title: AML genome hybridization to HG44A

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

institute: Jichi Medical University

summary:
CGH analysis was conducted for AML blasts with Agilent HG44A arrays.
Keywords: disease state analysis

overall_design: A total of 16 AML patients were analyzed. CD34-positive fractions were used as leukemic fractions, while CD34-negative fractions were used as control ones.


title: Three Reactive Compartments in Venous Malformations

status: Public on Mar 06 2007

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary:
Objective: Vascular malformations affect 3% of neonates. Venous malformations (VMs) are the largest group representing more than 50 % of cases. In hereditary forms of VMs gene mutations have been identified, but for the large group of spontaneous forms the primary cause and downstream dysregulated genes are unknown.

Methods and Results: We have performed a global comparison of gene
expression in slow-flow VMs and normal saphenous veins using human whole genome micro-arrays. Genes of interest were validated with qRT-PCR. Gene expression in the tunica media was studied after laser micro-dissection of small pieces of tissue. Protein expression in endothelial cells (ECs) was studied with antibodies. We detected 511 genes more than 4-fold down- and 112 genes more than 4-fold up-regulated. Notably, chemokines, growth factors, transcription factors and regulators of extra-cellular matrix (ECM) turnover were regulated. We observed activation and arterialization of ECs of the VM proper, whereas ECs of vasa vasorum exhibited up-regulation of inflammation markers. In the tunica media, an altered ECM turnover and composition was found.

Conclusions: Our studies demonstrate dysregulated gene expression in tunica interna, media and externa of VMs, and show that each of the three layers represents a reactive compartment. The dysregulated genes may serve as therapeutic targets.
Keywords: disease analysis

overall_design:
- 4 samples
- samples are replicates with dye swap

first: Chinedu

last: Ebenebe

first: Stefanie

last: Diehl

first: Katja

last: Bartnick

first: Hilmar

last: Dörge

first: Jürgen

last: Becker

first: Lothar

last: Schweigerer

first: Jörg

last: Wilting


title: Identification of epigenetically silenced genes in tumor endothelial cells

status: Public on Feb 28 2007

city: Maastricht

first: Debby

last: Hellebrekers

address: P Debyelaan 25

department: Pathology

country: Netherlands

institute: Maastricht University

summary:
Tumor angiogenesis requires intricate regulation of gene expression in endothelial cells (EC). We recently showed that DNA methyltransferase (DNMT)- and histone deacetylase (HDAC) inhibitors directly repress EC growth and tumor angiogenesis, suggesting that epigenetic modifications mediated by DNMTs and HDACs are involved in regulation of EC gene expression during tumor angiogenesis. To understand the mechanisms behind the epigenetic regulation of tumor angiogenesis, we used microarray analysis to perform a comprehensive screen to identify genes downregulated in tumor-conditioned versus quiescent EC, and re-expressed by 5-aza-2’-deoxycytidine and trichostatin A. Among the 81 genes identified, 77% harboured a promoter CpG island. Validation of mRNA levels of a subset of genes confirmed significant downregulation in tumor-conditioned EC and reactivation by treatment with a combination of 5-aza-2’-deoxycytidine and trichostatin A, as well as by both compounds separately. Silencing of these genes in tumor-conditioned EC correlated with promoter histone H3 deacetylation and loss of H3 lysine 4 methylation, however did not involve DNA methylation of promoter CpG islands. For six genes, downregulation in microdissected human tumor endothelium was confirmed. Functional validation by RNA interference revealed that clusterin, fibrillin 1 and quiescin Q6 are negative regulators of EC growth and angiogenesis. In summary, our data identify novel angiogenesis suppressing genes which become silenced in tumor-conditioned EC in association with promoter histone modifications and reactivated by DNMT- and HDAC inhibitors through reversal of these epigenetic modifications, providing a mechanism for epigenetic regulation of tumor angiogenesis.
Keywords: treated versus untreated

overall_design:
A commercial pool (a mixture of 32 donors) of HUVEC (Tebu-bio, Heerhugowaard, The Netherlands) was used for DNA microarray experiments. Total RNA was isolated using the RNeasy RNA isolation kit (Qiagen) according to the supplier's protocol. Possible genomic DNA contaminations were removed by on column DNase treatment with the RNase-free DNase set (Qiagen). The purified RNA was quantified using a Nanodrop spectrophotometer, and RNA quality was evaluated using the Agilent 2100 Bioanalyzer. cDNA synthesis was performed using the Agilent Fluorescent Direct Labelkit with direct incorporation of either cyanine 5 (Cy5) or Cy3 –dCTP nucleotides (Perkin Elmer) according to the manufacturer’s instructions. Labeled cDNA was purified using QIAquick PCR purification columns (Qiagen), followed by concentration by vacuum centrifugation. The Agilent human 1A cDNA microarray (Agilent Technologies, Amstelveen, The Netherlands) contained ~15000 cDNA probes. Labeled cDNA was resuspended in hybridisation buffer and hybridised to Agilent human 1A cDNA microarray for 17 h at 65°C, according to the Agilent protocols. All hybridisations were replicated with cy dyes switched. Two fluorescent microarray comparisons were performed: (1) A comparison of tumor-conditioned HUVEC and quiescent HUVEC and (2) a comparison of tumor-conditioned HUVEC treated with or without a combination of DAC and TSA.

Microarray data processing and statistical analysis
The image file was processed using Agilent's Feature Extraction software (version A.6.1.1, Agilent Technologies). This Feature Extraction program was used to identify pixels corresponding to fluorescent signal (as opposed to background) and to remove pixels with intensities that met the default criteria for outliers. The different normalisation routines applied (Local Background, Minimum signal (feature or background) & Average of all background areas) resulted in comparable results. For each identified area of signal and each of the two dyes, the basic measure of RNA abundance was taken to be the mean intensity over pixels in the identified signal area. The log ratio of the red to green intensities for each signal area was used for statistical analyses, with all subsequent analyses done using the R statistical software package (version 1.2). We selected fold change 1.5 as a threshold, since the 4 hybridisations increase the likelihood of statistical reliability.

middle: M

first: Veerle

last: Melotte

first: Emmanuelle

last: Viré

first: Elise

last: Langenkamp

first: Grietje

last: Molema

first: François

last: Fuks

first: James

middle: G

last: Herman

first: Wim

last: van Criekinge

first: Arjan

middle: W

last: Griffioen

first: Manon

last: van Engeland


title: Modulation of cardiomyocyte gene expression by n-3 PUFA supplementation

status: Public on Feb 21 2007

city: Bologna

first: Annalisa

last: Astolfi

address: via massarenti 11

department: "Giorgio Prodi" Cancer Research center

country: Italy

institute: University of Bologna

summary:
Despite the recognized protective effects of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in cardiovascular diseases, and the demonstration of the control of gene expression by polyunsaturated fatty acids (PUFAs), the effects of these n-3 fatty acids on the whole genoma has never been investigated in cardiac cells. Using rat arrays, the effects of Eicosapentaenoic acid (EPA) and Docosahexaenoic acid (DHA) supplementation on the global gene expression profile were evaluated in cultured neonatal rat cardiomyocytes.
Keywords: nutritional intervention, treatment response

overall_design: Primary cardiomyocyte cultures were obtained from the ventricles of newborn Wistar rats and grown in HAM F10 plus 10% fetal calf serum and 10% horse serum medium (controls), or in the same medium supplemented with 60 uM Eicosapentaenoic acid (EPA) or docosahexaenoic acid (DHA). Media were changed every 48 hrs; cells were grown until complete confluence, then they were scraped off in ice cold PBS, and RNA isolation, labeling of complementary RNA (cRNA), hybridization to Agilent 22K-gene arrays (Rat oligo array G4130A) and assessment of expression ratios were performed. About one million cells treated with RNAlater were homogenized and total RNA was extracted by column technology (Rneasy Protect mini kit) and analyzed on both a spectrophotometer and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Only samples with 28S/18S ratio of >2.0 and no evidence of ribosomal peak degradation were included. The cRNA was generated by in vitro transcription with the use of T7 RNA polymerase (Low RNA input fluorescent linear amplification kit) and labeled with Cy3-CTP  or Cy5-CTP.  Direct comparisons were performed between n-3 PUFAs supplemented cells versus unsupplemented ones (controls); each analysis was replicated swapping the labeling with the two cyanine dyes.

first: Alessandra

last: Bordoni

last: Pession

first: Luca

last: Morandi

first: Andrea

first: Mattia

last: Di Nunzio


title: Profiles of global gene expression in ionizing radiation-damaged human diploid fibroblasts

status: Public on Feb 01 2007

city: Morrisville

first: Tong

last: Zhou

state: NC

address: 133 Southcenter Court, Suite 400

department: Clincial Genetics

country: USA

institute: Gentris Corperation

summary:
Cell cycle arrest and transcriptional responses to ionizing radiation (IR)-induced DNA damage were quantified in telomerase-expressing human diploid fibroblasts. Assays of clonal expansion established 1.5 Gy IR as the D0 dose in three fibroblast lines and this dose was used in all subsequent analyses.  Fibroblasts exhibited >90% arrest of progression from G2 to M at 2 h and from G1 to S at 6 and 12 h post-IR. Normal rates of DNA synthesis and mitosis 6 and 12 h after irradiation caused the S and M compartments to empty by over 70% at 24 h. Microarray monitored global gene expression in IR-treated cells and a new microarray analysis algorithm, EPIG, identified nine IR-responsive patterns of gene expression including a dominant p53-dependent G1 checkpoint response. Many p53 target genes, like CDKN1A, GADD45, BTG2 and PLK3, were significantly up-regulated at 2 h post-IR while many genes whose expression is regulated by E2F family transcription factors, including CDK2, CCNE1, CDC6, CDC2, MCM2, were significantly down-regulated at 24 h post-IR. Numerous genes that participate in DNA metabolism were also markedly repressed in arrested fibroblasts as a result of cell synchronization behind the G1 checkpoint. However, cluster and principal component analyses of gene expression revealed a profile of gene expression 24 h after IR with similarity to that of G0 growth quiescence. These results demonstrate a highly stereotypic pattern of response to IR that reflects primarily synchronization behind the G1 checkpoint but with prominent induction of additional markers of G0 quiescence such as GAS1.
Keywords: time-course, DNA damgage responses

overall_design: Logarithmically growing cells were treated with 1.5 Gy IR or sham, and harvested at 2, 6 or 24 h after the treatment. Total RNA was isolated using Qiagen RNeasy kit. The quality of all RNA samples was confirmed using an Agilent 2100 Bioanalyzer. Microarray analysis was then performed: briefly, 1 µg of sample RNA and global reference RNA (Stratagene) were converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with either Cy3-dUTP or Cy5-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was evaluated using an Agilent 2100 Bioanalyzer prior to hybridization. 750ng of Cy3 and Cy5-labeled cRNA were used in the hybridization. The labeled cRNA from sham- or IR-treated samples was hybridized with the labeled global reference cRNA on an Agilent 22k human 1A array in a hybridization oven (Robbins Scientific Model 400, 1040-60-1AG) at 60oC for 17 h. Hybridization of sample RNA against reference RNA was done twice with dye swap. Following hybridization, the arrays were scanned using the Agilent DNA Microarray Scanner with SureScan® Technology and microarray images were analyzed using Agilent Feature Extraction Software (v7.1). The gene expression level was presented as ratio of sample intensity against reference intensity.

