title: roX RNAs are required for up-regulation of male X chromosome in Drosophila.

status: Public on Jan 06 2007

city: Detroit

first: Xinxian

last: Deng

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University

summary:
Drosophila males double transcription of their single X chromosome to equalize X-linked gene expression with females, which carry two X chromosomes.  Increased transcription requires the Male-Specific Lethal (MSL) complex.  One of the primary functions of the MSL complex is thought to be enrichment of H4Ac16 on the male X chromosome, a modification linked to elevated transcription. The roX1 and roX2 RNAs are essential but redundant components of the MSL complex.  Simultaneous removal of both roX RNAs reduces MSL X-localization and leads to ectopic binding of these proteins at autosomal sites and to the chromocenter.  Some H4Ac16 accumulates at these ectopic sites in roX1- roX2- males, suggesting the possibility of increased expression.  The global effect of roX mutations on gene expression was measured by microarray analysis.  We found that expression of the X chromosome was decreased by 26% in roX1- roX2- male larvae, supporting the involvement of roX RNAs in the up-regulation of X-linked genes.  This finding is broadly comparable to reports of reduced X chromosome expression following msl2 RNAi knockdown in S2 cells. In spite of strong MSL binding and H4Ac16 accumulation at autosomal sites in roX1- roX2- males, enhanced gene expression could not be detected at these sites by microarray analysis or reverse northern blotting.  Thus, failure to compensate X-linked genes, rather than inappropriate up-regulation of autosomal genes at ectopic sites of MSL binding, appears to cause male lethality upon loss of roX RNAs.
Keywords: effect of roX1-roX2- mutant on gene expression

overall_design: Total RNA was prepared from groups of 50 third instar larvae by TRIzol (Invitrogen) extraction and purified using the RNeasy kit (Qiagen).  Three independent RNA preparations for each genotype served as templates for probe synthesis.  Affymetrix Drosophila Genome 2.0 chips were hybridized to these probes (Santa Clara, CA).  The affymertrix Drosophila annotation of December 2004 was used to map genes to their cytological locations.  Genes were filtered for present/absent calls by a PM-MM (Perfect match- Mismatch) comparison.  Autosomal transcripts were normalized on a chip-by-chip basis to bring their median values to 100.  The identical degree of adjustment was used to normalize X-linked transcripts. Changes in gene expression were determined by comparing the mean signal intensities of genes on arrays hybridized with roX1SMC17A roX2- probes to those hybridized with roX1+ roX2- probes.

first: Victoria

middle: H

last: Meller


title: Identification of genes whose expression is modulated by the presence or absence of PTEN

status: Public on Nov 15 2006

city: Washington

first: JUNGSIK

last: KIM

state: DC

address: 3970 Reservoir Road

department: Oncology

country: USA

institute: GEORGETOWN UNIVERSITY

summary:
In an effort to identify genes whose expression is regulated by activated PI3K signaling, we performed microarray analysis and subsequent qRT-PCR on an isogenic set of PTEN gene-targeted human cancer cells. Numerous p53 effectors were upregulated following PTEN deletion, including p21, GDF15, PIG3, NOXA, and PLK2. Stable depletion of p53 led to reversion of the gene expression program.  Western blots revealed that p53 was stabilized in HCT116 PTEN-/- cells via an Akt1-dependent and p14ARF-independent mechanism. Stable depletion of PTEN in untransformed human fibroblasts and epithelial cells also led to upregulation of p53 and senescent-like growth arrest. Simultaneous depletion of p53 rescued this phenotype, enabling PTEN-depleted cells to continue proliferating. Next, we tested whether oncogenic PIK3CA, like inactivated PTEN, could activate p53. Retroviral expression of oncogenic human PIK3CA in MCF10A cells led to activation of p53 and upregulation of p53-regulated genes. Stable depletion of p53 reversed these PIK3CA-induced expression changes and synergized with oncogenic PIK3CA in inducing anchorage-independent growth. Finally, targeted deletion of an endogenous allele of oncogenic but not wild-type PIK3CA in a human cancer cell line led to a reduction in p53 levels and a decrease in the expression of p53-regulated genes. These studies demonstrate that activation of PI3K signaling by mutations in PTEN or PIK3CA can lead to activation of p53-mediated growth suppression in human cells, indicating that p53 can function as a brake on PIP3-induced mitogenesis during human cancer pathogenesis.
Keywords: PTEN genotype comparison

overall_design: Two HCT116 PTEN+/+ cell lines (parental cells and a clone with random integration of the targeting vector) and three independently-derived HCT116 PTEN-/- cell lines were studied


title: Up-regulation of translational machinery and distinct genetic subgroups characterize hyperdiploidy in multiple myeloma

status: Public on Jan 01 2007

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary:
Karyotypic instability, including numerical and structural chromosomal aberrations, represents a distinct feature of multiple myeloma (MM). 40-50% of patients displayed hyperdiploidy, defined by recurrent trisomies of non-random chromosomes. To characterize hyperdiploid (H) and nonhyperdiploid (NH) MM molecularly, we analyzed the gene expression profiles of 66 primary tumors, and used FISH to investigate the major chromosomal alterations. The differential expression of 225 genes mainly involved in protein biosynthesis, transcriptional machinery and oxidative phosphorylation distinguished the 28 H-MM from the 38 NH-MM cases. The 204 upregulated genes in H-MM mapped mainly to the chromosomes involved in hyperdiploidy, and the29% up-regulated genes in NH-MM mapped to 16q. The identified transcriptional fingerprint was robustly validated on a publicly available gene expression dataset of 64 MM cases; and the global expression modulation of regions on the chromosomes involved in hyperdiploidy was verified using a self-developed non-parametric statistical method. We showed that H-MM could be further divided into two distinct molecular and transcriptional entities, characterized by the presence of trisomy 11 and 1q-extracopies/chromosome 13 deletion, respectively. Our data reinforce the importance of combining molecular cytogenetics and gene expression profiling to define a genomic framework for the study of MM pathogenesis and clinical management.
Keywords: other

overall_design: This series of microarray experiments contains the gene expression profiles of purified plasma cells (PCs) obtained from 102 newly diagnosed multiple myeloma (MM). PCs were purified from bone marrow specimens, after red blood cell lysis with 0.86% ammonium chloride, using CD138 immunomagnetic microbeads. The purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases. 5 micrograms of total RNA was processed and, in accordance with the manufacturer's protocols, 15 micrograms of fragmented biotin-labelled cRNA were hybridized on GeneChip Human Genome U133A Arrays (Affymetrix Inc.). The arrays were scanned using the Agilent GeneChip Scanner G2500A. The images were acquired using Affymetrix MicroArray Suite (MAS) 5.0 software and the probe level data converted to expression values using the Bioconductor function for the Robust Multi-Array average (RMA) procedure (Irizarry et al, 2003), in which perfect match intensities are background adjusted and quantile-quantile normalised.

first: Sonia

last: Fabris

first: Silvio

last: Bicciato

first: Dario

last: Basso

last: Baldini

first: Fortunato

last: Morabito

first: Donata

last: Verdelli

first: Katia

last: Todoerti

first: Giorgio

last: Lambertenghi-Deliliers

first: Luigia

last: Lombardi

first: Antonino

last: Neri


title: Screening for differentially expressed genes in patients with a novel immunodeficiency syndrome

status: Public on Nov 21 2006

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary:
Lysosome-related organelles have versatile functions including protein and lipid degradation, signal transduction, and protein secretion. The molecular elucidation of rare congenital diseases affecting endosomal/lysosomal biogenesis has given insights into physiological functions of the innate and adaptive immune system.. Here, we describe a novel human primary immunodeficiency disorder and provide evidence that the endosomal adaptor protein p14, previously characterized as confining mitogen-activated-protein-kinase (MAPK) signaling to late endosomes, is critical for the function of neutrophils, B-cells, cytotoxic T-cells and melanocytes. Combining genetic linkage studies and transcriptional profiling analysis, we identified a homozygous point mutation in the 3’ UTR of p14 (also known as MAPBPIP), resulting in decreased protein expression. In p14-deficient cells, the distribution of late endosomes was severely perturbed, suggesting a novel role for p14 in endosomal biogenesis. These findings have implications for understanding endosomal membrane dynamics, compartmentalization of cell signal cascades, and their role in immunity.
Keywords: Interindividual comparison

overall_design: EBV-transformed B cell lines from 2 parents and 2 affected children

first: G

last: Bohn

first: R

first: C

last: Klein


title: Rus etal High Na Arabidopsis accessions mapping HKT1

status: Public on Nov 18 2006

city: St. Louis

first: Ivan

last: Baxter

state: MO

address: 975 North Warson Rd

department: PLant Genetics Research Unit

institute: USDA-ARS

summary:
Background:
Plants are sessile and therefore have developed mechanisms to adapt to their environment, including the soil mineral nutrient composition. Ionomics is a developing functional genomics strategy designed to rapidly identify the genes and gene networks involved in regulating how plants acquire and accumulate these mineral nutrients from the soil. Here we report on the coupling of high-throughput elemental profiling of shoot tissue from various Arabidopsis accessions with DNA microarray-based bulk segregant analysis (BSA) and reverse genetics, for the rapid identification of genes from wild populations of Arabidopsis that are involved in regulating how plants acquire and accumulate Na+ from the soil.

Methodology/Principal Findings:
Elemental profiling of shoot tissue from 12 different Arabidopsis accessions revealed that Ts-1 and Tsu-1 accumulate higher shoot levels of Na+ than Col-0 and other accessions. We identify AtHKT1, known to encode a Na+ transporter, as being the causal locus driving elevated shoot Na+ in both Ts-1 and Tsu-1. Furthermore, we establish that a deletion in a tandem repeat sequence ~5 kb upstream of AtHKT1 is responsible for the reduced root expression of AtHKT1 observed in these accessions. Reciprocal grafting experiments establish that this loss of AtHKT1 expression in roots is responsible for elevated shoot Na+. Interestingly, and in contrast to the hkt1-1 null mutant, under NaCl stress conditions this novel AtHKT1 allele not only does not confer NaCl sensitivity, but co-segregates with elevated NaCl tolerance. We also present all our elemental profiling data in a new open access ionomics database, the Purdue Ionomics Information Management System (PiiMS; www.purdue.edu/dp/ionomics).

