title: folic acid

status: Public on May 08 2005

city: Wageningen

first: Linette

last: Pellis

address: Bornsesteeg 45

institute: RIKILT-Institute of Food Safety

summary:
Caco-2, HT29, CCD841CoTr exposed to 10ng/mL, 100ng/mL and 4000ng/mL folic acid
Keywords: dose response


title: Effects of T3 on liver gene expression of wild type and TRbeta -/- mice

status: Public on May 04 2005

city: Stockholm

first: Amilcar

last: Flores

country: Sweden

institute: Karolinska Institute

summary:
Hypothyroids wild type and TRbeta -/- mice were treated with T3 and livers were collected and analysed using a microarray with 6500 cDNA probes. Expression ratios were calulated between 1) hypothyroids WT and TRbeta-/- mice 2) hypothyroid WT and hypothyroid TR beta-/- mice treated with T3 and 3) hypothyroid TRbeta-/- and hypothyroid TRbeta-/- treated with T3.
Keywords: other


title: Gene expression profile of human heart failure from different etiologies

status: Public on May 14 2005

city: Camperdown, Sydney

first: Masako

last: Tsubakihara

state: New South Wales, Australia

address: MRU, W103 Anderson Stuart Bldg (F13), Institute for Biomedical Research, University of Sydney

country: Australia

institute: University of Sydney

summary:
The goal of this experiment was to identify gene expression changes that are common in different heart failure (HF) types or specific to an etiology of HF. HF groups studied include doxorubicin induced cardiomyopathy, familial dilated cardiomyopathy, hypertrophic cardiomyopathy, idiopathic dilated cardiomyopathy, ischemic heart disease, peripartum cardiomyopathy, and viral induced cardiomyopathy.

Non-diseased left ventricles (LV) were obtained from donor hearts not used for transplantation (these were considered to be unsuitable for transplantation for a variety of reasons including the lack of a tissue-compatible recipient). Failing LV were obtained from patients undergoing heart transplantation. Transmural sections of LV anterior free wall were trimmed of fat, dissected into 1-1.5 gm pieces, and immediately frozen in the operating theater. 100-200 mg of frozen transmural LV was ground to a fine powder in liquid nitrogen using a mortar and pestle. Then total RNA was isolated by a method described by Wei and Khan (A Molecular Cloning Manual). The purity of the RNA extract was assessed by measuring the absorbance at 260 nm and 280 nm. Its quantity and integrity was then examined using RNA Nano Chips on a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). 10 ?g of RNA extracts and a universal human reference RNA (Stratagene, La Jolla, CA, USA) were reverse transcribed with Cy3-dUTP and Cy5-dUTP, respectively, to produce labeled cDNA probes using Thermoscript reverse transcriptase according Hwang JJ et. al. (Physiological Genomics 10: 31-44, 2002). Raw scanned images were processed using ScanAlyze version 2.50 (Michael Eisen, Stanford University, CA, USA). Cy3 and Cy5 scans were superimposed, local backgrounds were subtracted, and the fluorescence intensities of each spot were quantified. All further analyses of CardioChips were done using GeneSpring version 6.1 (Silicon Genetics, Redwood City, CA, USA). The data from each array was normalized first to the reference RNA and then a LOWESS curve was fit to the log-intensity versus log-ratio plot for each array and for each gene across all experiments. 40.0% of the data was used to calculate the LOWESS fit at each point. Differentially expressed genes in each HF group compared to donor hearts were identified by a one-way ANOVA test (P <0.05) with the benjamini and hochberg multiple testing corrections and we selected those genes with an average difference greater than 1.5 fold. A hierarchical clustering analysis was performed using pearson correlation with the separation ratio of 1.0 and minimum distance of 0.001 as similarity measure.

Using a cardiovascular-specific gene array (CardioChip) of 42 heart failure (HF) patients from a wide range of etiology groups and 8 non-failing donors, we have identified down-regulation of LIM domain protein which may be an important pathway for the clinical progression of HF. We identified six genes, encoding LIM domain and Homer proteins, that are down-regulated in terminally failing hearts. The LIM and cysteine rich domain 1 (LMCD1) gene, in particular, was significantly down-regulated in all HF samples. This novel finding suggests that the LMCD 1 is a universal biomarker for end-stage HF.  Other LIM domain genes were also down-regulated but only in non-familial dilated forms of cardiomyopathy. This is probably due to the fact that down-regulation of LIM protein expression may disrupt the cytoskeletal architecture, leading to dilated cardiomyopathy. In addition to identifying the LIM domain genes as possible regulatory genes involved in HF, we also demonstrated that the gene expression profile was able to classify multiple HF patients groups. This paper is the first to examine viral-induced cardiomyopathy, doxorubicin toxicity cardiomyopathy and perimartum cardiomyopathy and to perform the clustering analysis of those HF types providing new insights into human HF.
Keywords: other

first: Paul

middle: D

last: Allen

first: Cristobal

middle: G

last: dos Remedios

first: Victor

last: Dzau

first: C

middle: C

last: Liew


title: Gender differences in hepatic gene expression

summary:
Gene expression differences between mal and female rat livers (female/male).
Keywords: repeat sample


title: W23 and High altitude maize under solar and supplementary UV-B

status: Public on May 17 2005

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

summary:
Additional to GSE1807
A comparative analysis, by expression profiling of maize, was performed to identify novel components in the mechanisms of maize responses to UV-B. Five high-altitude landraces grown from 2,000 to 3,400 m naturally receive higher UV-B fluence than plants at lower altitudes and similar latitudes. These high-altitude landraces were compared directly with a low-altitude line and with literature reports for other temperate maize lines. A microarray analysis demonstrated that among the UV-B responsive transcripts, several types of gene implicated in chromatin remodeling are differentially expressed before and after UV-B treatment in high-altitude lines. RNAi transgenic plants with lower expression of four such chromatin-associated genes exhibited hypersensitivity to UV-B by measurements of leaf arching, increased leaf chlorosis and necrosis, and altered UV-B regulation of selected genes. These results collectively suggest that genes involved in chromatin remodeling are crucial for UV-B acclimation and that some high-altitude lines exhibit adaptations to this challenge.

first: Virginia

last: Walbot


title: Hepatic gene expression after minipump bGH treatment of male rats

summary:
male young rats treated with bGH (minipumps for a week before RNA was prepared from livers
Keywords: repeat sample


title: Serum Starvation/Refeeding RNA vs. RAP

city: San Diego

first: Yipeng

last: Wang

state: CA

country: USA

institute: Vaccine Research Institute of San Diego

summary:
Low abundance mRNAs are more difficult to examine using microarrays than high abundance mRNAs due to the effect of concentration on hybridization kinetics, signal-to-noise ratios, and interference between signals from mRNA isoforms. Individual sequences in LCRs are more highly represented than in the mRNA population from which they are derived, leading to favorable hybridization kinetics. LCR targets permit the measurement of abundance changes that are difficult to measure using oligo dT priming for target synthesis. An oligo dT-primed target and three LCRs detect twice as many differentially regulated genes as could be detected by the oligo dT-primed target alone, as serum-starved fibroblasts responded to the reintroduction of serum. Thus, this target preparation strategy considerably increases the sensitivity of spotted cDNA microarrays.
Keywords: parallel sample

first: Gaelle

last: Rondeau


title: Gene signature for relapse prediction in Dukes´B colon cancer

status: Public on May 07 2005

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

summary:
Purpose: The benefit of postoperative adjuvant chemotherapy in patients with Dukes´ B colorectal cancer is still uncertain and its routine use is not recommended. The five years survival rate is approximately 75% and identification of the patients at high risk of recurrence would represent an important strategy for the use of adjuvant chemotherapy.
In this study we identify new prognostic markers for tumor relapse in Dukes´ B colon cancer patients.
Patients and Methods: We retrospectively analyzed gene expression profiles in frozen tumor specimens from 16 patients with Dukes´ B colorectal cancer by using high density oligonucleotide microarrays. Data were normalized and subsequently analyzed with two different statistical procedures.  The intensity value associated to each spot is the result of subtracting a gaussian function of the noise from the foreground values {Kooperberg, 2002}. After this background subtraction, base 2 logarithms of all data were calculated and genes with more than two missing values were excluded from the analysis. The remaining missing values were replaced by using the KNN imputation method {Troyanskaya, 2001}.
The great number of genes present in the microarray allowed us to consider that the overall fluorescence intensity must be the same for all slides, as the vast majority of genes will not change their expression between the two conditions tested. So we used the quantile normalization method {Bolstad, 2003}, which equalizes not only the average intensity but also the range of intensity values between slides.
We decided to use two different statistical procedures in the search of significant differences in gene expression between the relapsed and non-relapsed  patients. Only the genes selected by both statistical procedures were considered as differentially expressed between relapsed and non-relapsed patients. The first test was a permutation t-test for comparison of two means {Dudoit, 2003} and the second one a variation of the Fisher test based on the work presented by Iizuka et al. {Iizuka, 2003} in which they searched for the optimal number of genes that could differentiate between two groups of samples. Briefly, we used the same algorithms for the calculation of the Fisher criterion, but instead of looking for the optimal subset of genes able to differentiate between groups, what requires a lot of computing capacity, we tried different numbers of candidate genes and selected a number which yielded very good classification results when evaluated by means of Fast ICA {Lee, 2003} and Hierarchical Clustering {Everitt, 1974}. The procedure consisted of selecting the 30 genes with the highest Fisher criterion value in 6 rounds of iteration, each round leaving one sample of the relapsed group and two of the non-relapsed group out of the calculations (a variant of the “leave one out” method). We selected the genes present in at least 3 of the iterations.
The intersection of the groups of genes selected by the two statistical procedures was selected as a prognostic signature for relapse in Dukes´stage B colon cancer.
Results: Our results show a group of 48 genes differentially expressed between the relapsed and non-relapsed groups with an associated probability below 0,001 in the t test. Another statistical  procedure based on the Fisher criterion resulted in 11 genes able to separate both groups. In order to minimize false positives we only considered a good gene signature the 8 genes selected by both statistical procedures. These genes are ribosomal protein S5, chromodomain helicase DNA binding protein 2, lysosomal ATPase V0 subunit A isoform 1, zinc finger protein 148, brain protein I3 (BRI3), hypothetical protein MGC23401 and one unknown clone. In order to verify the obtained results, the differential expression of the first two genes was confirmed by real time PCR.

