title: Altered cell lineage differentiation in fetal LGR5-null mice

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

institute: ULB

summary: The molecular mechanisms controlling stem cell renewal and lineage commitment are still poorly understood due to lack of reliable markers. In the adult small intestine, an example of high rate self-renewing tissue, four different epithelial cell lineages (enterocytes, Goblet, enteroendocrine and Paneth cells) are generated from a pool of stem cells localised at the bottom of the crypts of Lieberkühn. Recently, the orphan Leucine-rich repeat G protein-coupled receptor 5 (GPR49), a target of Wnt signalling, has been proposed as a marker for such cells. We investigated the role of LGR5 during intestinal development by using LGR5 null/LacZ-NeoR knock-in mice. We show that LGR5 deficiency leads to premature Paneth cell differentiation. X-gal staining on E18.5 intestine revealed that LGR5 expression is restricted to a few cells clustered within the intervillus region known to contain progenitor cells. In LGR5-null mice, expression from the LGR5 promoter was found upregulated, suggesting a loss of negative feedback control. However, neither epithelial cell proliferation nor cell migration appeared significantly impaired by LGR5 deficiency. Finally, transcriptional profiling of ileal mutant mice suggests that LGR5 plays a role in regulating the Wnt and Notch signalling pathways controlling progenitor renewal and differentiation.

overall_design: Microarray analysis was performed on four independent pairs of KO/WT E18.5-E19 embryos generated by three independent LGR5+/- couples. Ileum labeled RNA were hybridized to MEEBO arrays containing on average 38784 mouse 70mer oligonucleotide probes (Stanford University, US).

first: Marie-Isabelle

last: Garcia

first: Mariangela

last: Ghiani

first: Anne

last: Lefort

first: Frédérick

first: Gilbert

last: Vassart


title: bac2 mutant transcriptome modification during osmotic stress

status: Public on Oct 01 2009

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

summary:
rs08-05_bac2 - bac2-catma - We are studying the function of a gene encoding a mitochondrial basic amino acid carrier , BAC2 in Arabdopsis thaliana.This gene is expressed during osmotic and salt stresses, and dark-induced senescence. We wish to determine whether there are transcriptome modifications during osmotic stress in mutant plants (bac2) compared to wild-type plants . - Mutant and Wild-type plants were grown on grids for 7 days on plates containing MS/2 and saccharose. Plants were transferred for 24h to liquid medium containing MS/2 saccharose (untreated plants) or 0.4M mannitol MS/2 saccharose (treated plants).

Keywords: gene knock out,treated vs untreated comparison,wt vs mutant comparison

overall_design: 8 dye-swap - CATMA arrays

first: Jean-Pierre

middle: P

last: Renou

first: Pierre

last: Carol

first: Séverine

last: Planchais

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Gene profiling of young rats susceptible to malaria infection

city: Lille

first: Jamal

last: Khalife

address: 1 rue du Prof. Calmette

institute: Inserm U547

summary: The study was performed in order to determine molecular markers potentially involved in the susceptibility of young rats to the infection with Plasmodium berghei Anka

overall_design: In this study, we compared the microarrays of spleens (using the rat Codelink developed by Amersham Biosources) obtained from young rats infected by Plasmodium berghei Anka  with those of uninfected age matched controls.

first: Christine

last: Pierrot

first: Aurore

last: Acroute

first: Sophia

last: Lafitte

first: David

last: Hot


title: Expression analysis of Xylella fastidiosa PD Temecula strain grown in different media

status: Public on Oct 03 2009

city: Berkeley

first: Nabil

last: Killiny

state: CA

address: University of California

department: Environmental science, policy and management

country: USA

institute: UC-Berkeley

summary:
Investigation of whole genome gene expression level changes in Xylella fastidiosa grown in minimal media XFM and XFM supplied with pectin or glucan (Host polysaccharides) , compared to cell grown in the complex media PWG.
The cells grown in the minimal medium XFM supplied with host polysaccharides specially pectin are transmissible by the insect vector when delivered to the vector through artificial diet system. This does not happen with cells grown in the complex media.

overall_design: 4 (4 plex chips) study using total RNA recovered from 4 independents replicates for Xylella fastidiosa grown on PWG, XFM, XFM-glucan and XFM-pectin.

first: Rodrigo

last: Almeida


title: Gene expression differences between matched tumor and normal samples of NSCLC patients (qRT-PCR)

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

summary:
Gene expression differences between between matched tumor and normal samples were analyzed using paired t-test.
Keywords: disease state analysis

overall_design: he NSCLC patient collective was composed of the histological subtype adenocarcinoma (n=42) and squamous cell carcinoma (n=18). We subjected gene expression profiles of 34 AC and 11 SCC matched normal and tumor samples into qRT-PCR analysis. Expression analysis of 30 cell adhesion and EMT associated genes revealed strong differences between matched tumor and normal samples of NSCLC subtypes.

first: Holger

last: Sueltmann

first: Markus

last: Ruschhaupt

first: Andreas

last: Buness

first: Annemarie

last: Poustka

first: Hans

last: Hoffmann

first: Phillipp

last: Schnabel

first: Arne

last: Warth


title: ReproArray_Pmonodon

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

country: Thailand

institute: BIOTEC

summary:
To construct the first in-house version of cDNA microarrays for P. monodon, the ovary and testes EST libraries were used as templates for reproduction-specific cDNA microarray (ReproArray) fabrication.  ReproArray was used to analyze large-scale gene expression and to demonstrate capacity for studies of reproduction-relevant genes.

Keywords: time couse

overall_design: ReproArray was constructed to analyze large-scale gene expression of reproduction-relevant genes in the broodstocks (P. monodon).  The expression study of female brooders from different ovarian development stages was conducted to identify differential expression profiles and important genes. Stage I (Previtellogenic stage) was used as reference for comparison with Stages II, III, IV (Vitellogenic, Early cortical rod, and Late cortical rod). Two replicated data sets were averaged and analyzed.

first: Nitsara

last: Karoonuthaisiri

first: Kanchana

last: Sittikankaew

first: Rachanimuk

last: Preechaphol

first: Thidathip

last: Wongsurawat

first: Umaporn

last: Uawisetwatthana

first: Sergey

last: Kalachikov

first: James

middle: J

last: Russo

first: Jingyue

last: Ju

first: Sirawut

last: Klinbunga

first: Kanyawim

last: Kirtikara


title: Gene expression differences between adenocarcinoma and squamous cell carcinoma in human NSCLC (qRT-PCR)

first: Ruprecht

last: Kuner

summary:
Gene expression differences between the tumor subtypes AC and SCC were analyzed using t-test.
Keywords: disease subtype analysis

overall_design:
The NSCLC patient collective was composed of the histological subtype adenocarcinoma (n=42) and squamous cell carcinoma (n=18). We subjected gene expression profiles of 40 AC and 16 SCC tumor samples into qRT-PCR analysis. Expression analysis of 30 cell adhesion and EMT associated genes revealed strond differences between both NSCLC subtypes.

adenocarcinoma: 10T, 16T, 24T, 40T, 42T, 49T, 51T, 53T, 70T, 84T, 88T, 89T, 113T, 136T, 137T, 147T, 148T, 161T, 169T, 202T, 210T, 233T, 271T, 273T, 276T, 282T, 331T, 334T, 342T, 368T, 378T, 397T, 400T, 402T, 421T, 426T, 434T, 445T, 489T, 492T
squamous cell carcinoma: 22T, 25T, 30T, 37T, 55T, 77T, 95T, 165T, 188T, 215T, 248T, 301T, 347T, 364T, 390T, 412T

first: Holger

last: Sueltmann

first: Markus

last: Ruschhaupt


title: Gene regulation in Erbb2 transfected NIH3T3 cells after Azacytidine treatment

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

summary:
5-Azacytidine or 5-aza-2’-deoxycytidine is a chemical analogue of the cytosine nucleoside used in DNA and RNA. Cells in the presence of 5-azacytidine incorporate it into DNA during replication and RNA during transcription. The incorporation of 5-azacytidine into DNA or RNA inhibits methyltransferase thereby causing demethylation in that sequence, affecting the way that cell regulation proteins are able to bind to the DNA/RNA substrate. Inhibition of DNA occurs through the formation of stable complexes between the molecule and with DNA methyltransferases, thereby saturating the cells methylation machinery. 5-azacytidine is mainly used in the treatment of myelodysplastic syndrome. Changes in gene expression levels in Erbb2 transfected murine fibroblast cell line after treatment with Azacytidine in two different concentrations were analysed.
Keywords: cDNA microarray, murine fibroblast, azacytidine treatment, carcinogenesis

overall_design: Gene expression levels of Erbb2 transfected NIH3T3 cell lines treated with 5µM and 10µM Azacytidine were compared to Erbb2 transfected but non-treated NIH3T3 cell line. For each Azacytidine concentration 4-8 experiments were performed including 50% dye swaps. As a controll experiments gene expression levels of NIH3T3 cells with and without Azacytidine treatment were analysed

first: Johannes

last: Beckers

first: Marion

last: Horsch

first: Barbara

last: Seliger


title: A microarray-based method for the parallel analysis of genotypes and expression profiles in Eucalyptus grandis

city: Pretoria

first: Eugenia

last: Barros

state: Gauteng

address: Meiring Naude Rd

department: Building 20

country: South Africa

institute: CSIR

summary: Fast-growing Eucalyptus grandis trees are one of the most efficient producers of wood in South Africa. It is essential to maximize the effectiveness of these plantations by increasing their productivity, the quality and value of their products. We used microarray-based DNA-amplified fragment length polymorphism (AFLP) analysis in combination with expression profiling to develop fingerprints and profile gene expression of wood-forming tissue of seven individual E. grandis trees. A 1532-probe cDNA microarray was constructed by arraying 768 cDNA-AFLP fragments and 810 cDNA library clones from seven individual E. grandis trees onto silanised slides. The results revealed that 32% of the spotted fragments showed distinct expression patterns (with a fold change of at least 1.4 or -1.4 and a p value of 0.01) and could be grouped into clusters representing co-expressed genes. Evaluation of the binary distribution of cDNA-AFLP fragments on the array showed that the individual genotypes could be discriminated. A simple, yet general method was developed for genotyping and expression profiling of wood-forming tissue of E. grandis trees differing in their splitting characteristics and in their lignin contents. Evaluation of gene expression profiles and the binary distribution of cDNA-AFLP fragments on the chip suggest that the prototype chip developed could be useful for transcript profiling and for the identification of Eucalyptus trees with preferred wood quality traits in commercial breeding programmes.

overall_design: Transcriptional profiling and genotyping of seven E. grandis trees , namely (741-H (high lignin), 108-L (low lignin), 243-L (low lignin), 1/23/4-HS (high splitting), 1/71/6-HS (high splitting), 1/91/7-LS (low splitting) and 1/92/7-LS (low splitting), were performed with an in-house spotted cDNA microarray. All trees were characterized for their splitting qualities and lignin content and only the trees best corresponding to the selected traits were used for further analysis (Verryn and Turner 2000).  RNA was isolated and cDNA synthesis was performed. A reference design microarray experiment was conducted and tree 1/23/4-HS served as a reference. Samples were fluorescently labelled with Cy5 or Cy3 dye and co-hybridized overnight. Two biological and one technical replicate (using independent labelling reactions) was performed, each replication consisting of a reverse labelling experiment.