first: Jeff

last: Chou

first: William

last: Kaufmann


title: Gene expression analysis of liver and kidney following methapyrilene treatment in male Sprague-Dawley rats

status: Public on Mar 01 2007

city: Chapel Hill

middle: Todd

last: Auman

address: 3304 Kerr Hall, Campus Box 7360

department: Institute for Pharmacogenomics and Individualized Therapy

institute: University of North Carolina at Chapel Hill

summary:
This study was performed to gain insight into the hepatotoxicity of methapyrilene.  Gene expression changes in the kidney (non-target tissue for toxicity) were compared to those in the liver (target tissue for toxicity) to attribute gene expression changes to relevant biological processes (i.e. toxic response, non-specific acute response, pharmacological response, etc…).
Keywords: Time course, tissue comparison, liver toxicity, hepatotoxicity

overall_design:
Male Sprague-Dawley rats were treated with methapyrilene at two different doses (10 mg/kg/day and 100 mg/kg/day) for 1, 3, and 7 days.  Livers and kidneys were removed 24 hours after the last dose and flash frozen in liquid nitrogen.  Five hundred nanograms (500 ng) of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer’s protocol.  For each two color comparison, 750 ng each of Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v. 7.1) using defaults for all parameters.

Equal amounts of RNA was pooled from all of the animals in each group (n=4).  Each treated group was hybridized against its pooled time-matched and tissue-matched control group in quadruplicate (2 replicates + 2 fluor reversals).

middle: T

first: Kevin

last: Gerrish

first: Qihong

last: Huang

first: Supriya

last: Jayadev

first: Kerry

last: Blanchard


title: Transcriptional comparison of C. albicans WT and ACE2 knockout strains

status: Public on Feb 23 2007

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

summary:
Ace2 transcription factor family genes are found in many fungal genomes and are required for regulation of expression of genes involved in cell separation. We used transcriptional profiling to identify the targets of Ace2 in Candida albicans, and we show that these include several cell wall components, such as glucanases and glycosylphosphatidylinositol-anchored proteins. Expression is downregulated in ace2 deletion mutants in both yeast and hyphal cells. In addition, deleting ace2 results in dramatic changes in expression of metabolic pathways. Expression of glycolytic enzymes is reduced, while expression of respiratory genes (including those involved in the tricarboxylic acid cycle, oxidative phosphorylation, and ATP synthesis) is increased. Similar changes occur in both yeast and hyphal cells. In contrast, genes required for acetyl-coenzyme A and lipid metabolism are upregulated in an ace2 deletion mutant grown predominantly as yeast cells but are downregulated in hyphae. These results suggest that in wild-type strains, Ace2 acts to increase glycolysis and reduce respiration. This is supported by the observation that deleting ace2 results in increased resistance to antimycin A, a drug that inhibits respiration. We also show that Ace2 is required for filamentation in response to low oxygen concentrations (hypoxia). We suggest that filamentation is induced in wild-type cells by reducing respiration (using low oxygen or respiratory drugs) and that mutants with increased respiratory activity fail to undergo filamentation under these conditions.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Gene expression changes during murine mucosal mast cell in vitro differentiation

status: Public on Jan 31 2007

city: Budapest

first: Zoltan

last: Wiener

address: Nagyvarad ter 4.

department: Dept of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary:
The aim of the study was to find novel genes highly upregulated in mouse mucosal mast cells. To carry it out, differentiating progenitor cells were isolated on day4 of culturing and compared to mature mucosal mast cells obtained by day20.
Keywords: cell differentiation stage comparison

overall_design: The experiment was carried out on two microarrays. Array2 is a biological and technical replicate (dye-swap) of array1. In both cases, 3-3 samples were pooled, but of different origin.

first: Eva

last: Gorbe

first: Peter

last: Pocza

first: Anna

last: Gilicze

first: Barbara

last: Kohalmi

first: Judit

last: Jeager

first: Marton

last: Keszei

last: Papp

first: Andras

last: Falus


title: SR proteins in Drosophila

city: Montpellier

first: johann

last: Soret

address: 1919, route de Mende

department: Institut de Genetique Moleculaire

country: France

institute: CNRS

summary: This SuperSeries is composed of the SubSeries listed below.


title: Induced Senescence in HeLa Cells

status: Public on Jan 24 2007

city: New Haven

first: Kimberly

last: Johung

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University School of Medicine


title: Genes Directly Regulated by the Oncogene ZNF217 Using ChIP-chip Assays on ENCODE and Promoter Arrays and Expression Data

status: Public on Jan 25 2007

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

type: Genome binding/occupancy profiling by genome tiling array

relation:
SuperSeries of: GSE6624
SuperSeries of: GSE6625
SuperSeries of: GSE6627


title: Whole Genome array hippocampus_cocaine

status: Public on Jan 09 2007

city: Baltimore

first: Svetlana

middle: I

last: Novikova

state: MD

address: 666 W. Baltimore st

department: Biomedical Sciences

institute: University of Maryland

summary:
We explored the hypothesis that maternal cocaine exposure could alter the fetal epigenetic machinery sufficiently to cause lasting neurochemical and functional changes in the offspring.

These data were used as preliminary results for paper:
Maternal cocaine administration in mice alters DNA methylation and gene expression in hippocampal neurons of neonatal and prepubertal offspring.
Svetlana I. Novikova, Fang He, Jie Bai, Nicholas J. Cutrufello, Ashiwel S. Undieh and Michael S. Lidow
Keywords: whole genome gene expression, hippocampus, laser microdissection

overall_design: Pregnant CD1 mice were administered either saline or 20 mg/kg cocaine twice daily on gestational days 8-19. Male pups from each of ten litters of the cocaine and control groups were analyzed at 3 (P3) day postnatum. Pyramidal layer tissue from the right hemisphere of one of these brains (On every section, the pyramidal layer, encompassing the C1, C2 and C3 hippocampal regions, was carefully cut out)was used for analyzing gene expression. Laser microdissection was performed on a Leica ASLMD laser capture microdissection system (Leica Microsystems, Wetzlar, Germany).

first: Fang

last: He

first: Jie

last: Bai

first: Nicholas

middle: J

last: Cutrufello

first: Michael

middle: S

last: Lidow


title: mouse skeletal muscle study

status: Public on Jan 18 2007

first: Xiaodong

last: Mu

address: 108 N. Greene street

department: Biochemistry and Molecular Biology

institute: University of Maryland School of Medicine

first: Martin

middle: F

last: Schneider


title: Differential gene expression in the bone marrow of layer and broiler chickens

status: Public on Jan 01 2007

city: Ames

first: Diane

last: Spurlock

state: IA

address: 243 Kildee Hall

department: Animal Science

institute: Iowa State University

overall_design:
Refer to individual Series

The experiment was not designed to compare 15 vs. 60 week samples.


title: Gene expression during tumor enhancement by 3,3’-diindolylmethane in rainbow trout

status: Public on Dec 31 2006

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

overall_design:
Refer to individual Series.
Series GSE5643 and GSE5644 are part of the same study/publication but are not comparable.


title: Bis(2-chloroethoxy)methane-induced heart toxicity and recovery in male fisher rats

city: Durham

first: Joel

last: Parker

address: 2605 Meridian Parkway

institute: Constella Group

summary:
Specific gene changes after exposure to the heart toxin, bis(2-chloroethoxy)methane,  were analyzed to elucidate critical pathways associated with recovery from heart toxicity.   Bis(2-chloroethoxy)methane was administered  to male F344/N rats at 0, 200, 400, or 600 mg/kg by dermal exposure for up to 16 days.   Heart toxicity occurred at day 2 of exposure in all three regions of the heart (atrium, ventricle, interventricular septum) and was characterized by myofiber vacuolation, necrosis, mononuclear-cell infiltration,  and atrial thrombosis.  Ultrastructural analysis revealed that the primary site of damage occured in the mitochondrion.  Damaged mitochondria had disrupted cristae and loss of membrane structure, and distention of the myocardial sarcoplasmic reticulum.   By day 5, even though daily dosing was continued, the heart toxic lesions begin to resolved.  By day 16, even though BCEM treatment continued, the heart appeared normal.

RNA was extracted from control and dosed rats at day 2 and day 5, and analyzed for gene change by PCR. Gene changes associated with promoting cell growth including up regulation of growth factors and cell adhesion molecules were up regulated.    Temperature regulation was promoted by up regulation of uncoupling proteins.    Genes controlling the action potential of the heart, including ion flow and G protein signals, were altered. Because mitochondria are damaged by BCEM exposure, preserving and restoring energy function to the heart is considered to be essential, and up regulation of components of the ATP synthase unit occurred by day 5.

Significant gene changes included up regulation of transcription factors, growth factors, membrane bound G protein signals, and ion transport controls.    Multiple gene changes in the heart may contribute to restoration of heart function after exposure to environmental cardiotoxins.
Keywords: toxicity, recovery, cardiac, heart

overall_design:
Chemical and Animal exposures:

Bis(2-chloroethoxy)methane (CAS No. 11-91-1; lot B004160277) (Karl Industries, Aurora, OH) (Fig, 1) was found to be 98.5% pure (Dunnick et al. 2004a; Dunnick et al. 2004b) .   Solutions of BCEM were prepared in 95% ethanol for dosing by dermal administration daily to male F344 rats,  excluding weekends, for two weeks plus two consecutive dosages before the last sacrifice on study-day 16, at which animals had received  a total of 12 doses.   Fur from the site of application was clipped weekly.  Stock solutions prepared at concentrations of 0, 800, and 1200 mg/ml were stored in amber glass bottles at room temperature. The administrations were applied to the skin of the male rats at 0.5 ml/kg body to deliver doses of 0, 400, or 600 mg/kg body weight.  All dose formulations were determined to be within ±10% of target concentrations.  Approximately 45% of a dermal dose of CEM is adsorbed (NIEHS Contract NO1-ES-75407 2002). Male F344/N rats  (Taconic Laboratories, Germantown, NY) were placed on study at 5 weeks of age and housed one per cage in polycarbonate cages in rooms maintained at temperatures between  69 and 75°F with 35 – 65% relative humidity and a 12-hr light/dark cycle.  Control and treated groups received irradiated NTP-2000 diet (Zeigler Brothers, Gardners, PA) ad libitum.

