CD56+CD16+ NK subsets obtained from 9 healthy donors were analyzed for gene expression pattern. Each pooled NK subset sample was hybridized in replicates (A and B).
Keywords: other

first: Jacob

last: Hanna


title: Testing for gene expression differences between chromosomally stable and unstable isogenic clones

status: Public on Aug 01 2004

city: Baltimore

first: Andrew

last: Snyder

address: 655 West Baltimore Street

department: Radiation Oncology Research Laboratory

institute: University of Maryland, Baltimore

summary:
An irradiated but chromosomally stable CHO clone RT210B was used a reference to find differences in gene expression compared to radiation-induced chromosomally unstable isogenic clones.  Equal quantities of two unstable different unstable clones were mixed prior to RNA extraction.  Each mixture was tested twice versus the stable reference clone.  Two different two clone mixtures were tested against the same chromosomally stable clone
Keywords: repeat sample

middle: R


title: MicroRNA profiles of RISC sub-complexes

status: Public on Jul 30 2004

first: Scott

middle: M

last: Hammond

summary:
293 cells were tranfected with Myc-tagged argonaute family members and associated microRNAs quantitated by microarray analysis of immunoprecipitates. Human argonaute 1, 2, and 3, and a control immunoprecipitation were done. Two independent immunoprecipitations were performed, with two replicate points per immunoprecipitation. Ch1and Ch2 net values are median intensity, background subtracted, unnormalized. Normalized Ch2 values for argonaute immunoprecipitations are median center normalized. Normalized Ch2 values for control immunoprecipitates are normalized by a constant that is the average of the constants used for argonaute immunoprecipitates.
Keywords = microRNA
Keywords = miRNA
Keywords = argonaute
Keywords = RNAi
Keywords: repeat sample

first: Jidong

first: Michelle

last: Carmell

first: Fabiola

middle: V

last: Rivas

first: Carolyn

last: Marsden

first: John

last: Thomson

first: Ji-Joon

last: Song

first: Leemor

last: Joshua-Tor

first: Gregory

last: Hannon


title: HS-R5

city: Berne 9

first: Martin

last: Flück

state: Bern

address: Bühlstrase 26

department: Department of Anatomy

institute: University of Berne

summary:
14 days hindlimb suspended, 5 days reloaded m. soleus
RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis.
Keywords: time-course

first: Silvia

last: Schmutz

first: Matthias

last: Wittwer

first: Hans

last: Hoppeler

first: Dominique

last: Desplanches


title: Control vs. AngII Infusion: Heart

status: Public on Jul 22 2004

city: Boston

first: Faina

last: Schwartz

address: 700 Albany Street,W508

department: Medicine, Hypertension Section

institute: Boston University School of Medicine

summary:
C57Bl/6J mice received continuous administration of saline or Angiotensin II via implanted minipumps for 7 days, total RNA prepared from homogenized hearts, SAGE library constructed from heart RNA pooled from 6 mice.
Keywords: other

first: Arvi

last: Duka

first: Irena

first: Jing

last: Cui

first: Haralambos

last: Gavras


title: Transcriptional profiling with a Blood Pressure QTL interval-specific oligonucleotide array

status: Public on Jul 31 2004

first: Norman

middle: H

last: Lee

address: 9712 Medical Center Drive

department: Department of Mammalian Genomics

institute: The Institute for Genomic Research

summary:
Although the evidence for a genetic predisposition to human essential hypertension is compelling, the genetic control of blood pressure (BP) is poorly understood. The Dahl salt-sensitive (S) rat is a model for studying the genetic component of BP.  Using this model we previously reported the identification of 16 different genomic regions that contain one or more BP quantitative trait loci (QTLs). The proximal region of rat chromosome 1 contains multiple BP QTLs.  Of these, we have localized the BP QTL1b region to a 13.5cM (20Mb) region. Interestingly, five additional independent studies in rats and four independent studies in humans have reported genetic linkage for BP control by regions homologous to QTL1b.  To view the overall renal transcriptional topography of the positional candidate genes for this QTL, we sought a comparative gene expression profiling between a congenic strain containing QTL1b and control S rats by employing: (1) a saturated QTL1b interval specific oligonucleotide array, and (2) a whole genome cDNA microarray representing 20,465 unique genes that are positioned outside the QTL.  Results indicated that 19 out of the 231 positional candidate genes for this QTL are differentially expressed between the two strains tested.  Surprisingly, over 1,500 genes outside of QTL1b were differentially expressed between the two rat strains.  Integrating the results from the two approaches revealed at least one complex network of transcriptional control initiated by the positional candidate Nr2f2.  This network appears to account for the majority of gene expression differences occurring outside of the QTL interval.  Further substitution mapping is currently underway to test the validity of each of these differentially expressed positional candidate genes. These results demonstrate the importance of using a saturated oligonucleotide array for identifying and prioritizing differentially expressed positional candidate genes of a BP QTL.
Keywords: : rat, hypertension, genetics, polygenic trait, microarray, gene expression

overall_design: Pairs of Cy5 and Cy3 labeled targets were co-hybridized onto either the oligonucleotide microarray or a custom TIGR rat cDNA array consisting of 26,401 probe elements representing 20,465 unique non-QTL1b genes.  A “flip-dye” design was used as the experimental method of choice to account for potential dye-bias labeling effects.  Seven “flip dye” normalized files are submitted for the oligonucleotide array and twelve individual hybridizations are submitted for the cDNA array.