first: Sabine

last: Lezar


status: Public on Sep 30 2009

city: Vancouver

first: Bradley

last: Coe

state: BC

address: 675 West 10th Ave

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

type: Genome variation profiling by genome tiling array

summary:
DNA structural variation (SV) comprises a major portion of genetic diversity, but its biological impact is unclear. We propose that the genetic history and extraordinary phenotypic variation of dogs make them an ideal mammal in which to study the effects of SV on biology and disease. The hundreds of existing dog breeds were created by selection of extreme morphological and behavioral traits. And along with those traits, each breed carries increased risk for different diseases. We used array CGH to create the first map of DNA copy number variation (CNV) or SV in dogs. The extent of this variation, and some of the gene classes affected, are similar to those of mice and humans. Most canine CNVs affect genes, including disease and candidate disease genes, and are thus likely to be functional. We identified many CNVs that may be breed or breed class specific. Cluster analysis of CNV regions showed that dog breeds tend to group according to breed classes. Our combined findings suggest many CNVs are (1) in linkage disequilibrium with flanking sequence, and (2) associated with breed specific traits. We discuss how a catalog of structural variation in dogs will accelerate the identification of the genetic basis of canine traits and diseases, beginning with the use of whole genome association and candidate CNV/gene approaches.
Chen WK, Swartz JD, Rush LJ, Alvarez, CE. Mapping DNA structural variation in dogs. Genome Res. 2009. 19: 500 509 PMID: 19015322

overall_design: Array comparitive genomic hybridization analysis of structural variation in 9 dogs, and 1 lymphoma cell line.

first: Wei-Kang

last: Chen

first: Joshua

middle: D

last: Swartz

first: Laura

last: Rush

first: Carlos

last: Alvarez


title: Gene expression on different carbon sources in response to hxt1 deletion in Ustilago maydis

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

summary: Plant pathogenic fungi cause massive crop losses and therefore, severe economic deficits. The smut Ustilago maydis, a ubiquitous pest of corn, is highly adapted to its host to parasitize on its organic carbon sources. Recently, we identified the U. maydis sucrose transporter Srt1 to be of crucial importance for biotrophic development. Here we report the identification of Hxt1, a further member of the U. maydis sugar transporter family, which is of importance for full fungal virulence. Hxt1 mainly utilizes the hexoses glucose, fructose and mannose, but with lower affinity also secondary carbon sources like galactose and xylose. Deletion of hxt1 in U. maydis reduces virulence and growth on hexoses, in contrast growth on the secondary carbon sources is enhanced. Expression analysis revealed that monosaccharide-dependent regulation of transcription is hampered in hxt1 deletion mutants, leading to the expression of genes involved in the metabolism of secondary sugars and in the initiation of pathogenicity. Thus, we propose that Hxt1 has a dual function as monosaccharide-transporter and -sensor. While Hxt1 aids the initiation of pathogenicity by sensing starvation conditions on the plant surface as a receptor, it feeds the fungus in planta as a transporter.

overall_design: To analyze expression changes of SG200 and SG200∆hxt1 both strains were grown in glutamine minimal array media supplemented with 1% glucose or 1 %xylose to an OD600 of 1.0 for 6 h, respectively. For each experiment two independent replicates were conducted.

first: Ramon

last: Wahl


title: Gene expression in the barley spike during drought stress

city: Cedar Falls

first: Tilahun

last: Abebe

state: IA

address: 191 McCollum Hall

department: Biology

institute: University of Northern Iowa

summary: The photosynthetic organs of the barley spike (lemma, palea and awn) are  resistant to drought. This is a beneficial trait because they can sustain grain-filling when drought occurs at the reproductive stage. There is little information about gene expression in the spike organs under drought conditions. In this study, we compared gene expression in drought-stressed lemma, palea, awn and seed at the grain-filling stage using the Barley1 Genome Array in order to identify drought-regulated organ-specific genes.

overall_design: Barley plants were drough-stressed for 4 days at the grain-filling stage by withholding water. Lemma, palea, awn and seed were collected to determine gene expression during drought in each organ. For each organ three biological replications were collected on three different dates. On each of the three dates, one replication of each organ was collected from plants grown in separate pots using a randomized complete block design (RCBD). In ths design, organ type and drought treatment were treatment effects and date of sample collection (replication) was the block. To get enough tissue for RNA extraction, each replication for each organ was collected from four plants in the same pot. RNA from each replicate sample was hybridized to individual Barley1 GeneChips. Thus, for four organs with three replications (blocks) and two treatment levels, a total of 24 Barley1 GeneChips were used.


title: Specific growth rate dependent transcriptome profiling of Escherichia coli K12 MG1655 in accelerostat cultures

city: Tallinn

first: Ranno

last: Nahku

address: Akadeemia tee 15b

country: Estonia

institute: TFTAK

summary: Specific growth rate dependent gene expression changes of Escherichia coli K12 MG1655 were determined by microarray and real time PCR analyses. The bacteria were cultivated on glucose limited minimal medium using the accelerostat method (A-stat), where starting from steady state conditions in a chemostat culture, dilution rate is constantly increased. At specific growth rate (μ) 0.47 h-1, E. coli had focused its metabolism to glucose utilization by down-regulation of alternative substrate transporters expression compared to μ = 0.3 h-1. It was found that acetic acid accumulation began at μ = 0.34 ± 0.01 h-1 and two acetate synthesis pathways (phosphotransacetylase-acetate kinase (pta-ackA) and pyruvate oxidase (poxB)) contributed to the synthesis at the beginning of overflow metabolism, i.e. onset of acetate excretion. On the other hand, poxB, pta and ackA expression patterns suggest that pyruvate oxidase may be the only enzyme synthesizing acetate at μ = 0.47 h-1. Down-regulation of acs-yjcH-actP operon, the resulting loss of glucose and acetate co-utilization between specific growth rates 0.3 h-1 – 0.42 h-1 and acetic acid accumulation from μ = 0.34 ± 0.01 h-1 allows one to surmise that the acetate utilization operon expression might play an important role in overflow metabolism.

overall_design: DNA microarray analysis was performed from three A-stat cultivations, for which one has a technical replicate.

first: Petri-Jaan

last: Lahtvee

first: Kaspar

last: Valgepea

first: Sten

last: Erm

first: Kristo

last: Abner

first: Kaarel

last: Adamberg

first: Raivo

last: Vilu


title: Comparison of murine colonic mucosal DNA from postnatal day 90 (P90) to postnatal day 30 (P30) by MSAM

city: Houston

first: Richard

last: Kellermayer

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

type: Methylation profiling by genome tiling array

summary: DNA methylation profiling of colonic mucosal DNA between P90 and P30 mice. 0.5ug of DNA was serially digested with SmaI and XmaI followed by an adaptor ligation and adaptor mediated PCR amplification

overall_design: Two independent P90 to P30 comparisons were performed as follows. Samples were labelled with Cy3 (P30) and Cy5 (P90) and two independent P90 to P30 comparisons were done on a 2x105k methylation specific amplification microarray (MSAM) containing 90,535 probes, covering 77% of the 31,019 SmaI intervals between 200 bp and 2 kb in the mouse genome (average 3.8 probes per interval)

first: Lanlan

last: Shen


title: Transcriptome profiling of wheat caryopsis development

city: Albany

first: Debbie

last: Laudencia-Chingcuanco

address: 800 Buchanan Street

department: Western Regional Research Center

institute: USDA-ARS

summary:
Global gene expression analysis of 7,835 tentatively unique wheat genes during caryopsis development
Keywords: Time-course study; developing wheat caryopsis

overall_design: The expression of 7,835 genes in developing wheat caryopses was analyzed by direct RNA comparisons using an interconnected loop-design with 6 time-points X 3 biological replicates per time-point X dye-swap

first: Boryana

last: Stamova

first: Frank

last: You

first: Joseph

last: Pham

first: Sarah

last: Vela

first: Olin

last: Anderson


title: microRNA and aging

status: Public on Sep 29 2009

city: Rome

first: Massimo

last: Federici

address: Via Montpellier 1

country: Italy

institute: University of Tor Vergata

summary:
The critical role of the endothelium in governing vascular, tissues homeostasis and pathological processes is increasingly recognized (Deanfield et al., 2007). Cellular senescence of endothelial cells has been proposed to be involved in endothelial dysfunction and atherogenesis (Minamino T et al., 2007), although the mechanisms underlying the aging induced attenuation of endothelium dependent functions are yet to be clarified.
Recent evidences implicated overall miRNA levels and miRNA in regulating angiogenesis and endothelial function (Suarez et al., 2007; Kuehbacher et al., 2007; Harris et al., 2008; Fish et al. 2008; Wang et al., 2008).

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: To investigate the role of miRNAs in endothelial cell senescence, we first profiled the miRNA signature during HUVECs aging (Maciag et al.,1981), through DNA microarray containing 200 oligonucleotide probes complementary to mature forms of miRNAs of human, mouse, and rat origin.

first: Rossella

last: Menghini

first: Francesca

last: Amati


title: Microarray Innovations in LEukemia (MILE) study: Stage 2 data

city: Pleasanton

first: Wei-Min

last: Liu

address: 4300 Hacienda Drive

institute: Roche Molecular Systems

summary:
An International Multi-Center Study to Define the Clinical Utility of Microarray–Based Gene Expression Profiling in the Diagnosis and Sub-classification of Leukemia (MILE Study)

Established in 2005, the MILE (Microarray Innovations in LEukemia) study research program included 11 participating centers in three continents. This cohort of n=1,152 samples represents data on the retrospective whole-genome analysis phase.

This dataset is part of the MILE Study (Microarray Innovations In LEukemia) program, headed by the European Leukemia Network (ELN) and sponsored by Roche Molecular Systems, Inc.

overall_design: 1,152 blood or bone marrow samples of acute and chronic leukemia patients were hybridized to the Roche AmpliChip Leukemia Custom Microarray


title: Gene expression profiles in drug-induced hypersensitivity reactions with cutaneous involvement

city: Madrid

first: Teresa

last: Bellón

state: Madrid

address: Pº Castellana 261

department: Research Unit

country: Spain

institute: Hospital La Paz

summary:
Hypersensitivity reactions to medications constitute a growing problem in the clinical practice. In order to study the molecular basis underlying the pathogenesis of non-immediate hypersensitivity reactions to drugs, we characterized the gene expression profiles of PBMCs isolated from patients during the acute phase and upon resolution of the clinical symptoms using a cDNA array technology. Eighty five genes were found to be differentially expressed during the acute phase of drug-induced delayed hypersensitivity reactions. Furthermore, ninety two genes with distinct expression patterns during the acute phase of severe and benign diseases were identified.