Histopathology:
Animals were anesthetized with CO 2  and heart collected and preserved in 10% formalin. Slides were made from paraffin sections from rats treated with BCEM as previously described (Dunnick et al. 2004a).   Pathologic  analysis included comparing heart lesions in male rats after 2, 3, 5, and 16 days of treatment.

RNA Extraction Methods

RNA was extracted from hearts of three control animal at day 2, three control rats at day 5, three rats exposed to 200, 400, or 600 mg/kg BCEM at day 2 and three at day 5. Animals designated for heart RNA extraction were anesthetized with CO2/O2 on study days 2 and 5, exanguinated, and their hearts infused with RNAlater.   Total cardiac RNA was isolated from hearts using the QIAGEN Rneasy kit (QIAGEN, Valencia, CA).   The RNA was quantified through optical density measurements and agarose gel electrophoresis, and kept frozen at – 70 C.   RNA was extracted from control, 200, 400, and 600 mg/kg rats.

first: June

last: Dunnick

first: Pamela

last: Blackshear

first: Grace

last: Kissling

first: Abraham

last: Nyska


title: Aging Induced Alterations in Hepatic Gene Expression of the Male Fisher Rat

status: Public on Dec 17 2006

summary:
Toxicokinetic and metabolism studies are considered crucial to dose setting and interpretation of data from rodent carcinogenicity studies.  The metabolism and distribution studies are usually conducted in 6 to 8 week old rodents.  However cancer studies generally involve exposures from 6 weeks of age to 108 weeks or more of age.  It is recognized that age-related differences in sensitivities to some xenobiotics occur in several rodent models including the rat.  However, the potential for changes in metabolism with age has received little attention in the toxicology community especially in regard to extrapolation of rodent data to human risk assessment.  The advent of microarray technology has allowed a more global assessment of genes whose products are associated with xenobiotic metabolism.  We studied hepatic gene expression in 38 untreated F344/N rats at approximately 32, 58 and 84 weeks of age corresponding to 6, 12, and 18 months on study.  Statistical analysis of microarray (SAM) identified differential expression between the youngest and the oldest rats for genes whose products are involved in phase I and phase II metabolic pathways.  Fifteen of 30 cytochrome P450 genes from CYP families 1 – 4 showed marked decrease in expression at 84 weeks while only two showed increased expression.  The results of this study demonstrate prominent decreased expression in CYP family genes involved in xenobiotic metabolism in untreated rats as they age.  The assumption of a constant metabolic profile when extrapolating results from long-term chemical exposures needs to be reconsidered.
Keywords: :  Liver, rat, differential gene expression, microarray, transcriptome, aging, cytochrome P450, xenobiotic metabolism

overall_design:
Animals and Study Design. 	Male Fischer 344 rats approximately 36 ± 3 days old were supplied by Taconic laboratory animals (Germantown, NY) and were approximately six weeks old when placed in study rooms as sentinel animals for two-year studies.  All studies were conducted at Battelle Science and Technology International (Columbus, Ohio).  The livers from the male rat sentinels from three studies at six months (15 total rats), two studies at twelve months (10 total rats) and three studies at eighteen months (13 total rats) were used in this study.  The sampling times corresponded to approximately 32, 58 and 84 weeks of age for the rats. The studies in which the sentinels were a part were approved by Battelle’s Institute Animal Care and Use Committee and were conducted in accordance with the guide for the care and use of laboratory animals (ILAR 1996).  Details of the animal care and handling for studies conducted at Battelle have been reported previously (Boorman et al. 2005).
The rats were kept in a cage until necropsy.   The rats were anesthetized with CO2/O2, blood samples obtained for serology by cardiac puncture, the abdominal cavity was opened and the portal vein was severed.  The left liver lobe was promptly removed and a cross section was placed in 10% neutral buffered formalin (NFB).  The liver section was embedded, sectioned and stained with H&E and examined.  The remainder of the left lobe was processed for subsequent RNA isolation.
RNA isolation. 	The left hepatic lobe was cut into 0.5 cm cubes or smaller and immersed in RNALater® (Ambion, Austin, TX) within 4 minutes of necropsy.  The tissues were stored in RNALater® overnight at 4+/-30C, then stored at - 20+/-10C until RNA isolation (within 60 days).  Details of the RNA isolation procedures have been previous published (Boorman et al. 2005).  Briefly, the RNA samples were frozen at - 700 C and shipped to the NTP repository until transfer to Paradigm Array Labs (Icoria, Inc., A Clinical Data Inc. Company, RTP, NC) for microarray analysis.  RNA was isolated from individual rats.  Equal amounts of RNA from sixty-three male sentinel rats (25 rats at 32 weeks of age, 25 rats at 58 weeks of age and 13 rats at 84 weeks of age) were used to form a composite control pool for comparison with the individual rats at each age.
Microarray Hybridizations. 	One µg of total RNA from either an individual rat or from the pooled sample was amplified and labeled with a fluorescent dye (either Cy3 or Cy5) using the Low RNA Input Linear Amplification Labeling kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.  The amount and quality of the resulting fluorescently labeled cRNA was assessed using a Nanodrop ND-100 spectrophometer and an Agilent Bioanalyzer.  Equal amounts of Cy3- or Cy5-labeled cRNA were hybridized to the Agilent Rat Oligo Microarray (Agilent Technologies, Inc., Palo Alto, CA) for 17 hrs, prior to washing and scanning.  Data was extracted from the resulting images using Agilent’s Feature Extraction Software (Agilent Technologies, Inc., Palo Alto, CA).

first: Mori

last: Kazuhiko

middle: E

first: Edward

middle: K

last: Lobenhofer

first: Denise

middle: P

last: Orzech

first: Joseph

middle: H

last: Roycroft

first: Richard

middle: D

last: Irwin

first: Gary

middle: A

last: Boorman


title: Regulation of the stringent response is the essential function of the conserved bacterial G protein CgtA in V. cholerae

status: Public on Dec 28 2006

city: Boston

first: David

last: Raskin

state: MA

address: 200 Longwood Avenue

department: Microbiology & Molecular Genetics

institute: Harvard Medical School

summary:
The gene encoding the conserved bacterial G protein CgtA (Obg) is essential for viability in every organism in which it has been studied. CgtA has been reported to be involved in several diverse bacterial functions, including ribosome assembly, DNA repair, sporulation and morphological development. However, none of these functions have been identified as essential. Here we show that depletion of CgtA in Vibrio cholerae causes global changes in gene expression that are consistent with induction of a classical low nutrient stress response or “stringent” response. We show that depletion of CgtA leads to increased ppGpp levels which correlates with induction of the global stress response and cessation of growth. The enzyme RelA is responsible for synthesis of the alarmone ppGpp during the stringent response. We show that CgtA is no longer essential in a relA deletion mutant and thus conclude that the essentiality of CgtA is directly linked to its ability to affect ppGpp levels. The enzyme SpoT degrades ppGpp and here we show that SpoT is essential in a RelA+ CgtA+ background but not in a relA deletion mutant. We also confirmed that CgtA interacts with SpoT in a two-hybrid assay. We suggest that the essential function of CgtA is a repressor of the stringent response, and acts by regulating SpoT activity to maintain low ppGpp levels when bacteria are growing in a nutrient rich environment.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Cocaine-induced changes in the gene expression

status: Public on Jan 04 2007

first: Svetlana

last: Novikova

summary:
Several recent reports show that the cerebral cortex in humans and animals with altered expressions of Wnt/cadherin network-associate molecules display cytoarchitectural abnormalities reminiscent of cortical dysplasias seen in some (mouse-, rat-, and monkey-based) animal models of prenatal cocaine exposure. Therefore, we employed oligo microarrays followed by real-time RT-PCR to compare expressions of genes involved in Wnt and cadherin systems in the cerebral wall of 18-day-old (E18) fetuses from cocaine-treated (20 mg/kg cocaine, s.c., b.i.d., E8-18) and drug-naive (saline, s.c.) mice. The pregnant mice chronically treated with cocaine in the above-described manner represent one of the animal models producing offspring with widespread cortical dysplasias. Out of more than 150 relevant genes in the arrays, 32 were upregulated and 9 were downregulated in cocaine-exposed fetuses. The majority of these genes (30 out of 41) were similarly affected in the frontal and occipital regions of the cerebral wall. We also used Western immunoblotting to examine the ability of cocaine to regulate the protein levels of beta-catenin, the key functional component of both Wnt and cadherin systems. While the total cell levels of beta-catenin were increased throughout the cerebral wall of cocaine-exposed fetuses, its nuclear (gene-transcription driving) levels remained unaltered. This suggests a transcription-unrelated role for cocaine-induced upregulation of this protein. Overall, our findings point to an intriguing possibility that that cerebral cortical dysplasias observed in several animal models of prenatal cocaine exposure may be at least in part related to alterations in the Wnt/cadherin molecular network.

It has been demonstrated that exposure to cocaine increases cell death in the fetal CNS. To examine the molecular mechanisms of this effect, we employed mouse oligo microarrays followed by real-time reverse transcriptase-polymerase chain reaction (real-time RT-PCR) to compare expressions of apoptosis-related genes in the cerebral wall of 18-day-old (E18) fetuses from cocaine-treated (20 mg/kg cocaine, s.c., b.i.d., E8th-E18th) and drug-naive (saline, s.c.) mice. Out of approximately 400 relevant genes in the arrays, 53 showed alterations in expression in cocaine-exposed fetuses. Upregulation was observed in 35 proapoptotic and 8 antiapoptotic genes; 4 proapoptotic and 6 antiapoptotic genes were down-regulated. The affected genes encode a wide range of apoptosis-related proteins, including death receptors (NTF-R1, NTF-R2, DR3, DR5, LTbeta-R, GITR, P57 TR-1) and their adaptor and regulatory proteins (MASGE-D1, TRAF-2, SIVA, MET, FLIP, FAIM, IAP1, ATFA), members of transcription regulatory pathways (JNK, NF-kappaB, P53), members of BCL-2 family of proteins (BID, BAD, BAX, BIK, NIP21, NIP3, NIX, BCL-2), DNA damage sensor (PARP-1), caspases and their substrates and regulatory proteins (caspases 8, 4, 9, and 3, ACINUS, CIDE-A, CIDE-B, GAS2), mitochondrially released factors (cytochrome c, AIF, PRG3), specific endoplasmic reticulum- and oxidative stress-associated factors (BACH2, ABL1, ALG2, CHOP), members of cell survival AKT and HSP70 pathways (PIK3GA, PTEN, HSP70, BAG1, BAG2), and others. This suggests that cocaine affects survival of developing cerebral cells via multiple apoptosis-regulating mechanisms.
Keywords: Whole genome oligo microarray, Real time RT-PCR, gene expression analysis