Keywords: repeat sample

first: Eva

last: Bandrés

first: Elena

last: Cubedo

first: Jesús

last: Sola

last: García-Foncillas

first: Alberto

last: Labarga


title: Coho Salmon GH Transgenic Study

status: Public on May 01 2005

city: Milwaukee

first: Matthew

middle: Lawrence

last: Rise

state: WI

address: 600 E. Greenfield Ave.

department: Great Lakes WATER Institute

institute: University of Wisconsin - Milwaukee

summary:
Coho Salmon GH Transgenic Study
Keywords: other

platform_organism:
Oncorhynchus mykiss
Salmo salar

middle: L

first: Dionne

last: Sakhrani

first: Ben

middle: F

last: Koop

first: Robert

middle: H

last: Devlin


title: Agricultural sterol biosynthesis inhibitor fungicides

city: University

first: Isabelle

middle: Ann

last: Kagan

state: MS

address: University Ave.

department: US Department of Agriculture

institute: National Center for Natural Products Research

summary:
Resistance to agricultural fungicides in the field has created a need for discovering fungicides with new modes of action. DNA microarrays, because they provide information on expression of many genes simultaneously, could help to identify the modes of action. To begin an expression pattern database for agricultural fungicides, transcriptional patterns of Saccharomyces cerevisiae strain S288C genes were analysed following 2-h treatments with I50 concentrations of ergosterol biosynthesis inhibitors commonly used against plant pathogenic fungi. Eight fungicides, representing three classes of ergosterol biosynthesis inhibitors, were tested. To compare gene expression in response to a fungicide with a completely different mode of action, a putative methionine biosynthesis inhibitor (MBI) was also tested. Expression patterns of ergosterol biosynthetic genes supported the roles of Class I and Class II inhibitors in affecting ergosterol biosynthesis, confirmed that the putative MBI did not affect ergosterol biosynthesis, and strongly suggested that in yeast, the Class III inhibitor did not affect ergosterol biosynthesis. The MBI affected transcription of three genes involved in methionine metabolism, whereas there were essentially no effects of ergosterol synthesis inhibitors on methionine metabolism genes. There were no consistent patterns in other up- or downregulated genes between fungicides. These results suggest that inspection of gene response patterns within a given pathway may serve as a useful first step in identifying possible modes of action of fungicides.
agricultural sterol biosynthesis inhibitor fungicides.
Keywords = agriculture
Keywords = ergosterol
Keywords = methionine
Keywords = fungicide
Keywords = Saccharomyces cerevisiae S288C
Keywords = biosynthesis

middle: A

first: Albrecht

last: Michel

first: Anja

last: Prause

first: Brian

middle: E

last: Scheffler

first: Pat

last: Pace

first: Stephen

middle: O

last: Duke


title: Plasmodium falciparum W2/Dd2 Day 8 gametocytes

city: Rockville

first: Tetsuya

last: Furuya

state: MD

institute: National Institutes of Health

summary:
The sexual stages are vital phases in malaria parasite transmission and are the targets of various interventions such as transmission blocking vaccines. The molecular mechanisms underlying sexual development, however, remain poorly understood. We report mappping of a determinant previously linked to a male gametocyte development defect in the P. falciparum Dd2 parasite to an 82 kb region on chromosome 12. In order to find a critical gene in this region, we compared gene expression pattern in sexual stage of the parasite between Dd2 and its normal gametocyte-producing ancestor W2 clones. The region contains a sexual stage specific gene (pfmdv 1) that is expressed substantially at a lower level in the Dd2 than in W2 parasite. Disruption of pfmdv 1 results in a dramatic reduction in mature gametocytes, especially male gametocytes, with the majority of sexually committed parasites arrested at stage-I. The pfmdv-1 knockout parasites show an enlarged nucleus, often with separation of the inner and outer nuclear membranes and presence of multi-membrane vesicles in red blood cell cytoplasm. Mosquito infectivity of the knockout parasites is also greatly reduced, but not completely lost, suggesting presence of compensatory mechanisms in the sexual development pathways.
Data include Day 8 gametocytes of male defective Dd2 and parental W2 clones of Plasmodium falciparum. The series includes three biological repeats.
Keywords: repeat sample

first: Xin-zhuan

last: Su


title: Comparison analysis of rice and Arabidopsis photomorphogenesis

status: Public on May 02 2005

city: Pasadena

first: Yuling

last: Jiao

address: 1200 E California Blvd

department: Biology

institute: California Institute of Technology

summary:
Long oligonucleotide microarrays were used for the study of expression profile changes during seedling photomorphogenesis in rice and in Arabidopsis. Different light quality treatments were applied to seedlings. To dissect organ-specific light effects, we further profiled shoot and root organs in both species.
Keywords = rice
Keywords = Arabidopsis
Keywords = photomorphogenesis
Keywords: ordered

sample_organism:
Arabidopsis thaliana
Oryza sativa

platform_organism:
Arabidopsis thaliana
Oryza sativa

first: Ligeng

last: Ma

first: Xing-Wang

last: Deng


title: Effects of fescue toxicosis on rat hepatic tissue

status: Public on Apr 28 2005

city: Columbia

first: Raja

middle: S

last: Settivari

state: MO

address: 920 E Campus Drive

department: ASRC

institute: University of Missouri

summary:
Rats (n=24) were fed ad libitum diets containing either ground endophyte-free (E-) seed or endophyte–infected (E+) seed for five days at thermoneutrality (21°C).  Rats (n=24) with intraperitonial transmitters were used with core temperature (Tc) and general activity measured every 5 minutes during the study. At treatment end, the liver was removed, weighed and frozen in liquid nitrogen. Twelve rats were selected for microarray experiments, based on degree of sensitivity to fescue toxicosis.  Degree of sensitivity was based on changes in relative liver weights, feed intake, average daily gain, and Tc from pretreatment levels. RNA was extracted from liver samples, converted to cDNA, and hybridized with the printed oligonucleotide slides. The microarray data was analyzed using Wolfinger's two step ANOVA model.
Keywords: repeat sample

first: Eric

last: Antoniou

first: Leonard

middle: B

last: Hearne

first: Donald

last: Spiers


title: Neuroblastoma Neuro2A Cell Differentiation induced by retinoic acid-treatment

city: Kisarazu

first: Kazuhide

last: Imai

state: Chiba

address: 2-6-7 Kazusa-Kamatari

country: Japan

institute: Chiba Industry Advancement Center

summary:
To investigate a role of mKIAA genes in early stage of neurite outgrowth, in vitro time course experiment was performed using the mouse neuroblastoma Neuro2A cells and all-trans-retinoic acid. Six time points of 8 biological replicates were performed.These data were normalized by median intensities and subtracted background intensities. NOTE: Outlier involved several data were not deposited.
Keywords: time-course


title: Large-scale temporal gene expression profiling during gonadal differentiation and early gametogenesis in rainbow-trout

status: Public on Jun 01 2005

city: Rennes

first: Daniel

last: Baron

state: Brittany

department: Station Commune de Recherches en Ichtyophysiologie

country: France

institute: Institut National de la Recherche Agronomique-INRA

summary:
Animals and samplings:
Research involving animal experimentation has been approved by the author's institution (authorization number 35-14) and conforms to NIH guidelines. All-male and all-female rainbow trout populations were obtained from the INRA experimental fish farm (Drennec, France) using breeders from the Mirwart strain. At 55 days post-fertilization (55 dpf, i.e., the onset of the free swimming), a male and female batch of 1500 fry each were transferred in 0.3 m3 tanks with recirculating water conditions. They were held at 12°C under constant photoperiod (12h light : 12h dark) and fed ad libitum with a commercial diet (dry pellet food, BiomarTM, Brande, Denmark). In each group, from 20 to 100 gonads, depending on the age of the fish, were sampled and pooled in duplicates at various stages of development : the onset of the free swimming period after complete yolk resumption (Day 0 = D0), D7, D12 (around the first occurrence of oocyte meiosis), D27 (first ovarian lamellar structures), D60 (first previtellogenic oocytes), D90 and D110. There were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Additional gonads were sampled at the same dates for histological analysis performed as previously described.
Total RNA extraction and Reverse Transcription:
Total RNA was extracted using TRIzol reagent (Invitrogen, Cergy Pontoise, France). Total RNA concentration was determined with an Agilent 2100 Bioanalyzer and the RNA 6000 LabChip kit (Agilent Technologies, Stockport, UK) according to the manufacturer's instructions. For cDNA synthesis, 1µg of RNA was denaturated in the presence of random hexamers (0.5µg) for 5 min at 70°C, and then chilled on ice. Reverse transcription (RT) was performed at 37°C for 1 h using M-MLV reverse transcriptase (Promega, Madison, WI) as described by the manufacturer.
Primers design:
Trout candidate gene homologues were searched in international public databanks using a reciprocal blast hit strategy. Candidate genes were chosen according to a bibliographic analysis showing their direct or indirect involvement in the sex differentiation cascade in vertebrates. All the primers were purchased from Eurogentec (Eurogentec, Seraing, Belgium). These primers were manually designed respecting whenever possible the following restriction parameters : 21-23 bp length, no more than 4 identical successive nucleotides, 30-70% GC content, a maximum of 2 G or C among the five 3'-end bases, no primer dimers and a short amplicon size (70-150 bp). Secondary structures were searched with DNA mfold (http://bioinfo.math.rpi.edu/~mfold/DNA/form1.cgi). Whenever possible, each pair was chosen with at least one primer flanking an intron-exon boundary, in order to prevent genomic amplification.
Real-time RT-PCR
Real-time RT-PCR was carried out on an iCycler iQTM (BioRad, Hercules, CA). Reactions were performed in 20µl with 300nM of each primer, 5µl of a 1/50 dilution of the RT reaction and the SYBER-Green PCR master Mix (Eurogentec) according to the manufacturer's instructions. After two incubation steps (50°C 10 min, 95°C 2 min), the thermal cycling protocol was 95°C for 10 min followed by 40 cycles of PCR (95°C 30 s, 60°C or 65°C 1 min). For each primer set the efficiency of the PCR reaction (linear equation : y = slope + intercept) was measured in triplicate on serial dilutions of the same cDNA sample (pool of reverse transcribed RNA samples). Real-time PCR efficiencies for each reaction were then calculated using the formula : Efficiency (E)=[10(1/slope)]-1. Melting curve analysis was also performed for each gene to check the specificity and identity of the RT-PCR products. The relative amount of the target RNA called the Starting Quantity (SQ) was then determined using the I-Cycler IQ software by comparison with the corresponding standard curve for each sample run in duplicate. SQ were calculated as follow : SQ = [10((Ct -intercept)/slope))]-1 where Ct is the Cycle threshold of the unknown sample. Each transcript level was then normalized by division with the expression values of the constitutive elongation factor 1 alpha (EF1a) used as an internal standard.
Keywords: ordered

first: Remi

last: Houlgatte

first: Alexis

last: Fostier

first: Yann

last: Guiguen


city: Mountain View

first: Mark

last: Fielden

address: 325 East Middlefield Road

institute: Iconix Biosciences

summary:
Classification of a large micro-array dataset. Algorithm comparison and analysis of drug signatures.
These data support the publication titled "Classification of a large micro-array dataset. Algorithm comparison and analysis of drug signatures.". Some of the calculations in the publication were derived from an older version of the data available at http://www.iconixpharm.com
Copyright (c) 2005 by Iconix Pharmaceuticals, Inc.

Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf
Keywords: other

first: Georges

last: Natsoulis

first: Laurent

last: El Ghaoui

first: Gert

middle: R

last: Lanckriet

first: Alexander

middle: M

last: Tolley

first: Fabrice

last: Leroy

first: Shane

last: Dunlea

first: Barrett

middle: P

last: Eynon

first: Cecelia

middle: I

last: Pearson

first: Stuart

last: Tugendreich

first: Kurt

last: Jarnagin


title: underreplication

status: Public on Apr 22 2005

city: Novosibirsk

first: Stepan

last: Belyakin

country: Russia

institute: Institute of Cytology and Genetics

summary:
Identification of underreplicated areas in drosophila polytene chromosomes
Keywords: repeat sample

middle: N

first: George

middle: K

last: Christophides

first: Artyom

last: Alekseyenko

first: Evgenia

middle: V

last: Kriventseva

first: Elena

last: Belyaeva

first: Roman

last: Nanayev

first: Igor

last: Makunin

first: Heidelberg

last: Fly Array Consortium

first: Fotis

last: Kafatos

last: Zhimulev


status: Public on May 03 2005

city: La Jolla

first: Jennifer

last: Hammond

address: 10550 N. Torrey Pines Rd.

institute: The Scripps Research Institute

summary:
Activation of murine CD4+ and CD8+ T lymphocytes leads to dramatic remodeling of N-linked glycans.
Naïve and activated CD4 T cells, CD8 T cells and B cells were compared for their N-linked glycan structures by MALDI-TOF MS profiling and for expression of glycan transferase genes to assess the biosynthetic basis for any change observed.  The major change observed in activated CD4 and CD8 T cells was dramatic reduction of sialylated bi-antennary N-glycans carrying the terminal NeuGc?2-6Gal sequence, and corresponding increase in glycans carrying the Gal?1-3Gal sequence.  This change was accounted for by a decrease in the expression of the sialyltransferase ST6Gal, and increase in the expression of the galactosyltransferase ?1-3GalT.  Conversely, in B cells no change in terminal sialylation of N-linked glycans was evident, and the expression of the same two glycosyltransferases were increased and decreased, respectively.
Keywords = N-linked glycosylation, T cell, B cell, activation, glycosyltransferase, carbohydrate, glycomics, glycan, galactosyltransferase, sialyltransferase
Keywords: other

platform_organism:
Homo sapiens
Mus musculus

last: Comelli

first: Mark

last: Sutton-Smith

first: Qi

last: Yan

first: Margarida

last: Amado

first: Maria

last: Panico

first: Tim

last: Gilmartin

first: Thomas

last: Whisenant

first: Caroline

last: Lanigan

first: Steven

last: Head

first: David

last: Goldberg

first: Howard

last: Morris

first: Anne

last: Dell

first: James

middle: C

last: Paulson


title: Gene expression and phenotypic characterization of mouse heart after chronic constant or intermittent hypoxia

status: Public on Apr 18 2005

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

summary:
Chronic constant hypoxia (CCH), such as in pulmonary diseases or high altitude, and chronic intermittent hypoxia (CIH), such as in sleep apnea, can lead to major changes in the heart. The molecular mechanisms underlying these cardiac alterations are not well understood. We hypothesized that analysis on the changes in gene expression could help to delineate such mechanisms. In addition, the differences that can be anticipated between CCH and CIH could be potentially dissected.  Current study used CCH and CIH mouse models combined with cDNA microarrays to determine the changes of gene expression in CCH or CIH mice heart.
Keywords = heart
Keywords = hypoxia
Keywords = mouse
Keywords = microarray
Keywords: time-course

first: Chenghao

last: Fan

first: Dumitru

last: Iacobas

first: Qiaofang

last: Chen

last: Lai

first: Orit

last: Gavrialov

first: Gabriel

middle: G

last: Haddad


title: Exploring functional relationships between components of the gene expression machinery

status: Public on Jun 13 2005

city: Santa Cruz

first: Todd

last: Burckin

address: 1156 High Street

department: Molecular, Cell, & Developmental Biology

institute: University of California Santa Cruz

summary:
Splicing and expression analysis of a collection of 80 different mutations to the gene expression pathway in yeast
Keywords: other

first: Roland

last: Nagel

first: Yael

last: Mandel-Gutfreund

first: Lily

last: Shiue

first: Tyson

last: Clark

first: Jean-Leon

last: Chong

first: Tien-Hsien

last: Chang

first: Sharon

last: Squazzo

first: Grant

last: Hartzog

first: Manuel

last: Ares Jr.


title: Primary human neuroblastoma

status: Public on May 12 2005

city: Chiba

first: Akira

last: Nakagawara

address: 666-2 Nitona, Chuo-ku

institute: Chiba Cancer Center Research Institute

summary:
Reference1:
Ohira M, Oba S, Nakamura Y, Isogai E, Kaneko S, Nakagawa A, Hirata T, Kubo H, Goto T, Yamada S, Yoshida Y, Fuchioka M, Ishii S, Nakagawara A.
Expression profiling of human primary
Expression profiling using a tumor-specific cDNA microarray predicts the prognosis of intermediate risk neuroblastomas.
Cancer Cell. 2005 Apr;7(4):337-50.

To predict the prognosis of neuroblastoma patients and choose a better therapeutic protocol, we developed a cDNA microarray carrying 5340 genes obtained from primary neuroblastomas and examined 136 tumor samples. We made a probabilistic output statistical classifier that provided a high accuracy in prognosis prediction (89% at 5 years) and a highly reliable method to validate it. Kaplan-Meier analysis indicated that the patients in an intermediate group defined by existing markers are divided by microarray into two further groups with 5 year survivals for 36% and 89% of patients (p < 10(-4)), i.e., with unfavorably and favorably predicted neuroblastomas, respectively. According to these results, we developed a gene subset chip for a clinical tool, for which our classifier exhibited 88% prediction accuracy.

Datasets:
neuroblastomas by CCC-NB200-Chip: GSM42338-GSM42387

Expression profiling of human primary neuroblastomas by CCC-NB5000-Chip: GSM42391-GSM42526
Keywords = Neuroblastoma
Keywords: other

first: Miki

last: Ohira

first: Shigeyuki

last: Oba

first: Yohko

last: Nakamura

first: Eriko

last: Isogai

first: Setsuko

last: Kaneko

first: Atsuko

last: Nakagawa

first: Takahiro

last: Hirata

first: Hiroyuki

last: Kubo

first: Takeshi

last: Goto

first: Saichi

last: Yamada

first: Yasuko

last: Yoshida

first: Misa

last: Fuchioka

first: Shin

last: Ishii


title: miRNA combined

status: Public on May 11 2005

city: New Haven

first: Jun

last: Lu

state: CT

address: 10 Amistad St

department: Yale Stem Cell Center and Department of Genetics

institute: Yale University

summary:
miRNA expression data for the "MicroRNA expression profiles classify human cancers".
Keywords = miRNA
Keywords = microRNA
Keywords = normal
Keywords = tumor
Keywords = cell-line
Keywords = cancer
Keywords: other

sample_organism:
Homo sapiens
Mus musculus

first: Gad

last: Getz

first: Eric

last: Miska

first: Ezequiel

last: Alvarez-Saavedra

first: Justin

last: Lamb

first: David

last: Peck

first: Alejandro

last: Sweet-Cordero

first: Benjamin

middle: L

last: Ebert

first: Raymond

last: Mak

first: Adolfo

last: Ferrando

first: James

last: Downing

first: Tyler

last: Jacks

first: H

last: Horvitz

first: Todd

last: Golub

middle: Robert


title: Gene expression profiling of NOD mice and related congenic mice

status: Public on Apr 14 2005

city: Nashville

first: Zheng

last: Liu

state: TN

institute: Vanderbilt University

summary:
Functional liability conferred by gene expression profile can be a possible basis for diseases phenotype. By comparing gene expression profiles in splenic T cells from NOD, C57BL/6 mice and their congenic strains with altered MHCs (NOD.H2^h4 , B6.NOD/Idd1,5/), we identified that the NOD splenic T cells have a strain dependent, tissue specific unique gene expression profile that  can be but not necessarily be modulated by alternation of MHC. The NOD splenic T cells gene expression profile indicated a deregulated stress response system, especially heat shock protein family. We demonstrated that NOD splenic T cells have apoptosis defect in vivo and in vitro. Therefore, the gene expression profile may confer liability upon NOD splenic T cells to make them more susceptible to apoptosis, which can be a critical factor to lead to NOD lymphopenia. As recently described, compensatory homeostatic proliferation, driven by lymphopenia, generates autoimmunity in the NOD mouse.
Keywords: other

first: Thomas

last: Aune


title: mCGH of cervical cancer

status: Public on Apr 13 2005

city: New York

first: Veronique

last: Bourdon

state: NY

department: Human Genetics

institute: Memorial Sloan Kettering Cancer Center

summary:
Genomic alteration of cervical cancer samples.
Analysis by CGH array. Array spotted at AECOM (NY) with human ESTs.
Analysis as in Bourdon et al. Cancer Res. 2002 Nov 1;62(21):6218-23
Keywords: parallel sample


title: SAGE Profiles of Rat Lung Tissues

status: Public on Apr 09 2005

city: Shanghai

first: Yong Qing

last: Yang

address: 650 South Wanping Rd

department: Shanghai Research Institute of Acupuncture

country: China

institute: Shanghai University of Traditional Chinese Medicine

summary:
Thirty-two SD rats (male, 150 grams, 50days) were randomly divided into four groups: normal control group, asthma group, acupuncture-treated asthma group and acupuncture-treated normal group. The rat lungs were removed immediately after the rats were died. The rat lungs were conserved in liquid nitrogen. SAGE analyses were dependent on the classic protocol (Velculescu VE, et al, Serial Analysis of Gene Expression Detailed Protocol, version 1.0e, 2000) available at the SAGENET website.
Keyword = Rat
Keyword = Lung
Keyword = Asthma
Keyword = SAGE
Keyword = Acupuncture
Keywords: disease state analysis

first: Yong-Qing

first: Yan

last: Wang

first: Gong-Hao

last: Jiang

first: Ping

last: Wan

first: Yu

first: Yan-Yan

first: Wei-Rong

last: Jin

first: Lei-Jun

last: Zhuang


title: Effects of mutation in a soluble guanylyl cyclase gene

city: Mississauga

first: Zak

last: Razak

state: ON

address: 3359 Mississauga Road

department: Zoology Department

country: Canada

institute: University of Toronto

summary:
Genomic and behavioral investigations were performed to determine the effects of a mutation in a Drosophila soluble guanylyl cyclase gene.