Keywords: Comparison between disease and healty status

overall_design: Expression profiles of 11835 genes were analyzed in peripheral blood mononuclear cells from 13 patients with different clinical entities . Two samples were analyze from each patient. The first blood sample was drawn during the acute phase of the disease. The second blood sample was obtained upon resolutin of the clinical symptoms. The ratio between gene expression levels in both samples was calculated for each patient.

first: Luis

last: Álvarez

first: Miguel

last: Blanca


title: Role of Cryptococcus neoformans Sre1-pathway in low oxygen gene expression

city: Baltimore

first: Clara

last: Bien

state: MD

address: 725 N. Wolfe St Physiology rm #107

department: Cell Biology

institute: Johns Hopkins University

summary: Comparison of wild-type serotype A C. neoformans cells grown at 21% and 3% oxygen for 2 hours in rich medium.  Also comparison of wild-type and Sre1-pathway mutant strains grown at 3 % oxygen for 2 hours in rich medium.

overall_design: Two-condition experiment. Each comparison was performed in two biological replicates, each containing duplicate probes/array (=4 data points total per comparison).

first: Peter

last: Espenshade

first: June

last: Kwon-chung

first: Yun

last: Chang

first: David

last: Nes


title: Expression profiling of murine hemopoietic cell survival on cDNA arrays.

status: Public on Sep 26 2009

city: Adelaide

first: Anna

last: Tsykin

state: SA

address: Frome Road

department: Hanson Institute

country: Australia

institute: SA Pathology

summary: Deregulated cell survival programs are a classical hallmark of cancer. We have previously identified a serine residue (Ser585) in the beta-c subunit of the granulocyte-macrophage colony-stimulating factor (GM-CSF) receptor that selectively and independently promotes cell survival. We now show that Ser585 phosphorylation is constitutive in 20/23 (87%) acute myeloid leukemia (AML) patient samples indicating that this survival-only pathway is frequently deregulated in leukemia. We performed a global expression screen to identify gene targets of this survival pathway and report a 138-gene beta-c Ser585-regulated transcriptome. Pathway analysis defines a gene network enriched for PI 3-kinase target genes as well as a cluster of genes involved in cancer and cell survival.

overall_design: factorial design; factors: time x 2 & mutation, same RNA was used in both GSE18220 & GSE18221

first: Jason

middle: A

last: Powell

first: Daniel

last: Thomas

first: F

last: Barry

first: Chung

middle: H

last: Kok

first: Barbara

last: McClure

last: Tyskin

first: L

middle: B

last: To

last: Brown

first: Ian

last: Lewis

first: Kirsten

last: Herbert

first: Gregory

last: Goodall

first: Terence

last: Speed

first: Norio

last: Asou

first: Bindya

last: Jacob

first: Motomi

last: Osato

middle: N

last: Haylock

first: Susan

middle: K

last: Nilsson

first: Richard

last: D'Andrea

first: Angel

middle: F

last: Lopez

first: Mark

last: Guthridge


title: Capsule Mediates the Cell Shape of pcsB Mutants in Serotype 2 Streptococcus pneumoniae

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

institute: Indiana University

summary: PcsB is a protein of unknown function that plays a critical role in cell division in Streptococcus pneumoniae and other ovococcus species of Streptococcus. We constructed isogenic sets of mutants expressing different amounts of PcsB in laboratory strain R6 and virulent serotype 2 strain D39 to evaluate its cellular roles. Insertion mutagenesis in parent and pcsB+ merodiploid strains indicated that pcsB is essential in serotype 2 S. pneumoniae. Quantitative Western blotting of wild-type and epitope-tagged PcsB showed that all PcsB was processed into cell-associated and secreted forms of the same molecular mass. These analyses showed that PcsB bound to cells is present in relatively low amounts of only ≈ 300 molecules per cell. Controlled expression and complementation experiments indicated that there was a causative relationship between the severity of defects in cell division and decreasing PcsB amount. These experiments also indicated that perturbations of expression of the upstream mreCD genes did not contribute to the cell division defects of pcsB mutants and that mreCD could readily be deleted in these strains. Unexpectedly, the defects in cell division and cell shape in pcsB mutants or other mutants defective in cell wall biosynthesis, such as dacA, were strongly influenced by capsule. Underexpression of PcsB did not result in changes in the amounts or composition of lactoyl-muropeptides, which were markedly different in the R6 and D39 strains, and there was no correlation between decreased PcsB amount and sensitivity to penicillin. Finally, microarray analyses indicated that underexpression of PcsB may generate a signal that increases expression of the VicRK regulon, which includes pcsB.

overall_design: Four independent hybridizations using independent RNA preparations from the strain IU1533 (reference strain) and strain IU1979 (a strain with decreased expression of PcsB protein) were performed. Dye swap was performed with the reference strain labeled with Cy3 in two hybridizations and Cy5 in the other two hybridizations.

first: Skye

middle: M

last: Barendt

first: Adrian

last: Land

first: Lok-To

last: Sham

first: Wai-Leung

last: Ng

middle: T

first: Randy

last: Arnold

first: Malcolm

middle: E

last: Winkler


title: Expression profiling of murine hemopoietic cell survival on oligo arrays.

first: Anna

last: Tsykin

overall_design: factorial square; factors: time & mutation, same RNA was used in both GSE18220 & GSE18221

first: Jason

last: Powell

first: Daniel

last: Thomas

first: F

last: Barry

first: Chung

last: Kok

first: Barbara

last: McClure

last: Tyskin

first: L

last: To

last: Brown

first: Ian

last: Lewis

first: Kirsten

last: Herbert

last: Goodall

first: David


title: Gene expression profiling in drought tolerant Acala 1517-99 cotton (Gossypium hirsutum L.) under reduced irrigation field conditions

status: Public on Sep 25 2009

city: Las Cruces

first: Laura

last: Rodriguez-Uribe

state: NM

address: 945 College Dr. Skeen Hall RM 127

department: Plant and environmental Sciences

institute: New Mexico State University

summary: Cotton productivity is affected by water deficit and little is known about the molecular basis of drought tolerance in cotton. In this study, microarray analysis was carried out to identify drought responsive genes in functional leaves of the field-grown drought stressed cotton (Gossypium hirsutum L.) Acala 1517-99. The water stress was imposed after withholding irrigation for 9 days in the early squaring stage, which resulted in 10-15% reduction in plant growth compared to the well watered plants. A total of 110 drought responsive genes (0.5% of the total genes represented in the microarray) were identified, 79% (88 genes) of which were down-regulated and 21% (22 genes) were up-regulated by water stress. The responsiveness of 19 selected drought responsive genes was validated by real time PCR. The drought inducible genes were grouped into six functional categories only including stress related (10 genes, 9 of which are heat shock proteins), metabolism (3) and one each for transcription factor, proline biosynthesis and cellular transport. The down-regulated genes were classified into 14 functional categories including metabolism (20 genes), cellular transport (12), stress related (12), and regulation of gene expression (9) and transcription factor (4), signal transduction (7) and 2 genes each for biosynthesis of secondary compounds, cell wall, fatty acids/lipids and chlorophyll, and protein degradation. Most of the genes have been reported in other plants as drought tolerant/responsive and only 21 drought responsive genes (19%) were functionally unknown. The genes identified provides the first glimpse into the molecular basis of drought response in cotton.

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design:
Leaves from well-watered or drought-stressed cotton plants in the field were used for RNA extraction and generarion of cRNA probes for hybridization using Affymetrix Cotton GeneChips. Comparative microarray analysis was performed to identify drought-responsive genes in cotton.

The supplementary file 'GSE18253_differentially_expressed.txt' lists the differentially expressed genes.

first: Jinfa

last: Zhang


title: The role of the Ras- and cAMP-signaling pathways in stress response and sterol biosynthesis in Cryptococcus neoformans

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

summary: The cAMP-pathway plays a central role in regulation of growth, differentiation, and virulence of human pathogenic fungi, including Cryptococcus neoformans. Three major upstream signaling regulators of the adenylyl cyclase (Cac1), Ras, Aca1 (Adenylyl cyclase-associated protein 1) and G-alpha subunit protein (Gpa1), have been identified to control the cAMP-pathway in C. neoformans, but their functional relationship remains elusive. Here we performed genome-wide transcriptome analysis with C. neoformans ras1, gpa1, cac1, aca1, and pka1 pka2 mutants by DNA microarray. The aca1, gpa1, cac1, and pka1 pka2 mutants displayed similar transcriptome patterns to each other whereas the ras1 mutant exhibited distinctive transcriptome patterns compared to WT and the cAMP mutants. Interestingly, a number of environmental stress response genes are differentially modulated in the ras1 and cAMP mutants. In fact, the Ras1-signaling pathway was found to be involved in osmotic and genotoxic stress response, and maintenance of cell wall integrity via the Cdc24-dependent signaling pathway. Through this microarray analysis, we have identified a number of cAMP-dependent genes, including GRE2, HSP12, ENA1, TCO2, PKP2, CAT1, in C. neoformans. Notably, a majority of ergosterol biosynthesis genes were found to be upregulated in the cAMP mutants. Interestingly, the gpa1, cac1, and pka1 mutants, but not the aca1 and pka2 mutants were hypersensitive to amphotericin B, but resistant to fluconazole.  In conclusion, we demonstrated in this study that the Ras1- and cAMP-signaling pathways are involved in stress response and sterol biosynthesis of C. neoformans.

overall_design: There are more than 95% of genome homology between JEC21 and H99. Therefore 100 slides of JEC21 (cryptococcus neoformans var. neoformans serotype D) 70-mer oligo are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted with 6 strains from H99 (H99 Wild type strain (Cryptococcus neoformans var. grubii serotype A), ras1Δ, aca1Δ, gpa1Δ, cac1Δ, pka1Δpka2Δ), We use the mixed all of total RNAs from this experiment as a control RNA. We use Cy5 as Sample dye and Cy3 as a control dye. several sample are dye swaped.

first: Shinae

last: Maeng

first: Gyu-Bum

last: Kim

first: Young-Joon

last: Ko

first: Dong-Hoon

last: Yang

first: Kwang-Woo

last: Jung

first: Jeseph

last: Heitman


title: Microarray predictor of response to infliximab in rheumatoid arthritis (RA) patients

status: Public on Oct 02 2009

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

institute: Vall d'Hebron Hospital Research Institute

summary: We sought to find a gene-expression multigene predictor of response to infliximab therapy in Rheumatoid Arthritis patients. Using internal and external cross-validation systems we have built and validated an 8-gene predictor for response to infliximab.

overall_design: Blood RNA from 48 Rheumatoid Arthritis patients was extracted at baseline of anti-TNF alpha treatment with infliximab. From these 44 reached week 14 of treatment at which the clinical response was determined. Using 2/3 of the sample we built a multigene predictor using kNearest-Neighbour algorithm and Leave-One Out cross validation. The remaining 1/3 of the sample was used to estimate the precision accuracy of the predictor model.