overall_design:
Animals
Timed pregnant Swiss Webster (CFW; Charles River
Lab. Wilmington, MA) dams were maintained in individual
cages in a climate-controlled room on a 12/12-h light/
dark cycle. They were divided into two groups. The first
(experimental) group received subcutaneous (at the dorsum
of the neck) injections of 20 mg/kg cocaine hydrochloride
(Research Technology Branch, National Institute
of Drug Abuse, Rockville, MD) dissolved in 200 mkl of
0.9% saline, twice a day (at 8:00 AM and 8:00 PM) from
8th through 18th day of pregnancy (E8–E18). The second
(control) group was subjected to the same schedule of
0.9% saline only injections. The cocaine treatment was
designed to replicate the one capable of reducing cerebral
cortical mass in mouse offspring. Also, the
relatively protracted period the chronic treatment was
chosen to maximize the changes in the tissue expression
of cocaine-regulated genes of interest. Throughout the
treatment, all mice were weighed daily, and, from E8, the
control and experimental animals were pair-fed, with the
daily amount of food (Mouse Chow; Ralston Purina Saint
Louis, MO) provided to each control dam being matched
to that consumed by the paired experimental dam. Water
was available ad libitum. We found that this feeding
regiment resulted in similar weight gains from E8 to E18
in both experimental and control animal groups
(46.41F0.45% and 44.99F0.59% respectively). On E18,
1 h after the morning treatment, the animals were
anesthetized by peritoneal injection of 50 mg/kg sodium
pentobarbital (Abbott Lab., Abbott Park, IL) and their
uteri were removed. The frontal cerebral wall (containing
cerebral cortex and underlying transient cortical zones
anterior to the striatal level) and the occipital cerebral wall
(containing cerebral cortex and underlying transient
cortical zones posterior to the level of the hippocampus)
were dissected from the fetuses and stored in liquid
nitrogen prior to analysis. The animal experimentations
used in this study were approved by the University of
Maryland Animal Care and Use Committee.
Microarray
Tissue from two control and two experimental fetuses
were used in the processing of a single microarray slide
(Part G4121A, Agilent Technol). Five slides were processed
per region of the fetal cerebral wall. For a given region, the
tissue for each microarray slide was obtained from a
separate set of control and experimental litters. Total RNA
was isolated using TRIzol Reagent (Invitrogen, Carlsbad,
CA). The yield of total RNA was determined by absorbance
at 260 nm on a DU 640 Spectrophotometer (Beckman
Coulter, Fullerton, CA). The 260/280 nm ratios of the
samples were >1.8. For each assay, 5 mkg of RNA from
control tissue and 5 mkg of RNA from experimental tissue
were reverse transcribed using 3DNA Array Detection Kit
(Genesphere, Hatfield, PA) with primers containing different
dcaptureT sequences for control and experimental
samples. SuperScript II Reverse Transcriptase for these
reactions was purchased from Gibco BRL (Gaithersburg,
MD). The resultant cDNAs were hybridized to microarray
slides for 16 h in Agilent Hybridization Buffer (Agilent
Technol) at 60 8C. Upon completion of the hybridization,
the slides were washed for 10 min with 0.005% Triton in
6xsodium chloride/sodium citrate buffer (pH 7; SSC) at
room temperature and then for five more min with 0.005%
Triton in 0.1xSSC and 1 more minute in 0.1xSSC (pH 7),
both at 4 8C. Washed slides were air-dried for 30 s. For
fluorescent labeling of microarray-bound cDNA, the slides
were incubated for 3 h at 65 8C with Capture Reagent
Hybridization Mixture from 3DNA Array Detection Kit
(Genesphere). In this mixture, Alexa 546 fluorochromeincorporating
dendrimers contained single-stranded arms
complimentary to the dcaptureT sequences used in the
reverse transcription of RNA from control tissue, while
Alexa 647 fluorochrome-incorporating dendrimers contained
arms complimentary to the capture sequences used
in reverse transcription of RNA from experimental tissue.
The labeling reaction was terminated by washing of the
microarray slides at room temperature for 10 min with
0.005% Triton in 2xSSC and for another 10 min with in
0.2xSSC. After that, the slides were air-dried for 30 s. The
processed microarray slides were scanned at 10 Am
resolution on a GenePix 4100A scanner (Axon Instr., Union
City, CA) with the laser excitation at 532 nm [emission filter
575DF35 (green); photomultiplier voltage 550] for Alexa
546 (control samples) and the laser excitation at 635 nm
[emission filter 670DF40 (red); photomultiplier voltage
695] for Alexa 647 (experimental samples). The signals
were converted into 16-bits-per pixel resolution images,
providing color depth of 65,536 levels. The densitometry
was performed with GenePix Pro 4.1 software (Axon Instr.).
Background was subtracted using the dlocal background
correctionT procedure available in the software. Quality control utilized 255 positive controls, 161 negative controls
and 646 QC-spots present on Agilent’s arrays. For
replicates within a slide, median signal values were
calculated. For each array, the data were normalized in
Acuity 3.1 software (Axon Instr.) by applying locally
weighted scatterplot smoothing (LOWESS) transformation.
The between array scale normalization
was done using intensity log10 ratio distribution box plots (GeneSight
software, BioDiscovery, El Segundo, CA) for verification.
Statistical analysis of the normalized data was conducted
by the Significant Analyses for Microarray Algorithm
(SAM) using Excel macros available at the Stanford SAM website.
In the analyses of both frontal and occipital regions of the fetal cerebral wall,
the cut-off thresholds were set to identify the maximum
number of cocaine exposure-regulated genes at the minimal
false discovery rate (FDR) allowed by SAM for a given set
of microarray data. For both regions, the FDR rates were
<0.5%. The apoptosis and Wnt pathway-related genes were identified with Pathway Assist 2.0 software (Stratagene, La Jolla, CA).
This was followed by manual review of literature for each
identified gene.

first: Jie

last: Bai

first: Fang

last: He

first: Irina

last: Badan

last: Lidow

first: Michael


title: B. thetaiotaomicron or B. longum mono-association vs. bi-association

city: Saint Louis

first: Justin

middle: L.

last: Sonnenburg

state: MO

address: 4444 Forest Park

department: Center for Genome Sciences

institute: Washington University

sample_organism:
Bacteroides thetaiotaomicron
Bifidobacterium longum

middle: L

first: Christina

last: Chen

first: Jeffrey

last: Gordon


title: Effect of phthalate and terephthalate on Rhodococcus sp. RHA1

status: Public on Jan 19 2007

city: Vancouver

first: Hirofumi

last: Hara

state: BC

address: 2350 Health Science Mall

department: Microbilogy and Immunology

country: Canada

institute: University of British Columbia

first: Lindsay

last: Eltis

first: Julian

last: Davies

first: William

middle: W

last: Mohn


title: Temporal lobe epilepsy and Alzheimer's disease

status: Public on Jan 23 2007

city: New York

first: Erin

last: Heinzen

state: NY

department: Institute for Genomic Medicine

institute: Columbia University


title: The effect of lovastatin and fenofibrate in a short term diet-induced hyperlipidemia model in mice

status: Public on Feb 15 2007

city: Ljubljana

first: Drago

last: Kuzman

address: Verovskova 57

country: Slovenia

institute: Lek pharmaceuticals d.d.

summary:
C57BL/6 mice were fed ad libitum for the first 5 days of the experiments with high fat high cholesterol (HFC) diet only. The next 7 days of the experiments mice were continuously fed on a HFC diet and simultaneously vehicle (control group), fenofibrate (100 mg/kg) or lovastatin (30 mg/kg) were orally daily administered. At the end of the experiment (day 12) fenofibrate and lovastatin significantly decreased plasma LDL levels, while plasma cholesterol levels were significantly decreased by lovastatin only. Gene expression analysis of hyperlipidemic mouse liver revealed 391 significantly modulated genes when compared to standard diet fed mice. KEGG pathways related to modulated genes were identified and the most significant were biosynthesis of steroids, metabolism of xenobiotics by cytochrome P450 and linoleic acid metabolism. These pathways were modulated in a way, which increased the clearance of lipids and decreased endogenous synthesis of fatty acids and cholesterol. Additionally, genes involved in the regulation of detoxification pathways were significantly upregulated. The hepatic gene expression profiles of fenofibrate and lovastatin-treated HFC diet fed mice were compared to the vehicle-treated HFC diet fed mice. In the fenofibrate-treated group 124 genes and in the lovastatin-treated group 38 genes were significantly modulated. In the fenofibrate-treated group the top three significantly modulated pathways are fatty acid metabolism, propanoate metabolism and ascorbate and aldarate metabolism. While in the lovastatin-treated group the top three significantly modulated pathways are glycosphingolipid biosynthesis, tyrosine metabolism and metabolism of xenobiotics by cytochrome P450. Expert based classification revealed that both fenofibrate an lovastatin significantly down-regulated genes encoding sterol-C4-methyl oxidase like and 7-dehydrocholesterol reductase. Additionally, the regulation of cholesterol at the transcriptional level was also significantly augmented by fenofibrate and lovastatin, as judged by increased expression of  -1 and decreased expression of INSIG-2.
Keywords: Drug treatment

overall_design: 24 seven week old mice were randomly divided in four experimental groups. Control group (n = 6) was fed on a standard chow diet (diet 3430, Provimi Kliba AG, Kaiseraugst, Switzerland) and treated orally once daily with vehicle for 12 days. Remaining 18 mice were fed on HFC diet for 12 days. On day five HFC diet fed mice were treated orally once daily either with vehicle (HFC group, n=6), lovastatin (HFC lovastatin group, 30mg/kg, n=6) or fenofibrate (HFC fenofibrate group, 100mg/kg, n=6). Doses of lovastatin and fenofibrate were choosen according to the literature review. On day 12 liver were excised and immediately frozen in liquid nitrogen and stored at -80°C for the subsequent transriptome analyses

first: Luka

last: Peternel

first: Damjana

last: Rozman

first: Manica

last: Cerne


title: Identification of Helicobacter pylori genes contributing to stomach colonization.

status: Public on Dec 15 2006

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

summary:
Chronic infection of the human stomach with Helicobacter pylori leads to a variety of pathologic sequelae including peptic ulcer and gastric cancer, resulting in significant human morbidity and mortality. Several genes have been implicated in disease related to H. pylori infection including the vacuolating cytotoxin and the cag pathogenicity island. Other factors important for establishment and maintenance of infection include urease enzyme production, motility, iron uptake and stress response. We utilized a C57BL/6 mouse infection model to query a collection of 2400 transposon mutants in two different bacterial strain backgrounds for H. pylori genetic loci contributing to colonization of the stomach. Microarray based tracking of transposon mutants allowed us to monitor the behavior of transposon insertions in 758 different gene loci. Of the loci measured 223 (29%) had a predicted colonization defect. These include previously described H. pylori virulence genes, genes implicated in virulence in other pathogenic bacteria and 81 hypothetical proteins. We have retested 10 previously uncharacterized candidate colonization gene loci by making independent null alleles and confirmed their colonization phenotype using competition experiments and determination of the dose required for 50% infection. Of the genetic loci retested, 60% have strain specific colonization defects while 40% had phenotypes in both strain backgrounds for infection, highlighting the profound effect of H. pylori strain variation on the pathogenic potential of this organism.