first: Bina

last: Joe

first: Noah

last: Letwin

first: Michael

last: Garrett

first: Seema

last: Dhindaw

first: Bryan

last: Frank

first: Razvan

last: Sultana

first: Kathleen

last: Veratti

middle: P

last: Rapp


title: Genomic comparisons of Salmonella enterica serovar Paratyphi A isolates

status: Public on Jul 21 2004

city: Irvine

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary:
Comparative genomic analysis of a temporally and locally diverse set of S. enterica ssp I sv Paratyphi A isolates
Keywords: ordered

sample_organism: Salmonella enterica subsp. enterica serovar Paratyphi A

first: Steffen

last: Porwollik

first: Pui

last: Cheng

first: Carmen

last: Choy

first: Jerry

last: Reen


title: splitplotnestedANOVA

city: Wilmington

first: Ann

last: Stapleton

address: 601 S. College

department: Biological Sciences

institute: University of North Carolina Wilmington

summary:
Determination of significant differential expression was undertaken with analysis of variance (ANOVA) style models.  From the ideas provided by Kerr and Churchill (2001) and Wolfinger, et al. (2001),  and based on the specific design of this experiment, the following ANOVA models were constructed:

Model (1)

y_gijklr = \mu + L_i + A(L)_j(i) + T_k + LT_ik + D_l + AD_jl + \epsilon_gijklr

Model (2)

r_gijklr = GL_gi + GA(L)_gj(i) + GT_gk + GLT_gik + GD_gl + GS(A)_gr(j) + \epsilon_gijklr

In model (1), y is the logarithm (base 2) of the intensity for a particular spot. L, T and D are global effects due to differences in lines (Mo17 and B73), treatments (control and UV exposure) and dyes, respectively, while LT represents interaction between lines and treatments.  The AD interaction term is present as suggested by Wolfinger et al. to account for intensity scaling done on the two channels.  The nested term, A(L), accounts for variation across replicate arrays in a slightly different fashion than that set forth in Kerr and Churchill's ANOVA models.  Their approach considered connected designs; however, in this experiment, lines are not connected because no array has samples from two different lines hybridized to it.  The output from model (1) is given in the file "standardized".Model (2) takes residuals from model (1) as normalized response values and includes gene specific effects.  Additionally, it models replicate spot variation via the GS(A) term.
Both models were fit using the SAS/STAT® software's MIXED procedure, with model (2) being fit gene by gene.  Observed significance levels for all effects tests were adjusted for multiplicity of testing by use of the Sidak method.  Significance was assessed based on an experiment-wise significance level of 0.05.
The levels of expression of the SP10 negative controls were used to determine the log-ratio level for expression above background.  All cDNAs with all levels below the SP10 median were set to background, thus diminishing their influence on the final list of genes. Ten genes, that may have been otherwise called significant, were removed from the 5366 total using this criterion.  There are still 201 genes with at least one very low level; however, these were retained for significance testing as some may have significant expression level alterations in one line or condition.  There were six cDNAs with significant differences between lines but not interaction or treatment; these genes were not analyzed further.  A table of summary information for all genes is included as Table S1.    Cluster analysis on gene expression levels was performed using the SAS v. 8 Enterprise Miner software Cluster node, using the default settings except for specifying input cluster number as equal to the total sample number.  Clustering was performed separately on genes significant by interaction (Table S2) and genes significant by treatment (Table S3); the output cluster number is listed for each gene name in these tables.

The entire model (1) output file can be obtained by within the citation below.

first: James

last: Blum

first: Paula

last: Casati

first: Virginia

last: Walbot


title: AGAMOUS-GR time-course experiment

status: Public on Jul 15 2004

city: Pasadena

first: Frank

last: Wellmer

address: 1200 E. California Blvd.

department: Biology 156-29

institute: California Institute of Technology

summary:
Inflorescences of ag-1;35S::AG-GR plants were treated for 0,4,8,10, or 16 hours with dexamethasone or were mock-treated. Two biologically independent sets of samples were generated and RNA probes derived from these samples were co-hybridized to a cDNA array enriched for flower-specific transcripts.
Keywords: time-course


title: Steady state +/- Gly

status: Public on Jul 17 2004

city: Toronto

first: Andy

last: Bognar

address: 1 King's College Circle

department: Medical Genetics and Biology

institute: University of Toronto

summary:
Cells were grown to early log phase (OD600 ~ 0.2) at 30oC in 1 liter of minimal B medium (Cherest, H., and Surdin-Kerjan, Y. (1992) Genetics 130, 51-58) with or without supplementation with 10 mM glycine and harvested. All cells were harvested by rapid centrifugation at room temperature then flash frozen in liquid nitrogen. Arrays compared expression of Gly- cells to the Gly+ controls. Strain BY4741 was the wild type and several deletion strains were also used.
Keywords: parallel sample

first: Jonathan

middle: D

last: Lalich


title: A multigene analysis of the effects of L-arginine treatment in the hindlimb and diaphragm muscles of mdx mice.