Conclusions/Significance:
Using DNA microarray-based genotyping has allowed us to rapidly identify AtHKT1 as the causal locus driving the natural variation in shoot Na+ accumulation we observed in Ts-1 and Tsu-1, two coastal populations of Arabidopsis. Such an approach overcomes the limitations imposed by a lack of established genetic markers in most Arabidopsis accessions, and opens up a vast and tractable source of natural variation for the identification of gene function not only in ionomics but also in many other biological processes.
Keywords: genomics hybridization bulk segregant analysis

overall_design: Hybridizations from two sets of Bulk Segregant analysis. F2 populations from col-0 crossed to two High Na accessions: Ts-1 and Tsu-1 were analyzed. This series contains the 3 hybs from each accession that were used to identify Single Feature Polymorphisms, the 3 hybs of Col-0 they were compared to, and 1 hyb for each pool from the BSA mapping(High Na pool, low Na Pool).


title: An injected bacterial effector targets chromatin access for NF-kB as a strategy to shape transcription of immune genes

status: Public on Nov 19 2006

city: Paris

first: Thierry

last: Pedron

address: 28 rue du Docteur Roux

department: Biologie cellulaire et Infection

country: France

institute: Pasteur Institute

summary:
Phosphorylation of histone H3 at Serine 10 emerges as a mechanism increasing chromatin accessibility of the transcription factor NF-kB for a particular set of immune genes. Here we report that a bacterial pathogen uses this strategy to shape the transcriptional response of infected host cells. We identify the Shigella flexneri type III protein effector OspF as a Dual Specific Phosphatase. OspF dephosphorylates MAP kinases within the nucleus impairing histone H3 phosphorylation at Serine 10 in a gene-specific manner. Therefore, OspF reprograms the transcriptional response for inactivation of a subset of NF-kB responsive genes. This regulation leads to repression of polymorphonuclear leukocytes recruitment in infected tissues. Thus, pathogens have evolved the ability to precisely modulate host cell epigenetic information as a strategy to repress innate immunity.
Keywords: mutant strain

overall_design:
The wild-type (WT) invasive strain of S. flexneri serotype 5a. To construct the ospF mutant, a PCR amplified DNA fragment encompassing nucleotides 61 to 420 of ospF was cloned between the XbaI and EcoRI sites of the suicide plasmid pSW23T, giving raise to pSWOspFTr. This plasmid was transferred by conjugation to the WT strain WT-Sm. To complement the ospF mutant, we constructed pUC18-OspF containing a PCR fragment encompassing the ospF gene inserted between the EcoRI and HindIII sites of pUC18.
Cells were infected 2 hours with the differents strains. 2 biological replicates were done for each experimental conditions. After infection, cells were washed and total RNA was extracted using Rneasy mini kit from Qiagen. After cRNA synthesis and labeling with biotin, hybridizations were performed following Affymetrix procedures. After scanning, data were normalized with RMA (Quantile normalization).
Comparative analyses with dChip software between baseline (wild-type-infected cells) and experiment (mutant- or transcomplemented strain-infected cells) were done using an unpaired Welch t-test with a p-value threshold of 0.05 and a Signal Log Ratio (SLR) threshold of 0.6. This SLR threshold corresponds to a Fold Change of 1.5

first: Laurence

last: Arbibe

first: Dong-Wook

last: Kim

first: Eric

last: Batsche

first: Bogdan

last: Masteescu

first: Christian

last: Muchardt

first: Claude

last: Parsot

first: Philippe

middle: J

last: Sansonetti


title: Microarray analysis of gene expression from MDA-MB-231 cells

city: Ann Arbor

first: Bae Keun

last: Park

state: MI

address: 1011 N University Ave

department: BMS/Prosthodontics

institute: University of Michigan

summary:
We used human Affymetrix microarrays to identify the up- or down-regulated gene expressions from MDA-MB-231 cells infected with control vector or Flag-SR-IkBa
Keywords: microarray

overall_design: The pattern of gene expression from MDA-MB-231 cells transduced with retroviruses were analysed by RNA extraction and hybridization on Affymetrix microarrays. From expression profiles, we identified NF-kB target genes, and uncovered a novel and specific role of a gene in osteolytic bone metastasis.

first: Cun

middle: Y

last: Wang

first: Bae

middle: K


title: Airway epithelium, large airways, phenotypically normal smokers vs non-smokers, MAS5 (HG-U133A)

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Upregulation of Expression of the Ubiquitin Carboxyl Terminal Hydrolase L1 Gene in Human Airway Epithelium of Cigarette Smokers
The microarray data deposited here is from 11 HG-U133A GeneChips, from 5 normal non-smokers and 6 phenotypic normal smokers, large airways. Samples from the small airways of these individuals have been obtained and analyzed using the HG-U133A GeneChip; the small airway samples are in GEO Accession Number GSE 3320, and the data analysis is described in Harvey, B-G; Heguy, A.; Leopold, P.L.; Carolan, B.; Ferris, B. and Crystal R.G. Modification of Gene Expression of the Small Airway Epithelium in Response to Cigarette Smoking. J. Mol. Med (in press). These data are part of a study aimed at  understanding how cigarette smoking modifies neuroendocrine cells, in which microarray analysis with TaqMan confirmation was used to assess airway epithelial samples obtained by fiberoptic bronchoscopy from 81 individuals (normal nonsmokers, normal smokers, smokers with early COPD and smokers with established COPD). Of 11 genes considered to be neuroendocrine cell-specific, only ubiquitin C-terminal hydrolase L1(UCHL1), a member of the ubiquitin proteasome pathway, was consistently upregulated in smokers compared to nonsmokers. Up-regulation of UCHL1 at the protein level was observed with immunohistochemistry of bronchial biopsies of smokers compared to nonsmokers. Interestingly, however, while UCHL1 expression was present only in neuroendocrine cells of the airway epithelium in nonsmokers, UCHL1 expression was also expressed in ciliated epithelial cells in smokers, an intriguing observation in light of recent observations that ciliated cells can are capable of transdifferentiating to other airway epithelium. In the context that UCHL1 is involved in the degradation of unwanted, misfolded or damaged proteins within the cell and is overexpressed in >50% of lung cancers, its overexpression in chronic smokers may represent an early event in the complex transformation from normal epithelium to overt malignancy.
Keywords: smokers vs non-smokers

overall_design: comparison of gene expression in airway epithelial cells of the large airways of phenotypic normal smokers vs normal non-smokers

first: Brendan

last: Carolan

first: Adriana

last: Heguy

first: Ben-Gary

last: Harvey

first: Phil

last: Leopold

first: Barbara

last: Ferris

first: Ronald

last: Crystal


title: Silverleaf whitefly 2nd instar feeding on 7-week old Arabidopsis thaliana rosette leaves

status: Public on Dec 15 2006

city: Riverside

first: Linda

middle: L.

last: Walling

state: CA

address: 3401 Watkins Drive

department: Botany and Plant Sciences, CEPCEB

institute: University of California, Riverside

summary:
Phloem-feeding pests cause extensive crop damage throughout the world yet little is understood about how plants perceive and defend themselves from these threats. The silverleaf whitefly (SLWF; Bemisia tabaci type B) is a good model for studying phloem-feeding insect-plant interactions as SLWF nymphs cause little wounding and have a long, continuous interaction with the plant. Using the Arabidopsis ATH1 GeneChip, the global responses to Silverleaf Whitefly 2nd instar feeding were examined.
Keywords: stress response

overall_design:
The silverleaf whitefly colony (Bemisia tabaci type B; Bemisia argentifolii Bellows and Perring) was maintained on Brassica napus cv. “Florida broad leaf” grown under fluorescent and incandescent lights (180 μE m-2 s-1) 27°C with 55% relative humidity under long-day (16 hr light: 8 hr dark) conditions in the Insectory and Quarantine Facility at the University of California, Riverside. Adult whiteflies are collected from infested plants by aspiration into 15-ml falcon tubes.
	Individual Arabidopsis thaliana ecotype Columbia plants were grown for 21 days in 4-inch diameter, round pots under fluorescent and incandescent lights (180 μE m-2 s-1) with 50% relative humidity, 23° C and an 8 hr-light/16-hr dark cycle. One hundred adult whiteflies were collected into each 15-ml falcon tube and the tube was placed upright in each pot. Plants were individually encased with 5- by 10-inch nylon bags that were secured to each pot with a rubber band. The whiteflies were released by unscrewing the falcon tube. After seven days, the adult whiteflies were removed from the plants by aspiration. The infested and non-infested plants were caged for the remainder of the experiment to ensure any adults that escaped aspiration could not reach the plants. Rosette tissue was collected after 28 days, when 2nd and 3rd instars were observed on wild-type Columbia plants. Developmentally matched leaves were harvested from uninfested plants. Infestations were performed in two growth chambers; each chamber contained one replicate experiment, which included 10 control and 10 infested plants.  This experiment was repeated for a total of 8 biological replicate experiments.
Total RNA from the eight biological replicates was isolated using the RNAwiz protocol (Ambion Inc., Austin, TX) and purified using a RNAeasy column (Qiagen, Valencia, CA). RNA from the two biological replicates performed in each growth chamber were pooled to eliminate variance due to different environmental factors. This yielded the infested and control RNA pools used in the microarrays (Exp1 and Exp2) and RT-PCRs (Exp3 and Exp4). The quality of the RNA was determined by A260/A280 absorbance readings. RNA integrity (1 µg) was verified by fractionation on a 1% formaldehyde gel.

Hybridization

Biotin-labeled cRNAs were synthesized from infested and control RNAs for Exp1 and Exp2 at the UC Irvine Microarray Facility using the Affymetrix Eukaryotic One-Cycle Target Labeling Assay protocol (Affymetrix GeneChip Expression, Analysis Technical Manual, Affymetrix, Santa Clara, CA). The labeled cRNA was hybridized to Affymetrix Arabidopsis genome ATH1 Chip arrays, washed, and scanned using a Hewlett Packard Genearray scanner (Hewlett-Packard, Palo Alto, CA).