A mutant DGCalpha1[3] third chromosome was crossed into a natural rover (for[R]) or natural sitter (for[s]) genetic background. (See Osborne et al. 1997; PMID: 9242616.) First instar larvae were collected and grown on 60mm Petri plates containing 10 mL of food until mid-third instar. (Approximate density was 3 animals per mL food). Larvae were collected and washed quickly with distilled water and were flash frozen in liquid nitrogen. Co-reared larvae were tested for behavioural effects.  Four independent collections were made for each of the two conditions (Rover_DGCalpha1[3] or sitter_DGCalpha1[3]).
Keywords = Drosophila
Keywords = foraging
Keywords = behavior
Keywords = cGMP
Keywords = guanylyl cyclase
Keywords = genetic background
Keywords: other

first: Craig

last: Riedl

first: Scott

middle: J

last: Neal

first: Alain

last: Robichon

first: J

middle: T

last: Westwood

first: Marla

last: Sokolowski


title: Multiple Lab Comparison of Microarray Platforms

status: Public on Apr 12 2005

city: Baltimore

first: Rafael

last: Irizarry

institute: Johns Hopkins University

summary:
A consortium of ten labs from the DC and Baltimore area was formed to compare three leading platforms. Each lab was given identical RNA samples (A1 and B1) which were processed according to what each lab considered best practice. Five of the labs used Affymetrix GeneChips, three used two-color spotted cDNA arrays, and two used two-color long oligo arrays.
Keywords: repeat sample

middle: A


title: Tiling microarray analysis of japonica and indica rice chromosome 10

first: Xing-Wang

last: Deng

address: 165 Prospect

department: MCD Biology

type: Expression profiling by genome tiling array

summary:
This experiment was designed to identify transcribed regions of both japonica and indica rice chromosome 10. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of the chromosome were used to measure transcriptional activities. A total of 750,282 and 838,816 36mer oligonucleotide probes, positioned every 46 nt on average, were designed to interrogating the japonica and the indica chromosome, respectively. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA populations, namely, seedling roots, seedling shoots, panicles, and suspension cultured cells of the respective rice subspecies.
Keywords: other

first: Lei

last: Li

first: Xiangfeng

first: Mian

last: Xia

first: Viktor

last: Stolc

first: Ning

last: Su

first: Zhiyu

last: Peng

first: Songgang

first: Waraporn

last: Tongprasit

first: Jun

first: Xiping

first: Xingwang


title: Granulosa cell gene expression profiling of bovine cohort, dominant and subordinate follicles

status: Public on Apr 30 2005

city: Glasgow

first: Paul

last: Baker

address: Bearsden Road

department: Faculty of Veterinary Medicine

country: United Kingdom

institute: University of Glasgow

summary:
Bovine granulosa cells harvested from cohort follicles at 1.3 days after wave emergence, and from dominant and subordinate follicles at 2.6 days after wave emergence. Total RNA extracted from granulosa cells of 4 cohort, 4 dominant and 4 subordinate follicles was pooled for generation of each respective SAGE library.
Keywords: other

first: Monika

last: Mihm

first: Lynne

last: Fleming

first: Ana

last: Monteiro

first: Peter

last: O’Shaughnessy


title: Transcriptional responses of Escherichia coli to GSNO under defined chemostat conditions.

status: Public on Apr 06 2005

city: Sheffield

first: Jason

last: Barrett

state: South Yorkshire

address: Firth Court, Western Bank

department: Department of Molecular Biology and Biotechnology

institute: University of Sheffield

summary:
Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, GSNO was added to the chemostat culture and to the nutrient feed at a final concentration of 200 uM unless otherwise stated. Samples were taken immediately prior to the addition of GSNO and after a period of 5 min exposure to GSNO for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to
stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.
Equal quantities of RNA from control and GSNO-supplemented cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes. The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5). The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.
Keywords: dose response

first: Janet

last: Flately

first: Steven

last: Pullan

first: Martin

last: Hughes

first: Jeffrey

last: Green

first: Robert

last: Poole


title: Transcriptional responses of Anaerobically grown Escherichia coli to GSNO under defined chemostat conditions.

summary:
Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 h-1. In order to establish anaerobic growth, nitrogen was sparged through the chemostat medium prior to inoculation and throughout the course of the experiment at a rate of 0.2 l/min. No dissolved oxygen was detectable using the OxyProbe. Sodium fumarate was added to anaerobic medium at a final concentration of 50 mM to act as a terminal electron acceptor.  Cells were grown as above to steady-state, At steady-state, GSNO was added to the chemostat culture and to the nutrient feed at a final concentration of 200 uM unless otherwise stated. Samples were taken immediately prior to the addition of GSNO and after a period of 5 min exposure to GSNO for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.
Equal quantities of RNA from control and GSNO-supplemented cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes. The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5). The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.

Keywords: dose response


title: Spleen vs Neurokinin B (NEB) Treated B cell

status: Public on Apr 04 2005

city: Pasadena

first: Sangdun

last: Choi

address: 1200 E. California Blvd

institute: California Institute of Technology

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Neurokinin B (NEB) labeled with Cy5- time course with repeats
Keywords: ordered

first: Rebecca

last: Hart

first: Mi Sook

last: Chang

first: Jong-Woo

last: Kim

first: Yun Anna

last: Cao

first: Sun Young

last: Lee

first: Angela

last: Alexander

first: Joella

last: Grossoehme

first: Zhen

last: Yan

last: Hsueh


title: MicroRNA expression in lymphoma lines

status: Public on Mar 31 2005

city: Chapel Hill

first: Scott

last: Hammond

state: NC

department: Dept Cell and Developmental Biology

institute: University of North Carolina

summary:
MicroRNAs from lymphoma and leukemia cell lines with or without the 13q31 amplicon were quantitated using a custom microarray platform.  5ug total RNA from each line was labeled with cy3 and hybridized to a microarray that contains probes to 238 mouse and human mature microRNAs.  Four data sets per cell line are provided.  Data is presented as log (base 2) values median center normalized.
Keywords: other

first: Lin

last: He

first: Michael

last: Thomson

last: Hemann

first: Eva

last: Hernando-Monge

first: David

last: Mu

first: Summer

last: Goodson

last: Powers

first: Carlos

last: Cordon-Cardo

middle: W

last: Lowe

first: Gregory

last: Hannon


title: Global Gene Expression Profiling of Bovine Lymphocyte Populations

city: Ames

first: John

middle: D.

last: Neill

state: IA

address: 2300 Dayton Ave.

institute: National Animal Disease Center

summary:
Gene expression profiling of pooled lymphocyte populations from clinically normal cattle.  The T lymphocyte populations were purified from buffy coat and the immature B cells were prepared from isolated Peyer's patch follicles.
Keywords: other

middle: D

first: Julia

middle: F

last: Ridpath


title: Allelic Imbalances in bladder tumors based on high-density SNP array

status: Public on Apr 15 2005

city: Aarhus N

first: Karen

last: Koed

address: Brendstrupgaardsvej

department: Dept. of Clinical Biochemistry

country: Denmark

institute: Aarhus University Hospital, Skejby Sygehus

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
Comparison between germline (blood) and microdissected bladder tumors to determine allelic imbalances. The GeneChip® Mapping 10K Early Access Array Affymetrix, Santa Clara, CA was used to determine the number of heterozygous SNPs in DNA from blood compared to the number of heterozygous SNPs in DNA from tumor in the same patient.
Keywords: repeat sample


title: expression of SATs

city: Tsukuba

first: Shigeru

last: Iwase

department: BioResource center

institute: RIKEN

summary:
Expression of the sense-antisense transcripts (SATs).
Methods: The sequences of 60mer DNA specific to the sense and antisense genes were chosen by K.K. DNAFORM (Japan), and Agilent Technologies manufactured custom oligo DNA microarray chips by using this information. RNA was labeled and hybridized using Fluorescent Direct Label Kits (oligo dT-primed labeling) (Agilent Technologies), according to the manufacturer's protocols. For labeling with random nanomers, we used the CyScribe First-Strand cDNA Labeling Kit (Amersham). The RNA samples used for microarray experiments were from mouse ES cells, SL10 cells (fibroblast cell line), brain, heart, and testis. The total RNA of brain, heart, and testis for array experiments was purchased from Ambion. The total RNA of ES and fibroblast cells was isolated using Trizol reagent (Invitrogen). The same total RNA samples were reciprocally labeled with Cy3 or Cy5, hybridized to the oligo DNA on the chip, and dye-normalized, and processed signals were obtained using Feature Extraction software (Agilent Technologies).

Keywords: parallel sample

first: Hidenori

last: Kiyosawa

first: Nathan

last: Mise

first: Yoshihide

last: Hayashizaki

first: Kuniya

last: Abe


title: WT 14028 versus mutant

status: Public on Mar 30 2005

city: Austin

first: Rasika

last: Harshey

state: TX

department: Section of Molecular Genetics and Microbiology

institute: Institute of Cellular and Molecular Biology

summary:
WT 14028 versus mutant
Keywords: other

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

first: Tim

middle: Q

last: Wang

first: Jonathan

last: Frye

first: Steffen

last: Porwollik

last: McClelland


title: mSirt1 overexpression and knockdown in a pancreatic beta-cell line

status: Public on Apr 02 2005

city: St Louis

first: Andrew

middle: Alexander

last: Grimm

address: 660 S Euclid Ave, Campus Box 8103

department: Molecular Biology and Pharmacology

institute: Washington University School of Medicine

summary:
Cell culture and establishment of cell lines
The mouse pancreatic beta cell line MIN6 at passage 24 was obtained with permission from Dr. Jun-ichi Miyazaki at Osaka University (Miyazaki et al., 1990).  MIN6 cells were cultured as described previously (Miyazaki et al., 1990).  Two independent Sirt1-overexpressing MIN6 cell lines (MIN6-Sir2OE1 and Sir2OE2) were established by infection with the ecotropic pBabe-Sirt1 retrovirus carrying the mouse Sirt1 gene and a neomycin-resistant gene (Revollo et al., 2004) and selection in the presence of 280 micrograms/ml of G418 (Invitrogen).  Two control cell lines (MIN6-Neo1 and Neo2) were also established by infection with the pBabe-neo control retrovirus.  To establish Sirt1-knockdown MIN6 cell lines, small interfering RNAs (siRNAs) were designed against the Sirt1 gene, and each double-stranded siRNA template was cloned in the mU6pro vector (Yu et al., 2002, a gift from Dr. David L. Turner at University of Michigan, Ann Arbor).  Sirt1 siRNA sequences are available upon request.  Two independent Sirt1-knockdown MIN6 cell lines (MIN6-Sir2KD1 and KD2) were established by co-transfection with expression vectors carrying two different siRNAs and a neomycin-resistant marker plasmid and selection in the presence of 400 micrograms/ml G418.  A control cell line (MIN6-mU6pro) was also established using the mU6pro vector. All experimental and control cell lines were propagated carefully to ensure equivalent passage numbers and maintain healthy cellular morphology.

Microarray hybridizations and data collection
All cell lines were cultured in media containing 5 mM glucose for four days prior to RNA collection.  RNA samples were purified from two Sirt1-overexpressing (Sir2OE1 and Sir2OE2), two Sirt1-knockdown (Sir2KD1 and Sir2KD2), and three control (Neo1, Neo2 and mU6pro) MIN6 cell lines using Trizol (Sigma) according to the manufacturer’s protocol.  The quality of RNA was examined by capillary electrophoresis and denaturing agarose gel electrophoresis.  RNA from MIN6-Neo1 and Neo2 was combined prior to cDNA synthesis.  Eight micrograms of total RNA from each sample were converted to cDNA by using the 3DNA Array 350 Expression Array Detection Kit (Genisphere, PA) according to the manufacturer’s protocol.  Microarray hybridization was then conducted with Cy3- and Cy5-labeled dendrimers as described (Scearce et al., 2002) with the following modifications.  Hybridization was conducted at 42ºC for 18 h in MWG Coverslips Hybridization Buffer (MWG USA, NC), and all post-hybridization washes were carried out at 25ºC.  To increase the accuracy of the microarray analysis, we performed dye-swap experiments for each pair of cell lines (Sir2OE1 vs. Neo1+Neo2, Sir2OE2 vs. Neo1+Neo2, Sir2KD1 vs. mU6pro, and Sir2KD2 vs. mU6pro).  Microarray hybridizations were performed in duplicate for each pair with the exception that the Cy3-Cy5 labeling scheme was swapped between hybridizations, i.e., (control-Cy3, experimental-Cy5) and (experimental-Cy5, control-Cy3).  Including dye-swaps, four microarray slides were used for each pair-wise comparison.  A ScanArray Express HT scanner and accompanying software (PerkinElmer, MA) was used to scan the slides and analyze the raw data, including normalization according to the Lowess method (Yang et al., 2002).