status: Public on Aug 10 2004

city: Nantes

first: Nolwenn

last: Le Meur

address: 1 rue Gaston Veil

institute: INSERM

summary:
Diaphragm and hindlimb muscle samples from BL10 or MDX mice treated with L-arginine or untreated. Ages 3/5/9/12 weeks are represented in analysis.
Keywords = Muscular dystrophy
Keywords = mdx
Keywords = DNA microarrays
Keywords = L-arginine
Keywords = gene expression profiling
Keywords: other

first: Karl

last: Rouger

first: Martine

last: Le Cunff

first: Jean-Marie

last: Heslan

first: Jean

last: Leger

first: Jacques

last: Noireaud


title: PancChp-HSLKO and WT

status: Public on Jul 11 2004

city: Palo Alto

first: Wen-Jun

last: Shen

address: 3801 Miranda Avenue

institute: Stanford University

summary:
Microarray analysis of gene expression in islets of HSL-/- mice and wild type mice using PAncChip 2 array.
Keywords: repeat sample

first: Yu

last: Liang

first: Jenny

last: Wang

first: Kenji

last: Harada

first: Shailja

last: Patel

first: Jun-ichi

last: Osuga

first: Shun

last: Ishibashi

first: Fredric

middle: B

last: Kraemer


title: sok2 vs wild type colonies

city: Paris

first: Frederic

last: Devaux

institute: Ecole Normale Superieure

summary:
Time course analyses of gene expression in sok2 deleted vs wild type colonies during late developmental stages on plate.
Keywords = ammonia
Keywords = metabolism
Keywords = yeast
Keywords = stress
Keywords = transcriptome
Keywords: time-course

first: Libuse

last: Vachova

first: Helena

last: Kucerova

first: Marketa

last: Ricicova

first: Claude

last: Jacq

first: Zdena

last: Palkova


title: Wild-type and irr mutant Group A Streptococcus (GAS) strains

status: Public on Jul 14 2004

city: Hamilton

first: Frank

middle: R.

last: DeLeo

state: MT

address: 903 South 4th Street

department: Laboratory of Human Bacterial Pathogenesis

institute: National Institute of Allergy and Infectious Diseases

summary:
Wild-type (JRS4) and irr mutant (JRS550) Group A Streptococcus (GAS) strains growing in either early or late exponential phase
Keywords = Human
Keywords = Neutrophils
Keywords = Bacterial
Keywords = Gene Regulation
Keywords = Inflammation
Keywords: other

first: Jovanka

last: Voyich

first: Kevin

last: Braughton

first: Daniel

middle: E

last: Sturdevant

first: Cuong

last: Vuong

first: Scott

last: Kobayashi

first: Stephen

last: Porcella

first: Michael

last: Otto

first: James

last: Musser


title: Transgenic Arabidopsis expressing AtMYB23SRDX

status: Public on Jul 07 2004

city: Tsukuba

first: Kyoko

last: Matsui

department: Gene Function Research Center

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary:
Comparison of gene expression between wild type Arabidopsis ecotype Col-0 plants and transgenic Arabidopsis ecotype col-0 plants expressing AtMYB23SRDX.
Keywords: other

first: Masaru

last: Ohme-Takagi


title: Atlas Rat cDNA Expression Array - Zipf's Normalization

status: Public on Jul 03 2004

city: Kiel

first: Timothy

middle: TeHua

last: Lu

institute: Christian-Albrechts-University Kiel

summary:
Five microarrays from a larger dataset used to demonstrate a normalization technique base on Zipf's law. The original data set was generated by using Atlas Rat cDNA microarrays (Clontech, 588 genes) probed with rat brain tissue, from control (cerebellum n=10, olive n=10) and harmaline treated (cerebellum n=10, olive n=9) animals. Microarrays were probed according to established protocols and exposed to imaging plates overnight (BAS-MS 2325) and scanned at a 50  m resolution on a FLA-3000G phosphoimager (Raytest, Germany). Image gridding was carried out using VisualGrid® software (http://www.gpc-biotech.com).
Keywords: other

first: Tim

first: Christine

last: Costello

first: Peter

last: Croucher

first: Robert

last: Haesler

first: G.