This SuperSeries is composed of the SubSeries listed below.

first: David

last: Baldwin

first: N


title: Cold stress in sugarcane

status: Public on Dec 03 2006

city: Campinas

first: Fábio

middle: Tebaldi

last: Nogueira

department: CBMEG

country: Brazil

institute: Institute of Biology


title: Spleen vs Liver - cDNA - Single and Double

city: Pasadena

first: Sangdun

last: Choi

state: CA

address: 1200 E. California Blvd

department: Biology

institute: California Institute of Technology


title: Effects of laughter on gene expression profiles patients with type 2 diabetes (Tenri)

status: Public on Nov 23 2006

city: Minamidai, Kawagoe

first: Toshiro

last: Saito

state: Saitama

department: Life Science Group

country: Japan

institute: Hitachi, Ltd.

summary:
Sample tissue: peripheral blood

Samples for gene expression analysis were obtained before and after the event.
Keywords: time course, event response

overall_design: Event: watching a comic video or  spending tedious time.


title: Dissecting the rice genes responsible for long time changes of nitrogen supply forms and nitrogen starvation

status: Public on Dec 07 2006

city: Nanjing

first: Guohua

last: Xu

state: Jiangsu

address: Tongwei Road #1

department: Plant Nutrition

country: China

institute: Nanjing Agricultural University

summary:
In comparison with provision of either ammonium or nitrate alone, simultaneously supplying both forms of N results in superior growth and yield for the majority of plants including rice. Using a rice 22K oligo-array, we performed transcriptome analysis to identify genes of rice (Oryza sativa L. ssp. japonica) responsive to change of N-supply forms and N-starvation. Using the supply of ammonium nitrate (one to one molar ratio) as control, the total number of root genes that were equal or more than two fold up- or down- regulated was 445, 324, and 781 by upon supply of either ammonium or nitrate or continuous N starvation, respectively for 96 h. In the shoot the equivalent numbers were much smaller only 32, 58, and 165, respectively. Clustering of the rice genes associated with different environmental stresses revealed substantial organ specificity of the root and shoot to N starvation, and also to the N supply form. Genes encoding transporters for ammonium and nitrate, nitrate reductase, glutamate dehydrogenase, and aspartate amino transferase, showed great response to change of the N supply form, especially to N starvation. Some of the genes involved in chlorophyll metabolism, carbon fixation and assimilation, were enhanced by ammonium supply only, but significantly suppressed by N-starvation. In the shoot there was increased expression of more general stress genes under nitrate when compared to ammonium nutrition. In the root the reverse situation was true with more apparent stress under ammonium nutrition. The microarray approach has revealed new levels of complexity in the response of rice to the form of N supply.
Keywords: Rice; root; shoot; nitrogen starvation; nitrogen form; ammonium; nitrate; gene expression

overall_design:
Rice seedlings were grown in a hydroponic system in a growth chamber with control of both temperature and light. After normal growth for two weeks and for one week with completely avoiding any N source, the plants at four and a half leaf stage were re-supplied with ammonium nitrate (equal amount of either form of N), or only ammonium (ammonium sulphate and ammonium chloride), or only nitrate (calcium nitrate and magnesium nitrate), and continuing at zero N (N starvation). All the other essential nutrients were the same for all four treatments, except for sulfate and chloride which ranged between 1.1 – 2.6 mM and 0.5 – 2.5 mM, respectively. In Arabidopsis, addition of 3 mM Cl to ‘controls’ did not produce any changes in the expression of genes in an experiment investigating the re-supply of 3 mM nitrate (Scheible et al., 2004). In other microarray experiments, extra addition of 5 mM Cl for Arabidopsis (Wang et al., 2000; Wang et al., 2004) and 1.4 mM sulphate for tomato (Wang et al., 2001) were used to replace nitrate for identifying the N deprivation responsive genes. Therefore, we assume that the relative smaller difference in sulfate and chloride concentrations among the four treatments in the normal supply range for plants would not significantly affect the expression profile of genes responsible for changes in N supply form and starvation in our experiments.
For identifying the genes responding to the various N conditions by micro-array analysis, we extracted total RNA respectively from the roots and shoots at the 96 h after initiation of the four respective treatments. We used amplified and labeled cRNA from ammonium nitrate treatment as control, we performed array-hybridization for the cRNA from the treatment of single ammonium form, single nitrate form, or continuous N depletion, respectively. Agilent 60-mer oligonucleotide arrays containing 21,938 unique transcription units (Agilent Technologies, Tokyo, Japan) were used. Two biological replicates of each treatment were performed for microarray analyses.

first: Baozhen

last: Li

first: Kouji

last: Satoh

first: Qirong

last: Shen

first: Shoshi

last: Kikuchi


title: LPS timecourse

city: San Diego

first: Timothy

last: Ravasi

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California-San Diego


title: Response of gcr1 null mutant to glucose

status: Public on Nov 27 2006

city: Hattiesburg

first: Kellie

last: Barbara

state: MS

address: 118 College Dr. #5018

department: Biological Sciences

institute: Univ. of Southern MS

summary:
This experiment was done to detect the transcriptomic defects in the gcr1 null mutant, relative to an isogenic wild type, in the immediate response to glucose.
Keywords: time course

overall_design: Both gcr1 mutant and wild type cells were grown in YEP containing 3% pyruvate to early/mid log phase. The 0min sample was taken just prior to glucose addition. After addition of glucose, samples were taken at 20min and 60min. Total RNA was extracted for both strains and expression was measured by competitive hybridization of the mutant and wild type labeled cRNA for each time point.


title: UMRR vs Liver or Spleen


title: H3K4 trimethylation ChIP - ctk1 deletion and wild type

status: Public on Dec 01 2006

city: Pullman

first: John

middle: J.

last: Wyrick

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

type: Genome binding/occupancy profiling by array


title: Gene expression changes resulting from cdc25a over-expression

status: Public on Nov 13 2006

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

summary:
CDC25A is a critical target of checkpoint, and its overexpression is observed in various cancers.  Here we demonstrate that in vivo levels of Cdc25A expression determine the efficiency of transformation and tumorigenesis. Transgenic expression of CDC25A in murine mammary glands cooperates with tumorigenesis induced by expression of ras or neu.  CDC25A- overexpressing tumors display aggressiveness and genomic instability with changes in fragile chromosomal regions, including the region orthologous to human 1p32-36.
Keywords: genetic modification

overall_design: Tumors from two mice from each of two conditions (MMTV-cdc25a;MMTV-neu and MMTV-neu) were analyzed in a dye swap experiment.  A total of four hybridizations were performed.

first: Peter

middle: G

last: Fuhrken

first: Hiroaki

last: Kiyokawa

middle: T

first: Dipankar

last: Ray


title: The poloxamer P-407 chronic hyperlipidemia mouse model

status: Public on Nov 22 2006

first: Drago

last: Kuzman

summary:
We performed a systemic study of the poloxamer P-407-induced chronic hyperlipidemia in C57BL/6J mice. Mice were treated 96 days every third day.The poloxamer mostly elevates plasma triglycerides and cholesterol while change of the liver cholesterol is not significant.
Keywords: Disease model state analysis

overall_design: A group of 12 mice were administered 0.5 g/kg poloxamer P-407 by intraperitoneal (i.p.) injection (poloxamere group), a control group of 4 mice were injected every third day with normal saline. Total RNA from P-407 treated 12 mice has been pooled into 3 biological replicas (Smpl1, Smpl2 and Smpl3). Reference total RNA has been obtained by pooling 4 mice from control group. Each RNA sample has been splitted and hybridised in parallel on cDNA (G4104A) and oligonucleotide (G4120A) mouse microarrays (Agilent Technologies, CA, USA.

first: Manica

last: Cerne

first: Tadeja

last: Rezen

first: Damjana

last: Rozman


title: RpoS Controls the Vibrio cholerae Mucosal Escape Response

status: Public on Nov 03 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

first: N

last: Dolganov


title: Comparison of normal breast epithelium and stroma from reduction and I.D.C. cases

status: Public on Oct 20 2006

city: Montreal

first: Greg

last: Finak

state: QC

address: 3775 University

department: Mcgill Center For Bioinformatics

institute: McGill University

summary:
Histologically normal breast epithelium and stroma were laser capture microdissected from breast reduction specimens and from specimens of invasive ductal carcinoma. The objective of the study was to compare normal reduction tissues to tissues adjacent to I.D.C.  to determine whether adjacent normal tissues contained expression profiles correlated with characteristics of the primary tumor   and to identify markers of normal epithelium and stroma.
Keywords: disease state analysis

overall_design: common reference design. 66 samples  replicated twice as dye swaps  generating 132 arrays.


title: H3K36Ac ChIP chips

status: Public on Nov 01 2006

city: Chapel Hill

first: Jason

last: Lieb

state: NC

address: 203 Fordham Hall CB# 3280

institute: UNC-Chapel Hill

summary:
Histone lysine (K) acetylation is a major mechanism by which cells regulate the structure and function of chromatin, and new sites of acetylation continue to be discovered.  Here we identify and characterize histone H3K36 acetylation (H3K36ac).  By mass spectrometric analysis of H3 purified from Tetrahymena thermophila and S. cerevisiae (yeast), we find that H3K36 is acetylated in addition to being methylated.  Using an antibody specific to H3K36ac, we show that this modification is conserved in mammals.  In yeast, genome-wide ChIP-chip experiments show that H3K36ac is localized predominantly to the promoters of RNA polymerase II-transcribed genes, a pattern mutually exclusive to that of H3K36 methylation.  The pattern of H3K36ac localization is similar to that of other sites of H3 acetylation, including H3K9ac and H3K14ac.  Using histone acetyltransferase complexes purified from yeast, we show that the Gcn5-containing SAGA complex specifically acetylates H3K36 in vitro.  Deletion of GCN5 completely abolishes H3K36ac in vivo.  The regulation of H3K36ac by Gcn5 suggests a function for this modification in transcription.  These data expand our knowledge of the genomic targets of Gcn5, show H3K36ac is highly conserved, and raise the intriguing possibility that the transition between H3K36ac and H3K36me acts as a switch in chromatin function along transcription units.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Studying genome-wide distribution of H3K36acetylation in Saccharomyces cerevisae

first: Bhargavi

last: Rao


title: Temporal expression profile of megakaryocytic differentiation primary CD34+ cell culture

status: Public on Nov 08 2006

summary:
Little is known about the global transcriptional program underlying megakaryocytic (Mk) differentiation, maturation, and apoptosis.  Using DNA microarrays and Q-RT-PCR, we examined the transcriptional profile of Mk differentiation human CD34-positive hematopoietic stem and progenitor cells cultured with thrombopoietin, interleukin-3, and Flt3-ligand.  The goal this study was to identify genes involved in the various facets of Mk differentiation including commitment, polyploidization, proplatelet formation, and apoptosis.
Keywords: time course

overall_design: G-CSF mobilized peripheral blood CD34-positive cells were cultured with TPO, IL-3, and Flt3-L to induce Mk differentiation.  Samples prior to day 5, including uncultured starting cells,  were analyzed directly, whereas samples after and including day 5 were positively selected for CD41a expression immediately prior to RNA isolation.  Three biological replicate experiments were analyzed and approximately one-half of the samples from each experiment were technically replicated.  Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference RNA pool labeled with Cy5.