Microarray analysis
Spots used for statistical analysis satisfied the following criteria on at least three of the slides for both sets of comparisons: (1) ScanArray Express flag = 3, (2) Signal to noise ratio (defined as (mean foreground - mean background)/(standard deviation of background)) ≥ 2 in both channels.  Spot-specific dye bias was calculated as the arithmetic mean of the log2 transform of the Lowess-normalized ratio of the medians (Yang et al., 2002) across dye-swapped pairs of hybridizations for the given set of experiments (either Sirt1 overexpression or knockdown).  The spot-specific dye bias was subtracted from the log2 transform of the Lowess-normalized median of ratios of the foreground pixels in the Cy5 and Cy3 channels to obtain the log2 transform of the “expression ratio”.  For up-regulated genes, fold changes are equivalent to the expression ratio.  For down-regulated genes, fold changes are the negative inverse of the expression ratio.  In either case, fold change = ±2^|log2(expression ratio)|.  To reduce the effect of multiple hypothesis testing, significant changes were demarcated by a difference of least 3 standard deviations (99.74% of normally distributed data) from the control.  In addition, only genes that differed by at least 1.8-fold from the control were considered.

References
Miyazaki, J.-I., Araki, K., Yamato, E., Ikegami, H., Asano, T., Shibasaki, Y., Oka, Y., and Yamamura, K. (1990). Establishment of a pancreatic beta cell line that retains glucose-inducible insulin secretion: special reference to expression of glucose transporter isoforms. Endocrinology 127, 126-132.

Revollo, J. R., Grimm, A. A., and Imai, S. (2004). The NAD biosynthesis pathway mediated by nicotinamide phosphoribosyltransferase regulates Sir2 activity in mammalian cells. J Biol Chem 279, 50754-50763.

Scearce, L. M., Brestelli, J. E., McWeeney, S. K., Lee, C. S., Mazzarelli, J., Pinney, D. F., Pizaro, A., Stoeckert Jr., C. J., Clifton, S. W., Permutt, M. A., et al. (2002). Functional genomics of the endocrine pancreas: The pancreas clone set and PancChip, new resources for diabetes research. Diabetes 51, 1997-2004.

Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30, e15.

Yu, J.-Y., DeRuiter, S. L., and Turner, D. L. (2002). RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc Natl Acad Sci USA 99, 6047-6052.
Keywords = Sir2
Keywords = Sirt1
Keywords = Sir2[alpha]
Keywords = NAD-dependent deacetylase
Keywords = pancreatic ß cells
Keywords = BESTO
Keywords = beta cell-specific Sirt1-overexpressing transgenic mice
Keywords = transgenic
Keywords = glucose tolerance
Keywords = insulin secretion
Keywords = microarray
Keywords = gene expression profiling
Keywords = Ucp2
Keywords = ATP
Keywords = glucose sensitivity
Keywords = aging
Keywords = diabetes
Keywords: ordered

first: Kathryn

last: Moynihan

first: Marie

middle: M

last: Plueger

first: Ernesto

last: Bernal-Mizrachi

first: Eric

last: Ford

first: Corentin

last: Cras-Meneur

first: M

last: Permutt

first: Shin-ichiro

last: Imai


title: Heat, Cold and Stress adaptation in Potato

status: Public on Mar 19 2005

city: Rockville

first: Li

last: Zheng

address: 9712 Medical Center Dr.

institute: The Institute for Genomic Research

summary:
Potato seedlings were subjected to cold, heat and salt stress. Expression profiles were captured at three different time-points, 3h, 9h and 27h from two different tissues, roots and leaves. The experiment was preformed independently three times. Commercially available true potato seeds (Variety Gilroy) were germinated on rafts floating on hydroponic medium in Magenta boxes. Plants were grown for 5 weeks prior to stress application under long day conditions (16h light and 8h dark) at 25C with gentle agitation. To initiate stress the medium was replaced with fresh medium pre-chilled to 4C (cold stress), pre-heated to 35C (heat stress) or supplemented with 100mM NaCl (salt stress). Cold and heat stress were maintained for the duration of the experiment by placing the Magenta boxes on ice or in a water-bath at 35C. For every individual sample two boxes of plants were used pooling a total of 6 plants per sample. For each time-point a single control sample was used by changing the media in a similar way as for the stress induction. A total of six boxes were combined for the pooled reference samples. Plants were harvested at the appropriate time and snap-frozen in liquid nitrogen. Roots and aerial tissue was separated prior to freezing. The tissue was stored at -80C freezer until isolation. Total RNA was isolated using RNeasy isolation kit. The intactness of the RNA was verified on gel and the concentration was adjusted to 3ug/ul by ethanol precipitation and re-suspension.
Series_weblink: http://www.tigr.org/tdb/potato
Keywords = potato, Abiotic stress
Keywords: ordered

first: Willem

last: Rensink


title: Aquaporin-1 Knockout vs Wild type Mice (Re-spot found)

status: Public on Mar 18 2005

city: Tucson

first: Kevin

last: Greer

state: AZ

department: Biomedical Engineering

institute: University of Arizona

summary:
This dataset was derived (re-spot found) from the original images used in GSE1298. This experiment compared aRNA derived from the kidney inner medula of three mice lacking a functional aquaporin-1 gene to three wild type mice. Each sample was hybridized 4 times, against 4 of the other 5 samples, using an interwoven loop experimental design.
Keywords: repeat sample

first: Heddwen

last: Brooks


title: Round Spermatids and Pachytene Spermatocytes

status: Public on Mar 15 2005

city: Bethesda

first: Alan Lap-Yin

last: Pang

address: 49 Convent Drive, Room 2C08, MSC 4429

department: NICHD/LCG/SDG

institute: National Institutes of Health

summary:
Mouse Round Spermatids (Sptd) and Pachytene Spermatocytes (Spcy)
Keywords: repeat sample

first: Warren

last: Johnson

first: Neelakanta

last: Ravindranath

first: Martin

last: Dym

first: Owen

last: Rennert

first: Wai-Yee

last: Chan


summary:
Effect of U94 in Gene Expression in PC3 Cells
Keywords: repeat sample

first: Ekwere

last: Ifon

first: Alan

first: Kathleen

last: Cashman

first: Sharon

last: Zimmerman

first: Sumitra

last: Muralidhar

first: John

last: Casey

first: Leonard

last: Rosenthal


title: Effects of CRP on monocytes gene expression

status: Public on Mar 11 2005

city: Vandoeuvre

first: Dan

last: Longrois

institute: INSERM U684

summary:
Circulating blood monocytes isolated from healthy premenopausal women and men were stimulated ex vivo with 25 microg/ml purified CRP (Sigma) or vehicle for 12 hours before RNA extraction.

Keywords: repeat sample

first: Didier

last: Hanriot

first: Gaelle

last: Bello

first: Armelle

last: Ropars

first: Carole

last: Seguin-Devaux

first: Gael

last: Poitevin

first: Sandrine

last: Grosjean

first: Véronique

last: Latger-Cannard

first: Yvan

last: Devaux

first: Faiez

last: Zannad

first: Paul-Michel

last: Mertes

first: Ketsia

last: Hess


title: Immortalization of normal human cells

city: Hiroshima

first: Keiko

last: Hiyama

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Research Institute for Radiation Biology and Medicine

institute: Hiroshima University

summary:
A normal neonatal human diploid fibroblast strain MJ90 was cultured in Dulbecco's modified Eagle's minimal essential medium (DMEM; Sigma-Aldrich Japan) supplemented with 2 mM L-glutamine (Life Technologies) and 10% fetal calf serum (FCS; Life Technologies). A normal human umbilical vein endothelial cell strain HUE142-2 were grown in MCDB151 medium (Sigma-Aldrich Japan) supplemented with 15% fetal bovine serum, 5 µg/ml of heparin (Sigma), and 5 ng/ml of recombinant acidic fibroblast growth factor in a plastic flask (Corning) precoated with bovine fibronectin solution (1 µg/cm2, Wako).The 40 µg of plasmid hTRT/FLAG or hTERTn2 (from Prof. F. Ishikawa, Kyoto University)linealized by a single cut with a restriction enzyme NruI was transfected into 10^7 MJ90 cells at PDL 41 or the HUE142-2 cells at PDL 35 by electroporation (Invitrogen) at 330 V. Clones harboring the plasmids were obtained by 400 µg/ml of G418 selection (Wako) and named as TF1 from MJ90 and nTE4-5 from the HUE142-2 cells. The TF1 cells at PDL 104, 148, and 216 and nTE4-5 cells at PDL 105, 145, and 216 were collected and stored at –80°C until use. Total RNA was extracted from the cultured cells using an RNAeasy™ total RNA isolation kit (Qiagen) according to the protocols the manufacturer recommended. The poly(A)-RNA was isolated from the extracted total RNA using µMACS™ mRNA isolation kit(Miltenyi Biotec).One-microgram Poly(A)-RNA samples extracted from cell strains after hTERT induction were labeled with the fluorescent dye Cy-3 by random-primed reverse transcription. Similarly, 1-µg Poly(A)-RNA samples extracted from MJ90 cells at PDL 30 and the HUE 142-2 cells at PDL 38 before hTERT induction were labeled with Cy-5, and used as the expression references. Each pair of Cy-3 and cy-5 labeled cDNAs were hybridized as probes on RIKEN human 21K arrays. The array contained 21,168 spots in 48 blocks (4 x 12), each containing 441 spots (21 x 21). Among them, 20,784 spots are human cDNA clones purchased from ResGen™ (Invitrogen Corporation) and the remaining spots are the internal and exogenous controls spotted on every subgrid as positive and negative controls. All microarray analyses on the six pairs, i.e. MJ90 vs. TF1-PDL104, TF1-PDL148, or TF1-PDL216 and HUE142-2 vs. nTE4-5-PDL105, nTE4-5-PDL145, or nTE4-5 -PDL216 were carried out in duplicate. (_1 & _2). Arrays were laser-scanned using ScanArray 5000 confocal laser scanner (GSI Lumonics), and the fluorescence measurements were made separately by channels 1 and 2 for each dye at each spot on the array. Let CH1I and CH2I be spot intensities scanned by channels 1 and 2, respectively. Let Ch1B and CH2B be their background intensities. In this study, the values of CH1 = CH1I-CH1B and CH2 = CH2I – CH2B were used as gene expression levels in each sample. Each result of the duplicated microarray experiment was independently subjected to global normalization and new normalization (Ohtaki et al., Technical Report Series of Statistical Research Group, Hiroshima Univershity, No.04-07).
Keywords: time-course

last: Otani

first: Megu

last: Ohtaki

first: Kenichi

last: Satoh

first: Tsutomu

last: Kumazaki

first: Tomoko

last: Takahashi

first: Youji

last: Mitsui

first: Yasushi

last: Okazaki

first: Yoshihide

last: Hayashizaki

first: Keiji

last: Tanimoto

first: Masahiko

last: Nishiyama


title: Acid sensitivity and opp transport regulation in L. acidophilus

city: Raleigh

first: Todd

last: Klaenhammer

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

summary:
A whole-genome microarray containing 97.4 % of the annotated genes of L. acidophilus was employed to compare genome-wide patterns of transcription at varying pHs between the wild type parent and a histidine protein kinase mutant
Keywords: ordered