last: Deuschl

first: Stefan

last: Schreiber


title: Human UniGene Set RZPD 1 - Zipf's Normalization

summary:
Five microarrays from a larger dataset used to demonstrate a normalization technique base on Zipf's law. The original data-set generated using a global genome-wide cDNA clone set (Human UniGene clone set RZPD 1 - http://www.rzpd.de - Build 138, NCBI), which consisted of ~33,792 cDNA clone inserts spotted in duplicate onto membranes (18). These microarrays (n=31) were hybridized with 33P-labeled cDNA derived from total RNA extracted from biopsy material from the sigmoidal colon of normal (control, n=11), and patients with Crohn's disease (condition A, n=10) and ulcerative colitis (condition B, n=10). Microarrays were probed according to established protocols and exposed to imaging plates overnight (BAS-MS 2325) and scanned at a 50  m resolution on a FLA-3000G phosphoimager (Raytest, Germany). Image gridding was carried out using VisualGrid® software (http://www.gpc-biotech.com).
Keywords: other


title: Overlapping gene regulation by cytosine methylation and histone deacetylation

status: Public on Aug 06 2004

first: Shuang

last: Chang

state: MO

department: Biology

institute: Washington University

summary:
Testing the hypothesis that cytosine methylation and histone deacetylation regulate an overlapping set of genes.
Keywords: other

first: C

last: Pikaard


title: TFB5 (YDR079c-a) Knockout Study

status: Public on Jun 28 2004

city: Seattle

first: Bruz

last: Marzolf

state: WA

institute: Institute for Systems Biology

summary:
RNA expression analysis of polyA+ RNA isolated from a TFB5 (YDR079c-a) deletion strain and an isogenic wild type strain.
Comparison of RNA expression levels in TFB5 deletion strain compared to a wild type strain at 30C in YPD medium
Keywords: repeat sample

first: Jeffrey

middle: A

last: Ranish

first: Steven

last: Hahn

first: Yu

first: Eugene

middle: C

last: Yi

first: Xiao-jun

last: Li

first: Jimmy

last: Eng

first: Ruedi

last: Aebersold


title: In vivo selection of diverging tumor phenotypes

status: Public on Jul 02 2004

city: Bar Harbor

first: Janet

last: Pereira

state: ME

address: 600 Main St.

department: Gene Expression Service

institute: The Jackson Laboratory

summary:
Mammary carcinomas arising in mice transgenic for c-Myc gave were selected in vivo for the following phenotypes: (1) glandular carcinomas; (2) solid /comedo carcinomas; (3) solid/comedo carcinomas with metastases; (4) spindle cell carcinomas. Gene arrray were ran on 5-6 tumors from each of these groups.
Keywords = In vivo selection
Keywords = transgenic
Keywords = mouse
Keywords = mammary
Keywords = breast
Keywords: other

first: Igor

last: Mikaelian


title: MADSCAN evaluation using heart disease patients

first: Nolwenn

last: Le Meur

summary:
Data set for microarray data processing tool evaluation.
Patients affected by valvular heart disease and coronary artery disease, or idiopathic dilated cardiomyopathy.
Keywords = Myochip
Keywords = MADSCAN
Keywords: other

first: Guillaume

last: Lamirault


title: LEAFY-GR time-course experiment in callus

first: Frank

last: Wellmer

state: CA

summary:
Callus derived from 35S:LFY-GR plants was treated with dexamethasone- or was mock-treated for 0,2,4,6,8,10,12, or 22 hours. Four biologically independent sets of samples were generated and RNA probes derived from these samples were co-hybridized to a cDNA array enriched for flower-specific transcripts.
The data were analyzed with Rosetta Resolver as described in Wagner et al. (2004).
Keywords: time-course


title: GM00156 EMETINE TIME COURSE

status: Public on Jun 24 2004

city: Gaithersburg

first: Jeff

last: Kiefer

state: MD

address: 20 Firstfield Rd,  Suite 110

department: CDDL

institute: Translational Genomics Research Institute (TGen)

summary:
GM00156 (Coriell) cells were treated with and without 100?g/ml Emetine Dihydrochloride Hydrate (Fluka, Buchs, Swizerland).  Both Emetine-treated and untreated control cells were then incubated at 37°C for 10 hours. After the incubation, the first time point (0 min) was harvested for both treated and untreated cells. Simultaneously, Actinomycin D (Sigma-Aldrich, St Louis, MO) with the final concentration of 5ug/ml, was added to the remaining treated and untreated cells to stop new transcription. Time points of 10min, 30min, 1h, and 8h were harvested in both groups for most of the cell lines. Cell pellets were snap-frozen and mRNA extracted by using FastTrack kit (Invitrogen) according to the manufacturer’s instructions.
For each time point, the untreated sample was hybridized against the Emetine-treated equivalent. Four ug of untreated mRNA was labeled with Cy5-dUTP and four ug of Emetine-treated mRNA with Cy3-dUTP (Amersham Biosciences, Piscataway, NJ) as previously described (Mousses et al, 2000). Image analysis was done by DeArray software. Average intensities of the tumor samples were divided by the average intensities of the reference sample at each microarray spot after background intensity subtraction. Within-slide normalization was performed with ratio statistics method using housekeeping genes as described previously (Chen et al, 1997). The data were quality filtered with ratio quality method (Chen et al, 2002), which computes a quality value for each ratio. The scale for the quality values is from zero (poor quality) to one (good quality). Here, all ratios having quality value below 0.5 were discarded from the subsequent analysis.
Keywords: time-course