first: Chi

last: Chen

first: William

middle: M

last: Miller


title: Effect of biphenyl, ethylbenzene, and benzoate on Rhodococcus sp. RHA1

first: Michael

last: McLeod

state: British Columbia

address: 4506 - 2350 Health Sciences Mall

department: Microbiology & Immunology

overall_design: Refer to individual Series


title: Analysis of gene expression changes in MSCs and BMCs that occur with Staph aureus mastitis

status: Public on Dec 06 2006

city: Guelph

first: Wenjing

last: Tao

state: ON

address: Gordon street

department: Department of Pathobiology

institute: University of Guelph


title: NB4 cells treated with lethal toxin

status: Public on Oct 07 2006

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary:
Bacillus anthracis lethal toxin (LT) exposure on NB-4 cells
Keywords: time course

overall_design: color-swap dye-reversal

first: Amanda

last: Ozin

first: Stefan

last: Kaufmann


title: Bacterial lipopolysaccharides induce defense responses associated with Programmed cell death in rice cell

status: Public on Sep 28 2006

city: Kawasaki

first: Hanae

last: Kaku

state: Kanagawa

address: 1-1-1, Higashi-Mita, Tama-ku

department: Life Sciences

institute: Meiji University

summary:
PAMP (Pathogen-Associated Molecular Pattern) recognition plays an important role in innate immune responses both in plants and animals. Lipopolysaccharides (LPS) of gram-negative bacteria are a typical PAMP molecule and have been reported to induce defense-related responses such as suppression of hypersensitive responses, defense gene espression and systemic resistance in plant. However the detailed analysis of these cellular responses and the molecular machinery involved in the perception and transduction of LPS molecule largely remains to be studied. Furthermore, the biological activities of LPS on plants have so far been reported only for dicots and no information is available on the action of LPS on monocots. We report here that bacterial LPSs, both from plant pathogens and non-pathogens, could induce various defense responses in rice cells, including reactive oxygen generation and defense gene expression. Global analysis of gene expression induced by two PAMP elicitors, LPS and chitin oligosaccharide elicitor, showed a close correlation between the gene responses induced by these elicitors, indicating the convergence of signaling cascades downstream of corresponding receptors. Further, we show that the defense responses induced by LPS are associated with programmed cell death, a finding so far not reported for LPS action on plant cells.
Keywords: elicitor, defense, LPS, rice cell

overall_design: 1. LPS treatment (WT), 2. LPS treatment (WT) color-swap, 3. N-acetylchitooctaose treatment (WT), 4. N-acetylchitooctaose treatment (WT) color-swap


title: Identification of transcriptome of nst1-1 nst3-1 plant

status: Public on Oct 28 2006

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary:
Wood is one of the most important and enormous biomass that is widely used in our life. It is formed by successive addition of secondary xylem that develops continuously from cambium. The transcriptome of nst1 nst3 “double-knockout” lines was examined to know the effect of mutations on wood formation.
Keywords: mutant vs wt comparison

overall_design: Total RNA was extracted from the base 4 cm part of inflorescence stems whose heights were between 12 and 17 cm of three independent nst1-1 nst3-1 double T-DNA tagged lines and the whole transcriptome was compared with that of wild-type plant.

first: Akira

last: Iwase

first: Hiroyuki

last: Yamamoto

first: Masato

last: Yoshida

first: Motoaki

last: Seki

first: Kazuo

last: Shinozaki

first: Masaru

last: Ohme-Takagi


title: The protective role of silicon in the Arabidopsis-powdery mildew pathosystem

status: Public on Sep 30 2006

city: Jouy en Josas

first: Florian

last: Chain

address: Domaine de Vilvert

department: Institut Micalis

institute: INRA

summary:
The role and essentiality of silicon (Si) in plant biology has been debated for over 150 years in spite of numerous reports describing its beneficial properties. To obtain unique insights regarding the effect of Si on plants, we performed a complete transcriptome analysis of both control and powdery mildew-stressed Arabidopsis plants, with or without Si application, using a 44K microarray. Surprisingly, the expression of all but two genes was unaffected by Si in control plants, a result contradicting reports of possible direct effect of Si as a fertilizer. In contrast, inoculation of plants, treated or not with Si, altered the expression of a set of nearly 4,000 genes. Following functional categorization, many of the up-regulated genes were defense-related whereas a large proportion of down-regulated genes were involved in primary metabolism. Regulated defense genes included R genes, stress-related transcription factors, genes involved in signal transduction, the biosynthesis of stress hormones (SA, JA, ethylene), and the metabolism of reactive oxygen species. In inoculated plants treated with Si, the magnitude of down-regulation was attenuated by over 25%, an indication of stress alleviation. Our results demonstrate that Si treatment had no effect on the metabolism of unstressed plants suggesting a non essential role for the element, but that it has beneficial properties attributable to modulation of a more efficient response to pathogen stress.
Keywords: compound effect, stress response

overall_design: A loop design with complete dye-swap was used as experimental design for comparing plants submitted to four treatments and three biological replicates for a total of 24 Agilent Arabidopsis 3 microarrays. Two factors experimental factors : response to a compound (Silicon, treated or not treated) and disease state (Erysiphe cichoracearum, normal vs. diseased). Each factor had two levels. For each of the four combinations of factors, three plants were randomly selected. Thus a total of 12 plants were used for the experiment. RNA was extracted from rosette leaves.

first: François

last: Fauteux

last: Belzile

first: James

last: Menzies

first: Richard

last: Bélanger


title: Transcriptomic adaptations in rice suspension cells under sucrose starvation

status: Public on Sep 20 2006

city: Taipei

first: Huei-Jing

last: Wang

state: Taipei

address: Academia Road, 128, Sec.2, Nankang

department: Inst of plant and microbial biology

country: Taiwan

institute: Academia sinica

summary:
Sugar is an important resource for energy generation and developmental regulation in plants, and sucrose starvation causes enormous changes in cellular morphology, enzyme activities and gene expression.  Genome-wide gene expression profiling provides a comprehensive knowledge into gene expression under nutrients depletion and senescence, however, that of monocot model plant rice under sucrose depletion is still under investigation.  Here, the time-course monitoring of gene expression profiles in sucrose-starved rice (Oryza sativa cv Tainung67) suspension cells was investigated by 21495 probes-containing Agilent rice chip.  In sucrose-starved cells, the induced vacuolar biogenesis was coincided with the significantly upregulated expression of genes encoding H+-pyrophosphatase, delta-TIP, one putative alpha-TIP, several vacuolar proteases and proteinase inhibitors, and one OsATG3.  To survey the overall metabolic adaptations under sucrose depletion the genes significantly alternating expression level were incorporated into multiple metabolic pathways.  The majority of genes encoding enzymes involved in biosynthesis and degradation pathways of various macromolecules were comprehensively down- and upregulated, respectively, by sucrose starvation.  Transcriptional regulation of gene expression is important for the physiological adaptations to environmental stress and many transcription factors, including bZIPs, NACs, and WRKY showed significant increase in transcript levels under sucrose starvation.  Concurrently, statistical analysis reveals that their corresponding consensus cis-elements, such as ABA-responsive element, CACG, ACI, ACII and CTTATCC, are frequently found in the promoter regions of many Suc starvation-upregulated genes.  Particle bombardment-mediated transient promoter activity assays further showed that the CTTATCC, derived form TATCCA, and the AC motifs, are the promising sucrose starvation responsive activators in sucrose-starved rice suspension cells.
Keywords: stress response

overall_design: We used Agilent rice gene chips to investigate the gene expression profiling in rice cells after periods of 12, 24 and 48 h Suc starvation.  To eliminate the effect of osmotic stress on alternation of gene expression, an additional set of control, 88 mM Sorbitol in MS medium verse Suc-free samples for 12 h Suc starvation, was also applied for array analysis.

first: Ai-Ru

last: Wan

first: Chia-Mei

last: Hsu

first: Kuo-Wei

last: Lee

first: Su-May

last: Yu

first: Guang-Yuh

last: Jauh


title: The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate-limiting

status: Public on Oct 19 2006

city: Boston

first: Nikos

last: Reppas

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard University

type: Expression profiling by genome tiling array

summary: This SuperSeries is composed of the SubSeries listed below.


title: 10 Strain, 7 Brain Region

status: Public on Sep 12 2006

first: Jessica

last: Nadler

address: 103 Mason Farm Rd.

department: Genetics

institute: University of North Carolina

summary:
Survey of gene expression in ten common inbred strains of laboratory mouse.  Seven brain regions examined:  amygdala, basal ganglia, cerebellum, frontal cortex, hippocampus, cingulate cortex, olfactory bulb.
Keywords: Genetic background and brain region
Sample data tables were removed because the ID_REF identifiers did not match the platform IDs

overall_design: Tissue from three animals was pooled on each array.  Three biological replicates per strainxregion condition.  Animals were 4-5 weeks of age.

middle: J

first: Fei

last: Zou

first: Hanwen

last: Huang

first: Fred

last: Wright

first: Terry

middle: R

last: Magnuson


title: Temporal expression profile of CHRF-288 cell line after phorbol ester stimulation

first: Eleftherios

last: Papoutsakis

summary:
Little is known about the global transcriptional program underlying megakaryocytic (Mk) differentiation, maturation, and apoptosis.  Using DNA microarrays and Q-RT-PCR, we examined the transcriptional profile of phorbol-ester-induced Mk differentiation of the megakaryoblastic CHRF-288-11 (CHRF) cell line – a model system for investigating megakaryopoiesis.  The goals of this study were to (1) verify the megakaryocytic nature of the CHRF cell line at the transcriptional level, and (2) extract novel insights into the key facets of Mk maturation including polyploidization, proplatelet formation, and apoptosis.
Keywords: time course

overall_design: CHRF-288 cells were cultured in the presence of 10 ng/mL phorbol ester (PMA) or equivalent volume of DMSO solvent (0.02%).  Unstimulated control cells from time zero (exponentially growing CHRF cells) were also analyzed.  For PMA treated legs, only the adherent cells were included in the transcriptional analysis.  Two biological replicate experiments were analyzed and approximately one-half of the samples with each experiment were technically replicated.  Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference RNA pool labeled with Cy5.