first: Maria

last: Azcarate-Peril

first: Olivia

last: McAuliffe

first: Eric

last: Altermann

first: Sonja

last: Lick

first: William

last: Russell

middle: R


title: P.falciparum strain 3D7, SIR2 knockout

status: Public on Mar 08 2005

city: Parkville

first: Ken

last: Simpson

state: Victoria

address: 1G Royal Parade

department: Genetics and Bioinformatics

institute: The Walter and Eliza Hall Institute

summary:
This experiment studies the effect of knocking out the transcriptional regulator SIR2 in 3D7 parasites.  RNA was harvested from ring-stage parasites at 8 hours post-infection.
Keywords = SIR2
Keywords = epigenetic regulation
Keywords = antigenic variation
Keywords = var
Keywords = Plasmodium falciparum
Keywords: other

first: Manoj

last: Duraisingh

first: Till

middle: S

last: Voss

first: Allison

last: Marty

first: Michael

last: Duffy

first: Robert

last: Good

first: Jennifer

middle: K

last: Thompson

first: Lucio

middle: H

last: Freitas-Junior

first: Artur

last: Scherf

first: Brendan

last: Crabb

first: Alan

last: Cowman


title: Adult mouse testis

city: Prague

first: Petr

last: Divina

address: Videnska 1083

department: Mammalian Molecular Genetics

country: Czech Republic

institute: Institute of Molecular Genetics, Academy of Sciences

summary:
SAGE libraries generated from total testes of adult mouse males.
Keywords = testis
Keywords: other

first: Jiri

last: Forejt

first: Cestmir

last: Vlcek


title: Expression Analysis of Rice Chromosome 4 Using Tiling Microarray

status: Public on Mar 05 2005

first: Yuling

last: Jiao

state: CA

address: 1200 E California Blvd

department: Biology

summary:
We analyzed the transcriptional activity of rice chromosom 4 using a tiling path microarray based on PCR-generated genomic DNA fragments. Five organ samples from various developmental stages and cultured cells were examined.
Keywords: ordered

first: Peixin

last: Jia

first: Xiangfeng

last: Wang

first: Suliang

last: Yu

first: Bin

last: Han


status: Public on Apr 07 2005

city: Shanghai

first: Zhengjun

last: Chen

state: Shanghai

address: 320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology

summary:
Proteomic analysis of pervanadate-induced tyrosine-phosphorylated proteins in hepatocellular carcinoma WRL 68 cells
Protein tyrosine phosphorylation plays critical roles in modulating biological processes such as cellular proliferation, differentiation, migration, apoptosis and metabolism. To profile tyrosine phosphorylated (pTyr) proteins as well as search novel pTyr proteins as cross-talk points among different cellular pathways, we developed a rapid and efficient approach to identify cellular pTyr proteins and their complexes by a combination of subcellular proteomics approach with signal transduction strategies. Human hepatocytic cells from WRL68 cell line were treated with pervanadate (POV), subfractionated into four fractions and then subjected to immunoaffinity purification with anti-pTyr antibody. The eluted mixtures of the anti-pTyr purification were identified by LC-MS/MS.
Subcellular fractionation and affinity purification of tyrosine-phosphorylated proteins:
WRL68 cells were first grown to 80% confluence in MEM complete medium and then the medium replaced with serum free media. After 15 h, the cells were either untreated or stimulated with 0.1 mM pervanadate (1 mM sodium orthovanadate, 3 mM H2O2) for 10 min. 150-mm cultures of WRL 68 cells were rinsed twice with 4? PBS and then scraped from the dish in 750?l of hypotonic buffer (10 mM Tris, 1 mM NaF, 10 mM IAA, pH 7.5) containing a cocktail of protein inhibitors. After a 20-min incubation on ice, the cells were passed about five times through a 25-g needle. The resulting lysate was subjected to a 15min centrifugation at 1000 rpm at 4?, after which the pellet was resuspended in 250?l of hypotonic buffer and re-extracted by a second round of the trituration and centrifugation. The supernatants of the first and second spins were combined, adjusted to 0.25 M NaCl, and separated into cytosolic (supernatant) and membrane (pellet) fractions bycentrifugation at 19,000 rpm (43,000 g) for 90 min at 4?. All the pellets and total cell lysate were resuspended in RIPA buffer (50 mM Tris-HCl, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid sodium) containing 1mM pervanadate with a cocktail of protein inhibitors with sonication aid. Cleared cell lysates were incubated overnight at 4? with 30?l monoclonal anti-phosphotyrosine-agrose (Sigma). Precipitated immune complexes were washed three times with 1×HNTG (20 mM HEPES, 150 mM NaCl, 0.1% Triton X-100, 10% Glycerol, pH 7.5) and then eluted with 100 mM phenyl phosphate (Sigma) in lysis buffer at 4?.
Enzyme digestion, mass spectrometry and protein identification:
The sample was digested according to the published method. Chromatography was performed using a surveyor LC system (Thermo Finnigan,SanJose,CA) on C18 reverse phase column(RP, 180 µm x 150 mm, BioBasic® C18, 5 µm, Thermo Hypersil-Keystone). The pump flow rate is split 1:100 for a colum flow rate of 1.5 µL/min.The column effluent is directly electrosprayed using the orthogonal metal needle source without further splitting.Mobile phase A is 0.1% formic acid in water,and the B mobile phase is 0.1% formic acid in acetonitrile. The separation of peptides obtained by enzymatic digest of bile sample was achieved with a gradient of 2-80% B over 360 min.The column effluent from the reverse phase column was analyzed by LCQ Deca XP ion-trap mass spectrometer.The micro-electrospray interface uses a 30 µm metal needle that is orthogonal to the inlet of the LCQ.The mass spectrometer was set that one full MS scan was followed by three MS/MS scans on the three most intense ion from the MS spectrum with the following Dynamic Exclusion™ settings: repeat count, 1; repeat duration, 0.5 min; exclusion duration, 3.0 min. The acquired MS/MS spectra were automatically searched against protein database for human proteins (SWISS-PROT/TrEMBL) using the TurboSEQUEST program in the BioWorks™ 3.0 software suite. An accepted SEQUEST result had to have a ?Cn score of at least 0.1 (regardless of charge state) and Xcorr (one charge?1.5, two charges?2.0, three charges?2.5). Single peptides that alone identify a protein were manually validated after meeting the above criteria.
Bioinformatics analysis:
The pI and MW of the proteins were analyzed using ExPASy proteomics tools accessed from http://cn.expasy.org/tools/#proteome. The grand average hydropathicity (GRAVY) values were determined according to Kyte-Doolittle. The protein subcellular location annotation was from SwissProt &TrEMBL protein database (http://us.expasy.org/sprot/). The protein function family was categorized according to Gene Ontology (GO) annotation terms extracted by InterPro (http://www.ebi.ac.uk./interpro/). The annotation of protein phosphorylation was from SwissProt &TrEMBL protein database (http://us.expasy.org/sprot/) and PhosphoSite (http://www.phosphosite.org). The kinases were annotated according to human kinome.
Keywords: other

first: Yiguo

first: Dan

last: Du

first: Longhou

last: Fang

first: Rongxia

last: Li

first: Haixin

last: Yuan

first: Guang

last: Yang

first: Rong

last: Zeng

first: Friedrich

last: Lottspeich

first: Axel

last: Ullrich


title: carbon utilization in E. coli

city: Madison

first: Mingzhu

last: Liu

state: WI

institute: University of Wisconsin-Madison

summary:
The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÒ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com).
Keywords: parallel sample

first: Tim

last: Durfee

first: Julio

last: Cabrera

first: Kai

last: Zhao

first: Ding

last: Jin

first: Frederick

last: Blattner


title: Detection of gene expression changes in S. Choleraesuis infected porcine lung using an oligonucleotide microarray

first: Christopher

last: Tuggle

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

summary:
Piglets were raised in isolation facilities from 10 days to 7 weeks of age at the National Animal Disease Center.  Bacteriological culture of rectal swabs was performed twice to confirm that all pigs were free of Salmonella spp. Three control pigs were necropsied on experimental day -3.  On day 0, pigs in the infected group were intranasally challenged with 1 x 109 CFU S. Choleraesuis X3246. Lung samples were aseptically collected from three 24 h and three 48 h post infection pigs and immediately frozen in liquid nitrogen for future mRNA isolation. In the microarray experiment, the nine animals were randomly assigned to three loops so that each loop included one animal from each infection status category. A total of 9 slides (3 slides per loop) were used to obtain a total of 18 measurements from the three control and six infected pigs. A mixed model analyses was also used  to identify differentially expressed genes.  The mixed model included fixed effects for dye (Cy3 or Cy5), time point (control, 24 hour, and 48 hour infection) as well as random effects for slide and animal.
Keywords: repeat sample

first: Shu-Hong

first: Justin

last: Recknor

first: Daniel

last: Kuhar

last: Nettleton

first: Joan

last: Lunney

first: Sarah

last: Orley

first: Jolita

last: Uthe

first: Shawn

last: Bearson

first: Harry

last: Dawson

first: Joilta


title: Gene expression in normal tissues to validate the first generation porcine oligonucleotide microarray

summary:
Lung, liver, muscle (Semitendinosus), small intestine (duodenum; approximately 5 cm from stomach) were collected from six cross-bred white pigs (three 15 week old and three 17 week old). Total RNAs were isolated from these tissues to study gene expression by using the first generation of porcine long oligonucleotide microarray. In the experimental design, tissue samples from the six animals were assigned to six loops (three for younger animals and three for older animals). One sample from each of the four tissues from a single animal was used in each loop.  The order of the tissues in each loop was varied so that all pairs of tissues were represented together on a slide an equal number of times.  Dye balance was used throughout so that each tissue was measured an equal number of times with each dye. Data from 48 measurements from 24 slides were collected, with 12 measurements for each tissue. The mixed model included fixed effects for dye, tissue, animal age, and age-by-tissue interaction as well as random effects for slide, animal, and animal-by-tissue interaction. Genes with expression significantly higher in one tissue than in each of the others will be referred to as tissue-selective genes.  To identify such genes, pair-wise comparisons of normalized signal intensities between tissues were conducted as part of our mixed model analyses for each gene.
Keywords: repeat sample

first: Dan


title: GABAB-R evoked changes in mRNA transcription

city: Bristol

first: Mohamed

middle: T.

last: Ghorbel

address: Level 7, BRI, Marlborough street

department: Bristol Heart Institute

institute: University of Bristol

summary:
Aim: To gain insight into the pathways by which GABABR activation may influence long-term changes in synaptic plasticity and neuronal growth and morphology we investigated changes in gene expression in cultured hippocampal neurones evoked by the GABABR agonist baclofen.  We used cDNA microarray gene expression profiling to identify candidate genes that are differentially expressed in the hippocampal neurones following GABABR activation.
Experimental design:	The cDNA microarray used in the present study is the NIA Neuroarray containing 1152 genes relevant to neurobiology. NIA Neuroarray probes were hybridised in triplicate with targets derived from control and baclofen-treated neurones.
Conclusion: Our novel data on down-stream, late phase consequences of GABABR signalling provide a basis for future studies to investigate these changes in gene expression at the protein, cell biology and functional levels.  Furthermore, the changes in gene expression identified will shed light on the multiple roles of GABABRs.