first: Sara

last: Marsal


title: Comparative analyses of chromosome alterations in metastases in castration-resistant prostate cancer patients

city: Seattle

middle: J.

last: Trask

state: WA

address: 1100 Fairview Avenue N., C3-168, P.O. Box 19024

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: Androgen deprivation is the mainstay of therapy for progressive prostate cancer. Despite initial and dramatic tumor inhibition, most men eventually fail therapy and die of metastatic castration-resistant (CR) disease. Here, we characterize the profound degree of genomic alteration found in CR tumors using array CGH, gene expression arrays, and FISH. By cluster analysis, we show that the similarity of the genomic profiles from primary and metastatic tumors is driven by the patient. Using data adjusted for this similarity, we identify numerous high-frequency alterations in the CR tumors, such as 8p loss and chromosome 7 and 8q gain. By integrating array CGH and expression array data, we reveal genes whose correlated values suggest they are relevant to prostate cancer biology. We find alterations that are significantly associated with the metastases of specific organ sites, and others with CR tumors versus the tumors of patients with localized prostate cancer, not treated with androgen deprivation. Within the high-frequency sites of loss in CR metastases, we find an over-representation of genes involved in cellular lipid metabolism, including PTEN. Finally, using FISH we verify the presence of a gene fusion between TMPRSS2 and ERG suggested by chromosome-21 deletions detected by array CGH. We find the fusion in 54% of our CR tumors, and 81% of the fusion-positive tumors contain cells with multiple copies of the fusion. Our investigation lays the foundation for a better understanding of and possible therapeutic targets for CR disease, the poorly responsive and final stage of prostate cancer.

overall_design: The aim of this study was to characterize the genomic changes identified in a set of matched castrate-resistant primary and metastatic prostate cancers. Tumor cells were isolated by laser-capture microdissection from 14 patients, a total of 54 tumor samples. LCM capture samples were isolated from multiple metastastases from all but one patient from whom a single metastasis was available. Primary prostate tumor samples were collected from 12 patients. DNA was amplified by either ligation-mediated PCR (LMP) or WGA (Sigma-Aldrich, St. Louis, MO, USA). Reference DNA was isolated from peripheral blood from a single female individual.

first: Ilona

last: Holcomb

first: Janet

last: Young

first: Ilsa

last: Coleman

first: Keyan

last: Salari

first: Douglas

middle: I

last: Grove

first: Li

last: Hsu

first: Lawrence

last: True

first: Martine

last: Roudier

first: Colm

last: Morrissey

first: Celestia

middle: S

last: Higano

first: Peter

last: Nelson

first: Robert

last: Vessella


title: THE EFFECTS OF ALCOHOLISM ON THE HUMAN BASOLATERAL AMYGDALA

status: Public on Sep 24 2009

city: St Lucia

first: Rosemarie

middle: Lotte

last: Kryger

state: Qld

address: Sir Fred Schonell Drive

department: Biochemistry

institute: University of Queensland

summary: Alcohol affects gene expression in several brain regions. The amygdala is a key structure in the brain’s emotional system and in recent years the crucial importance of the amygdala in drug-seeking and relapse has been increasingly recognized. In this study gene expression screening was used to identify genes involved in alcoholism in the human basolateral amygdala. The results show that alcoholism affects a broad range of genes and many systems including genes involved in synaptic transmission, neurotransmitter transport, structural plasticity, metabolism, energy production, transcription and RNA processing and the circadian cycle. In particular, genes involved in the glutamate system were affected in the alcoholic patients. In the amygdala the glutamate system is involved in the acquisition, consolidation, expression and extinction of associative learning, which is a vital part of addiction, and in alcohol abusers it is associated with withdrawal anxiety and neurodegeneration. Downregulation of the excitatory amino acid transporters GLAST, GLT-1 and the AMPA glutamate receptor 2 (GluR2) revealed by the microarray were confirmed by Western blots. The decreased expression of GLAST, GLT-1 and GluR2 in the alcoholic patients may increase glutamate tone and activity in the basolateral amygdala and this may contribute to neurodegeneration as well as the expression of associative memories and anxiety which underlie continued drug-seeking and chronic relapse.

overall_design: Two-condition experiment, alcoholics vs controls. Biological replicates: 6 alcoholics  6 controls,  one replicate per array.

last: Wilce


title: Transcriptomic and physiological responses of Bacillus cereus to organic and inorganic acid down-shocks

city: Wageningen

first: Maarten

last: Mols

address: Bomenweg 2

department: ATV

country: Netherlands

institute: Wageningen University

summary: Comparative phenotype and transcriptome analyses were performed with Bacillus cereus ATCC 14579 exposed to acid down-shock to pH 5.5 set with different acidulants. When acidified with hydrochloric acid (HCl), growth was diminished, whereas 2 mM undissociated lactic acid (HL) or acetic acid (HAc) stopped growth without inactivation (bacteriostatic condition), and 15 mM undissociated HAc caused growth arrest and, finally, cell death, as reflected by a 3 to 4 log inactivation (bactericidal condition). Within the first 60 min after pH down-shock, the intracellular ATP levels of cultures shocked with HCl were increased. The bacteriostatic pH shocks did not result in increased nor decreased intracellular ATP levels, indicating that the high energy status within the stressed aerobically grown B. cereus cells could be maintained. In contrast, exposure to 15 mM undissociated HAc resulted in significant lower ATP levels, which was in accordance with the observed inactivation. The transcriptomic responses pH down-shocked cultures were studied in the same time frame. The analyses revealed general and specific responses coupled to the different phenotypes and the acidulant used. The general acid stress response, shown in all different pH shocks, involves modulation of pyruvate metabolism and an oxidative stress response. The shifts in pyruvate metabolism include induction dehydrogenases of a butanediol fermentation pathway under non-lethal acid stress conditions and of lactate, formate, and ethanol fermentation pathways under 15 mM HAc stress. Other 15 mM HAc-specific responses were induction of the alternative electron-transport systems, including cydAB, and fatty acid biosynthesis genes. Differences in gene expression for the bacteriostatic organic acid stress conditions compared to the growth-retarded inorganic stress condition indicated a more stringent oxidative stress response, including induction of an additional catalase gene and a gene encoding a Dps-like protein. Moreover, modulations in amino acid and oligopeptide transport were also found for the 2 mM HAc and HL shocks. HL-specific and HAc-specific responses both involve amino acid metabolism. Our study on the genome-wide responses of aerobically grown B. cereus pH 5.5 shocks provides a unique overview of the different responses induced by three acidulants relevant for food preservation.

overall_design: Per acid down-shock three exposure times (i.e., 10, 30 and 60 min) were each compared with non-exposed cells (i.e., t0). In total 4 different pH 5.5 acid down-shocks were applied. pH 5.5 was reached by adding different acidulants i.e., hydrochloric acid (HCl), lactic acid (HL) resulting in 2 mM undissociated HL, acetic acid (HAc) resulting in 15 mM undissociated HAc, and a combination of acetic acid and hydrochloric acid (HAc/HCl) resulting in 2 mM undissociated HAc. The experiments were performed in duplicate and the duplicate samples were hybridised with a dye-swap.

first: Richard

last: van Kranenburg

first: Marcel

last: Tempelaars

first: Willem

last: van Schaik

first: Roy

last: Moezelaar

first: Tjakko

last: Abee


title: tRNA Over-Expression in Breast Cancer

city: Chicago

first: Tao

last: Pan

state: IL

address: 929 East 57th street

department: Biochemistry & Molecular Biology

institute: University of Chicago

summary: Increased proliferation and elevated levels of protein synthesis are characteristic of transformed and tumor cells. Though components of the translation machinery are often misregulated in cancers, how tRNA plays a role in cancer cells has not been explored. We compare genome-wide tRNA expression in tumorigenic versus non-tumorigenic breast cell lines, as well as tRNA expression in breast tumors versus normal breast tissues. In tumorigenic versus non-tumorigenic cell lines, nuclear-encoded tRNAs increase by up to 3-fold and mitochondrial-encoded tRNAs increase by up to 5-fold. In tumors versus normal breast tissues, both nuclear and mitochondrial-encoded tRNAs increase by up to 10-fold. This tRNA over-expression is selective and coordinates with the properties of cognate amino acids. Nuclear- and mitochondrial-encoded tRNAs exhibit distinct expression patterns, indicating that tRNAs can be used as biomarkers for breast cancer.

platform_organism:
Saccharomyces cerevisiae
Homo sapiens
Caulobacter vibrioides

overall_design: We analyzed tRNA expression levels in 2 non-tumorigenic breast cell lines, 6 tumorigenic breast cancer cell lines, 3 normal breast tissue samples, and 9 breast tumor samples. We used a non-tumorigenic breast cell line (MCF10A) as a reference sample in all hybridizations. All data is dye-swapped.

first: Mariana

last: Pavon

first: Suzanna

last: Gomes

first: Renaud

last: Geslain

first: Qing

last: Dai

first: Marsha

last: Rich Rosner


title: miRNA Profiling from total blood of lung cancer and control samples

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

summary: This project aims at the detection of specific patterns of miRNAs in peripheral blood samples of lung cancer patients. As controls, blood of donors without known affection have been tested. Using the miRNA patterns we hope to detect a diagnostic pattern for the non-invasive diagnosis of non-small cell lung carcinoma.

overall_design: In this study, we compared 17 lung cancer samples to 19 control samples using the sanger miRBAse 12.0 miRNA biochip manufactured by febit. Samples were analyzed with the Geniom Realtime Analyzer (GRTA, febit gmbh, Heidelberg, Germany) using the Geniom Biochip miRNA Homo sapiens. Each array contains 7 replicates of 866 miRNAs and miRNA star sequences as annotated in the Sanger miRBase 12.0. To benchmark the platform, we tested technical replicates using bought total RNA of brain and liver samples (ambion), achieving a correlation of 0.97.

first: Petra

last: Leidinger

first: Anke

last: Wendschlag

first: Matthias

last: Scheffler

first: Eckart

last: Meese

first: Frank

last: Wucherpfennig

first: Hanno

last: Huwer

first: Anne

last: Borries


title: Drosophila elevated CO2 (hypercapnia) microarray

city: Evanston

first: Taneli

last: Helenius

address: 2205 Tech Drive

department: BMBCB

institute: Northwestern University

summary: The effects of elevated CO2 (hypercapnia) on organisms are not well known, nor are the molecular pathways by which organisms sense CO2. We have performed microarray analysis on Drosophila in order to develop a genetic model for better understanding the effects of CO2.

overall_design: Equal numbers of 5-day old male and female flies (at least 40 total) were exposed to 13% CO2 or air for 24h and RNA extracted. Gene expression changes in CO2 compared with air were analyzed. Experiments were performed in triplicate and the 3 separate microarray experiments are included.