title: LNCaP EMETINE TIME COURSE

summary:
LNCaP prostate cancer cells were treated with and without 100?g/ml Emetine Dihydrochloride Hydrate (Fluka, Buchs, Swizerland).  Both Emetine-treated and untreated control cells were then incubated at 37°C for 10 hours. After the incubation, the first time point (0 min) was harvested for both treated and untreated cells. Simultaneously, Actinomycin D (Sigma-Aldrich, St Louis, MO) with the final concentration of 5ug/ml, was added to the remaining treated and untreated cells to stop new transcription. Time points of 10min, 30min, 1h, 2h, and 4h were harvested in both groups for most of the cell lines. Cell pellets were snap-frozen and mRNA extracted by using FastTrack kit (Invitrogen) according to the manufacturer’s instructions.
For each time point, the untreated sample was hybridized against the Emetine-treated equivalent. Four ug of untreated mRNA was labeled with Cy5-dUTP and four ug of Emetine-treated mRNA with Cy3-dUTP (Amersham Biosciences, Piscataway, NJ) as previously described (Mousses et al, 2000). Image analysis was done by DeArray software. Average intensities of the tumor samples were divided by the average intensities of the reference sample at each microarray spot after background intensity subtraction. Within-slide normalization was performed with ratio statistics method using housekeeping genes as described previously (Chen et al, 1997). The data were quality filtered with ratio quality method (Chen et al, 2002), which computes a quality value for each ratio. The scale for the quality values is from zero (poor quality) to one (good quality). Here, all ratios having quality value below 0.5 were discarded from the subsequent analysis.
Keywords: time-course


status: Public on Jul 01 2004

first: Timothy

middle: Richard

last: Hughes

address: 112 College St.

department: Banting and Best Department of Medical Research

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
Exploration of essential gene functions via titratable promoter alleles.
Collection of microarray experiments described in Mnaimneh et al. 2004.
Keywords = Yeast
Keywords = Saccharomyces cerevisiae
Keywords = oligonucleotide
Keywords = dual channel
Keywords: other


title: Mammary carcinomas in c-Myc transgenic mice

status: Public on Jun 27 2004

summary:
We compared gene microarray data of mammary carcinomas arising in mice transgenic for the myelocytomatosis oncogene (c-Myc). These neoplasms belonged to three groups: (1) the first group was composed of neoplasms that were exclusively comprised of neoplastic cells with an epithelial phenotype (n=5); (2) the second group was composed of neoplasm that were almost entirely composed of cells with an epithelial phenotype and that also contain minute areas of epithelial to mesenchymal transition (n=5); the third group was composed of neoplasms that contained areas of epithelial to mesenchymal transition that accounted for >10% of these neoplasms (n=5). A neoplasm composed exclusively of cells with an epithelial phenotype was subsequently excluded from the first group based on gene array data that indicated a salivary origin for this neoplasm.
Keywords: parallel sample


title: Time course of glycine addition or withdrawal

first: Andy

middle: L

last: Bognar

state: Ontario

summary:
+Gly 20, 40, 80: Cells were grown to early log phase (OD600 ~ 0.2) at 30oC in 1 liter of minimal B medium (Cherest, H., and Surdin-Kerjan, Y. (1992) Genetics 130, 51-58) and t=0 time point samples were harvested (250 ml). The remainder of the medium was supplemented with 10 mM glycine incubated at 30oC and samples (250 ml) harvested at 20, 40 and 80 minutes. All cells were harvested by rapid centrifugation at room temperature then flash frozen in liquid nitrogen.
-Gly 20, 40, 80: Cells were grown to early log phase (OD600 ~ 0.2) at 30oC in 1 liter of minimal B medium (Cherest, H., and Surdin-Kerjan, Y. (1992) Genetics 130, 51-58) supplemented with 10 mM glycine and t=0 time point samples were harvested (250 ml). The remainder of the medium was filtered and the cells were rapidly resuspended in 750 ml of pre-warmed B minimal medium, incubated at 30oC and samples (250 ml) harvested at 20, 40 and 80 minutes. All cells were harvested by rapid centrifugation at room temperature then flash frozen in liquid nitrogen.
Keywords: time-course