Keywords: repeat sample

first: Kevin

middle: G

last: Becker

first: Jeremy

last: Henley


title: aerobic_to_anaerobic_shift

status: Public on Feb 28 2005

city: Urbana

first: Kurt

middle: E

last: Kwast

state: IL

address: 407 S. Goodwin Ave.

department: Molecular & Integrative Physiology

institute: University of Illinois at Urbana-Champaign

summary:
The wild-type (grown on galactose or glucose) or msn2/4 mutant (grown on galactose) strains were grown aerobically.  At time zero (generation 0) the sparge gas was switched from air to O2-free N2 and samples were harvested after 0 (aerobic control), 0.04, 0.08, 0.19, and 2 generations of anaerobic growth.
Keywords: time-course

first: Liang-Chuan

last: Lai

first: Alexander

middle: L

last: Kosorukoff

first: Patricia

middle: V

last: Burke


title: E-Predict Training Data Set and Examples

status: Public on Mar 01 2005

city: San Francisco

first: Joe

last: DeRisi

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary:
This series includes a 32-array training dataset used to evaluate E-Predict normalization and similarity metric parameters as well as 13 microarrays used as examples in (Urisman, et. al 2005). Training data set includes 15 independent HeLa RNAhybridizations (microarrays 1-15), 10 independent nasal lavage samples positive for Respiratory Syncytial virus (microarrays 16-25), and 7 independent nasal lavage samples positive for Influenza A virus (microarrays 26-32). Examples iclude a serum sample positive for Hepatitis B virus (microarray 33), a nasal lavage sample positive for both Influenza A virus and Respiratory Syncytial virus (microarray 34), and culture samples of 11 distinct Human Rhinovirus serotypes (microarrays 35-45).
Keywords = virus detection, E-Predict, species identification, metagenomics
Keywords: other

first: Anatoly

last: Urisman

first: Kael

last: Fischer

first: Charles

middle: Y

last: Chiu

first: Amy

last: Kistler

first: Shoshannah

last: Beck

first: Joseph


title: Wild type 4 hours exposure to congo red (cell wall chip)

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

institute: Facultad de Farmacia (UCM)

summary:
S. cerevisiae was grown on YEPD. For Congo Red experiments, yest cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 µg/ml. Cells were collected at 4hours of growth, frozen at -80 °C and processed for RNA extraction.
Keywords: repeat sample

first: Jose

last: Rodríguez-Peña

first: Rosa

last: Pérez-Díaz

first: Sara

last: Alvarez

first: Clara

last: Bermejo

first: Raúl

last: García

first: Catalina

last: Santiago

first: César

last: Nombela


city: Berkely

first: Sanchita

last: Bhattacharya

address: 1 Cyclotron Rd

institute: MIT

summary:
Gene Expression profiles of E.coli grown in LB and Minimal medium (DM) at OD 600 =1
Keywords: ordered

first: Paolo

last: Boccazzi

first: Andrea

last: Zanzotto

first: Nicolas

last: Szita

first: Klavs

last: Jensen

first: Anthony

last: Sinskey


title: Abiotic stress

status: Public on Mar 02 2005

city: Yongin

first: Ju-Kon

last: Kim

state: Kyonggi-do

address: 38-2 Nam-dong

department: Division of Bioscience and Bioinformatics

country: South Korea

institute: Myongji University

summary:
To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNA.
Keywords = abiotic stress
Keywords: repeat sample

first: Se-Jun

last: Oh

first: Minjeong

first: Yeon-Ki

first: Baek-Hie

last: Nahm


title: Wild type yellow experiment (cell wall chip)

first: Javier

last: Arroyo

summary:
S. cerevisiae was grown on YEPD. For yellow experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 6h. At this time cells were collected. Experiment was carried out hybridising the cDNA from the same RNA (from this culture) with both Cy3 and Cy5.
Keywords: repeat sample

first: Jose

first: Rosa


title: Cytokine expression in macrophages and splenic CD4+ T-cells

status: Public on Feb 25 2005

city: Knoxville

first: Bin

last: Wan

institute: University of Tennessee, Knoxville

summary:
This experiment was designed to study the cytokine gene expression profile of macrophage under 50uM DU exposure. the experiment was repeated three time, with duplicate spots for each gene on the array.
Conclusion: DU exposure induces the expressions of IL-10, NF-kBP65, and Midkine and other cytokine genes, indicating the immunomodulation abilities of DU.  (GSM43230-GSM43241)

This experiment was designed to study the cytokine gene expression of splenic CD4+ T-cells under 100uM DU exposure in 24 hours.
Conclusion: DU induces Th2 cytokine gene expression (eg. IL-5), and midkine, as well as other cytokine genes, indicating the abilities of DU in promoting Th2 shifting during differtiation. (GSM43242 to GSM43253)


title: Diff_cell_shift

status: Public on Mar 23 2005

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

summary:
Immortalised lines created from different cell types from the human breast were induced to undergo senesecence by inactivation of the immortalising LT antigen.
Keywords: ordered

first: Louise

last: Mansfield

first: Alan

last: Mackay

first: Mike

last: O'Hare

first: Parmjit

last: Jat


title: Promyelocytic cells response to Anaplasma phagocytophilum infection

city: Stillwater

first: Patricia

middle: J

last: Ayoubi

state: OK

address: 246 NRC

department: Biochemistry and Molecular Biology

institute: Oklahoma State University

summary:
Gene expression profiling of human promyelocytic cells in response to infection with Anaplasma phagocytophilum.
Total RNA derived from 3DPI Anaplasma phagocytophilum-infected HL-60 cells was labeled with A647 and total RNA derived from 3DPI Mock-infected HL-60 cells was labeled  with A546.  For each, 5 µg of total RNA was labeled using Genisphere Array900, Alexa Fluor dyes and SuperscriptII.   Slide scanned with ScanArray Express and images processed with GenePix Pro version 4.0.  Normalized log ratios VALUES determined using R-project statistical environment (http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) through the GenePix AutoProcessor (GPAP, http://darwin.biochem.okstate.edu/gpap) website (P. Ayoubi, unpublished results).
Keywords: time-course

last: de la Fuente

first: Edmour

last: Blouin

first: Consuelo

last: Almazán

first: Victoria

last: Naranjo

first: Katherine

last: Kocan


title: Variation in tissue-specific gene expression among natural populations of Fundulus heteroclitus

status: Public on Feb 18 2005

city: Miami

first: andrew

last: whitehead

state: FL

institute: University of Miami, RSMAS

summary:
Examination of the expression of a selected suite of 192 metabolic genes in brain, heart and liver in three populations of the teleost fish Fundulus heteroclitus using a highly replicated experimental design.
Keywords: other

first: A

last: Whitehead

first: D

last: Crawford


title: Gene expression of lung macrophages in mice instilled with Silica, TiO2 or Saline

city: Missoula

first: Corbin

last: Schwanke

state: MT

department: Biomedical and Pharmaceutical Sciences

institute: University of Montana

summary:
Mice were intranasally instilled at 6 weeks of age with silica, titanium dioxide, or saline control and macrophages were harvested by broncho-alveolar lavage at 14 weeks of age.  RNA was isolated using RNeasy Mini kits (Qiagen).  Due to low yield of RNA, mRNA was amplifed by RiboAmp kits (Arcturus) and resulting aRNA was indirectly labeled with Alexa-Fluor 647 dye (Molecular Probes).  This was hybridized against Universal Mouse Reference RNA (Stratagene) which was indirectly labeled with Alexa-Fluor 555 dye (Molecular Probes).  Slides were printed in house using PCR product cDNA targets on GAPS slides (Corning).  Slides were scanned with an Axon GenePix 4000B scanner and data was analyzed using GenePix Pro 4.0 software and Iobion GeneTraffic Duo software.  Data was normalized to a total 1:1 ratio of read to green dye.
Keywords: parallel sample

first: Jared

last: Brown

first: Mark

last: Pershouse

first: Andrij

last: Holian


title: Arabidopsis Whole Genome 36-mer

status: Public on Feb 10 2005

city: Moffett Field

first: Waraporn

last: Tongprasit

institute: NASA Ames Research Center

summary:
Identification of novel transcribed sequences in Arabidopsis thaliana using high density genome tiling arrays.
Keywords: other

first: Viktor

last: Stolc

first: Manoj

middle: P

last: Samanta

first: Himanshu

last: Sethi

first: Shoudan

last: Liang

first: David

middle: C

last: Nelson

first: Adrian

last: Hegeman

first: Clark

last: Rancour

first: Sebastian

last: Bednarek

first: Eldon

last: Ulrich

first: Qin

last: Zhao

first: Russell

last: Wrobel

first: Craig

last: Newman

first: Brian

last: Fox

first: George

last: Phillips

first: John

last: Markley

first: Michael

last: Sussman


title: Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by oligonucleotide array analysis

status: Public on Feb 04 2005

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

state: MO

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

summary:
Microarray technology permits high throughput comparisons of gene expression in different parasite stages or sexes. We now report the first use of this technology for analysis of gene expression in filarial worms. The slide array (comprised of 65 mer oligos representing 3569 EST clusters) was spotted with sequences selected from the extensive Brugia malayi EST database (http://nema.cap.ed.ac.uk/nematodeESTs/nembase.html#Annotation). Arrays were hybridized with male and female cDNA and developed with Cy5- and Cy3-fluorescent 3DNA capture reagents. The experimental design included both biological and technical (dye-flip) replicates.
Keywords: repeat sample

first: Ben-wen

last: Li

first: Amy

last: Rush

middle: D

first: Wes

last: Warren

first: Steven

middle: A

last: Williams

first: Gary

last: Weil


title: LPS Blood Time course

status: Public on Feb 09 2005

city: Durham

first: Rick

middle: David

last: Fannin

state: NC

address: 111 T.W. Alexander Drive

department: Office of the Director

institute: The National Institute of Environmental Health Sciences

summary:
cDNA microarray study of gene expression changes in whole blood from LPS treated rats, 2 and 6 hours after I.P. injection of 5 mg/kg
Keywords: time-course

first: James

middle: T

last: Auman

first: Maribel

last: Bruno

first: Stella

middle: O

last: Sieber

first: Sandra

middle: M

last: Ward

first: Charles

last: Tucker

first: Bruce

last: Merrick

first: Richard

last: Paules


title: Identification of neural genes using Xenopus DNA microarrays

city: Irvine

first: Yongchol

last: Shin

address: 4115 McGaugh Hall

department: Developmental and Cell Biology

institute: University of California, Irvine

summary:
In order to isolate novel genes regulating neural induction, we utilized a DNA microarray approach.  As neural induction is thought to occur via the inhibition of BMP signaling, BMP signaling was inhibited in ectodermal cells by overexpression of a dominant-negative receptor. RNAs were isolated from control animal cap explants and from dominant-negative BMP receptor expressing animal caps and subjected to a microarray experiment using newly generated high-density Xenopus DNA microarray chips.
Keywords = neural induction
Keywords = BMP
Keywords = nervous system
Keywords = Xenopus
Keywords = microarray
Keywords: parallel sample

first: Atsushi

last: Kitayama

first: Tetsuya

last: Koide

first: Daniel

last: Peiffer

first: Makoto

last: Mochii

first: Arnold

last: Liao

first: Naoto

last: Ueno

first: Ken

middle: W

last: Cho


title: NHBE exposed to cigarette smoke

status: Public on Feb 23 2005

city: Oklahoma City

first: Stewart

middle: Alan

last: Shields

address: 825 NE 13th St

department: Arthritis/Immunology

institute: Oklahoma Medical Research Foundation

summary:
normal human bronchial epithelial cultures from two cultures in parallel exposed to cigarette smoke (CS) or air (mock) at timepoints 4 hours and 24 hours.
Keywords = cigarette smoke
Keywords = microarray
Keywords = bronchial cell
Keywords = tobacco
Keywords: time-course

first: Ellen

last: Jorgensen

first: Sean

last: Turner

first: Diana

last: Gietl

first: Mary

last: Ellexion-Turner

first: Yuhon

last: Tang

first: Andy

last: Stinson

first: Michael

last: Centola

first: Anthony

last: Albino


title: Cross species comparison of expression patterns

status: Public on Jan 25 2005

city: New Haven

first: Yoav

last: Gilad

state: CT

address: 333 Cedar St.