title: Profiling of spatio-temporally regulated transcripts during cerebral corticogenesis in the mouse

city: UPM Serdang

first: King

middle: Hwa

last: Ling

state: Selangor Darul Ehsan

address: Faculty of Medicine and Health Sciences

department: Department of Obstetrics and Gynaecology

country: Malaysia

institute: Universiti Putra Malaysia

summary: The cerebral cortex plays an important role in cognitive function and specialized perception in mammals and its development requires highly specific spatio-temporal control of gene expression. The study identified stage- and region-specific markers throughout cerebral corticogenesis at various important stages of cerebral cortex development; embryonic day (E) 15.5, E17.5, postnatal day (P) 1.5 and 4-6 months old.

overall_design: The study involved the analysis of 12 SAGE libraries, which were generated from the mouse cerebral cortex of E15.5 (n=3), E17.5 (n=2), P1.5 (n=1) and 4-6 month old (n=6). N denotes biological replicates.

first: Chelsee

last: Hewitt

first: Tim

last: Beissbarth

first: Lavinia

last: Hyde

first: Kakoli

last: Banerjee

first: Pike

last: Cheah

first: Ping

middle: Z

last: Cannon

first: Christopher

last: Hahn

first: Paul

middle: Q

last: Thomas

first: Gordon

last: Smyth

first: Seong

last: Tan

first: Hamish

last: Scott


title: The profile of cellular and KSHV microRNAs in AIDS_KS biopsies (and normal skin control biopsies)

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building, Huntley Street

department: Cancer Institute

country: United Kingdom

institute: UCL

summary: Kaposi sarcoma is the most common cancer in AIDS patients and is typified by red skin lesions. The disease is caused by the KSHV virus (HHV8) and is recognisable by its distinctive red skin lesions. The lesions are KSHV-infected spindle cells, most commonly the lymphatic endothelial and blood vessel endothelial cells (LEC and BEC), plus surrounding stroma. Here we study the microRNA profiles of the KS lesion biopsies in AIDS patients (including both the cellular and KSHV microRNA).

overall_design: There are  (n=3) normal skin biopsies from healthy patients and (n=5) AIDS-KS biopsies. Three of the AIDS-KS biopsies were technically replicated and 2 were single hybridisations.

first: Amy

last: Hansen

first: Dimitrios

last: Lagos


title: Gut microbiota regulate xenobiotic metabolism in the liver

status: Public on Sep 22 2009

city: Singapore

first: Martin

middle: Lloyd

last: Hibberd

address: 60 Biopolis Street, #02-01, Genome

country: Singapore

institute: Genome Institute of Singapore

summary:
Germ-free (GF) mice can be used as a powerful tool to investigate the role of the intestinal commensal flora in metabolism and immune tolerance. In this study we have used whole genome transcriptome analyses to compare expression levels systemically in liver of germ-free mice and specific pathogen free (SPF) mice.

Keywords: Mouse liver tissue germ-free or specific pathogen free vs universal mouse reference

Specific Pathogens Excluded from the SPF mice:

Virus

1.	Mouse Hepatitis Virus (MHV)
2.	Mouse Rotavirus (EDIM)
3.	Parvoviruses
Minute virus of mice (MVM)
Mouse parvo virus (MPV)
4.	Pneumonia virus of mice (PVM)
5.	Sendai virus
6.	Theiler's encephalomyelitis virus
7.	Ectromelia virus
8.	Lymphocytic choriomeningitis virus (LCMV)
9.	Mouse adenovirus
10.	Mouse cytomegalovirus
11.	Reovirus type 3

Bacteria

1.	Citrobacter rodentium
2.	Clostridium piliforme (Tyzzer’s disease)
3.	Corynebacterium kutscheri
4.	Mycoplasma pulmonis
5.	Pasteurellaceae
6.	Salmonella spp.
7.	Streptococci-β-haemolytic
8.	Streptococcus pneumoniae
9.	Helicobacter spp.
10.	Streptobacillus moniliformis

Parasite

1.	Ectoparasites
2.	Endoparasites

overall_design: Two-condition experiment, GF mice liver vs. SPF mice liver. Biological replicates: 4 GF mice liver, 4 SPF mice liver. Each replicate was hybridized on 2 arrays with dyeswap. GSMxxx.gpr test is Cy5. GSMxxxdyeswap.gpr test is Cy3.

first: Sven

last: Pettersson

first: Britta

last: Björkholm

first: Chek

last: Bok

first: Annelie

last: Lundin

first: Joseph

last: Rafter

first: Annika

last: Samuelsson


title: S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation, dual-channel dataset

status: Public on Sep 20 2009

city: Los Angeles

first: Susan

last: Forsburg

state: CA

address: 1050 Childs Way, RRI 201B

department: Molecular and Computational Biology

institute: University of Southern California

summary: Analysis of histone acetyl transferases (HATs) from the MYST and GNAT families in S. pombe to identify functional differences or overlap with regard to gene expression. Mutations were made to Elp3 and Gcn5 (GNAT family), and to Mst2 (MYST family). Mutants showed distinct phenotypes which were repressed or enhanced by mutant combinations.

overall_design: Mutations were made to Gcn5 (GNAT family), and to Mst2 (MYST family) in S. pombe. A treatment of 1M KCl was applied for 60min to some samples. RNA was extracted from the various mutants and hybridized on Eurogentec arrays.

first: Rebecca

last: Nugent

first: Anna

last: Johnsson

first: Brian

last: Fleharty

first: Madelaine

last: Gogol

first: Yongtao

last: Xue-Franzén

first: Chris

last: Seidel

first: Anthony

last: Wright

middle: L


title: Transcriptome profiles of a riboflavin-producing B.subtilis RH33 and wild type B.subtilis 168

city: Tianjin

first: shuobo

last: shi

address: Weijin Road

country: China

institute: Tianjin University

summary: The transcriptome profiles of a riboflavin-producing recombinant Bacillus subtilis RH33 and wild type Bacillus subtilis 168 were compared using DNA microarrays to identify the target genes for further enhancing riboflavin production.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Transcriptome profiles of a riboflavin-producing B. subtilis RH33 were compared with those of the wild-type B. subtilis 168 as a control strain during exponentially growing period on LBG medium. These conditions corresponded to the state of high riboflavin production, which was growth related. For each comparison, two independent cultivations on LB medium with 1% glucose were performed, and exponentially growing cells (OD600 3–6) were harvested. The synthesis of cDNA and biotin-labeled cRNA were carried out exactly as described in the Affymetrix GeneChip Expression Analysis Technical Manual (2000).

first: Shuobo

last: Shi

first: Tao

last: Chen

first: Xun

first: Xueming

last: Zhao


title: Transcriptional profiling of 2 outbreak strains of E. coli O157:H7 following exposure to epithelial cells

status: Public on Sep 17 2009

city: East Lansing

first: galeb

last: abu-ali

state: MI

address: NFSTC

department: NFSTC

institute: michigan state university

summary: Two outbreak strains of E. coli O157:H7 differ phylogenetically, in gene content, and in epidemiological characteristics. The working hypothesis in this experiment was that these strains will also differ in the transcription of shared virulence genes. Indeed, following a 30 minute exposure to epithelial cells, strain TW14359 overexpressed major and ancillary virulence genes, relative to strain Sakai.

overall_design:
E. coli O157:H7 strains were physiologically normalized by growth to stationary phase, twice, in MOPS minimal media. Cultures were then transferred to DMEM media for adaptation. After 3 h of growth in DMEM, O157:H7 cultures were used to infect monolayers of MAC-T epithelial cells. 30 min following incubation, aliquots of suspended, non-adherent bacteria were used for RNA extraction. Five biological replications of the experiment were performed with each strain and, together with dye-swaps, 10 array hybridizations were carried out.
Array data were fitted to a mixed model ANOVA using the following linear model: array+dye+sample (biological replicate)+strain+error.

first: Galeb

last: Abu-Ali

first: Lindsey

last: Ouellette

first: Scott

last: Henderson

first: Thomas

last: Whittam

first: Shannon

middle: D

last: Manning


title: Expression profiling of human adipose tissue derived stem cells cultured at various oxygen tensions

city: Aalborg

first: Vladimir

last: Zachar

address: Fredrik Bajers Vej 3B

country: Denmark

institute: Aalborg University

summary:
Adipose tissue is a plentiful and easily accessible source of mesenchymal stem cells that have been shown to be multi potent and possibly have immuno suppressive capacity(Zuk, Zhu et al. 2002; McIntosh, Zvonic et al. 2006; Prichard, Reichert et al. 2008). Several studies have identified hypoxia and the molecular effector of reduced oxygen tension, HIF1α to be essential in the differentiation processes, stem cell proliferation and survival as well as in maintenance of stem cell characteristics (Lennon, Edmison et al. 2001; Goda, Ryan et al. 2003; Wang, Fermor et al. 2005; Lin, Lee et al. 2006; Malladi, Xu et al. 2007; Ohnishi, Yasuda et al. 2007).  The fact that oxygen has a central role in cell development and metabolism makes the regulation of oxygen tension a valuable tool in the attempt of exploiting stem cells to their full potential.  In the current study we investigate the transcriptional changes caused by two weeks of monolayer hypoxic expansion of human adipose tissue derived stem cells (ASCs). Application of the XVivo hypoxic workstation (BioSpherix, Redfield, NY) made it possible to conduct the expansion of six ASC lines at four different hypoxic conditions in parallel covering the range from mild (15% oxygen) to full hypoxic (1% oxygen) conditions. In this comprehensive investigation the Illumina bead microarray platform was employed to give a profound and new insight in the molecular changes effectuated by hypoxic expansion.  The findings of this study demonstrate the significance of biologic variation in the transcriptional response to mild hypoxic expansion and display evidence that full hypoxic growth conditions at 1% oxygen tension selects for a more prolific cell population of reduced chondrogenic potential.

Keywords: hypoxia response

overall_design: To investigate the transcriptional response to hypoxia, adipose tissue derived stem cells (ASCs) from six female individuals were cultured for 14 days at different oxygen tensions (ambient, 15%, 10%, 5% and 1%). Gene expression levels at each oxygen tension were compared to ambient conditions (Ambient oxygen tension) using Illumina Human-6 v2.0 microarrays.

first: Linda

last: Pilgaard

first: Pia

last: Lund

first: Meg

last: Duroux

first: Helen

last: Lockstone

first: Jennifer

last: Taylor

first: Jeppe

last: Emmersen

first: Trine

last: Fink

first: Ioannis

last: Ragoussis


title: Analysis of severe feather pecking behavior in a high feather pecking selection line

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

institute: Aarhus University, Faculty of Agricultural Sciences

summary:
Even though feather pecking (FP) in laying hens has been extensively studied, a good solution to prevent chickens from this behavior under commercial circumstances has not been found. Selection against FP behavior is possible, but for a more effective selection across different populations, it is necessary to characterize the genetic mechanism associated with this behavior. In this study, we use a high FP selection line, which has been selected for 8 generations. We present evidence of the presence of a major dominant allele affecting the FP behavior by using an argument based on the presence of mixture in the distribution of the observed FP and by studying the evolution of the proportion of very high FP along the sequence of 8 generations. This hypothesis is further supported by the fact that the gene transcription profile of the birds performing high FP differs from the profile of the other birds performing FP (456 genes differentially expressed from a total of 14,077 investigated genes).