MAS 5.0 was performed using the standard parameters (Affymetrix GeneChip Expression, Analysis Technical Manual, Affymetrix, Santa Clara, CA.) Genes with “absent” calls in replicate experiments were removed from further analysis.

first: Louisa

middle: A

last: Kempema

first: Xinping

last: Cui

first: Frances

middle: M

last: Holzer

middle: L


title: AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors

status: Public on Jan 08 2007

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana (Hybridisations done at NASC)
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Series 2: Base line experiment for pathogen infection. Growth and infection conditions: Seeds will be stratified for 3 days at 4°C and sown on soil. Plants are grown at 22°C under a 8/16 hour light/dark regime in Percival growth chambers. All pathogen treatments will be performed on leaves of 5-weeks old plants. Bacterial infiltrations will be performed with 10-8 cfu/ml in 10 mM MgCl2. 5x105 spores of Phytophthora infestans in water will be applied to leaf surfaces. LPS (100 µg/ml), HrpZ (1 µM), NPP1 (2 µM) or flagellin (1 µM flg22) will be applied in water. Experiments should be performed in triplicate at the time points indicated below.
Experimenter name = Frederic Brunner  , Thorsten Nürnberger
Experimenter institute = AtGenExpress
Keywords: genetic_modification_design;  organism_part_comparison_design; development_or_differentiation_design

overall_design: 42 samples were used in this experiment

first: Frederic

last: Brunner

first: Thorsten

last: Nürnberger

first: Henrik

last: Townsend

first: Zoe

last: Emmerson

first: Beatrice

last: Schildknecht


title: EC_interferon

status: Public on Dec 28 2006

city: Genova

first: Ulrich

last: Pfeffer

address: L. Benzi 10

institute: IRCCS AOU San Martino - IST

summary:
IFNs are highly pleiotropic cytokines also endowed with marked anti-angiogenic activity. In this study, the mRNA expression profiles of endothelial cells (EC) exposed in vitro to IFN-alpha, IFN-beta, or
IFN-gamma were determined. We found that in HUVEC as well as in other EC types 175 genes were upregulated (>2-fold increase) by IFNs, including genes involved in the host response to RNA viruses, inflammation, and apoptosis. Interestingly, 41 genes showed a >5-fold higher induction by IFN-alpha in EC compared to human fibroblasts; among them, the gene encoding the angiostatic chemokine CXCL11 was selectively induced by IFN-alpha in EC along with other genes associated
with angiogenesis regulation, including CXCL10, TRAIL, and guanylate binding protein 1 (GBP-1). These transcriptional changes were confirmed and extended by quantitative PCR analysis and ELISA; whereas IFN-alpha and IFN-beta exerted virtually identical effects on transcriptome modulation, a differential gene regulation by type I and type II IFN emerged, especially as far as quantitative aspects were concerned. In vivo, IFN-alpha-producing tumors over-expressed murine CXCL10-11,
GBP-1 and TRAIL, with evidence of CXCL11 production by tumor-associated EC. Overall, these findings improve our understanding of the anti-angiogenic effects of IFNs by showing that these cytokines trigger an anti-angiogenic transcriptional program in EC. Moreover, we suggest that quantitative differences in the magnitude of the transcriptional activation of IFNresponsive genes could form the basis for cell-specific transcriptional signatures.
Keywords: class comparison

overall_design: comparison of interferon effects on endothelial cells (HUVEC, HMVEC) and fibrobloasts

first: Stefano

last: Indraccolo

first: Sonia

last: Minuzzo

first: Emilia

last: Gola

first: Nicoletta

last: Ferrari


title: Differential gene expression patterns in the phosphate deficient mutant, pho 1

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary:
Background: The UK horticultural and agricultural industries routinely apply large amounts of inorganic fertiliser to maintain crop yield and quality, since chemical assays of soil nutrients are unreliable. Excessive fertiliser applications are costly and can lead to unnecessary pollution. A possible solution is to use sensor (GM or non-GM) technologies that exploit the changes in plant gene expression under incipient nutrient deficiency.
Aim: The aim of this project is to use mutants with reduced leaf phosphate contents to identify genes upregulated in response to phosphate stress. Preliminary gene expression analysis has identified several phosphate responsive genes to be upregulated in the pho1 mutant. However, further replicates of the experiment are required to confirm these changes.
Methods: Arabidopsis mutant pho1 (N8507) and its parent ecotype Columbia 2 (N907) will be grown on MS agar under identical conditions. RNA will be extracted from the rosette leaves of both parent and mutant and the same growth stage. By comparing the expression profiles, we will be able to differentiate between genes that are upregulated in leaves experiencing phosphate stress. Previously, two GeneChips have been used (mutant and parent) to provide preliminary data. A further two biological replicates are now required to confirm these results. Promoters and transcripts of these genes will underpin the development of novel sensor technologies, and knowledge of the gene expression profiles will improve our understanding of the physiology of plant mineral nutrition.

Experimenter name = John Hammond
Experimenter phone = 01789 470382
Experimenter fax = 01789 470552
Experimenter address = Plant Sciences Division
Experimenter address = School of Biosciences
Experimenter address = University of Nottingham
Experimenter address = Sutton Bonington Campus
Experimenter address = Loughborough
Experimenter zip/postal_code = LE12 5RD
Experimenter country = UK
Keywords: genetic_modification_design

overall_design: 6 samples were used in this experiment

first: John

last: Hammond

first: Malcolm

last: Bennett


title: Functional studies of a new Arabidopsis SH2 domain-containing gene

summary:
The protein modules known as SH2 (Src-homology-2) domains are key players in the signal transduction of animals. Two questions arise: Do such modules exist in plants, and when did SH2 domains evolve? Here I show that the Arabidopsis genome contains three strong candidates for plant SH2 proteins (referred to as PASTA1, 2 and 3 : GI:25513455, At1g78540, At1g17040 respectively) with homology to the SH2 domains and the adjacent linker region of STAT proteins (Signal Transducer and Activator of Transcription). The three characteristics features of a STAT protein sequence1, namely, (i) the SH2 domain with a conserved arginine residue crucial for binding to a phospho-tyrosine residue (ii) a tyrosine residue outside the C-terminus of the SH2-domain  for phosphorylation during signalling and (iii) a DNA-binding domain, are conserved in the PASTA3 protein. However, PASTA 1 and 2 proteins lack a tyrosine in a similar position. PASTA proteins are not homologous to STAT proteins outside the SH2 and linker regions. The three PASTA proteins are 70 to 80 % identical to one another. Gene expression studies with PASTA2 reveal that it is expressed in roots, stem, leaves, flowers and green siliques. Preliminary indications are that plants homozygous for PASTA2 do not have any obvious phenotype, most likely due to redundancies.
This microarray experiment is an attempt to compare the gene expression of a mutant plant  homozygous for PASTA2 with that of the wild type plant. This might give clues about the possible function of PASTA2 in Arabidopsis.

Experimenter name = Latha Kadalayil
Experimenter phone = 023-8059 5512
Experimenter department = University of  Southampton
Experimenter address = School of Biological Sciences
Experimenter address = Univ.  Southampton
Experimenter address = Bassett Crescent East
Experimenter address = Southampton
Experimenter zip/postal_code = SO16 7PX
Experimenter country = UK
Keywords: genetic_modification_design

overall_design: 2 samples were used in this experiment

first: Latha

last: Kadalayil


title: Gene expression in Stage 1,2 Normal and Tumor kidney cancer

status: Public on Nov 23 2006

city: Jacksonville

last: Copland

state: FL

address: 4500 San Pablo Road

department: Biochemistry & Molecular Biology

institute: Mayo Clinic College of Medicine

summary:
Although renal cell carcinoma (RCC) is the sixth-leading cause of cancer death, the molecular events leading to disease onset and progression are not well understood. Genomic profiling of clear cell RCC (cRCC) patients indicated that loss of a negative regulator of the Wnt pathway, secreted frizzled-related protein 1 (sFRP1), occurred in the majority of more than 100 patients tested. To our knowledge, this is the first report of loss of sFRP1 expression in patients diagnosed with cRCC; this loss occurs in early stage cRCC, suggesting that it may be an important early event in renal carcinogenesis. Genomic profiling of patient matched normal and cRCC tissues identified Wnt regulated genes to be aberrantly increased in cRCC tissues suggesting sFRP1 suppresses Wnt signaling in cRCC. In order to test the hypothesis that sFRP1 acts as a tumor suppressor in cRCC, we have stably expressed sFRP1 in cRCC cells. sFRP1 expression in cRCC cells resulted in decreased growth in cell culture, inhibition of anchorage-independent growth, and decreased tumor volume in a nude mouse model. Together these data suggest an important role for sFRP1 as a tumor suppressor in cRCC.
Keywords: Disease state analysis

overall_design:
5pts on Stg1 Normal and Tumor and 5pts on Stg2 normal and tumor each

Additional information may be found in the following supplementary files:

1) GSE6344_Combofiles.zip - contains all text files for combination tables.
2) GSE6344_Dataframe.TXT - contains the Dataframe after filters and normalizations for differential testing.
3) GSE6344_MethodsDetails.PDF - describes the steps for creating the combination tables from HG-U133 A, B set and also the method for normalizations and filters.
4) GSE6344_a1way_StageTumor_@95(@99).txt - contain results from Anova 1 way at p-values<=0.05 and 0.01.


title: IM CD34+ progenitors cells

status: Public on Oct 06 2006

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

summary:
IM CD34+ vs BM CD34+ cells
Keywords: parallel sample

overall_design: Differential gene expression profiling of CD34+ cells purified from the PB of  15 IM patients (3 distinct pools) and from the BM of 15 healthy subjects (3 distinct pools)

first: Paola

last: Guglielmelli

first: Roberta

last: Zini

first: Costanza

last: Bogani

first: Marie-Caroline

last: Le Bousse-Kerdilès

first: Simona

last: Salati

first: Alessandro

last: Pancrazzi

first: Elisa

last: Bianchi

first: Francesco

last: Mannelli

first: Sergio

first: Alberto

last: Bosi

first: Gianni

last: Barosi

first: AnnaRita

last: Migliaccio

last: Vannucchi


title: Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions

status: Public on Oct 20 2006

city: Copenhagen

first: Adrian

middle: P.

last: Bracken

address: Fruebjergvej 3

country: Denmark

institute: Biotech Research & Innovation Centre (BRIC)

summary:
The Polycomb group (PcG) proteins form chromatin-modifying complexes that are essential for embryonic development and stem cell renewal and are commonly deregulated in cancer. Here, we identify their target genes using genome-wide location analysis in human embryonic fibroblasts. We find that Polycomb-Repressive Complex 1 (PRC1), PRC2, and tri-methylated histone H3K27 co-occupy >1000 silenced genes with a strong functional bias for embryonic development and cell fate decisions. We functionally identify 40 genes derepressed in human embryonic fibroblasts depleted of the PRC2 components (EZH2, EED, SUZ12) and the PRC1 component, BMI-1. Interestingly, several markers of osteogenesis, adipogenesis, and chrondrogenesis are among these genes, consistent with the mesenchymal origin of fibroblasts. Using a neuronal model of differentiation, we delineate two different mechanisms for regulating PcG target genes. For genes activated during differentiation, PcGs are displaced. However, for genes repressed during differentiation, we paradoxically find that they are already bound by the PcGs in nondifferentiated cells despite being actively transcribed. Our results are consistent with the hypothesis that PcGs are part of a preprogrammed memory system established during embryogenesis marking certain key genes for repressive signals during subsequent developmental and differentiation processes.
Keywords: polycomb, development, differentiation, cell fate, stem cells, siRNA

overall_design: Total RNA was extracted from mock, EZH2, EED, SUZ12, and BMI-1 siRNA-transfected cells. For each treatment, RNA was prepared from six independent experiments and was pooled into one sample to reduce the experimental variation. Targets for microarray hybridization were synthesized accordingly to the supplier’s instructions (Affymetrix). The human GeneChip array U133A (Affymetrix), which interrogates 33,000 transcripts, was used for gene expression profiling. Fifteen GeneChip arrays U133A were used for this analysis; for each different condition, three separate arrays were hybridized with pooled cRNA. Hybridization, washing, staining, scanning, and data analysis were performed at The Affymetrix Microarray Unit at the IFOM-IEO campus, Milan, Italy, according to the manufacturer’s instructions. Expression levels were analyzed using Microarray Analysis Suite (MAS) 5.0 statistical algorithm software (Affymetrix), using the default parameters and scaling (TGT Value) signal intensities for all the GeneChip arrrays to a value of 500. The mock siRNA treatment was used as a baseline condition for comparison with the polycomb siRNA-treated samples.