institute: Yale

summary:
Comparison of expression in liver samples of human, chimp, orang and rhesus, by using a novel multi-species cDNA array
Keywords: other

sample_organism:
Macaca mulatta
Pan troglodytes
Pongo pygmaeus
Homo sapiens

first: Scott

last: Rifkin

first: Paul

last: Bertone

first: Mark

last: Gerstein

first: Kevin

last: White


title: Microarray Analysis of Gene Expression in Human Normal and Breast Cancer Cells

status: Public on Jan 20 2005

city: Kenilworth

first: Wei

last: Ding

state: NJ

address: 2015 Galloping Hill Road

department: Discovery Technology

institute: Schering Plough Research Institute

summary:
Differential gene expression between normal breast epithelial cells and the malignant counterpart was studied using microarray technique. We utilized GeneAlbum GEM 1-6 from Incyte Pharmaceuticals, Inc., which contains which contains 65,873 cDNA clones (57,172 clones excluding controls), representing 33,515 individual genes. The normal human mammary epithelial cells (HMEC) from 3 donors were used to search different gene expression patterns among individuals, ages and races. In addition, 8 well-established breast cancer cell lines were used as probes against a common normal HMEC from 50 years old donor
Keywords: other

first: Qun

last: Wu

first: Asra

last: Mirza

first: Tish

last: Van Arsdale

first: Iris

last: Wei

first: Robert

last: Bishop

first: Andrea

last: Basso

first: Terri

last: McClanahan

first: Lin

last: Luo

last: Kirschmeier

first: Eric

last: Gustafson

first: Marco

last: Hernandez

first: Suxing

last: Liu


title: Gene expression in rat kidney following recovery from acute renal failure (ARF)

status: Public on Jan 26 2005

city: Milwaukee

first: David

middle: P.

last: Basile

address: 8701 Watertown Plank

department: Physiology

institute: Medical College of Wisconsin

summary:
This experiment was designed to study the alteration in expression of mRNA is kidney following recovery from transient acute renal failure.

The model used was a 52 min. bilateral renal artery clamping, followed by reperfusion, which resulted in a transient loss of renal function, followed by a functional recovery.   All tissue in this study was harvested 35 days post-surgery, when renal function was restored, and renal structure largelyy normal. For controls, sham-operated animals were used.  An N of 6 post-ischemia reperfusion animals were used with 6 sham-operated controls.

For hybridization studies, RNA from one of six post-ischemic acute renal failure animals were compared with with RNA from kidney of six sham-operated control animals.  Each ARF vs. sham-operated comparison was performed twice, alternating the cy3 and cy5 label between the two hybridizations for each pair.

A second set of hybridizations was carried out using sham vs. sham hybridizations.  This was done to get a quantitative analysis of the variation of the biological and microarry platform.

Keywords: parallel sample

first: Katherine

last: Fredrich


title: Histone H4 N-terminal tail mutants

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

summary:
A series of yeast carrying K->R mutations in the histone H4 N-terminal tail were profiled by gene expression array in mid-log phase.
Keywords: repeat sample

first: Michael

middle: F

last: Dion

first: Steven

last: Altschuler

first: Lani


title: Solar UV-B regulation of high altitude maize

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

institute: Universidad Nacional de Rosario

summary:
To initiate a genomic scale analysis of high altitude maize, we performed expression-profiling experiments using Unigene I cDNA arrays from the Maize Gene Discovery Project that contain 5664 cDNAs printed in triplicate spots; a triplicate set for nearly all cDNAs was printed in at least one additional location on each slide, thus there is a minimum of 6 spots for each cDNA per slide. Four-week-old maize plants grown in the field under the three irradiation regimes no UV-B, solar UV-B or UV-B supplemental were used for the experiments. Samples were collected from adult leaves 9 and 10; samples from 6 plants were pooled for preparation of poly(A)+ RNA.
Keywords: parallel sample

overall_design:
Statistical analysis of array data was undertaken with analysis of variance (ANOVA) style models essentially as previously described (Blum et al, 2004).  As before, the following ANOVA models were constructed:

ygijklr= µ+Li+A(L)ji+Tk+LTik+Dl+ADjl+εgijklr	      (1)

rgijklr=GLgi+GA(L)gj(i)+GTgk+GLTgik+GDgl+GS(A)gr(j)+ εgijklr       (2)

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, treatments and dyes, respectively while LT represents interaction between lines and treatments.  The AD interaction term is present to account for intensity scaling done on the two channels.  The nested term, A(L), accounts for variation across replicate arrays, as in this experiment, lines are not connected since no array has samples from two different lines hybridized to it; the arrays are arranged in a split-plot design, with line being the whole plot factor and treatment the split-plot factor.
Model (2) takes residuals from model (1) as normalized response values and includes gene specific effects.  Additionally, it models replicate spot variation with the GS(A) term.
Both models were fit using the Mixed procedure (SAS 9.0, SAS Institute, Cary, NC) with model (2) being fit gene by gene.  Observed significance levels for all effects tests were adjusted for multiplicity of testing by the False Discovery Rate (FDR) method.  Background (threshold) levels for the arrays were set at median value in all conditions lower than the median values for the SP array control genes; this is a conservative threshold that retains genes with low expression levels in even a single treatment/line combination.  Additional low-expression genes (with normalized log2 levels less than -2) were flagged.

first: Virginia

last: Walbot

first: Stapleton

middle: E

last: Ann

first: Blum

last: James


title: Endothelial cells and exposure to enviromental tobacco

city: Dallas

first: John

middle: G

last: Maresh

state: TX

address: 5323 Harry Hines

department: Internal Medicine

institute: U.T. Southwestern Medical Center

summary:
Endothelial cells from mice exposed to enviromental tobacco smoke for 1 or 6 weeks.
Keywords: parallel sample


title: Wheat Freeze-Tolerance

first: Kelsi

last: Rotter

address: 4444 Forest Park Pkwy.

institute: Washington University School of Medicine

summary:
Comparison of gene expression levels in non-hardened (NH), cold-hardened (CH) and subzero-hardened (SZH) Triticum aestivum L. cv Jackson crowns with Affymetrix GeneChip Barley Genome Array.
Keywords = wheat
Keywords = crowns
Keywords = cold tolerance
Keywords = freezing resistance
Keywords = Triticum aestivum L. cv Jackson
Keywords: repeat sample

first: Eliot

last: Herman

last: Livingston


title: Development stages of Lentinula edodes

city: Shatin

first: Hoi Shan

last: Kwan

state: Hong Kong SAR

department: Biology

institute: The Chinese University of Hong Kong

summary:
Gene expression profiles at different development stages and different growth medium of Lentinula edodes (L54) are comparied.
Keywords: time-course

first: Wing Yan Winnie

last: Chum

first: Ai Min

last: Ma


title: HCC formation in rat

status: Public on Feb 01 2005

city: Tokyo

first: Fumiyuki

last: Uematsu

state: Tokyo

address: 2-2 Kanda-surugadai, Chiyoda

department: Department of Pathology

institute: Sasaki Institute

summary:
A total of 10 male Fischer 344 rats, 5 weeks old, were purchased from Charles River Japan, Incorporated, Atsugi, Kanagawa, Japan.  Rats were divided into 2 groups each consisting of 5 animals housed in a plastic cage with white flake bedding in an air-conditioned room.  Rats were used for the experimentation after a 1-week acclimation on a basal diet (CRF-1, Oriental Yeast Corporation, Itabashi, Tokyo, Japan) and allowed free access to food and tap water throughout the acclimation and experimental periods.  Body weight, food consumption, and water intake were monitored weekly.  The CDAA diet was obtained from Dyets, Bethlehem, PA.
After acclimation, group 1 rats were administered the basal diet, while group 2 rats were placed on the CDAA diet for 70 weeks and then sacrificed.  The livers were taken and macroscopically examined.  Portions of group 1 livers, as well as the macroscopic tumors and their surrounding, non-cancerous tissues of group 2 livers were fixed in 10% neutrally-buffered-formalin for 24 hours, embedded in paraffin, processed for the routine hematoxylin-and-eosin staining procedure, and histologically examined.  Remaining portions of these 3 types of liver tissues were immediately frozen in liquid nitrogen and stored at -80C.  Group 1 liver tissues, group 2 liver tissues from non-cancerous areas, and group 2 liver tissues from tumors (after histologically diagnosed as HCCs; see the results section) were used as normal liver samples, surrounding non-cancerous liver samples, and HCC samples, hereafter referred to as CON, NC, and CA, respectively.  The microarray and RT-PCR experiments and the subsequent data analysis were performed using 5 CON samples from individual group 1 rats and 5 matched pairs of NC and CA samples from individual group 2 animals.
RNA Isolation and Probe Labeling.  Total RNA from liver tissues was isolated using RNeasy Midi kits (QIAGEN, Hilden, Germany).  The integrity of the RNA was checked by electrophoresis on 1% agarose-formaldehyde gels. Five micrograms of total RNA from individual samples were labeled with Cy3 (Amersham Biosciences, Uppsara, Sweden) using BD Atlas Powerscript Fluorescent Labeling kits (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer’s protocols.
Hybridization, Scanning, and Quantification.  Cy3-labeled probes were hybridized to Atlas Rat 3.8 I microarrays (BD Biosciences Clontech) containing 3757 genes for 16 hours at 50C.  After hybridization, microarrays were washed, dried, and scanned using a GMS 418 confocal laser scanner (Genetic MicroSystems, Woburn, MA).  Fluorescence intensities of the Cy3 channels were quantified using ImaGene 4.0 software (BioDiscovery, El Segundo, CA).
Data analysis was performed using the GeneSpring software, version 5.1 (Silicon Genetics, Redwood City, CA), including appropriate statistics.  Dividing by the median calculated from all of the signal intensities for the Cy3 in a given sample normalized the fluorescence signal for each gene.  The VALUEs for each gene was then calculated by dividing the normalized signal by the median of each gene to offset differences in expression levels between genes.
Keywords: parallel sample

first: Masakazu

last: Takahashi

first: Midori

last: Yoshida

first: Maki

last: Igarashi

first: Naoto

last: Watanabe

first: Noriko

last: Suzuki