Keywords: severe feather pecking , selection , modeling , inheritance pattern

overall_design: From each selection line (high feather pecking line, low feather pecking line and control line) 60 animals were randomly selected. Within each line the birds were randomly assigned to a cage of 20. The cages were kept in a randomized block design. Number of samples analyzed in total: 179 (60 high feather pecking line, 60 low feather pecking line, 59 control line samples. Common reference design using total-RNA purified from brain from a single F1 cross between the high and low feather pecking line as reference.

first: R

last: Labouriau

first: J

middle: B

last: Kjaer

first: G

middle: C

last: Abreu

first: A

middle: J

last: Buitenhuis


title: Gene expression profile of mesenchymal stem cells from paired umbilical cord units: cord is different from blood

status: Public on Sep 18 2009

city: Sao Paulo

first: Yuri

middle: Barros

last: Moreira

state: SP

address: Av. Prof. Lineu Prestes 748 sala 1200

country: Brazil

institute: Universidade de Sao Paulo

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

summary: Mesenchymal stem cells (MSC) are multipotent cells which can be obtained from several adult and fetal tissues including human umbilical cord units.  We have recently shown that umbilical cord tissue (UC) is richer in MSC than umbilical cord blood (UCB) but their origin and characteristics in blood as compared to the cord remains unknown.  Here we compared, for the first time, the exonic protein-coding and intronic noncoding RNA (ncRNA) expression profiles of MSC from match-paired UC and UCB samples, harvested from the same donors, processed simultaneously and under the same culture conditions. The patterns of intronic ncRNA expression in MSC from UC and UCB paired units were highly similar, indicative of their common donor origin. The respective exonic protein-coding transcript expression profiles, however, were significantly different.  Hierarchical clustering based on protein-coding expression similarities grouped MSC according to their tissue location rather than original donor. Genes related to systems development, osteogenesis and immune system were expressed at higher levels in UCB, whereas genes related to cell adhesion, morphogenesis, secretion, angiogenesis and neurogenesis were more expressed in UC cells. These molecular differences verified in tissue-specific MSC gene expression may reflect functional activities influenced by distinct niches and should be considered when developing clinical protocols involving MSC from different sources.  In addition, these findings reinforce our previous suggestion on the importance of banking the whole umbilical cord unit for research or future therapeutic use.

overall_design:
Cy5- and Cy3-labeled cRNAs were obtained using 300 ng total RNA as template for amplification of poly(A) RNA by T7-RNA polymerase with the Agilent Low RNA Input Fluorescent Linear Amplification kit. The T7-polymerase amplified cRNA labeling approach advantageously replaces the reverse-transcriptase cDNA labeling used in early microarray experiments, because T7-RNA polymerase labeling of cRNA preserves the strand orientation of the original mRNA template. Reverse-transcriptase labeling can eventually generate a complementary cDNA second strand and cause artifactual labeling of a target with the opposite sense to that of the original message.
Hybridization of 825 ng of Cy3- or Cy5-labeled RNA (dye swap technical replicate) from each UC sample with its paired UCB sample was performed with Agilent in situ Hybridization kit-plus, as recommended by the manufacturer, using a total of 4 intron-exon 44K expression oligoarrays. This array comprises a total of 13,699 exonic probes representing different protein-coding genes, along with custom-designed intronic probes for the antisense or sense strand. Slides were washed and processed according to the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol (Version 5.5) and scanned on a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA). Fluorescence intensities were extracted using Feature Extraction (FE) software (version 9.0; Agilent). A gene was considered expressed if its probe intensity was significantly higher than the local background intensity, as calculated by the FE software. Then, the software applies local background subtraction and corrects for unequal dye incorporation using the default LOWESS (locally weighted linear regression) method.

first: Mariane

last: Secco

first: Y

first: Eder

last: Zucconi

first: Natassia

last: Vieira

first: Tatiana

last: Jazedje

first: Alysson

middle: R

last: Muotri

first: Oswaldo

middle: K

last: Okamoto

first: Sergio

last: Verjovski-Almeida

first: Mayana

last: Zatz


title: Challenge of vaccinated and unvaccinated salmon with Aeromonas salmonicida

status: Public on Sep 16 2009

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: The study searched for the correlates of vaccine protection against furunculosis. After pathogen challenge of vaccinated (V) and unvaccinated (N) fish, hepatic gene expression was compared in salmon with high resistance (HR, individual samples) and low resistance (LR, pooled samples)

overall_design: Two-condition experiment - vaccinated and unvaccinated salmon, HR vs. LR livers. Biological replicates (HR): 6 vaccinated, 5 unvaccinated, pooled samples of LR were used as reference. One replicate per array.

first: Stanko

last: Skugor


title: DamID profiling of neural transcription factor binding in Drosophila melanogaster embryos

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

type: Genome binding/occupancy profiling by genome tiling array

summary: Paper abstract: Neural stem cells must strike a balance between self-renewal and multipotency, and differentiation. Identification of the transcriptional networks regulating stem cell division is an essential step in understanding how this balance is achieved. We have shown that the homeodomain transcription factor, Prospero, acts to repress self-renewal and promote differentiation. Amongst its targets are three neural stem cell transcription factors, Asense, Deadpan and Snail, of which Asense and Deadpan are repressed by Prospero. Here we identify the targets of these three factors throughout the genome. We find a large overlap in their target genes, and indeed with the targets of Prospero, with 245 genomic loci bound by all factors. Many of the genes have been implicated in vertebrate stem cell self-renewal, suggesting that this core set of genes is crucial in the switch between self-renewal and differentiation. We also show that multiply bound loci are enriched for genes previously linked to nervous system phenotypes, thereby providing a short-cut to  identifying genes important for nervous system development.

overall_design: Each Dam-fusion-derived sample is compared to a control Dam-only sample. Four biological replicates were performed for Prospero (with 2 dye-swaps). For Asense, Deadpan and Snail, two biological replicates were performed.

first: Andrea

middle: H

last: Brand


title: Gene expression profiles of Themis-deficient thymocytes

status: Public on Sep 14 2009

city: Bethesda

first: Andy

last: Johnson

address: 9000 Rockville Pike

country: USA

institute: NIAID/NIH

summary: Determine the biochemical cause of impaired development of Themis-deficient thymocytes.

overall_design: We isolated three thymocyte populations (three populations: CD4+CD8+CD5loCD69lo, CD4+CD8+CD5+CD69+, and CD4+CD8-CD24hiH2Klo) from Themis-deficient and WT mice. 8 or 9 individual biological replicates were analyzed for each population. An aliquot of cDNA from each sample was pooled and used as a reference.


title: MicroRNA Profiling Identifies Potential Diagnostic and Prognostic Markers in Prostate Cancer

status: Public on Sep 15 2009

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: Prostate cancer is the second leading cause of cancer death in the United States and Europe. Diagnosis and risk estimation of cancer recurrence is often critical with the common clinicopathologic parameters of prostate-specific antigen, tumor stage and grade. Therefore it is mandatory to develop new diagnostic and prognostic markers for prostate cancer. miRNAs have been shown to be novel markers in a series of other cancer types. We show for the first time, that good overall classification of normal and malignant prostate tissue was possible with combination of just two miRNAs (hsa-miR-205, hsa-miR-183). Further, hsa-miR-96 is shown to be associated with the recurrence-free interval after radical prostatectomy.

overall_design: Tumor tissue and normal adjacent tissue with untreated prostate carcinoma were collected after radical prostatectomy between 2001 and 2005 at Charité University Hospital, Berlin.  Matched malignant (#PC (e.g. 09PC)) and non-malignant (#PN (e.g. 09PN)) tissue samples from men (mean age 63 years, range 49-74 years; mean pre-operative concentration of prostate-specific antigen (PSA) 8.21 µg/l, range 0.92-41.9 µg/l) with untreated prostate carcinoma were profiled.

first: Klaus

last: Jung

first: Monika

first: Annika

last: Schäfer

first: Carsten

last: Stephan

first: Michael

last: Lein

first: Glen

last: Kristiansen


title: Affymetrix exon array analysis of control and hnRNP H knockdown in 293T cells

status: Public on Sep 13 2009

city: Cambridge

first: Xinshu

last: Xiao

state: MA

address: 77 Mass Ave. MIT, 68-211

department: Biology

institute: MIT

summary:
Splice site strength and the presence of splicing regulatory elements (SREs) play central roles in the control of pre-mRNA splicing1-3 and in exon evolution4.  However, the degree to which SRE function is dependent or independent of the strength of nearby splice sites is not well understood.  Here, we show that the activity of a major class of mammalian SREs is highly sensitive to the strength of the adjacent 5' splice site (5'ss) sequence, with important functional and evolutionary implications.  Using extensive splicing reporter assays, we found that activity of identical 'G-run' intronic splicing enhancers (ISEs)5, 6 was higher by ~4-fold for 5'ss of intermediate strength relative to weak 5'ss, and higher by ~1.3-fold relative to strong 5'ss, based on established 5'ss scoring criteria7.  This dependence on 5'ss strength was supported both by comparative genomic analyses and by high-throughput transcriptome sequencing analyses of splicing changes following RNAi against the G-run-binding factor heterogeneous nuclear ribonucleoprotein (hnRNP) H.  This pattern and an inverse pattern of 5'ss-dependent activity observed for G-run exonic splicing silencers (ESSs) enables G-runs and hnRNP H to buffer 5'ss mutations and to function as effective evolutionary capacitors8 of splicing change.  Human exons flanked by G-runs exhibited increased 5'ss polymorphism and a ~30% increased frequency of evolutionary change between constitutive and alternative splicing, supporting a role in facilitating splicing-level evolution.  Evolutionary conservation indicated a substantially greater role for intronic elements generally in splicing of exons with weak and intermediate 5'ss, and supported 5'ss strength-dependent activity for several other intronic motifs, suggesting widespread functional and evolutionary differences between exons of differing 5'ss strength.