middle: P

first: Nikolaj

last: Dietrich

first: Diego

last: Pasini

first: Klaus

last: Hansen

first: Kristian

last: Helin


title: A Mitochondria-K+ Channel Axis Is Suppressed in Cancer & Its Normalization Promotes Apoptosis and Inhibits Cancer Growth

status: Public on Oct 11 2006

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary:
The unique metabolic profile of most cancers (aerobic glycolysis) might confer apoptosis-resistance and be therapeutically targeted. Compared to normal cells, several human cancers have high mitochondrial membrane potential and low expression of the K+ channel Kv1.5, both contributing to apoptosis-resistance. Dichloroacetate (DCA), an inhibitor of the mitochondrial pyruvate dehydrogenase kinase (PDK), shifts metabolism from glycolysis to glucose oxidation, decreases mitochondrial membrane potential, increases mitochondrial-H2O2 and activates Kv channels in all cancer, but not normal cells; DCA upregulates Kv1.5 by an NFAT1-dependent mechanism. DCA induces apoptosis, decreases proliferation and tumor growth in vitro and in vivo, without apparent toxicity. Molecular inhibition of PDK2 by siRNA mimics DCA. The mitochondria-NFAT-Kv axis and PDK are important therapeutic targets in cancer; the orally available DCA is a novel selective anticancer agent.
Keywords: treatment

overall_design: lung carcinoma and brain glioblastoma cells were analalyzed, with microarrays run both for control and treatment with DCA

first: Sebastien

last: Bonnet

first: Stephen

last: Archer

first: Joan

last: Allalunis-Turner

first: Alois

last: Haromy

first: Christian

last: Beaulieu

first: Richard

last: Thompson

first: Christopher

middle: T

last: Lee

first: Gary

middle: D

last: Lopaschuk

first: Lakshmi

last: Puttagunta

first: Sandra

first: Gwyneth

last: Harry

first: Kyoko

last: Hashimoto

last: Porter

first: Miguel

last: Andrade-Navarro

first: Bernard

last: Thebaud

first: Evangelos

last: Michelakis


title: 5`aza-dC demethylation of three short term cultured glioblastomas

status: Public on Nov 03 2006

city: Berlin

first: Wolf

middle: C

last: Mueller

address: Amrumer Str. 1

department: Neuropathology

institute: Charité Universitätsmedizin Berlin

type:
Expression profiling by array
Methylation profiling by array

summary:
Glioblastoma, the most aggressive and least treatable form of malignant glioma, is the most common human brain tumor. Although many regions of allelic loss occur in glioblastomas, relatively few tumor suppressor genes have been found mutated at such loci. To address the possibility that epigenetic alterations are an alternative means of glioblastoma gene inactivation, we coupled pharmacological manipulation of methylation with gene profiling to identify potential methylation-regulated, tumor-related genes. Triplicates of three short-term cultured glioblastomas were exposed to 5μM 5-aza-dC for 96 hours followed by cRNA hybridization to an oligonucleotide microarray (Affymetrix U133A). We based candidate gene selection on bioinformatics, RT-PCR, bisulfite sequencing, methylation-specific PCR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Two genes identified in this manner, RUNX3 and Testin (TES), were subsequently shown to harbor frequent tumor-specific epigenetic alterations in primary glioblastomas. This overall approach therefore provides a powerful means to identify candidate tumor suppressor genes for subsequent evaluation and may lead to the identification of genes whose epigenetic dysregulation is integral to glioblastoma tumorigenesis.
Keywords: expression profile following global demethylation

overall_design: Duplicates of three short term cultured glioblastoma cell lines (internal IDs: GLI56;GLI60;GLI72) were either exposed to 5umol 5`aza-dC for 96h or left untreated. Total RNA was extracted of treated and untreated cells after 96h and hybridized to U133A chip. Gene expression profiles of treated and untreated cells were compared. Upregulation of gene expression in the treated (demethylated) samples was interpreted as potentially being regulated by methylation - pointing towards hypermethylation in the related cell line. Identification of novel tumor suppressor genes, regulated by methylation, was the overall goal.

first: David

middle: N

last: Louis


title: Detection of cardiac allograft rejection and response to immunosuppressive therapy with peripheral blood gene expression

status: Public on Oct 04 2006

city: Philadelphia

first: Thomas

last: Cappola

state: PA

address: 6 Penn Tower, 3400 Spruce Street

department: Penn Cardiovascular Institute

institute: Univeristy of Pennsylvania School of Medicine

summary:
BACKGROUND: Assessment of gene expression in peripheral blood may provide a noninvasive screening test for allograft rejection. We hypothesized that changes in peripheral blood expression profiles would correlate with biopsy-proven rejection and would resolve after treatment of rejection episodes. METHODS AND RESULTS: We performed a case-control study nested within a cohort of 189 cardiac transplant patients who had blood samples obtained during endomyocardial biopsy (EMB). Using Affymetrix HU133A microarrays, we analyzed whole-blood expression profiles from 3 groups: (1) control samples with negative EMB (n=7); (2) samples obtained during rejection (at least International Society for Heart and Lung Transplantation grade 3A; n=7); and (3) samples obtained after rejection, after treatment and normalization of the EMB (n=7). We identified 91 transcripts differentially expressed in rejection compared with control (false discovery rate <0.10). In postrejection samples, 98% of transcripts returned toward control levels, displaying an intermediate expression profile for patients with treated rejection (P<0.0001). Cluster analysis of the 40 transcripts with >25% change in expression levels during rejection demonstrated good discrimination between control and rejection samples and verified the intermediate expression profile of postrejection samples. Quantitative real-time polymerase chain reaction confirmed significant differential expression for the predictive markers CFLAR and SOD2 (UniGene ID No. 355724 and No. 384944). CONCLUSIONS: These data demonstrate that peripheral blood expression profiles correlate with biopsy-proven allograft rejection. Intermediate expression profiles of treated rejection suggest persistent immune activation despite normalization of the EMB. If validated in larger studies, expression profiling may prove to be a more sensitive screening test for allograft rejection than EMB.
Keywords: human, peripheral blood, before and after therpay, untreated control

overall_design: Case- control study with three groups.  Patients with rejection (r1-r7), follow-up samples after treatment of rejection (post1-7), and controls with no rejection (con1-7)

first: Philip

last: Horwitz

first: Jonathan

last: Epstein

first: Emily

last: Tsai

first: Mary

middle: E

last: Putt


title: Influence of beverages on blood gene expression

city: Basel

first: Florent

last: Baty

address: Petersgraben 4

department: Pneumology

country: Switzerland

institute: Universitätsspital Basel

summary:
The aim of this study was to measure the influence of beverages on blood gene expression. We wanted to explore the underlying mechanisms of the cardioprotective effects of red wine.
Keywords: Treatment effect

overall_design: Six healthy volunteers participated in this randomized controlled cross-over experiment. On 4 independent days they had 4 different beverages (500mL each: grape juice, red wine, 40g diluted ethanol, water). Blood samples were taken at baseline, 1, 2, 4, 12 hours after the drink together with standardized nutrition. RNA of 120 PBL samples was hybridized on Affymetrix microarrays. Three sources of variations were examined: individual, time and beverage.

first: Michaël

last: Facompré

first: Jan

last: Wiegand

first: Joseph

last: Schwager

first: Christian

last: Müller

first: Martin

last: Brutsche


title: CD34+ and Treatment with UTP and CXCL12

first: Rossella

last: Manfredini

summary:
Homing and engraftment of hematopoietic stem cells (HSCs) to the bone marrow (BM) involve a complex interplay between chemokines, cytokines, and non-peptide molecules. Extracellular nucleotides and their cognate P2 receptors are emerging as key-factors of inflammation and related chemotactic responses. In this study, we investigated the activity of extracellular adenosine-triphosphate (ATP) and uridine-triphosphate (UTP) on CXCL12-stimulated CD34+ HSC chemotaxis. In vitro, UTP significantly improved HSC migration, inhibited cell membrane CXCR4 down-regulation of migrating CD34+ cells and increased cell adhesion to fibronectin. In vivo, pre-incubation with UTP significantly enhanced the BM homing efficiency of human CD34+ cells in immunodeficient mice. Pertussis toxin blocked CXCL12- and UTP-dependent chemotactic responses, suggesting that G-protein alpha-subunits (Gαi) may provide a converging signal for CXCR4- and P2Y-activated transduction pathways. In addition, gene expression profiling of UTP-treated CD34+ cells and in vitro inhibition assays demonstrated that Rho guanosine 5’-triphosphatases (GTPase) Rac2 and downstream effectors Rho GTPase–activated kinases 1 and 2 (ROCK1/2) are involved in UTP-promoted/CXCL12-dependent HSC migration. Our data suggest that UTP may physiologically modulate the migration of HSCs and their homing to the BM, in concert with CXCL12, via the activation of converging signaling pathways between CXCR4 and P2Y receptors, involving Gαi proteins and RhoGTPases.
Keywords: treatment comparison

overall_design: Highly purified CD34+ cells from 6 healthy donors were seeded at 1000000 cells/ml in serum free medium (EX vivo 15) w/o cytokines and treated with 10 mM UTP, 150ng/ml CXCL12, or 10 mM UTP plus 150ng/ml CXCL12 respectively for 24 hours. As a control, CD34+ untreated cells were maintained in the same culture conditions at the same time.


title: Transcription data from Normal Skin and Nonlesional and Lesional Atopic Dermatitis/Eczema Skin

status: Public on Oct 01 2006

city: Rochester

first: Douglas

last: Plager

state: MN

address: 200 First Street SW

department: Dermatology

institute: Mayo Clinic Rochester

summary:
Atopic dermatitis (AD) is a common pruritic dermatitis with macroscopically nonlesional skin that is often abnormal.  Therefore, we used high-density oligonucleotide arrays to identify cutaneous gene transcription changes associated with early AD inflammation as potential disease control targets.  Skin biopsy specimens analyzed included normal skin from five healthy nonatopic adults and both minimally lesional skin and nearby or contralateral nonlesional skin from six adult AD patients.
Keywords: disease state analysis

overall_design: We used high-density oligonucleotide Affymetrix Human U133A GeneChip arrays to identify cutaneous gene transcription changes associated with early AD inflammation as potential disease control targets.  Skin biopsy specimens analyzed included normal skin from five healthy nonatopic adults and both minimally lesional skin and nearby or contralateral nonlesional skin from six adult AD patients.

first: Alexey

last: Leontovich

first: Gabriel

middle: F

last: Sciallis II

first: Mark

middle: R

last: Pittelkow


title: Expression data from H157 non-small cell lung carcinoma cells with and without DJ-1 expression knocked-down

city: Chapel Hill

first: Casey

last: Clements

state: NC

department: Lineberger Cancer Center

institute: UNC Chapel Hill

summary:
DJ-1 expression protects H157 cells from cell death, using siRNA oligomers we knocked down DJ-1 and evaulated gene expression using Affymetrix U133A GeneChip arrays.
Keywords: siRNA comparison

overall_design: H157 cells were transfected every 24 hours with siRNA oligomers for 3 consecutive days, lysed 96 hours after the first transfection, and total RNA extracted.  cRNA was generated and used to probe Affymetrix U133A GeneChip microarrays.