first: Peter

last: Fuhrken

first: William

last: Miller


title: Normal, sluggish and recovered fermentation

status: Public on Sep 15 2006

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary:
Gene expression analysis of time course experiment of [1] a synthetic must (nitrogen-rich) fermentation by a natural wine yeast; [2] a synthetic must (nitrogen-poor) fermentation by a natural wine yeast; and [3] a synthetic must (nitrogen-poor) fermentation by a natural wine yeast, supplemented at 72 hours with 200 mg/l of nitrogen.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series, and to genomic hybridization of the individual membranes used for normalizing single samples.


title: Time course response of Synechocystis PCC 6803 to dehydration/desiccation and UV irradiation

status: Public on Sep 04 2006

city: Blacksburg

first: Malcolm

last: Potts

state: VA

address: W. Campus Drive

department: Biochemistry

institute: Virginia Tech


title: Induction of pluripotent-like cells derived from MEF by defined factors

status: Public on Aug 21 2006

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

summary:
Differentiated cells can be reprogrammed to an embryonic-like state by transfer of their nuclear contents into oocytes or by fusion with embryonic stem (ES) cells. Little is known about the factors that induce this reprogramming. Here we show that the combination of four factors, Oct3/4, Sox2, c-Myc, and Klf4, can generate pluripotent-like stem cells directly from mouse embryonic or adult fibroblast cultures. Unexpectedly, Nanog was dispensable in this process. These cells, which we designated iPS (induced pluriopotent-like stem) cells, exhibit the morphology and growth properties of ES cells and express ES cell marker genes. Subcutaneous transplantation of iPS cells into nude mice resulted in tumors containing a variety of tissues from all three germ layers. Following injection into blastocysts, iPS cells contributed to mouse embryonic development. These data demonstrate that pluripotent-like cells can be directly generated from fibroblast cultures by the addition of only a few defined factors.
Keywords: cell type comparison

overall_design: Total RNAs were isolated from indicated cells and labeled with Cy3. Hybridization was performed once for each sample.

first: Kazutoshi

last: Takahashi

first: Megumi

last: Kumazaki


title: Platelet Activating Factor Receptor and Innate Immunity

status: Public on Aug 17 2006

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

summary:
This data series contains spotted oligo microarray data from 10 different experiments using Agilent Rat v2 microarrays. This data is being made public in support of Fillon S et al. Journal of Immunology, (2006).
Proinflammatory bacterial components are at least partially responsible for causing the clinical features of sepsis, a syndrome that causes >100,000 deaths each year in the US (1). In the case of Gram positive infection, a key bacterial element recognized by the innate immune system is the cell wall, a complex network of peptidoglycan covalently linked to teichoic acids, proteins and lipoproteins. The current model of innate immune recognition of Gram positive bacteria suggests bacterial cell wall interacts with host recognition proteins, such as toll-like receptors (TLR) and Nod proteins. We describe an additional recognition system mediated by the platelet activating factor receptor (PAFr) and directed to the pathogen associated molecular pattern (PAMP) phosphorylcholine that results in uptake of bacterial components into host cells. Intravascular choline-containing cell walls bound to endothelial cells and caused rapid lethality in wild type, Tlr2-/- and Nod2-/- mice, but not in Pafr-/- mice. Cell wall exited the vasculature into the heart and brain, accumulating within endothelial cells, cardiomyocytes and neurons in a PAFr-dependent way. Physiological consequences of the cell wall/PAFr interaction were cell specific, being noninflammatory in endothelial cells and neurons, but causing rapid loss of cardiomyocyte contractility that contributed to death. Thus, PAFr shepherds phosphorylcholine-containing bacterial components such as cell wall into host cells from where the response ranges from quiescence to severe pathophysiology.
Keywords: Competitive hybridizations

overall_design:
The ten experiments in this series comprise of four distinct experiments, two of which were performed as biological triplicates and two as biological duplicates. The table below describes the overall design in detail:

File Name						Experiment

16011868017643v41_GEO_format.txt		RBCEC Replicate 1
16011868017644v41_GEO_format.txt		RBCEC Replicate 2
251186821865v41_GEO_format.txt			Neuron Replicate 1
16011868021377v41_GEO_format.txt		Neuron Replicate 2
251186821690v41_GEO_format.txt			CW/Lyt44 Replicate 1
251186821691v41_GEO_format.txt			CW/Lyt44 Replicate 2
251186821692v41_GEO_format.txt			CW/Lyt44 Replicate 1
251186821693v41_GEO_format.txt			CW+TNF/Lyt44+TNF Replicate 1
251186821694v41_GEO_format.txt			CW+TNF/Lyt44+TNF Replicate 2
251186829677v41_GEO_format.txt			CW+TNF/Lyt44+TNF Replicate 3

first: Elaine

last: Tuomanen

first: Sophie

last: Fillon


title: B. thetaiotaomicron in glucose, galactose, lactose, and from the cecum of NMRI mice

status: Public on Sep 01 2006

city: St. Louis

first: Magnus

middle: K

last: Bjursell

state: MO

address: 4444 Forest Park Ave

department: Molecular Biology and Pharmacology

institute: Washington University School of Medicine

platform_organism:
Bacteroides thetaiotaomicron
Bifidobacterium longum


title: MDA-MB-435 Cells treated with 2-methoxyestradiol versus control DMSO

status: Public on Sep 08 2006

first: Nancy

last: DeMore

address: 3010 Old Clinic Rd., CB 7213

department: Surgery

institute: UNC @ Chapel Hill

summary:
MDA-MB-435 breast cancer cells were treated with 2ME2 (2 µM) or vehicle alone. RNA was extracted and genomic profiling was performed using 22k Agilent microarrays.
Keywords: Treatment-response


title: Effects of laughter on gene expression profiles of patients with type 2 diabetes

status: Public on Jul 29 2006

city: Minamidai, Kawagoe

first: Toshiro

last: Saito

department: Life Science Group

institute: Hitachi, Ltd.

summary:
Sample tissue: peripheral blood
Disease: normal subject, patients with type 2 diabetes (diabetic nephropathy +, -)
Samples for gene expression analysis were obtained before and after the event.
Keywords: equivalent probe, disease response

overall_design: Event: a comedy show or a monotonous VTR.


title: Prediction of breast cancer prognosis by gene expression profile of TP53 status.

status: Public on Aug 23 2006

city: Sendai

first: Shin

state: Miyagi

address: 4-1, Seiryo-chou, Aobaku

department: Clinical Oncology

institute: Tohoku Univ.

summary:
TP53 mutations are a poor prognostic factor in breast cancers. This study sets out to identify the gene set that determine expression signature of the TP53 status (TP53 signature) and to correlate it with clinical outcome. Using comprehensive expression analysis and DNA sequencing of the TP53 gene in 38 Japanese breast cancer patients, we have isolated a gene set of 33 genes from differentially expressed genes in the learning set (n=26), depending on the TP53 status. Predictive accuracy of TP53 status by gene expression profile was 83.3% in the test set (n=12). As independent external datasets, two published datasets were introduced for validation of TP53 status prediction (251 Swedish samples) and survival analysis (both the Swedish and 295 Dutch samples). TP53 signature has the ability to predict recurrence-free survival (RFS) of 29 stage I and II Japanese breast cancers (log rank, P = 0.032), and RFS, overall survival of two independently published datasets (log rank, both P < 0.0001). Multivariate analysis has shown an independent and significant prognostic factor with a hazard ratio (HR) for recurrence and survival in two external datasets (P < 0.0001). The TP53 signature is also a strong prognostic factor in the subgroups: estrogen-receptor positive, lymph node (LN) positive and negative, intermediate/high risk in St. Gallen criteria, and high risk in National Cancer Institute (NCI) criteria (log rank, P < 0.0001). TP53 signature is a reliable and independent predictor of the outcome of disease in operated breast cancer.
Keywords: Tumor sample comparison

overall_design:
Microarray hybridizations (Agilent: Whole Human Genome Oligo Microarray; 41k unique probe) were carried out with 1μg Cy3 labeled cRNA and 1 μg Cy5 labeled cRNA, both prepared from each sample and reference pool, respectively.
Fluorescent intensities of scanned images were quantified by ArrayVision Ver.8 rev.4 (Imaging research).
The gene expression data was quantified and analyzed by GeneSpring 6.2 (Silicon Genetics). To identify the TP53 status predictor gene set, a Wilcoxon rank sum test along with Benjamini and Hochberg false discovery rate (FDR) was used.

first: Takuya

last: Moriya

first: Takanori

last: Ishida

first: Hiroyuki

last: Shibata

first: Hironobu

last: Sasano

first: Noriaki

last: Ohuchi

first: Chikashi

last: Ishioka


title: Comparative transcriptome analysis of early interaction events in Scots pine root tissues following challenge

status: Public on Jul 31 2006

city: Raleigh

first: Chris

last: Smith

address: 840 Main Campus Dr

department: Bioinformatics Research Center

institute: NCSU


title: Yeast FAIRE Study_Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters.

status: Public on Aug 11 2006

first: Jason

last: Lieb

address: 203 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

first: Gregory

last: Hogan

first: Cheol

last: Lee


title: thrombopoietin-induced megakaryocyte differentiation with and without nicotinamide

status: Public on Aug 25 2006

city: Newark

first: Eleftherios

last: Papoutsakis

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

summary:
Culture of hematopoietic stem and progenitor cells in the presence of thrombopoietin induces megakaryocytic differentiation.  Addition of nicotinamide to thrombopoietin-stimulated cultures results in significant increases in megkaryocytic differentiation including greater polyploidization and enhanced proplatelet formation.  This study focuses on understanding the differences in the temporal gene expression pattern during differentiation with and without nicotinamide.  Nicotinamide was added on day 5.
Keywords: treatment response

overall_design: Two biological experiments were analyzed.  For each experiment, a sample was taken on day 5, before nicotinamide addition, and on days 6, 8, and 10 from both nicotinamide and control treated cultures.  Each sample was analyzed in duplicate for a total of 14 hybridizations per culture or 28 total hybridizations.

first: Peter

last: Fuhrken

first: Lisa

last: Giammona

first: William

last: Miller


title: Shipyard Creek gene expression: 2000-2005

city: Ocean Springs

first: Jonathan

last: Roling

address: 703 East Beach Dr

department: Department of Coastal Sciences

institute: University of Southern Mississippi

platform_organism:
Fundulus heteroclitus
Pseudopleuronectes americanus


title: Androgen receptor coregulators

status: Public on Oct 12 2006

city: Kiel

first: Paul-Martin

last: Holterhus

address: Campus Kiel, Schwanenweg 20

department: Pädiatrische Endokrinologie und Diabetologie

institute: Universitätsklinikum Schleswig-Holstein


status: Public on Apr 01 2007

city: Oslo

first: Esten

last: Nakken

address: Kirkeveien 166

department: Ulleval university Hospital

country: Norway

summary:
Molecular factors governing liver pathology in abcb4 (-/-) mice.