Keywords: gene expression array-based, exon and protein coding gene analysis

overall_design: Three arrays for biological replicates of control siRNA transfection; three arrays for biological replicates of hnRNP H siRNA transfection


title: Hematopoietic Transcriptional Comparison of HSC from B10.BR/JRep and B10.BR/J (drifted) mice

city: Hackensack

last: Appel

state: NJ

address: 30 Prospect AVE-room 350

department: Oncology Research

institute: Hackensack University Medical Center

summary: Divergence has occured between the B10.BR-H2k H2-T18a/SgSnJJrep and B10.BR-H2k H2-T18a/SgSnJ (drifted) mouse strains, resulting in altered antigenic recognition and differential bone marrow engraftment capability. The microarray data demonstrate that the transcriptional profile of genes associated with hematopoiesis differs between lineage negative (as a marker for hematopoietic stem cells) bone marrow cells isolated from the B10.BR-H2k H2-T18a/SgSnJJrep and B10.BR-H2k H2-T18a/SgSnJ (drifted) mouse strains.

overall_design: Bone marrow cells from ten male mice of each strain, aged 10-12 weeks, were harvested.  One pooled sample was analyzed for each strain.

first: Stacey

last: Fanning

middle: Y

first: Stephanie

middle: A

last: Berger

first: Robert

last: Korngold

first: Thea

middle: M

last: Friedman


title: Comparative transcriptional profiling of organs of the barley spike

city: Cedar Falls

first: Tilahun

last: Abebe

state: IA

address: 191 McCollum Hall

institute: University of Northern Iowa

summary: The lemma, the palea and the awn of a barley spike are photosynthetic organs and supply the developing seed with carbohydrates. In addition, the lemma and the palea cover the seed and protect it from pathogens and insects. In this study, we compared gene expression among the lemma, the palea, the awn and the developing seed of barley at the grain-filling stage (Zadok scale 83) using the Barley1 Genome Array in order to identify genes that determine the primary function of these organs.

overall_design: Lemma, palea, awn and seed were collected at grain-filling stage (Zadok scale 83) to compare differences in gene expression. For each organ three biological replications were collected on three different dates. On each of the three dates, one replication of each organ was collected from plants grown in separate pots using a randomized complete block design (RCBD). In ths design, organ type was the treatment effect and date of sample collection (replication) was the block. To get enough tissue for RNA extraction, each replication for each organ was collected from four plants in the same pot. RNA from each replicate sample was hybridized to individual Barley1 GeneChips. Thus, for four organs with three replications (blocks), a total of 12 Barley1 GeneChips were used.


title: FRUM and EcR-regulated expression during Drosophila development

status: Public on Sep 21 2009

first: Matthew

middle: S

last: Lebo

address: 1040 Child's Way

department: Molecular and Copmutational Biology

summary: In Drosophila, male-specific FRU (FRUM) is required to establish the potential for courtship behaviors, but the downstream effectors of FRUM during development are largely unknown.  A microarray-based approach identified genes that are differentially expressed as a consequence of FRUM in pupae, in both whole body and CNS tissues.  Genes were also identified that are sex-differentially expressed in CNS tissues. The FRUM-regulated sets were significantly overrepresented with genes also regulated by the ecdysone regulatory pathway. Two EcR isoforms (EcRA and EcRB1) are expressed in FRUM-expressing neurons during distinct periods of metamorphosis.  Males with abrogated EcRA function in FRUM-expressing neurons aggressively court other males.  Transcriptional profiles of mutants with abrogated EcRA function in the fru circuit demonstrate that EcR and FRUM regulate common gene sets, including the early gene broad.  These results demonstrate a novel role for EcR in specifying male courtship behavior through its actions specifically in the FRUM neural circuitry.

overall_design: All microarrays were dual channel with direct comparisons of male versus female, wild type versus mutant, or experimental versus control. For each experiment, four to eight independent biological samples were analyzed using a dye-swap design.  Samples consisted of whole body pupae or dissected CNS collected either at 0 hour After Pupal Formation (APF), 48 hour APF, or 0-24 hour adults.

first: Laura

middle: E

last: Sanders

first: Justin

last: Dalton

first: Fengzhu

last: Sun

first: Michelle

middle: N

last: Arbeitman


title: FIA plasma induces arthritis in naïve mice

status: Public on Sep 12 2009

city: Stanford

first: William

last: Robinson

address: 269 Campus Dr

institute: Stanford University

summary: Plasma collected from mice with FIA were pooled, and 0.3 ml was injected intravenously into 6-week-old naïve SJL mice on days 0 and 2. Synovial antigen array profiling of plasma from the arthritic recipient mice demonstrated autoreactive B-cell responses against peptides representing native fibrinogen and citrullinated fibrinogen, and further epitope spreading resulting in additional targeting of fibronectin, collagen type V, cartilage gp39, and clusterin.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Custom-spotted protein slides were probed with plasma samples from individual mice. Four slides were probed with plasma derived from naïve mice and four slides were probed with plasma derived from mice injected with FIA plasma.

first: Peggy

middle: P

last: Ho

first: Lowen

last: Lee

first: Xiaoyan

last: Zhao

first: Beren

last: Tomooka

first: Ricardo

middle: T

last: Paniagua

first: Orr

last: Sharpe

first: Maya

last: BenBarak

first: Wolfgang

last: Hueber

first: Piyanka

last: Chandra

first: Lawrence

last: Steinman


title: Fibrinogen-reactive T cells transfer disease to naïve mice

summary: Splenocytes harvested from mice with FIA were cultured in vitro and stimulated with 0.01 mg/ml fibrinogen for 3 days.  Enriched T cells were transferred into 6-week-old naïve SJL mice, which developed visible signs of arthritis within 2 weeks.  Synovial array profiling of plasma from the arthritic recipient mice demonstrated autoreactive B cell responses against peptides representing native fibrinogen, and further spreading of the responses to target collagen type V, cartilage gp39, and citrullinated vimentin.

overall_design: Custom-spotted protein slides were with plasma samples from individual mice. Four slides were probed with plasma derived from naïve mice and five slides were probed with plasma derived from mice injected with FIA T cells.


title: Gene expression profiling of canine osteosarcoma reveals genes associated with short and long survival times

city: Utrecht

first: Gayathri

middle: Thevi

last: Selvarajah

state: Utrecht

address: Yalelaan 104

department: Clinical Sciences of Companion Animals

institute: University Utrecht

summary: Osteosarcoma (OS) accounts for approximately 80% of all malignant bone tumors in the dog. Tumors are highly metastatic and long-term survival is poor. This study aims to investigate the prognosis associated gene expression profile in primary canine OS. Canine specific cDNA microarray representing 20,313 genes was used to analyze expression profiles in a panel of thirty-two primary osteosarcoma to identify genes associated with survival. The 32 tumours were classified into two groups of prognosis based on survival time (ST). They were defined as short survivors (dogs with poor prognosis that survived less than 6 months) and long survivors (dogs with better prognosis that survived longer than 6 months). Fifty-one genes were found to be differentially expressed, with common up regulation of these genes in the short survivors. The overexpression of these genes in short survivors suggests a possible role for increased proliferation, drug resistance or metastasis. Several deregulated pathways were identified in the present study includes Wnt signaling, Integrin signaling and Chemokine / cytokine signaling which were comparable to the pathway analysis conducted on human OS, adding more value for the dog as an excellent model to study human OS. Our results suggest that a molecular-based method for discrimination of outcome for short survivors and long survivors of canine OS may be useful for future prognostic stratification of dogs at initial diagnosis, where genes and pathways associated with cell cycle/ proliferation, drug resistance and metastasis could be potential targets for therapy that may not just be beneficial for dogs but also for humans.

overall_design: Thirty-two histologically confirmed canine OS with available survival data, that were presented at the University Clinic for Companion Animals in Utrecht from 1996 – 2003 were selected in this study. These dogs were not subjected to any sort of therapy prior to harvesting of the tumor tissue. Tumor samples were harvested under sterile conditions during surgery (amputation / marginal resection / total resection). Samples were snap-frozen in liquid nitrogen and stored in sterile tubes at -70°C. Various clinical and pathological parameters were evaluated retrospectively for the dogs included in this study. Thirty-two tumors were assigned into two groups of prognosis based on survival time (ST). They were defined as short-term survivors (SS; 16 dogs with poor prognosis that survived less than 6 months) and long-term survivors (LS; 16 dogs with better prognosis that survived longer than 6 months). A common reference cRNA pool consisting of equal quanitity of cRNA from all 32 tumors was used to hybridize against each tumor on the array. Equal numbers of samples per tissue group were labelled with Cy3 and Cy5 (dye swap).

first: Jolle

last: Kirpensteijn

first: Monique

last: van Wolferen

first: Jan

last: Mol


title: Actinobacillus pleuropneumoniae during a natural infection in pigs

city: St-Hyacinthe

first: Vincent

last: Deslandes

state: Quebec

address: 3200 rue Sicotte

department: Groupe de Recherche sur les Maladies Infectieuses du Porc

institute: Université de Montréal - Faculté de Médecine Vétérinaire

type:
Expression profiling by array
Genome variation profiling by array

summary: Actinobacillus pleuropneumoniae is the etiological agent of porcine pleuropneumonia, a respiratory disease which causes great economic losses worldwide. Many virulence factors are involved in the pathogenesis, namely capsular polysaccharides, RTX toxins, LPS and many iron acquisition systems. In order to identify genes that are expressed in vivo during a natural infection, we undertook transcript profiling experiments with an A. pleuropneumoniae DNA microarray, after recovery of bacterial mRNAs from serotype 5b-infected porcine lungs.

platform_organism: Actinobacillus pleuropneumoniae serovar 5b str. L20

overall_design: Comparative Genomic Hybridizations between Actinobacillus pleuropneumoniae serotype 5b strain L20 (ref) and serotype 5b fresh field isolate 896-07, recovered from infected pig lung tissues following natural acute infection. Two condition transcript profiling experiments : infectious 5b field strain isolated directly from lungs of naturally deceased pigs after acute infection vs infectious 5b field strain grown in BHI broth to an OD600 of 0.300.

first: Martine

last: Denicourt

first: Josée

last: Harel

first: John

last: Nash

first: Mario

last: Jacques


title: Identification of HP0244 regulon at different pH conditions

first: Yi

last: Wen

address: 11301 Wilshire Blvd., Bldg.113, Rm. 324

department: Physiology Department

institute: UCLA/VAGLAHS

summary:
Transcriptional profiling of Helicobacter pylori comparing 26695 wild-type strain and a HP0244-deficient mutant 26695/∆HP0244::km treated at three different pH conditions (pH 7.4, pH 4.5 without urea, or pH 2.5 with 30 mM urea) for 30 min to define the HP0244 acid-responsive regulon

Keywords: Genetic modification and stress response

sample_organism:
Helicobacter pylori
Helicobacter pylori 26695

overall_design: Wild type vs HP0244-deficient mutant at three different pH conditions (pH7.4, pH4.5 without urea, and pH2.5 with 30 mM urea).  Three biological replicates for each pH condition: 3 wild type and 3 mutant, independently grown, pH treated, and harvested.

first: George

last: Sachs


title: Transcriptome of GATA3 knocked-down and normal keratinocytes after 1 cGy X irradiation

city: LYON

first: Jerome

last: Lamartine

address: 7 passage du Vercors

country: France

institute: Université Lyon I

summary: To characterize the consequences of the GATA3 silencing on the transcriptome of X-rays irradiated keratinocytes. Oligonuclotide microarrays were used to assess transcriptional changes over a time-course between 3 and 72h post-irradiation in a GATA3 knocked-down background (shGATA3) or in a normal background (ShSCR).  Primary human keratinocytes were cultured in a semi-defined medium and then infected either with shGATA3 or with ShSCR lentiviral particles . Cells were then cultured 5 to 8 days up to confluence and then submitted to an 1 cGy dose of X-rays. Total RNA was extracted 4, 24, 48 or 72 hours after irradiation. After RNA amplification and labeling, gene profiling was performed using oligonucleotide microarrays (26 068 probes) to compare 1 cGy irradiated cells to sham-irradiated cells at individual times.