first: Jonathan

last: Lalich


title: PC3 EMETINE TIME COURSE

summary:
PC3 prostate cancer cells were treated with and without 100?g/ml Emetine Dihydrochloride Hydrate (Fluka, Buchs, Swizerland).  Both Emetine-treated and untreated control cells were then incubated at 37°C for 10 hours. After the incubation, the first time point (0 min) was harvested for both treated and untreated cells. Simultaneously, Actinomycin D (Sigma-Aldrich, St Louis, MO) with the final concentration of 5ug/ml, was added to the remaining treated and untreated cells to stop new transcription. Time points of 10min, 30min, 1h, 2h, and 4h were harvested in both groups for most of the cell lines. Cell pellets were snap-frozen and mRNA extracted by using FastTrack kit (Invitrogen) according to the manufacturer’s instructions.
For each time point, the untreated sample was hybridized against the Emetine-treated equivalent. Four ug of untreated mRNA was labeled with Cy5-dUTP and four ug of Emetine-treated mRNA with Cy3-dUTP (Amersham Biosciences, Piscataway, NJ) as previously described (Mousses et al, 2000). Image analysis was done by DeArray software. Average intensities of the tumor samples were divided by the average intensities of the reference sample at each microarray spot after background intensity subtraction. Within-slide normalization was performed with ratio statistics method using housekeeping genes as described previously (Chen et al, 1997). The data were quality filtered with ratio quality method (Chen et al, 2002), which computes a quality value for each ratio. The scale for the quality values is from zero (poor quality) to one (good quality). Here, all ratios having quality value below 0.5 were discarded from the subsequent analysis.
Keywords: time-course


title: MeJA treatment in sugarcane

status: Public on Jul 23 2004

city: Campinas

first: Vicente

middle: Eugenio

last: De Rosa Junior

state: SP

department: CBMEG

country: Brazil

institute: Unicamp

summary:
Using nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp.) exposed to the phytormone methyl jasmonate (MeJA) for 0-12 h. 26 ESTs were differentially expressed, including novel genes and also genes that had not previously been reported as being MeJA-inducible. Data are for two independent experiments.
Keywords = sugarcane
Keywords = methyl jasmonate
Keywords = nylon arrays
Keywords: time-course

first: VICENTE

last: de Rosa Jr

first: FABIO

middle: T

last: Nogueira

first: MARCELO

last: Menossi

first: EUGENIO

last: Ulian

first: PAULO

last: Arruda


title: Gene expression profile of abf1-1 mutant at 36 degrees C

status: Public on Jun 23 2004

city: Charlottesville

first: Tsuyoshi

last: Miyake

state: VA

address: 1300 Jefferson Park Ave.

department: Biochemistry & Molecular Genetics

institute: Univ. Virginia

summary:
The abf1-1 mutant and wild type cells were grown at 30 degrees C in YPAD until OD600 reached 1.0-1.2. The same volume of 42 degrees C preheated YPAD was added for each flask. After 45 min incubation at 36 degrees C, cells were harvested and RNA was isolated. Four repeats of microarray results are in this series.
Keywords: repeat sample

first: Justin

last: Reese

first: Christian

last: Loch

first: David

last: Auble

first: Rong

last: Li


title: EV110+111, Histone 3 Lysine 9 methylation in ddm1 Arabidopsis thaliana seedlings

status: Public on Jun 12 2004

city: Austin

first: Matthew

middle: Wayne

last: Vaughn

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

type: Genome binding/occupancy profiling by genome tiling array

summary:
This is a biological replicate of EV59+60.
The purpose of the chromatin immunoprecipitation/microarray (ChIP/chip) experiment is to determine which regions of a genome are enriched for a particular histone modification in a single Arabidopsis thanliana genotype.
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) or dimethyl histone-H3 lysine-4 (H3mK4) is performed on a selected genotype.  This purified DNA from each immunoprecipiation (mH3K9, mH3K4, no antibody control) is used for random amplification to increase the quantity of DNA for microarray hybridization.
The amplified DNA from each experimental sample is then labeled with Cy5 and hybridized against total input DNA from the corresponding genotype, labeled in Cy3.  In a single hybridization, the total input DNA serves as a baseline and is compared to the immunoprecipitated samples. Ratios of normalized signal intensities were calculated to identify enrichment of a particular sequence after immunoprecipitation, in comparison to the total input DNA. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
The two samples in this series are complementary hybridizations in a dye-swap analysis.
These data were normalized and subjected to hypothesis testing. Error rate was controlled by Benjamini and Hochberg's step-up procedure for limiting the False Discovery Rate.

Wild-type seedlings, 9 days old
This is the normalized result of the paired dye swap samples EV110 and EV111.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using false discovery rate (FDR) controlling methods. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found after hypothesis-testing with a controlled error rate to be significantly enriched or depleted for H3K9 methylation compared to mean values found in euchromatic regions are flagged in the column. No family-wise error rate methods were used to analyze this sample.
Keywords: other

first: Zachary

last: Lippman

first: Anne-Valerie

last: Gendrel

first: Mik

last: Black

middle: W


title: Histone 3 Lysine 9 methylation in wild-type Arabidopsis thaliana seedlings

summary:
This is a biological replicate of EV51+52.
The purpose of the chromatin immunoprecipitation/microarray (ChIP/chip) experiment is to determine which regions of a genome are enriched for a particular histone modification in a single Arabidopsis thanliana genotype.
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) or dimethyl histone-H3 lysine-4 (H3mK4) is performed on a selected genotype.  This purified DNA from each immunoprecipiation (mH3K9, mH3K4, no antibody control) is used for random amplification to increase the quantity of DNA for microarray hybridization.
The amplified DNA from each experimental sample is then labeled with Cy5 and hybridized against total input DNA from the corresponding genotype, labeled in Cy3.  In a single hybridization, the total input DNA serves as a baseline and is compared to the immunoprecipitated samples. Ratios of normalized signal intensities were calculated to identify enrichment of a particular sequence after immunoprecipitation, in comparison to the total input DNA. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
The two samples in this series are complementary hybridizations in a dye-swap analysis
These data were normalized and subjected to hypothesis testing. Error rate was controlled by Benjamini and Hochberg's step-up procedure for limiting the False Discovery Rate.