first: Richard

middle: S

last: McNally

first: Brian

last: Conti

first: Tak

middle: W

last: Mak

first: Jenny

last: Ting


title: Gene Expression Analysis in Malaria Infection

city: Rockville

first: Maryanne

last: Vahey

state: MD

address: 1600 East Gude Drive

institute: Walter Reed Army Institute of Research

summary:
Using genome-wide expression profiles from persons either experimentally challenged with malaria-infected mosquitoes or naturally-infected with Plasmodium falciparum malaria, we present details of the transcriptional changes that occur with infection and that are either commonly shared between subjects with pre-symptomatic and clinically apparent malaria or that distinguish these two groups. Our findings confirm and extend aspects of the earliest responses to malaria infection at the molecular level and which may be informative in elucidating how innate and adaptive immune responses may be modulated in different stages of infection.
Keywords: Human PBMC samples from natural and experimentally (clinical trial) induced malaria

overall_design: Compared samples from patients with naturally acquired malaria infection to those from volunteers in a challenge model vaccine trial.

last: Ockenhouse


title: Expression data from native ZAP-70+CD38+ vs. ZAP-70-CD38- CLL cells

status: Public on Sep 22 2006

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
B-cell chronic lymphocytic leukemia (B-CLL) is a heterogenous disease with a highly variable clinical course and analysis of ZAP-70 and CD38 expression on B-CLL cells allowed for identification of patients with good (ZAP-70-CD38-), intermediate (discordant expression of ZAP-70 and CD38) and poor (ZAP-70+CD38+) prognosis. In an attempt to identify a molecular basis that may underly this diverse clinical behaviour DNA microarray technology was employed to compare eight ZAP-70+CD38+ with eight ZAP-70-CD38- B-CLL cases.
We used microarrays to detail the global programme of gene expression distinguising B-CLL from patient with good (samples 1 to 8) and poor prognosis (sample 9 to 16) and identified distinct classes of up- and down-regulated genes.
Keywords: Disease progression

overall_design: To compare the transcriptosomes of good prognosis CLL cases (ZAP-70-CD38-) to poor prognosis cases (ZAP-70+CD38+), we purified CD19+ cells from peripheral blood samples by immunomagnetic isolation using MidiMacs,  resulting in >95% purity of leukemic cells as detected by FACS analysis of CD19+CD5+ cells. The leukemic cells were freshly purified from untreated patients and RNA was directly isolated from fresh cells without further ex vivo treatment of the cells. Eight immunomagnetically purified peripheral blood derived  ZAP-70+CD38+ CLL cases were compared with eight ZAP-70-CD38- B-CLL cases.

first: Andreas

last: Huettmann

first: Juergen

last: Thomale

first: Rene

last: Deenen

first: Alexander

last: Carpinteiro

first: Holger

last: Nueckel

first: J

last: Edelmann

last: Sellmann

first: Ulrich

last: Duehrsen

last: Duerig


title: Rapamycin treated CEM-C1 cells 3 hours

status: Public on Sep 14 2006

city: Boston

first: Scott

middle: A.

last: Armstrong

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Children's Hospital

summary:
Drug resistance remains a major obstacle to successful cancer treatment. Here we use a novel approach to identify rapamycin as a glucocorticoid resistance reversal agent. A database of drug-associated gene expression profiles was screened for molecules whose profile overlapped with a gene expression signature of glucocorticoid (GC) sensitivity/resistance in Acute Lymphoblastic Leukemia (ALL) cells. The screen indicated the mTOR inhibitor rapamycin profile matched the signature of GC-sensitivity. We thus tested the hypothesis that rapamycin would induce GC sensitivity in lymphoid malignancy cells, and found that it sensitized cells to glucocorticoid induced apoptosis via modulation of antiapoptotic MCL1. These data indicate that MCL1 is an important regulator of GC-induced apoptosis, and that the combination of rapamycin and glucocorticoids has potential utility in ALL. Furthermore this approach represents a novel strategy for identification of promising combination therapies for cancer.
Keywords: drug treatment

overall_design: CEM-C1 cells were treated with 10 nM rapamycin for 3 hours and compared to DMSO treated cells


title: Rapamycin treatment of CEM_C1 cells 24 hours

overall_design: CEM-C1 cells were treated with 10 nM rapamycin or DMSO and harvested for microarray analysis at 24 hours


title: Connectivity Map dataset (build01)

status: Public on Sep 27 2006

city: Cambridge

first: Justin

last: Lamb

address: Seven Cambridge Center

institute: Broad Institute

summary:
A reference collection of genome-wide transcriptional expression data for bioactive small molecules.
Keywords: small molecule perturbation

overall_design: The current collection (build01) contains data for 164 distinct small molecules applied to freely cycling human cell lines, represented by 453 individual treatment and matched vehicle control pairs.


title: Identification of rapamycin as a glucocorticoid resistance reversal agent

summary:
Drug resistance remains a major obstacle to successful cancer treatment. Here we use a novel approach to identify rapamycin as a glucocorticoid resistance reversal agent. A database of drug-associated gene expression profiles was screened for molecules whose profile overlapped with a gene expression signature of glucocorticoid (GC) sensitivity/resistance in Acute Lymphoblastic Leukemia (ALL) cells. The screen indicated the mTOR inhibitor rapamycin profile matched the signature of GC-sensitivity. We thus tested the hypothesis that rapamycin would induce GC sensitivity in lymphoid malignancy cells, and found that it sensitized cells to glucocorticoid induced apoptosis via modulation of antiapoptotic MCL1. These data indicate that MCL1 is an important regulator of GC-induced apoptosis, and that the combination of rapamycin and glucocorticoids has potential utility in ALL. Furthermore this approach represents a novel strategy for identification of promising combination therapies for cancer.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


status: Public on Sep 15 2006

city: Cork

first: Fergal

last: O'Gara

address: College Road

department: Microbiology

country: Ireland

institute: University College Cork

summary:
Global expression profiling of airway epithelial cells infected with Pseudomonas aeruginosa and the rsmA mutant.
Recent work in our laboratory investigated the impact of RsmA on a number of airway epithelial cell phenotypes including actin depolymerization, cytotoxicity and invasion. These cellular phenotypes were influenced by the positive effect of RsmA on the expression of the TTSS in P. aeruginosa (Mulcahy et al. 2006. Infect. Immun.).

Pseudomonas aeruginosa is an important opportunistic pathogen which is capable of causing both acute and chronic infections in immunocompromised patients. Successful adaptation of the bacterium to its host environment relies on the ability of the organism to tightly regulate gene expression. RsmA, a small RNA-binding
protein, controls the expression of a large number of virulence-related genes in P. aeruginosa, including those encoding the type III secretion system and associated effector proteins, with important consequences for epithelial cell morphology and cytotoxicity. In order to examine the influence of RsmA-regulated functions in
the pathogen on gene expression in the host, we compared global expression profiles of airway epithelial cells in response to infection with P. aeruginosa PAO1 and an rsmA mutant. The RsmA-dependent response of host cells was characterized by significant changes in the global transcriptional pattern, including the increased expression of two Kruppel-like factors, KLF2 and KLF6. This increased expression was mediated by specific type III effector proteins. ExoS was required for the enhanced expression of KLF2, whereas both ExoS and ExoY were required for the enhanced expression of KLF6. Neither ExoT nor ExoU influenced the expression of the transcription factors. Additionally, the increased gene expression of KLF2 and KLF6 was associated with ExoS-mediated cytotoxicity. Therefore, this study identifies for the first time the human transcription factors
KLF2 and KLF6 as targets of the P. aeruginosa type III exoenzymes S and Y, with potential importance in host cell death.
Keywords: Expression profiling, Pseudomonas aeruginosa, microbial infection, airway epithelial cells, cystic fibrosis, exoenzymes, ExoS, ExoT, ExoU, ExoY, Kruppel-like factors, KLF2, KLF6

overall_design:
RNA isolation and microarray sample preparation
Biological samples from two independent infection experiments were used in two independent microarray experiments as outlined below. Total RNA was isolated from epithelial cells using a RNeasy Kit (Qiagen) according to manufacturer's instructions. Genomic DNA was removed using DNA-free (Ambion) and confirmed by PCR to be free of DNA, prior to cDNA synthesis. Isolated RNA was used in the preparation of fragmented cRNA for microarray hybridization according to the manufacturer's protocol (Affymetrix). Briefly, 8.5ug of RNA was converted to double stranded cDNA by reverse transcription, using a Superscript cDNA synthesis kit (Invitrogen), with an oligo dT primer containing a T7 RNA polymerase site added 3' of the poly (T) (Affymetrix). After second strand synthesis, cDNA was converted to biotin-labelled cRNA by in vitro transcription (Enzo). The labelled cRNA was purified using Genechip clean up module (Qiagen). Total cRNA quality and yield was measured using a GeneQuant spectrophotometer and 20ug of cRNA was fragmented at 94ºC for 35 mins in fragmentation buffer (40 mM tris acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate). Full length and fragmented cRNA sample integrity was assessed by electrophoresis on a 1% agarose-TBE gel visualized by staining with SyBr green. Fragmented cRNA was sent to MRC geneservice (Cambridge, UK) for assessment of RNA quality using a Bioanalyzer (Agilent) before hybridization and scanning. The arrays were washed and stained in a fluidics station and scanned according to the manufacturer's protocols (Affymetrix).