overall_design: Dye-swap hybridization were performed. Slides were scanned with a Genepix 4000 microarray scanner (Axon Instruments, Molecular devices, Sunnyvale, CA). For each hybridized spot, the Cy3 and Cy5 fluorescence values were obtained by using Genepix Pro 4.0 software (Axon Instruments) and were saved as a result file

first: Florian

last: Bonin

first: Manuella

last: Molina

first: Odile

last: Berthier

first: Michèle

last: Martin

first: Claude

last: malet


title: Mice with FIA develop anti-native and anti-in vitro citrullinated fibrinogen antibodies

first: William

last: Robinson

summary: Synovial antigen arrays were probed with 1:150 dilutions of plasma derived from SJL mice immunized with fibrinogen emulsified in CFA or with CFA alone.  Autoantibody binding was detected with a Cy3-conjugated goat-anti-mouse IgG/M secondary antibody.  SAM was applied to identify antigens with statistically significant differences in array reactivity between FIA and CFA control plasma (q < 0.01) obtained from mice before boosting. The SAM hits were subjected to hierarchical cluster analysis and are displayed as a heatmap.  Synovial array profiling of FIA plasma demonstrated autoreactive B-cell responses against peptides representing native fibrinogen, and B-cell epitope spreading resulting in additional targeting of citrullinated fibrinogen in the samples obtained before boosting.

overall_design: Custom-spotted protein slides were probed with plasma samples from individual mice. Four slides were probed with plasma derived from mice immunized with CFA and six slides were probed with plasma derived from mice immunized with fibrinogen emulsified in CFA.

first: Peggy

last: Ho

first: Lowen

last: Lee

first: Xiaoyan

last: Zhao

first: Beren

last: Tomooka

first: Ricardo

last: Paniagua

first: Orr

last: Sharpe

first: Maya

last: BenBarak

first: Wolfgang

last: Hueber

first: Piyanka

last: Chandra

first: Lawrence

last: Steinman


title: Meiotic time-course expression profile

status: Public on Sep 23 2009

city: Chicago

first: Sean

middle: Erik

last: Hanlon

address: 920 E. 58th Street – CLSC 515E

department: Department of Human Genetics

institute: University of Chicago

summary: To investigate the dynamics of the meiotic transcriptome and to ensure meiotic synchrony of our samples, we measured RNA abundance in vegetative cells, respiratory (pre-meiotic) cells and in synchronously sporulating cells at various times after transfer to sporulation media (SM).

overall_design:
SK1 yeast strain SHy002 (MATa/MATα ho::LYS2/ho::LYS2 leu2::hisG/leu2::hisG lys2/lys2 ura3/ura3)

Meiotic Time Course with samples collected during vegetative growth (YPD), respiratory growth (pre-meiotic/YPA 8 hours) and 0 hr, 1.5hr, 3hr, 4.5hr, 6hr, 9hr and 12hr after transfer to sporulation media (SM).

3 separate biological replicates were used for each condition/time-point.

Total RNA from each sample was hybridized competitively with a genomic DNA common reference.

The expression analysis was carried out from the same biological samples as the FAIRE analysis.

first: Luke

last: Berchowitz

first: Jason

middle: D

last: Lieb

first: Gregory

last: Copenhaver


title: Gene expression study after 1 and 3 days of salt exposure in a Solanum tuberosum cultivar called PS3

status: Public on Sep 11 2009

city: Belvaux

first: Danièle

last: Evers

address: 41, rue du Brill

department: EVA

country: Luxembourg

institute: CRP-Gabriel Lippmann

summary: The molecular response to salt exposure was studied in the leaves of a S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon a 150 mM NaCl exposure in potato leaves occurred in the photosystem apparatus and Calvin cycle: many transcripts coding for proteins belonging to photosystems I and II and chlorophyll synthesis were repressed. On the other hand, we observed the induction of various kinds of transcription factors implicated in osmotic stress response via ABA-dependent or ABA-independent pathways but also in plant defense pathways. This revealed a crosstalk between abiotic and biotic stress responses during salt exposure, which activated several adaptation mechanisms including HSP, LEA, dehydrins and PR proteins. Gene expression changes related to carbohydrate and amino acid metabolism were also observed, pointing at putative modifications at the metabolic level.

overall_design: Gene expression has been followed at two different time-points (one and three day after salinity treatment) and conditions: salt-treatment (150 mM NaCl) and control conditions. For each time-point and conditions 3 independent biological replicates were sampled.

first: Sylvain

last: Legay

first: Didier

last: Lamoureux

first: Jean-François

last: Hausman

first: Lucien

last: Hoffmann


title: Response of Henle 407 cells during Toxoplasma gondii infection

city: Ithaca

first: Chia-Hsin

last: Ju

state: NY

address: VMC C5 151 Cornell University

institute: Cornell University

summary: The innate immune response of mucosal epithelial cells during pathogen invasion plays a central role in immune regulation in the gut.   Toxoplasma gondii (T. gondii) is a protozoan intracellular parasite that is usually transmitted through oral infection. Although much of the information on immunity to T. gondii has come from intra-peritoneal infection models, more recent studies have revealed the importance of studying immunity following infection through the natural per-oral route. Oral infection studies have identified many of the key players in the intestinal response; however, they have relied on responses detected days to weeks following infection. Much less is known about how the gut epithelial layer senses and reacts during initial contact with the pathogen. Given the importance of epithelial cells during pathogen invasion, this study uses an in vitro approach to isolate the key players and examine the early response of intestinal epithelial cells during infection by T. gondii. We show that human intestinal epithelial cells infected with T. gondii elicit rapid MAPK phosphorylation, NF-κB nuclear translocation, and secretion of interleukin (IL)-8.   Both ERK1/2 activation and IL-8 secretion responses were shown to be MyD88 dependent and TLR2 was identified to be involved in the recognition of the parasite regardless of the parasite genotype.  Furthermore, we were able to identify additional T. gondii-regulated genes in the infected cells using a pathway-focused array.  Together, our findings suggest that intestinal epithelial cells were able to recognize T. gondii during infection, and the outcome is important for modulating intestinal immune responses.

overall_design: Oral infection studies have demonstrated an increase in several cytokines and chemokines in response to T.gondii infection; however, the mixed population of the intestinal mucosa did not allow for the determination of the relative role that specific cell populations play in the production of these mediators.  To address the role of intestinal epithelial cells to modulate the cytokine environment early following infection, we used specific pathway arrays to identify cytokines and chemokines induced 4 hours after exposure to T. gondii.  At this time point most cells have become infected, but the parasites have not replicated.

first: Cynthia

last: Leifer


title: Effect of VirR/VirS-VR-RNA regulatory cascade on the expression of chromosomal genes of Clostridium perfringens

city: Fukuoka

first: Hideki

last: Hirakawa

state: Fukuoka

address: 6-10-1, Hakozaki, Higashi-ku

department: Faculty of Agriculture

country: Japan

institute: Kyushu University

summary:
The microarrays were subjected to two-color hybridization using Cy5 and Cy3 dyes incorporated in the cDNAs synthesized from total RNA samples of strains.  We compared each gene’s transcription level between the wild-type (WT) strain 13 (labeled by Cy5) and the VirR-mutant strain (TS133) or VR-RNA-mutant strain (TS140) (both labeled by Cy3) on a single DNA microarray.

Keywords: gene regulation in time course

overall_design: Each sample represent data calculated from 3 to 4 biological  replicates of independent experiments. Each biological replicate contains duplicated data.

first: Shimizu

last: Tohru

first: Kaoru

last: Ohtani

first: Satoru

last: Kuhara

first: Kosuke

last: Tashiro

first: Kiyoshi

last: Yamamoto

first: Akiko

last: Enomoto


title: ChIP to AIRE regulated genes in HEK 293 cells

city: Tartu

first: Tõnis

last: Org

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

summary: The Autoimmune Regulator (AIRE) protein is expressed in thymic medullary epithelial cells, where it promotes the ectopic expression of tissue-restricted antigens needed for efficient negative selection of developing thymocytes. Mutations in AIRE cause APECED syndrome, which is characterized by a breakdown of self-tolerance. The molecular mechanism by which AIRE increases the expression of a variety of different genes remains unknown. Here, we studied AIRE-regulated genes using whole genome expression analysis and chromatin immunoprecipitation. We show that AIRE preferentially activates genes that are tissue-specific and characterized by low levels of initial expression in stably transfected HEK293 cell model and mouse thymic medullary epithelial cells. In addition, the AIRE-regulated genes lack active chromatin marks, such as histone H3 trimethylation (H3K4me3) and acetylation (AcH3), on their promoters.  We also show that during activation by AIRE, the target genes acquire histone H3 modifications associated with transcription and RNA polymerase II. In conclusion, our data show that AIRE is able to promote ectopic gene expression from chromatin associated with histone modifications characteristic to inactive genes.

overall_design: We compared the gene expression profiles of HEK293 cell-lines expressing either YFP (NC) or AIRE (AIRE1) proteins using Illumina BeadChips (GSE16877). Based on these results we chose more than 50 genes that where upregulated in the presence of AIRE and used chromatin immunoprecipitation and custom made Nimblegen tiling arrays to study the regions of 200kb up-and downstream of the genes in HEK293 cells expressing either YFP or AIRE protein. The following antibodies where used in the ChIP experiments: H3K4me3, AcH3, H3K27me3, H3, PolII and AIRE.

first: Ana

last: Rebane

first: Kai

last: Kisand

first: Martti

last: Laan

first: Uku

last: Haljasorg

first: Reidar

last: Andreson

first: Pärt

last: Peterson


title: The transcriptional response of Drosophila melanogaster to infection with the sigma virus (Rhabdoviridae)

city: Planegg-Martinsried

first: Stephan

last: Hutter

state: Bavaria

address: Grosshaderner Strasse 2

department: Department of Biology II

institute: University of Munich

summary: Bacterial and fungal infections induce a potent immune response in Drosophila melanogaster, but it is unclear whether viral infections induce a similar immune response. Using microarrays, we examined the changes in gene expression in Drosophila that occur in response to infection with the sigma virus, a negative-stranded RNA virus (Rhabdoviridae) that occurs in wild populations of D. melanogaster. We detected many changes in gene expression in infected flies, but found no evidence for the activation of the Toll, IMD or Jak-STAT pathways, which control immune responses against other pathogens. We identified a number of functional categories of genes, including serine proteases, ribosomal proteins and chorion proteins that were overrepresented among the differentially expressed genes. We also found that the sigma virus alters the expression of many more genes in males than in females. In contrast to previous results, our data suggest that either Drosophila do not mount an immune response against the sigma virus, or that the immune response is not controlled by known immune pathways. The genes which we identified as differentially expressed after infection are promising candidates for controlling the host’s response to the sigma virus.

overall_design: We used dual channel microarrays to compare genome-wide expression profiles of adult males and females infected with the sigma virus to uninfected controls. In total 10 hybidizations were performed for males and 8 for females, including dye-swaps.

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