Wild-type seedlings, 9 days old
This is the normalized result of the paired dye swap samples EV108 and EV109.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using false discovery rate (FDR) controlling methods. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found after hypothesis-testing with a controlled error rate to be significantly enriched or depleted for H3K9 methylation compared to mean values found in euchromatic regions are flagged in the column. No family-wise error rate methods were used to analyze this sample.
Keywords: other


title: DU 145 EMETINE TIME COURSE

first: Jeff

last: Kiefer

summary:
DU 145 prostate cancer cells were treated with and without 100?g/ml Emetine Dihydrochloride Hydrate (Fluka, Buchs, Swizerland).  Both Emetine-treated and untreated control cells were then incubated at 37°C for 10 hours. After the incubation, the first time point (0 min) was harvested for both treated and untreated cells. Simultaneously, Actinomycin D (Sigma-Aldrich, St Louis, MO) with the final concentration of 5ug/ml, was added to the remaining treated and untreated cells to stop new transcription. Time points of 10min, 30min, 1h, 2h, 4h and 8h were harvested in both groups for most of the cell lines. Cell pellets were snap-frozen and mRNA extracted by using FastTrack kit (Invitrogen) according to the manufacturer’s instructions.
For each time point, The untreated sample was hybridized against the Emetine-treated equivalent. Four ug of untreated mRNA was labeled with Cy5-dUTP and four ug of Emetine-treated mRNA with Cy3-dUTP (Amersham Biosciences, Piscataway, NJ) as previously described (Mousses et al, 2000). Image analysis was done by DeArray software. Average intensities of the tumor samples were divided by the average intensities of the reference sample at each microarray spot after background intensity subtraction18. Within-slide normalization was performed with ratio statistics method using housekeeping genes as described previously (Chen et al, 1997). The data were quality filtered with ratio quality method (Chen et al, 2002), which computes a quality value for each ratio. The scale for the quality values is from zero (poor quality) to one (good quality). Here, all ratios having quality value below 0.5 were discarded from the subsequent analysis.
Keywords: time-course


title: Total-body irradiation dose response

status: Public on Jun 17 2004

city: New York

first: Sally

last: Amundson

department: Center for Radiological Research

institute: Columbia University

summary:
Duplicate hybridizations with fluorochrome switching were performed following the first two fractions of total body irradiation for accumulated doses of 1.5 Gy and 3.0 Gy.  Control samples for all hybridizations were from the same patient before the beginning of treatment.
Keywords: dose response

first: Marcy

last: Grace

first: Christopher

last: McLeland

first: Michael

last: Epperly

first: Andrew

last: Yeager

first: Qimin

last: Zhan

first: Joel

middle: S

last: Greenberger

first: Albert

middle: J

last: Fornace


title: EV59+60, Histone 3 Lysine 9 methylation in ddm1 Arabidopsis thaliana seedlings

summary:
The purpose of the chromatin immunoprecipitation/microarray (ChIP/chip) experiment is to determine which regions of a genome are enriched for a particular histone modification in a single Arabidopsis thaliana genotype.
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) or dimethyl histone-H3 lysine-4 (H3mK4) is performed on a selected genotype.  This purified DNA from each immunoprecipiation (mH3K9, mH3K4, no antibody control) is used for random amplification to increase the quantity of DNA for microarray hybridization.
The amplified DNA from each experimental sample is then labeled with Cy5 and hybridized against total input DNA from the corresponding genotype, labeled in Cy3.  In a single hybridization, the total input DNA serves as a baseline and is compared to the immunoprecipitated samples. Ratios of normalized signal intensities were calculated to identify enrichment of a particular sequence after immunoprecipitation, in comparison to the total input DNA. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
The two samples in this series are complementary hybridizations in a dye-swap analysis
These data were normalized and subjected to hypothesis testing. Error rate was controlled by Benjamini and Hochberg's step-up procedure for limiting the False Discovery Rate.