Microarray data analysis
Raw image analysis was performed using Microarray Suite v5.0 software (Affymetrix). Downstream data analysis was performed using GeneSight software version 2.7 (Biodiscovery). For all analyses, the signal intensities from two independent infection and microarray experiments were used. Statistically significant changes in gene expression were identified by firstly performing analysis of variance (ANOVA), for comparison between multiple groups, with a P value of < 0.05. The list of transcripts generated using ANOVA was then subjected to a Student's t-test, for comparison between two groups, with a P value of < 0.05. To identify different levels of gene expression compared to baseline, a fold change cut-off of greater than or equal to 1.5 was applied to this data.

first: Eoin

last: O'Grady

first: Heidi

last: Mulcahy

first: Julie

last: O'Callaghan

first: Claire

last: Adams


title: Expression data from Drosophila subjected to artificial selection on aggression

status: Public on Aug 30 2006

city: Raleigh

first: Alexis

last: Edwards

address: Campus Box 7614

department: Genetics

institute: North Carolina State University

summary:
Genes relevant to manifestion of and variation in aggression behavior might be differentially expressed in lines selected for divergent levels of aggression.
Keywords: selection group

overall_design: Drosophila males were assessed for their aggression levels in a behavioral assay that quantified aggressive encounters.  A subset of the sampled population was selected as parents for the next generation, with High, Low, and Control selection groups maintained.  This artificial selection was continued for 28 generations, with a variety of other behavioral and life history traits assessed for correlation with response to selection for aggression.  At generation 28, male and female flies were collected for RNA extraction and subsequent gene expression analysis.

first: Theodore

middle: J

last: Morgan

first: Stephanie

last: Rollmann

first: Trudy

last: Mackay


title: Gene expression profiles of primary tumors from patients with metastatic neuroblastoma lacking MYCN amplification

status: Public on Sep 06 2006

city: Los Angeles

first: Shahab

last: Asgharzadeh

address: 4650 Sunset Boulevard, Mail Stop #57

department: Hematology-Oncology

institute: Childrens Hospital Los Angeles

summary:
Metastatic neuroblastomas lacking amplification of the MYCN proto-oncogene vary in their clinical behavior. Those diagnosed before one year of age are least aggressive and those diagnosed after two years are most aggressive. To improve current risk stratification and gain insight into the biological processes that account for this phenomenon, we analyzed expression profiles from 102 primary untreated neuroblastomas. A 55 gene model classified patients diagnosed after 12 months of age based on molecular risk with an error rate of 17.5%. The progression-free survival for this group was 16% and 79% if their tumors had molecular high or low risk profiles (p<0.001). Expression profiles of tumors with molecular high-risk features included genes relating to regulation of growth and programmed cell death. This series also includes 15 samples obtained at disease relapse.  Fourteen out of the fifteen samples had molecular high risk features.
Keywords: repeat

overall_design: 102 samples obtained at diagnosis were analyzed for model generation and compared to 15 obtained at relapse, using Affymetrix HG-U133A (GPL96) and HG-U133B (GPL97) platforms.

first: Robert

last: Seeger


title: Human ischemic cardiomyopathy, idiopathic cardiomyopathy, and nonfailing controls

status: Public on Sep 04 2006

first: Thomas

last: Cappola

summary:
Left ventricular myocardium was snap-frozen at time of cardiac transplantation from patients with advanced idiopathic or ischemic cardiomyopathy, or at time of harvest from unused donor heart that serve as a nonfailing control.  No subjects received mechanical support devices.
Keywords: disease state analysis (case:control)

overall_design: All arrays were normalized together using RMA (www.Bioconductor.org)

first: Kenneth

middle: B

last: Margulies

first: Mary

last: Putt

first: Sridhar

last: Hannenhalli


title: The Genome Wide Distribution of Acetylated Histone H4 Remodelled through Human Primary Myoblast Differentiation

status: Public on Aug 28 2006

last: Perkins

type: Genome binding/occupancy profiling by SNP array

summary:
The simultaneous genotyping of tens of thousands of SNP using SNP microarrays is a very important tool that is revolutionizing genetics and molecular biology. In this work, we present a new application of this technique by using it to assess chromatin immunoprecipitation (CHIP) as a means to assess the multiple genomic locations bound by a protein complex recognized by an antibody. We illustrate the use of this technique with an analysis of the change in histone H4 acetylation, a marker of open chromatin and transcriptionally active genomic regions, which occur during the differentiation of human myoblasts into myotubes. Our results are validated by the observation of a significant correlation between the histone modifications detected and the expression of the nearby genes, as measured by DNA microarrays.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
This super series is composed of the following subset series:
GSE4131: Triplicate Affymetrix HGU133A/B expression chips were hybridized to RNA extracted from myoblasts and myotubes.
GSE4132: Triplicate Affymetrix 10K ax 13339 SNP chips were hybridized to DNA from myoblasts and myotubes.


title: col0,gun1,abi4-102, w/wo lincomycin

status: Public on Sep 09 2006

city: La Jolla

first: Joanne

last: Chory

address: 10010 N. Torrey Pines Road.

department: Plant Biology Laboratory

institute: The Salk Institute for Biological Studies

summary:
To test the relationship between GUN1 and ABI4
Keywords: does response, mutant

overall_design: 2*3 factorial design, two factors (1) treatment: with/without lincomycin (2) genotype: col0, gun1, abi4-102

first: Shai

last: Koussevitzky


title: Differential Gene Induction by Type I And Type II Interferons and Their Combination

status: Public on Aug 15 2006

city: Bloomington

first: Milton

last: Taylor

state: IN

address: 343 Jordan Hall

department: Biology

institute: Indiana University

summary:
Type I and type II interferons (IFNs) bind to different cell surface receptors but activate overlapping signal transduction pathways.  We examined the effects of a type I IFN (IFN-acon1) and a type II iFN (IFN-g1b) on gene experession in A549 cells and demonstrate that there is a common set of genes modulated by both IFNs as well as a set of gene specifically regulated by each, reflecting the activation of different signaling pathways.  In particualr, IFN-g induced many more genes of the signaling pathways, apoptosis, and cytokine interactions than did IFN-a.  Even with genes induced by both IFNs there were distinctive quantitativive differences in expression. IFN-g1b plays a major role in the induction and regulation of the complement pathway.  Previous work has shown a synergistic antivral and antiproliferative effect of type I and type II IFNs in cell culture and in the treament of tumors in mice.  We demonstrate that a majority of genes showed and additive effect of IFN-acon1 and IFN-g1b, but a subset of gene is synergistically induced;  these incluce ISG10, MX2, OAS2, and other genes known to be involved in the antiviral response, TRAIL (TNFSF10) and caspases involved in apoptosis and chemokine genes RANTES, CXCL10, and CXCL11.  Greater than additive transcription of some of these genes in the presence of both IFNs was confirmed by real-time kinetic RT-PCR.  Elevated induction of many of these genes may be sufficient to explain the synergistic antiviral and antitumor effects of this combination of IFNS in vivo.
Keywords: comparison of  2 treatments, combination, and untreated at two time points

overall_design: 4 cell culture replicates per treatment group.

first: Corneliu

last: Sanda

first: Patrick

last: Weizel

first: Takuma

last: Tsukahara

first: Joel

last: Schaley

first: Howard

last: Edenberg

first: Matthew

middle: A

last: Stephens

first: Jeanette

last: McClintick

first: Lawrence

last: Blatt

first: Lang

last: Li

first: Leonid

last: Brodsky


title: Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL-1 and glucocorticoid resistance

first: Scott

last: Armstrong

summary:
Drug resistance remains a major obstacle to successful cancer treatment. Here we use a novel approach to identify rapamycin as a glucocorticoid resistance reversal agent. A database of drug-associated gene expression profiles was screened for molecules whose profile overlapped with a gene expression signature of glucocorticoid (GC) sensitivity/resistance in Acute Lymphoblastic Leukemia (ALL) cells. The screen indicated the mTOR inhibitor rapamycin profile matched the signature of GC-sensitivity. We thus tested the hypothesis that rapamycin would induce GC sensitivity in lymphoid malignancy cells, and found that it sensitized cells to glucocorticoid induced apoptosis via modulation of antiapoptotic MCL1. These data indicate that MCL1 is an important regulator of GC-induced apoptosis, and that the combination of rapamycin and glucocorticoids has potential utility in ALL. Furthermore this approach represents a novel strategy for identification of promising combination therapies for cancer.
Keywords: drug resistance comparison

overall_design: primary acute lymphoblastic leukemia samples were determined to be sensitive or resistant to in vitro treatment with glucocorticoids. Samples were then hybrized to affymetrix microarrays


title: Skin biopsies from atopic eczema and healthy controls

status: Public on Oct 13 2006

city: Gothenburg

first: Mikael

last: Benson

address: Smorslottsgatan

department: Paediatrics

country: Sweden

institute: Queen Silvia Children's Hospital

summary:
The aim of this study was to find disease-associated genes in atopic eczema.
Keywords: Skin biopsy, DNA microarray, atopic eczema

overall_design: Skin biopsies were analyzed from ten patients with active atopic eczema and ten healthy controls.


title: red illumination w/o lincomycin

summary:
To identify putative regulatory elements enriched in the promoters of target genes of the PGE-dependent retrograde signaling pathway, we analyzed 500 bp regions of sequence upstream of genes whose expression was down-regulated by lincomycin. We treated dark-grown Arabidopsis seedlings with lincomycin, sampled them before or after a short illumination and examined the genomic response using Affymetrix ATH1 oligonucleotide microarrays. Differentially regulated genes were ranked based on descending degree of significance (p-value) and the top 50 genes affected by lincomycin in dark grown seedlings and top 50 genes affected by the antibiotic after illumination were selected for further analysis.
Keywords: does response

overall_design: 2*2 factorial design, two variables are (1) with/without lincomycin treatment (2) with/without red  illumination. There are 2 replicates for each condition.

first: Pablo

last: Cerdan

first: Kunhua

last: Chen

first: Jianping

last: Hu


title: Over-expression of MBF1c enhances stress tolerance

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

summary:
Multiprotein bridging factor 1c MBF1c (At3g24500) is a stress-response transcription co-activator. To test the function of MBF1c, we over-expressed it in transgenic Arabidopsis plants using the 35S-CaMV promoter. T4 seeds form 3 independent lines were tested for their tolerance to biotic and abiotic stress conditions. Constitutive expression of MBF1c in Arabidopsis enhanced the tolerance of transgenic plants to bacterial infection, salinity, heat and osmotic stress. Moreover, the enhanced tolerance of transgenic plants to osmotic and heat stress was maintained even when these two stresses were combined. The expression of MBF1c in transgenic plants augmented the accumulation of a number of sugars and defense transcrtipts in response to heat stress. Transcriptome profiling and inhibitor studies suggest that MBF1c expression enhances the tolerance of transgenic plants to heat and osmotic stress by partially activating, or perturbing, the ethylene-response signal transduction pathway. MBF1 proteins could be used to enhance the tolerance of plants to different abiotic stresses. Suzuki et al., 2005 Plant Physiology, submitted.

Experimenter name = Ron Mittler
Experimenter phone = 1-775-784-1384
Experimenter fax = 1-775-784-1650
Experimenter department = Dept. of Biochemistry
Experimenter institute = University of Nevada
Experimenter address = MS200
Experimenter address = Reno
Experimenter address = Nevada
Experimenter zip/postal_code = 89557
Experimenter country = USA
Keywords: genetic_modification_design; stimulus_or_stress_design

overall_design: 6 samples were used in this experiment

first: Ron

last: Mittler

first: Henrik

last: Townsend

first: Zoe

last: Emmerson

first: Beatrice

last: Schildknecht


title: Targets of AtWRKY27  in Arabidopsis leaves

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary:
The Arabidopsis transcription factor WRKY27 was found to be involved in plant defense towards Ralstonia solanacearum GMI1000. To identify target genes of WRKY27, we introduced a functional tagged version of WRKY27 into two independent Arabidopsis wrky27 knockout lines (ecotype Columbia) under the control of the estrogen receptor-based chemical-inducible system. 18 days old  plants grown on soil (Metro Mix 200) at 22oC under a 10/14 h light/dark cycle were treated for 6h with 10 microM beta-estradiol after which RNA was immediately isolated. The two independent knockout lines transformed with the empty vectors (pMD::XVE-SALK and pMD::XVE-ETL)  served as controls and were grown under the same conditions and treated identically as the experimental plants.