Dr. Nakken, Karl Esten, Dr. Berge, Knut E., Dr. Knut J. Labori, Ståle Nygård, Dr. Terese Haaland , professor Morten G. Ræder. Institute for Experimental Medical Research and Department of Pathology, Ulleval University Hospital, Oslo, Norway and Institute for Medical Genetics, National Hospital, Oslo, Norway; E-mail: k.e.nakken@medisin.uio.no.

Background and Aims: Abcb4 (mdr2) (-/-) mice secrete phosphatidylcholine-free bile and develop chronic cholangitis. This study aims at identifying differentially transcribed genes that govern liver pathology during this disease.
Methods: Hepatic gene transcription was measured in  3, 6, 9 and 20 week old abcb4 (-/-) mice (FVB.129P2-abcb4tm1Bor/J) using cDNA microarrays; FVB/NJ abcb4 (+/+) mice serving as controls. Altered gene transcriptions were verified by real-time polymerase chain reaction. Attention focused on genes coding for chemokines and cytokines of potential pathogenic importance and on matrix housekeeping genes, growth factors and genes regulating wound healing, epithelial morphogenesis and tissue development. Disease phenotype was characterized by histopathology scoring.
Results: Transcription of  serpina3 genes showed early downregulation. Genes exhibiting upregulated transcription included: Cxcl10, Ccl2, Ccl20, Ctgf, Elf3, Lgals3, Mmp12, Mmp15, Spp1, Loxl2, Pdgfa, Pdgfrb, Sparc, Tgfbi, Tgfbr2.
Conclusions: During early phases of chronic cholangitis in abcb4 (-/-) mice, hepatic downregulation of  serpina3 genes  and enhanced transcription of genes sustaining inflammatory processes contribute to fashioning the portal tract pathology. Later, enhanced transcription of genes governing tissue repair consolidate the portal tract pathology.
Keywords: Disease state analysis, time course

overall_design: A time-series where 5 male mice were sacrificed at time-points 3,6,9 and 20 weeks, both sick knockouts and healthy controls. Including one dye-swap there were a total of 6 arrays at each time-point.

first: Karl

middle: E

first: Ståle

last: Nygård

first: Knut

last: Berge

first: Kristin

last: Arnkværn

first: Terese

last: Haaland

last: Labori

first: Morten

last: Ræder


title: Transcriptional effect of various iron treatments on Caco-2 cells.

status: Public on Jul 14 2006

city: rennes

first: chicault

last: celine

address: 2 avenue du Pr Leon Bernard

summary:
We investigated transcriptional response of CaCo-2 cells to iron treatments, we studied hemin effect by adding hemin to DMEM-FBS medium and iron deficiency effects in using an iron free medium compared to the same supplemented with FAC (ferric ammonium citrate).
Keywords: various iron treatment, differential gene expression, hemin treatment, iron-free

overall_design: Biological replicates were used (3 samples) of each iron treatments (SF-FAC, SF-0, DMEM-FBS, DMEM-Hemin). Each sample was labelled with cy5 and a pool of each sample was constituted and labelled with cy3.

first: Céline

last: Chicault

first: Bertrand

last: Toutain

first: Annabelle

last: Monnier

first: Marc

last: Aubry

first: Patricia

last: Fergelot

first: André

last: LeTreut

first: Marie-Dominique

last: Galibert

first: Jean

last: Mosser


title: Translation State Array Analysis

status: Public on Jul 27 2006

city: Salt Lake City

first: Douglas

middle: I.

last: Schmid

state: UT

department: HMBG

institute: University of Utah


title: Expression profile comparison among Listeria monocytogenes strains

status: Public on Jul 03 2006

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

institute: Universidade de São Paulo

summary:
The aim of this study is to contribute to the understanding of L. monocytogenes virulence and survival capabilities using global gene expression profiling by means of DNA macroarrays.
Keywords: strain comparison; correlation between expression and behaviour

overall_design: The nylon membrane contains probes for all L. monocytogenes (EGDe strain) genes plus some 4b specific genes.  All hibridizations were performed as 4-plicates. Since macroarray is a 'one-color' technology, there is no competitve hybridization, dye-swap and so on.

last: Severino


title: Comparing control and TGF-beta treated cord blood-derived human mast cells

status: Public on Jun 23 2006

city: Budapest

first: Zoltan

last: Wiener

address: Nagyvarad ter 4.

department: Dept of Genetics, Cell- and Immunobiology

institute: Semmelweis University

summary:
Cord blood-derived stem cells were in vitro cultured in the presence of 40 ng/ml SCF, 20 ng/ml IL6 and 2 microM lysophosphatidic acid for 5 week. Then mast cells were magnetically isolated and further cultured for 4 days in the presence or absence of 2 ng/ml TGF-betaI. Total RNA was isolated and processed according to the Agilent Low-input RNA Linear Amplification Kit and microarray hybridization protocol.
Keywords: Agilent Whole Human Genome, dual channel, LogRatio values are log(10) values

overall_design: 5 biological replicates from 5 donors and one technical replicate (dye-swap)

first: Barbara

last: Kohalmi

first: Gergely

last: Tolgyesi

first: Eva

last: Gorbe

first: Judit

last: Jeager

first: Peter

last: Pocza

first: Sara

last: Toth

last: Papp

first: Andras

last: Falus


title: Genome-wide expression profile in rat model of renal isografts from brain dead donors

status: Public on Jun 21 2006

city: Toyoake

first: Mamoru

last: Kusaka

state: Aichi

address: 1-98 Kutsukake

department: Department of Urology

institute: Fujita-Health University

summary:
The clinical results obtained with organ allografts from marginal or extended donors are less satisfactory over both the short-term and long-term than the outcome of grafting from living donors. Early postoperative graft function depends on several pretransplant factors, with the major donor influences being brain death (BD) and ischemia/reperfusion(I/R) injury. The effects of BD and I/R injury not only reduce the number of functioning nephrons, but also trigger a host immune response to the grafted kidney. It has been hypothesized that allografts from marginal sources may not be biologically inert at the time of surgery, but may already be programmed to initiate or amplify a host response. To exclude the effects of allogenicity, we established a rat renal isograft model using dead donors and compared the results with those obtained after grafting from living donors. In this study, we performed an analysis of the changes of gene expression in rat kidney isografts using samples obtained at 0(pre-transplant) and 1 hour time points since transplantation procedure. The results enhanced our insight into the pathways and cascades that are activated or down-regulated by BD and/or I/R injury. Better knowledge of the key components of BD or I/R injury will provide clues to the factors triggering progression that leads to a decline of organ viability, as well as ideas on how to overcome such graft failures. Such data may also allow us to identify novel biomarkers as predictors of adverse outcomes.
Keywords: disease state analysis

overall_design:
Inbred male Lewis rats were used for these experiments as recipients and donors. The left kidney was transplanted orthotopically by end-to-end anastomosis. The contralateral right kidney was removed at the time of transplantation. The time of operative ischemia for transplantation was 30 min, which did not vary between animals. Donor animals were divided into two groups. The experimental group received kidneys from BD rats, while kidneys from living donors were used in the control group. Brain death was produced by gradually increasing the intracranial pressure that led to brain stem herniation. The rats were mechanically ventilated for a period of 6 hours. We compared the gene expression profiles of renal isografts from BD donors and grafts from living donors using a high-density oligonucleotide microarray that contained approximately 20,500 genes.
For DNA microarray experiments, 200 ng aliquots of total RNA were labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Product) according to the manufacturer's instructions. RNA purified from each kidney graft was used for microarray analysis (Cy3-labeled), with pooled RNA derived from normal kidneys as a template control (Cy5-labeled). After checking the labeling efficiency, 1ug aliquots of Cy5-labeled normal control RNA and Cy3-labeled RNA from individual grafts (control 0 hour, 1 hour, BD 0 hour, BD 1 hour, n=3/group) were mixed, and then hybridized to Agilent Rat Oligo Microarrays (Product No. G4130A). After washing, the microarray slides were analyzed with an Agilent Microarray scanner and software (scanner model G2565BA). Data analysis was performed using Agilent Feature Extraction software (Ver. A.7.1.1), and Excel 2003 (Microsoft). The data were imported into GeneSpring 7.0 (Silicon Genetics, Redwood City, CA), with per spot, per chip, and intensity dependent (lowess) normalization being applied for each array. The ratio of the normalized channels (Cy3/Cy5) was used to assess the level of expression.


title: Arabidopsis stn7 and stn8 single and double mutants vs WT

status: Public on Jul 07 2006

city: Chicago

first: christos

last: Noutsos

institute: University of Chicago

overall_design: Refer to individual Series


title: Arabidopsis CAF-1 depletion / gamma-irradiation

status: Public on Jun 20 2006

city: Tsukuba

first: Masaki

last: Endo

address: 2-1-2 Kannondai

department: Division of Plant Sciences

institute: National Institute of Agrobiological Sciences

summary:
CAF-1 is involved in nucleosome assembly following DNA replication and nucleotide excision repair. In Arabidopsis thaliana, the 3 CAF-1 subunits p150, p60 and p48 are encoded by FAS1, FAS2 and, most likely, MSI1, respectively.fas mutants exhibited increased levels of DNA double-strand breaks, a G2 phase retardation, and elevated levels of mRNAs coding for proteins involved in homologous recombinational repair. The same genes that were transcriptionally up-regulated in the fas mutants were also found to have a higher steady state level of transcription in wild-type Arabidopsis plants exposed to gamma-irradiation.
Keywords: stress response, genetic modification

overall_design: Total RNA prepared from 4-week-old seedlings (without the roots i.e. true leaves with cotyledon and hypocotyls) using an RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Four-week-old sterile seedlings of wild-type plants (ecotype Nossen) were irradiated with 100 Gy of gamma-rays at a dose rate of 300 Gy/h. Six and 12 hours after irradiation, samples were frozen in liquid nitrogen and immediately ground for total RNA isolation. After confirming its quality, extracted RNA was prepared for microarray analysis. An Arabidopsis 2 Oligo Microarray kit (Agilent Technology, CA, USA) was used in this study. After confirming its quality, extracted RNA was prepared for microarray analysis as described by the manufacturer (Agilent) using the suggested chemicals and reagents.

first: Seiichi

last: Toki