Ddm1 seedlings, 9 days old
This is the normalized result of the paired dye swap samples EV59 and EV60.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using false discovery rate (FDR) controlling methods. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found after hypothesis-testing with a controlled error rate to be significantly enriched or depleted for H3K9 methylation compared to mean values found in euchromatic regions are flagged in the column. No family-wise error rate methods were used to analyze this sample.
Keywords: other


title: EV51+52, Histone 3 Lysine 9 methylation in wild-type Arabidopsis thaliana seedlings

summary:
The purpose of the chromatin immunoprecipitation/microarray (ChIP/chip) experiment is to determine which regions of a genome are enriched for a particular histone modification in a single Arabidopsis thaliana genotype.
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) or dimethyl histone-H3 lysine-4 (H3mK4) is performed on a selected genotype.  This purified DNA from each immunoprecipiation (mH3K9, mH3K4, no antibody control) is used for random amplification to increase the quantity of DNA for microarray hybridization.
The amplified DNA from each experimental sample is then labeled with Cy5 and hybridized against total input DNA from the corresponding genotype, labeled in Cy3.  In a single hybridization, the total input DNA serves as a baseline and is compared to the immunoprecipitated samples. Ratios of normalized signal intensities were calculated to identify enrichment of a particular sequence after immunoprecipitation, in comparison to the total input DNA. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
The two samples in this series are complementary hybridizations in a dye-swap analysis
These data were normalized and subjected to hypothesis testing. Error rate was controlled by Benjamini and Hochberg's step-up procedure for limiting the False Discovery Rate.

Wild-type seedlings, 9 days old.
This is the normalized result of the paired dye swap samples EV51 and EV52.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using false discovery rate (FDR) controlling methods. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found after hypothesis-testing with a controlled error rate to be significantly enriched or depleted for H3K9 methylation compared to mean values found in euchromatic regions are flagged in the column. No family-wise error rate methods were used to analyze this sample.
Keywords: other


title: Molecular mechanisms in Day 11 and Day 12 pre-implantation porcine embryos

city: Beltsville

first: Jane

middle: Garlow

last: McDougal

address: 10300 Baltimore Avenue, BARC-East, Bldg 200, Rm 101A

department: USDA

institute: ANRI

summary:
Comparison of gene expression in in vivo derived pre-implantation porcine embryos in order to define molecular mechanisms involved in embryo development.
Keywords: parallel sample

first: Le Ann

last: Blomberg

first: Kurt

last: Zuelke


title: EV104+105, Histone 3 Lysine 4 methylation in ddm1 Arabidopsis thaliana seedlings

summary:
This series is a biological replicate of EV55+56
The purpose of the chromatin immunoprecipitation/microarray (ChIP/chip) experiment is to determine which regions of a genome are enriched for a particular histone modification in a single Arabidopsis thanliana genotype.
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) or dimethyl histone-H3 lysine-4 (H3mK4) is performed on a selected genotype.  This purified DNA from each immunoprecipiation (mH3K9, mH3K4, no antibody control) is used for random amplification to increase the quantity of DNA for microarray hybridization.
The amplified DNA from each experimental sample is then labeled with Cy5 and hybridized against total input DNA from the corresponding genotype, labeled in Cy3.  In a single hybridization, the total input DNA serves as a baseline and is compared to the immunoprecipitated samples. Ratios of normalized signal intensities were calculated to identify enrichment of a particular sequence after immunoprecipitation, in comparison to the total input DNA. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
The two samples in this series are complementary hybridizations in a dye-swap analysis
These data were normalized and subjected to hypothesis testing. Error rate was controlled only by Benjamini and Hochberg's step-up procedure for limiting the False Discovery Rate.

Ddm1 seedlings, 9 days old.
This is the normalized result of the paired dye swap samples EV104 and EV105.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using false discovery rate (FDR) controlling methods. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found after hypothesis-testing with a controlled error rate to be significantly enriched or depleted for H3K4 methylation compared to mean values found in euchromatic regions are flagged in the FDR column. No family-wise error rate method was used to analyze this sample.
Keywords: other


title: Ev106+107, Histone 3 Lysine 4 methylation in WT Arabidopsis thaliana seedlings

summary:
This series is a biological replicate of EV49+50.
The purpose of the chromatin immunoprecipitation/microarray (ChIP/chip) experiment is to determine which regions of a genome are enriched for a particular histone modification in a single Arabidopsis thanliana genotype.
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) or dimethyl histone-H3 lysine-4 (H3mK4) is performed on a selected genotype.  This purified DNA from each immunoprecipiation (mH3K9, mH3K4, no antibody control) is used for random amplification to increase the quantity of DNA for microarray hybridization.
The amplified DNA from each experimental sample is then labeled with Cy5 and hybridized against total input DNA from the corresponding genotype, labeled in Cy3.  In a single hybridization, the total input DNA serves as a baseline and is compared to the immunoprecipitated samples. Ratios of normalized signal intensities were calculated to identify enrichment of a particular sequence after immunoprecipitation, in comparison to the total input DNA. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
The two samples in this series are complementary hybridizations in a dye-swap analysis
These data were normalized and subjected to hypothesis testing. Error rate was controlled only by Benjamini and Hochberg's step-up procedure for limiting the False Discovery Rate.

WT seedlings, 9 days old
This is the normalized result of the paired dye swap samples EV106 and EV107.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using false discovery rate (FDR) controlling methods. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found after hypothesis-testing with a controlled error rate to be significantly enriched or depleted for H3K4 methylation compared to mean values found in euchromatic regions are flagged in the FDR column. No family-wise error rate method was used to analyze this sample.
Keywords: other