Experimenter name = Shahid Mukhtar
Experimenter phone = +49-221-5062-310
Experimenter fax = +49-221-5062-353
Experimenter address = Max.Planck-Institute for Plant Breeding
Experimenter address = Dept. Plant Microbe Interactions
Experimenter address = Carl-von-Linne Weg 10
Experimenter address = Koeln
Experimenter zip/postal_code = 50829
Experimenter country = Germany
Keywords: genetic_modification_design

overall_design: 4 samples were used in this experiment

first: Shahid

last: Mukhtar

first: Imre

last: Somssich


title: Response to cold, soil grown plants

summary:
This experiment was annotated by TAIR (http://arabidopsis.org).

This experiment looks at changes in gene expression in Col-0 plants grown in soil in response to low temperature over time.

Experimenter name = Jonathan Vogel
Experimenter phone = 517-355-2299
Experimenter fax = 517-353-5174
Experimenter department = MSU-DOE Plant Research Lab
Experimenter institute = Michigan State University
Experimenter address = East Lansing
Experimenter zip/postal_code = MI 48824
Experimenter country = USA
Keywords: time_series_design

overall_design: 8 samples were used in this experiment

first: Jonathan

last: Vogel

first: Michael

last: Thomashow


title: Determination of myotube and myoblast expression levels

city: Ottawa

first: Theodore

last: Perkins

institute: Ottawa Hospital Research Institute

summary:
Gene expression was determined for both myotubes and myoblasts using Affymetrix HG-U133 A/B arrays.
Keywords: Comparative expression

overall_design:
Triplicate Affymetrix HG-U133A/B expression chips were hybridized to RNA extracted from myoblasts and myotubes.
12 samples in total.


title: Cell Specific Expression & Pathway Analyses Reveal Novel Alterations in Trauma-Related Human T-Cell & Monocyte Pathways

first: Wenzhong Xiao

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

summary:
Monitoring genome-wide, cell-specific responses to human disease, although challenging, holds great promise for medicine’s future.  Patients with injury severe enough to develop multiple organ dysfunction syndrome (MODS) are known to have multiple immune derangements, including T-cell apoptosis and anergy combined with depressed monocyte antigen presentation.  Genome-wide expression analysis of highly-enriched circulating leukocyte subpopulations, combined with cell-specific pathway analyses, offers a previously unavailable opportunity to discover novel leukocyte regulatory networks in critically injured patients.  Severe injury induced significant changes in the T-cell, monocyte, and total leukocyte transcriptome, with only 12% of these genomic changes common to all three cell populations.  T-cell-specific pathway analyses identified increased gene expression of several novel inhibitory receptors (PD-1, CD152, NRP-1, Lag3), and concomitant decreases in stimulatory receptors  (CD28, CD4, IL-2Ralpha).  Functional analysis of T-cells and monocytes confirmed reduced T-cell proliferation and increased cell surface expression of negative signaling receptors paired with decreased monocyte costimulation ligands. Thus, genome-wide expression from highly-enriched cell populations combined with knowledge-based pathway analyses leads to the identification of novel regulatory networks differentially expressed in injured patients.  Importantly, application of cell separation, genome-wide expression, and cell specific pathway analyses can be used to discover novel pathway alterations in human disease.
Keywords: Gene expression profiling of circulating total blood leukocytes, T-Cells, and Monocytes in severe trauma patients and healthy subjects.

overall_design:
Type of experiment: Gene expression profiling of circulating total blood
leukocytes, T-Cells, and Monocytes in severe trauma patients and healthy subjects.
Experimental factors: Healthy subjects, 7 severely traumatized patients
and 7 healthy subjects for transcriptome analysis. Venous blood samples
were collected. Total blood leukocytes were isolated, and T-cell and
monocyte populations were obtained from two subsequent aliquots of the
leukocytes. Total leukocytes, enriched T-cells, and enriched monocytes were analyzed using Affymetrix GeneChip arrays.
Number of hybridizations: 42 Human U133A GeneChip arrays (Affymetrix)

first: Krzysztof

last: Laudanski

first: Carol

last: Miller-Graziano

first: Wenzhong

last: Xiao

last: Mindrinos

first: Daniel

last: Richards

first: Asit

last: De

first: Lyle

last: Moldawer

first: Ronald

middle: V

last: Maier

first: Paul

last: Bankey

first: Henry

last: Baker

first: Bernard

middle: H

last: Brownstein

first: J

last: Cobb

first: Steve

last: Calvano

last: Davis

middle: G

last: Tompkins


title: Tissue Type Arrays of Columbia-0

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
This experiment has been annotated by TAIR (http://arabidopsis.org).

In this experiment, different tissue preparations of wild type Columbia-0 Arabidopsis thaliana plants were hybridized and run on the ATH1 Affymetrix platform.

Experimenter name = Chris Somerville
Experimenter phone = 650-325-1521 ext203
Experimenter fax = 650-325-6857
Experimenter address = Plant Biology
Experimenter address = Carnegie Institution
Experimenter address = 260 Panama Street
Experimenter address = Stanford
Experimenter zip/postal_code = CA 94305-1297
Experimenter country = USA
Keywords: organism_part_comparison_design;

overall_design: 11 samples were used in this experiment

first: Chris

last: Somerville

first: Henrik

last: Townsend

first: Zoe

last: Emmerson

first: Beatrice

last: Schildknecht


title: Arabidopsis E2F target genes

summary:
Entry into the S phase of the cell cycle is controlled by the E2F transcitption factors that induce the transcription of genes required for cell cycle progression and DNA replication. To identify E2F target genes of Arabidopsis on a genome-wide scale, the transcriptome of wild-type plants was compared with that one of plants ectopically expressing the E2Fa-DPa genes. In four independent experiments, E2Fa-DPa overexpressing plants were grown side-to-side with wild type (Col-0) plants. RNA was extracted from 6-day-old seedlings. Each biological sample was harvested and processed independently, and finally all probed individually to Affymetrix ATH1 microarrays, resulting into 8 hybridization signals for each probeset.

Experimenter name = Lieven De Veylder
Experimenter phone = +32 9 3313961
Experimenter fax = +32 9 3313809
Experimenter address = Technologiepark 927
Experimenter address = B-9052 Gent
Experimenter zip/postal_code = B-9052
Experimenter country = Belgium
Keywords: genetic_modification_design

first: Lieven

last: De Veylder

first: Dirk

last: Inze


title: Response to cold, plate grown plants

summary:
This experiment was annotated by TAIR (http://arabidopsis.org).

This experiment looks at changes in gene expression in Col-0 plants grown in plates in response to low temperature over time.

Experimenter name = Jonathan Vogel
Experimenter phone = 517-355-2299
Experimenter fax = 517-353-5174
Experimenter department = MSU-DOE Plant Research Lab
Experimenter institute = Michigan State University
Experimenter address = East Lansing
Experimenter zip/postal_code = MI 48824
Experimenter country = USA
Keywords: time_series_design

first: Jonathan

last: Vogel

first: Michael

last: Thomashow


title: Gene Expression During Recovery from Freezing

summary:
Freezing causes physiological changes even in a hardy, cold-acclimated wild type. During recovery from freezing, gene expression will reflect the induction of damage-repair processes distinct from the damage-prevention associated with cold acclimation. This will be detected by observing the wild-type transcriptome at two time points during recovery from a freezing episode. The appropriate control is the unfrozen, cold-acclimated wild type.

Experimenter name = Glenn Thorlby
Experimenter phone = 01874 443770
Experimenter address = School of biological Sciences
Experimenter address = Bourne Building
Experimenter address = Royal Holloway
Experimenter address = Egham
Experimenter zip/postal_code = TW20 0EX
Keywords: growth_condition_design;

overall_design: 3 samples were used in this experiment

first: Glenn

last: Thorlby


title: Hydrogen peroxide stress and Zat12 over-expression in Arabidopsis.

summary:
In this experiment we tested the transcriptome of transgenic Arabidopsis seedlings (5-day-old) constitutively expressing the zinc-finger protein Zat12 (At5g59820) under the control of the 35S-CaMV promoter (Zat12). The transcriptome of these seedlings was compared to that of wild type seedlings grown under the same conditions (WT) and to that of wild type seedlings grown under the same conditions and subjected to a hydrogen peroxide stress (WT+H2O2). Hydrogen peroxide treatment was performed by applying 20 mM hydrogen peroxide for 1 hour. In parallel to these experiments transgenic plants expressing Zat12 were subjected to a similar hydrogen peroxide stress (Zat12+H2O2). All treatments were performed with similar size and age seedlings grown in liquid culture (MS) and sampled at the same time as described by Davletova et al., 2005.

Experimenter name = Ron Mittler
Experimenter phone = 1-775-784-1384
Experimenter fax = 1-775-784-1650
Experimenter department = Dept. of Biochemistry
Experimenter institute = University of Nevada
Experimenter address = MS200
Experimenter address = Reno
Experimenter address = Nevada
Experimenter zip/postal_code = 89557
Experimenter country = USA
Keywords: genetic_modification_design; stimulus_or_stress_design

overall_design: 12 samples were used in this experiment

first: Ron

last: Mittler


title: Comparative ABA-treatment of Col-O vector control and transgenic plants

summary:
The aim of this experiment is to understand the impact of overexpression of ERD15 on the transcriptome of Arabidopsis thaliana. ERD15 was isolated from a screen for genes rapidly induced after pathogen treatment from Arabidopsis. This gene was originally found as early responsive to drought (Kiyosue et al., 1994, Plant Physiol 106, 1707). ABA is central phytohormone in drought response, but increasing information is pointing to its significant role in pathogen responses as well.
We are interested to see the effect of this hormone on plants overexpressing ERD15 compared to control plants. The samples (rosette leaves)will be harvested from 3-week old soil grown plants 90 min after spraying with 100 micromolar ABA. Comparison will be made with non-treated plant samples.

Experimenter name = Elina Helenius
Experimenter phone = +358 9 191 59085
Experimenter fax = +358 9 191 59079
Experimenter institute = University of Helsinki
Experimenter address = Viikinkaari 5 D
Experimenter address = P.O.Box 56
Experimenter address = Helsinki
Experimenter zip/postal_code = 00014
Experimenter country = Finland
Keywords: compound_treatment_design

first: Elina

last: Helenius

first: Tapio

last: Palva


title: Transcriptional Programs of Early Reproductive Stages in Arabidopsis

summary:
The life cycle of flowering plants alternates between a diploid sporophytic and a haploid gametophytic generation. After fertilization of each the egg and central cells by one male gamete, the development of both fertilization products occurs coordinated with the maternally derived seed coat and carpel tissues forming the fruit. The reproduction program is likely to involve the concerted activity of many genes. To identify genes with specific functions during reproduction, we have analyzed the expression profile of more than 22,000 genes present on the Arabidopsis ATH1 microarray during three stages of flower and fruit development. We found 1,886 genes regulated during reproductive development and 1,043 genes that were specifically expressed during reproduction. When compared to cells from an Arabidopsis suspension culture, S-phase genes were underrepresented and G2 and M-phase genes were strongly enriched in the set of specific genes, indicating that important functions during reproduction are exerted in the G2 and M phases of the cell cycle. Many potential signaling components, such as receptor-like protein kinases, phosphatases, and transcription factors, were present in both groups of genes. Members of the YABBY, MADS box, and Myb transcription factor families were significantly overrepresented in the group of specific genes, revealing an important role of these families during reproduction. Furthermore, we found a significant enrichment of predicted secreted proteins smaller than 15 kD that could function directly as signaling molecules or as precursors for peptide hormones. Our study provides a basis for targeted reverse-genetic approaches aimed to identify key genes of reproductive development in plants.
During evolution, both animals and plants developed distinct pathways of sexual reproduction. The haploid life cycle starts with the formation of the meiotic products, for instance arrested primary oocytes and spermatocytes in mammals or micro- and megaspores in plants. The haploid phase ends when a sperm cell fuses with an egg cell to form the diploid zygote, which initiates embryo development. In animals, gametes are derived from a population of germ cells committed early during development to their reproductive fate and which usually rest until the onset of sexual maturity. By contrast, stem cells in shoot apical meristems of flowering plants divide continuously during postembryonic development. Only after formation of vegetative organs, the meristem produces specialized reproductive organs in which meiosis occurs, the stamens and carpel-borne ovules of the flower (for review, see Bowman and Eshed, 2000; Carles and Fletcher, 2003). As early as 1790, Goethe suggested that floral organs are derived from leaves and adapted to their specialized tasks (Goethe, 1790).
Animal gametes differentiate directly from the products of meiosis, whereas in plants the meiotic products (spores) typically undergo two or three mitotic divisions to give rise to the male or female gametophytes, respectively (Drews et al., 1998; Grossniklaus and Schneitz, 1998). In several plant species, including Arabidopsis, the female gametophyte consists of seven cells: three antipodal cells, two synergid cells, one egg cell, and one central cell that contains two polar nuclei (Drews et al., 1998; Grossniklaus and Schneitz, 1998). The mature male gametophyte comprises two sperm cells contained within a vegetative cell (McCormick, 1993; da Costa-Nunes and Grossniklaus, 2003).
During fertilization one sperm cell nucleus fuses with the egg cell nucleus, giving rise to the diploid embryo, whereas the other sperm cell fuses with the homodiploid central cell nucleus, generating the triploid endosperm (Drews and Yadegari, 2002). Subsequent seed and fruit development are highly coordinated processes between the embryo and endosperm, as well as the maternally derived testa (seed coat) and carpels. Because of the significant economical importance of flowers, seeds, and fruits, the complex processes involved in plant reproduction are not only of academic interest but also of high economic relevance.
Many genes have been identified genetically that have a function in plant reproduction. The establishment of floral organ identity and initiation of seed development have been studied extensively, and many regulators of these processes have been identified (McElver et al., 2001; Zik and Irish, 2003; for review, see Chaudhury et al., 2001). High-throughput RNA profiling technologies can now complement the genetic and molecular approaches to provide new insights into plant reproduction. In particular, oligonucleotide-based microarrays can produce reliable, high-quality data (Lockhart et al., 1996; Hennig et al., 2003) to establish new biological knowledge on the transcriptional programs that are active during developmental processes (Spellman et al., 1998; Harmer et al., 2000; Becker et al., 2003; Honys and Twell, 2003).
Here, we report a comprehensive Affymetrix GeneChip analysis of the Arabidopsis transcriptome at key steps of reproductive development. We identified 1,043 genes that were specifically expressed during reproduction. Among those genes were many potential signaling components, such as receptor-like protein kinases, phosphatases, and transcription factors. In addition, we found a significant enrichment of predicted secreted proteins smaller than 15 kD that could function directly as signaling molecules or as precursors for peptide hormones. Our study provides the basis for targeted reverse-genetic approaches aimed to identify important regulators of reproductive development in plants.

Experimenter name = Lars Hennig
Experimenter phone = +41 1 632 22 44
Experimenter fax = +41 1 632 10 44
Experimenter department = Plant Science C
Experimenter institute = Institute of Plant Sciences and Zurich-Basel
Experimenter address = Swiss Federal Institute of Technology
Experimenter address = ETH Center
Experimenter address = Zurich
Experimenter zip/postal_code = CH-8092
Experimenter country = Switzerland
Keywords: organism_part_comparison_design;

first: Lars

last: Hennig

first: Wilhelm

last: Gruissem


title: Signaling of Neisseria meningitidis MC58 mutants to primary human umbilical vein endothelial cells (HUVEC)

status: Public on Sep 01 2006

city: Prague 4

first: Marek

last: Basler

address: Videnska 1083

department: Cell and Molecular Microbiology Division

country: Czech Republic

institute: Institute of Microbiology, Czech Academy of Sciences

summary:
We examined the adherence-mediated signaling of meningococci to human cells by comparing gene expression profiles of primary human umbilical vein endothelial cells (HUVEC) infected by piliated and adherent wild-type (WT), frpC/frpA-deficient mutant, or the non-adherent (ΔpilD) N. meningitidis MC58 bacteria defective in production of the type IV pilus, respectively. Surprisingly, no significant difference was found between the transcriptomes of HUVECs infected by bacteria producing, or not the RTX FrpC and FrpA proteins, thus failing to provide any hints on their biological activity. In contrast, pili-mediated adhesion of meningococci resulted in alterations of expression levels of human genes known to regulate apoptosis, cell proliferation, inflammatory response or adhesion. In particular, genes for signaling pathway proteins involved in early embryonic development, such as transforming growth factor-β (TGF-β)/Smad, Wnt/β-catenin, and Notch/Jagged were found to be upregulated upon adhesion of N. meningitidis together with genes for a number of transcription factors. This reveals that adhering piliated meningocci manipulate signaling pathways controlling human cell proliferation, survival and defense mechanisms, while establishing a commensal relationship with the host.
Keywords: time course, infection response, genetic modification

overall_design: Time courses of gene expression profiles of primary human umbilical vein endothelial cells (HUVEC) during infection with piliated and adherent wild-type (WT), frpC/frpA-deficient mutant, or the non-adherent (ΔpilD) Neisseria meningitidis MC58 bacteria defective in production of the type IV pilus, were analyzed respectively. Total RNA isolated from uninfected HUVEC (reference) and HUVEC after 1, 4 or 6 hours of infection with N. meningitidis mutants was labeled according to standard Affymetrix protocol and hybridized to HG-U133A GeneChips. Data were analyzed by Robust Multi-array Analysis algorithm. For every condition at least two biological replicates were analyzed, totally representing 23 Affymetrix GeneChips.

first: Irena

last: Linhartova

first: Jeffrey

last: Ichikawa

first: Vladimir

last: Pelicic

first: Radim

last: Osicka

first: Stephen

last: Lory

first: Xavier

last: Nassif

first: Peter

last: Sebo


title: Responses to overexpression of wild type and constitutively active Arabidopsis MAP Kinase Kinase 2

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
This experiment has been annotated by TAIR (http://arabidopsis.org).

We examined transcript profiles triggered by three different arabidopsis R genes that recognize distinct Peronospora parasitica isolates.

Experimenter name = Thomas Eulgem
Experimenter phone = 43 1 4277 54622
Experimenter fax = 43 1 4277 9546
Experimenter department = Institute of Microbiology and Genetics
Experimenter address = Institute of Microbiology and Genetics
Experimenter address = Dr. Bohrgasse 9
Experimenter address = Vienna
Experimenter zip/postal_code = A-1030
Experimenter country = Austria
Keywords: strain_or_line_design

first: Thomas

last: Eulgem

first: Jeff

last: Dangl

first: Henrik

last: Townsend

first: Zoe

last: Emmerson

first: Beatrice

last: Schildknecht


title: Transcriptome changes of Arabidopsis during pathogen and insect attack

summary:
Plant defenses against pathogens and insects are regulated differentially by cross-communicating signaling pathways in which salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) play key roles. To understand how plants integrate pathogen- and insect-induced signals into specific defense responses, we monitored the dynamics of SA, JA, and ET signaling in Arabidopsis after attack by a set of microbial pathogens and herbivorous insects with different modes of attack. Arabidopsis plants were exposed to a pathogenic leaf bacterium (Pseudomonas syringae pv. tomato), a pathogenic leaf fungus (Alternaria brassicicola), tissue-chewing caterpillars (Pieris rapae), cell-content-feeding thrips (Frankliniella occidentalis), or phloem-feeding aphids (Myzus persicae). Monitoring the signal signature in each plant-attacker combination showed that the kinetics of SA, JA, and ET production varies greatly in both quantity and timing. Analysis of global gene expression profiles demonstrated that the signal signature characteristic of each Arabidopsis-attacker combination is orchestrated into a surprisingly complex set of transcriptional alterations in which, in all cases, stress-related genes are overrepresented. Comparison of the transcript profiles revealed that consistent changes induced by pathogens and insects with very different modes of attack can show considerable overlap. Of all consistent changes induced by A. brassicicola, P. rapae, and F. occidentalis, more than 50% were also induced consistently by P. syringae. Notably, although these four attackers all stimulated JA biosynthesis, the majority of the changes in JA-responsive gene expression were attacker-specific. All together our study shows that SA, JA, and ET play a primary role in the orchestration of the plant's defense response, but other regulatory mechanisms, such as pathway cross-talk or additional attacker-induced signals, eventually shape the highly complex attacker-specific defense response.
In the experimental set up we intended to select for genes that showed a more than 2-fold change in the same direction(up or down)at two time points after pathogen or insect attack.
The results are described in the following paper:
De Vos, M., Van Oosten, V.R., Van Poecke, R.M.P., Van Pelt, J.A., Pozo, M.J., Mueller, M.J., Buchala, A.J., Metraux, J.-P., Van Loon, L.C., Dicke, M. and Pieterse, C.M.J. (2005). Signal signature and transcriptome changes in Arabidopsis upon pathogen and insect attack. Molecular Plant-Microbe Interactions.

Experimenter name = Corne Pieterse
Experimenter phone = +31 30 253 3013
Experimenter fax = +31 30 251 8366
Experimenter department = Section Phytopathology
Experimenter institute = Utrecht University
Experimenter address = Department of Biology
Experimenter address = Utrecht University
Experimenter address = Sorbonnelaan 16
Experimenter address = Utrecht
Experimenter zip/postal_code = 3584CA
Experimenter country = The Netherlands
Keywords: time_series_design;  pathogenicity_design

overall_design: 14 samples were used in this experiment

first: Corne

last: Pieterse